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22| Nitrogen Assimilation, Biosynthetic Use, and Excretion © 2013 W. H. Freeman and Company

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Page 1: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

22| Nitrogen Assimilation Biosynthetic Use and Excretion

copy 2013 W H Freeman and Company

CHAPTER 22 Nitrogen Assimilation Biosynthetic Use

and Excretion

ndash Nitrogen fixation

ndash Incorporation of ammonia into biomolecules

ndash Biosynthesis of amino acids

ndash Biosynthesis of heme

ndash Biosynthesis of nucleotides

ndash Catabolism of purines and pyrimidine

Key topics C1 transfer amino gr transfer

Genetic diseases chemotherapy

Asn Met Thr Lys Aspartate

Oxaloacetate -Ketoglutarate

Glu

Gln Pro Arg

Trp Phe Tyr

Pyruvate

3-Phosphoglycerate

Serine

Glycine Cysteine

Histidine

Ala Val Leu Ile Citrate

Phosphoenolpyruvate

Erythrose 4-phosphate

Glucose Glucose 6-phosphate Ribose-5-phosphate

Amino acid의 생합성

1) 필수aa 음식으로부터 섭취가능

ex)Val Leu Trp Phe His Met Thr Lys Ile

2) aa 생합성의 개관

Importance of Nitrogen in Biochemistry

bull Nitrogen (with H O and C) is a major elemental constituent of living organisms

bull Mostly in nucleic acids and proteins

bull But also found in ndash several cofactors (NAD FAD biotin hellip )

ndash many small hormones (epinephrine)

ndash many neurotransmitters (serotonin)

ndash many pigments (chlorophyll)

ndash many defense chemicals (amanitin)

The Nitrogen Cycle

Ammonia is incorporated into biomolecules through Glu and Gln

bull Glutamine is made from Glu by glutamine synthetase in a two-

step process

Glu + ATP -glutamyl + NH4+ Gln + Pi

phosphate

bull Phosphorylation of Glu creates a good leaving group that can be

easily displaced by ammonia

H3N

NH2

O

COOH3N

O

O

COO H3N

O

O

COO

P

O

O

O

OH

P

O

O

O+ -+ -

ATP

+ -

NH3 +

Structure of Gln Synthetase

6X2=12 subunits

Regulation of Gln Synthetase―by Six Endpoints of Gln Metabolism

Gln synthetase is also inhibited by adenylylation

Adenylylation (attachment of AMP) to Tyr-397 assists in inhibition

ndash Increases sensitivity to inhibititors

ndash Adenylation via adenylyltransferase(AT)

ndash Part of complex cascade that is dependent on [Glu] [-ketoglutarate] [ATP] and [Pi]

ndash Activity of adenylyltransferase regulated by binding to regulatory protein PII

Covalent Modification of Gln Synthetase

PII is regulated by uridylylation

(Remember that PII regulates adenylyltransferase(AT) which helps inhibit Gln synthetase)

bull When PII is uridylylated adenylyltransferase stimulates deadenylylation of Gln synthetase (increasing the latterrsquos activity)

bull ALSO uridylylated PII upregulates transcription of Gln synthetase

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 2: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

CHAPTER 22 Nitrogen Assimilation Biosynthetic Use

and Excretion

ndash Nitrogen fixation

ndash Incorporation of ammonia into biomolecules

ndash Biosynthesis of amino acids

ndash Biosynthesis of heme

ndash Biosynthesis of nucleotides

ndash Catabolism of purines and pyrimidine

Key topics C1 transfer amino gr transfer

Genetic diseases chemotherapy

Asn Met Thr Lys Aspartate

Oxaloacetate -Ketoglutarate

Glu

Gln Pro Arg

Trp Phe Tyr

Pyruvate

3-Phosphoglycerate

Serine

Glycine Cysteine

Histidine

Ala Val Leu Ile Citrate

Phosphoenolpyruvate

Erythrose 4-phosphate

Glucose Glucose 6-phosphate Ribose-5-phosphate

Amino acid의 생합성

1) 필수aa 음식으로부터 섭취가능

ex)Val Leu Trp Phe His Met Thr Lys Ile

2) aa 생합성의 개관

Importance of Nitrogen in Biochemistry

bull Nitrogen (with H O and C) is a major elemental constituent of living organisms

bull Mostly in nucleic acids and proteins

bull But also found in ndash several cofactors (NAD FAD biotin hellip )

ndash many small hormones (epinephrine)

ndash many neurotransmitters (serotonin)

ndash many pigments (chlorophyll)

ndash many defense chemicals (amanitin)

The Nitrogen Cycle

Ammonia is incorporated into biomolecules through Glu and Gln

bull Glutamine is made from Glu by glutamine synthetase in a two-

step process

Glu + ATP -glutamyl + NH4+ Gln + Pi

phosphate

bull Phosphorylation of Glu creates a good leaving group that can be

easily displaced by ammonia

H3N

NH2

O

COOH3N

O

O

COO H3N

O

O

COO

P

O

O

O

OH

P

O

O

O+ -+ -

ATP

+ -

NH3 +

Structure of Gln Synthetase

6X2=12 subunits

Regulation of Gln Synthetase―by Six Endpoints of Gln Metabolism

Gln synthetase is also inhibited by adenylylation

Adenylylation (attachment of AMP) to Tyr-397 assists in inhibition

ndash Increases sensitivity to inhibititors

ndash Adenylation via adenylyltransferase(AT)

ndash Part of complex cascade that is dependent on [Glu] [-ketoglutarate] [ATP] and [Pi]

ndash Activity of adenylyltransferase regulated by binding to regulatory protein PII

Covalent Modification of Gln Synthetase

PII is regulated by uridylylation

(Remember that PII regulates adenylyltransferase(AT) which helps inhibit Gln synthetase)

bull When PII is uridylylated adenylyltransferase stimulates deadenylylation of Gln synthetase (increasing the latterrsquos activity)

bull ALSO uridylylated PII upregulates transcription of Gln synthetase

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 3: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Asn Met Thr Lys Aspartate

Oxaloacetate -Ketoglutarate

Glu

Gln Pro Arg

Trp Phe Tyr

Pyruvate

3-Phosphoglycerate

Serine

Glycine Cysteine

Histidine

Ala Val Leu Ile Citrate

Phosphoenolpyruvate

Erythrose 4-phosphate

Glucose Glucose 6-phosphate Ribose-5-phosphate

Amino acid의 생합성

1) 필수aa 음식으로부터 섭취가능

ex)Val Leu Trp Phe His Met Thr Lys Ile

2) aa 생합성의 개관

Importance of Nitrogen in Biochemistry

bull Nitrogen (with H O and C) is a major elemental constituent of living organisms

bull Mostly in nucleic acids and proteins

bull But also found in ndash several cofactors (NAD FAD biotin hellip )

ndash many small hormones (epinephrine)

ndash many neurotransmitters (serotonin)

ndash many pigments (chlorophyll)

ndash many defense chemicals (amanitin)

The Nitrogen Cycle

Ammonia is incorporated into biomolecules through Glu and Gln

bull Glutamine is made from Glu by glutamine synthetase in a two-

step process

Glu + ATP -glutamyl + NH4+ Gln + Pi

phosphate

bull Phosphorylation of Glu creates a good leaving group that can be

easily displaced by ammonia

H3N

NH2

O

COOH3N

O

O

COO H3N

O

O

COO

P

O

O

O

OH

P

O

O

O+ -+ -

ATP

+ -

NH3 +

Structure of Gln Synthetase

6X2=12 subunits

Regulation of Gln Synthetase―by Six Endpoints of Gln Metabolism

Gln synthetase is also inhibited by adenylylation

Adenylylation (attachment of AMP) to Tyr-397 assists in inhibition

ndash Increases sensitivity to inhibititors

ndash Adenylation via adenylyltransferase(AT)

ndash Part of complex cascade that is dependent on [Glu] [-ketoglutarate] [ATP] and [Pi]

ndash Activity of adenylyltransferase regulated by binding to regulatory protein PII

Covalent Modification of Gln Synthetase

PII is regulated by uridylylation

(Remember that PII regulates adenylyltransferase(AT) which helps inhibit Gln synthetase)

bull When PII is uridylylated adenylyltransferase stimulates deadenylylation of Gln synthetase (increasing the latterrsquos activity)

bull ALSO uridylylated PII upregulates transcription of Gln synthetase

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 4: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Importance of Nitrogen in Biochemistry

bull Nitrogen (with H O and C) is a major elemental constituent of living organisms

bull Mostly in nucleic acids and proteins

bull But also found in ndash several cofactors (NAD FAD biotin hellip )

ndash many small hormones (epinephrine)

ndash many neurotransmitters (serotonin)

ndash many pigments (chlorophyll)

ndash many defense chemicals (amanitin)

The Nitrogen Cycle

Ammonia is incorporated into biomolecules through Glu and Gln

bull Glutamine is made from Glu by glutamine synthetase in a two-

step process

Glu + ATP -glutamyl + NH4+ Gln + Pi

phosphate

bull Phosphorylation of Glu creates a good leaving group that can be

easily displaced by ammonia

H3N

NH2

O

COOH3N

O

O

COO H3N

O

O

COO

P

O

O

O

OH

P

O

O

O+ -+ -

ATP

+ -

NH3 +

Structure of Gln Synthetase

6X2=12 subunits

Regulation of Gln Synthetase―by Six Endpoints of Gln Metabolism

Gln synthetase is also inhibited by adenylylation

Adenylylation (attachment of AMP) to Tyr-397 assists in inhibition

ndash Increases sensitivity to inhibititors

ndash Adenylation via adenylyltransferase(AT)

ndash Part of complex cascade that is dependent on [Glu] [-ketoglutarate] [ATP] and [Pi]

ndash Activity of adenylyltransferase regulated by binding to regulatory protein PII

Covalent Modification of Gln Synthetase

PII is regulated by uridylylation

(Remember that PII regulates adenylyltransferase(AT) which helps inhibit Gln synthetase)

bull When PII is uridylylated adenylyltransferase stimulates deadenylylation of Gln synthetase (increasing the latterrsquos activity)

bull ALSO uridylylated PII upregulates transcription of Gln synthetase

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 5: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

The Nitrogen Cycle

Ammonia is incorporated into biomolecules through Glu and Gln

bull Glutamine is made from Glu by glutamine synthetase in a two-

step process

Glu + ATP -glutamyl + NH4+ Gln + Pi

phosphate

bull Phosphorylation of Glu creates a good leaving group that can be

easily displaced by ammonia

H3N

NH2

O

COOH3N

O

O

COO H3N

O

O

COO

P

O

O

O

OH

P

O

O

O+ -+ -

ATP

+ -

NH3 +

Structure of Gln Synthetase

6X2=12 subunits

Regulation of Gln Synthetase―by Six Endpoints of Gln Metabolism

Gln synthetase is also inhibited by adenylylation

Adenylylation (attachment of AMP) to Tyr-397 assists in inhibition

ndash Increases sensitivity to inhibititors

ndash Adenylation via adenylyltransferase(AT)

ndash Part of complex cascade that is dependent on [Glu] [-ketoglutarate] [ATP] and [Pi]

ndash Activity of adenylyltransferase regulated by binding to regulatory protein PII

Covalent Modification of Gln Synthetase

PII is regulated by uridylylation

(Remember that PII regulates adenylyltransferase(AT) which helps inhibit Gln synthetase)

bull When PII is uridylylated adenylyltransferase stimulates deadenylylation of Gln synthetase (increasing the latterrsquos activity)

bull ALSO uridylylated PII upregulates transcription of Gln synthetase

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 6: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Ammonia is incorporated into biomolecules through Glu and Gln

bull Glutamine is made from Glu by glutamine synthetase in a two-

step process

Glu + ATP -glutamyl + NH4+ Gln + Pi

phosphate

bull Phosphorylation of Glu creates a good leaving group that can be

easily displaced by ammonia

H3N

NH2

O

COOH3N

O

O

COO H3N

O

O

COO

P

O

O

O

OH

P

O

O

O+ -+ -

ATP

+ -

NH3 +

Structure of Gln Synthetase

6X2=12 subunits

Regulation of Gln Synthetase―by Six Endpoints of Gln Metabolism

Gln synthetase is also inhibited by adenylylation

Adenylylation (attachment of AMP) to Tyr-397 assists in inhibition

ndash Increases sensitivity to inhibititors

ndash Adenylation via adenylyltransferase(AT)

ndash Part of complex cascade that is dependent on [Glu] [-ketoglutarate] [ATP] and [Pi]

ndash Activity of adenylyltransferase regulated by binding to regulatory protein PII

Covalent Modification of Gln Synthetase

PII is regulated by uridylylation

(Remember that PII regulates adenylyltransferase(AT) which helps inhibit Gln synthetase)

bull When PII is uridylylated adenylyltransferase stimulates deadenylylation of Gln synthetase (increasing the latterrsquos activity)

bull ALSO uridylylated PII upregulates transcription of Gln synthetase

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 7: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Structure of Gln Synthetase

6X2=12 subunits

Regulation of Gln Synthetase―by Six Endpoints of Gln Metabolism

Gln synthetase is also inhibited by adenylylation

Adenylylation (attachment of AMP) to Tyr-397 assists in inhibition

ndash Increases sensitivity to inhibititors

ndash Adenylation via adenylyltransferase(AT)

ndash Part of complex cascade that is dependent on [Glu] [-ketoglutarate] [ATP] and [Pi]

ndash Activity of adenylyltransferase regulated by binding to regulatory protein PII

Covalent Modification of Gln Synthetase

PII is regulated by uridylylation

(Remember that PII regulates adenylyltransferase(AT) which helps inhibit Gln synthetase)

bull When PII is uridylylated adenylyltransferase stimulates deadenylylation of Gln synthetase (increasing the latterrsquos activity)

bull ALSO uridylylated PII upregulates transcription of Gln synthetase

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 8: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Regulation of Gln Synthetase―by Six Endpoints of Gln Metabolism

Gln synthetase is also inhibited by adenylylation

Adenylylation (attachment of AMP) to Tyr-397 assists in inhibition

ndash Increases sensitivity to inhibititors

ndash Adenylation via adenylyltransferase(AT)

ndash Part of complex cascade that is dependent on [Glu] [-ketoglutarate] [ATP] and [Pi]

ndash Activity of adenylyltransferase regulated by binding to regulatory protein PII

Covalent Modification of Gln Synthetase

PII is regulated by uridylylation

(Remember that PII regulates adenylyltransferase(AT) which helps inhibit Gln synthetase)

bull When PII is uridylylated adenylyltransferase stimulates deadenylylation of Gln synthetase (increasing the latterrsquos activity)

bull ALSO uridylylated PII upregulates transcription of Gln synthetase

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 9: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Gln synthetase is also inhibited by adenylylation

Adenylylation (attachment of AMP) to Tyr-397 assists in inhibition

ndash Increases sensitivity to inhibititors

ndash Adenylation via adenylyltransferase(AT)

ndash Part of complex cascade that is dependent on [Glu] [-ketoglutarate] [ATP] and [Pi]

ndash Activity of adenylyltransferase regulated by binding to regulatory protein PII

Covalent Modification of Gln Synthetase

PII is regulated by uridylylation

(Remember that PII regulates adenylyltransferase(AT) which helps inhibit Gln synthetase)

bull When PII is uridylylated adenylyltransferase stimulates deadenylylation of Gln synthetase (increasing the latterrsquos activity)

bull ALSO uridylylated PII upregulates transcription of Gln synthetase

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 10: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Covalent Modification of Gln Synthetase

PII is regulated by uridylylation

(Remember that PII regulates adenylyltransferase(AT) which helps inhibit Gln synthetase)

bull When PII is uridylylated adenylyltransferase stimulates deadenylylation of Gln synthetase (increasing the latterrsquos activity)

bull ALSO uridylylated PII upregulates transcription of Gln synthetase

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 11: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

PII is regulated by uridylylation

(Remember that PII regulates adenylyltransferase(AT) which helps inhibit Gln synthetase)

bull When PII is uridylylated adenylyltransferase stimulates deadenylylation of Gln synthetase (increasing the latterrsquos activity)

bull ALSO uridylylated PII upregulates transcription of Gln synthetase

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 12: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

End Result of Multiple Levels of Control of Gln Synthetase

bull When Gln is high Gln synthetase is less active

ndash Need less NH4+ conversion to Gln

bull When Gln is low and substrates -ketoglutarate and ATP are available Gln synthetase is more active

ndash To convert more NH4+ to Gln

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 13: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of Amino Acids and Nucleotides―Three Types of Reactions

1 Transaminations and rearrangements using pyridoxal phosphate (PLP)

ndash PLP is active form of Vit B6

ndash Catalyzed by amidotransferases

ndash PLP has aldehyde group that forms Schiff base with Lys of aminotransferase

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 14: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

2 Transfer of 1-C groups using tetrahydrofolate (H4 folate) or S-adenosylmethionine (adoMet)

ndash Both can act as carbon donors

3 Transfer of amino groups derived from amide of Glu

All three of these categories of reactions use glutamine amidotransferases

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 15: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Glutamine Amidotransferases Catalyze Bisubstrate Reactions

bull Two domains

ndash One binds Gln

ndash Other is amino group acceptor and binds substrate

bull Cys acts as nucleophile to cleave amide bond of Gln

ndash Forms glutamyl-enz intermediate

bull Then second substrate binds to accept amino group from enzyme

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 16: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Proposed Mechanism for Glutamine Amidotransferases

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 17: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Amino Acid Biosynthesis―Overview

bull Source of N is Glu or Gln

bull Derive from intermediates of

ndash Glycolysis

ndash Citric acid cycle

ndash Pentose phosphate pathway

bull Bacteria can synthesize all 20

bull Mammals require some in diet

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 18: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Amino Acid Synthesis Overview

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 19: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

All amino acids derive from one of seven precursors

(See Table 22-1 and Figure 22-11)

bull CAC(citric acid cycle TCA cycle)

ndash -ketoglutarate oxaloacetate

bull Glycolysis

ndash Pyruvate 3-phosphoglycerate phosphoenolpyruvate erythrose 4-phosphate

bull Pentose phosphate pathway

ndash Ribose 5-phosphate

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 20: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Several pathways share 5-phosphoribosyl-1-pyrophosphate (PRPP) as an intermediate

bull Synthesized from ribose 5-phosphate of PPP via ribose phosphate pyrophosphokinase

ndash A highly regulated allosteric enzyme

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 21: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of Ser and Gly from 3-Phosphoglycerate

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 22: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of Cys from Homocysteine and Ser in Mammals

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 23: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Reminder of Essential Amino Acids

bull Humans cannot synthesize Met Thr Lys Val Leu Ile Phe Trp His

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 24: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Asn Thr

Lys

Met

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 25: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Ile Val Leu

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 26: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 27: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria methionine threonine lysine isoleucine valine and leucine

필수 aa

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 28: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

The bacteria-derived enzyme asparaginase is a chemotherapy agent

bull Childhood acute lymphoblastic leukemia (ALL) dependent on serum Asn

bull Asparaginase removes Asn 95완화

bull Has side-effects

bull Being used in conjunction with inhibitor of human Asn synthetase (개발 시도)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 29: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

bull Amino acid로부터 유도되는 여러 가지 분자

- aa의 역할 단백질 구성단위 hormone cofactor nucleotide alkaloids

세포벽 중합체 porphyrin antibiotics pigment (색소) 싞경전달물질의 전구체

1) Porphyrin의 생합성

① 전구체 Glycine

② 역할 Hb cytochrome과 같은 heme 단백질 중의 porphyrin핵의 구성성분

③ 유전적 결함 ldquoPorphyriardquo rArr 적혈구 혈액 간에서 porphyrin 전구체의 축적을 야기하는 glycine으로부터 porphyrin에 이르는 생합성에서의 효소의 결핍

2) 담즙색소

heme의 분해 rarr bilirubin 생성 혈청 albumin과 결합 간으로 rarr bilirubin diglucuronide (담즙색소) 소장으로 분비

- bilirubin 간 기능 손상의 결과로 담즙 분비가 폐쇄될 때 혈중으로 새어 나와 황달

( jaundice) 야기

- GeorgeⅢ과 협혈귀 치아형광 소변적색 heme 부족

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 30: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Synthesis of -Aminolevulinate in Higher Eukaryotes

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 31: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of heme from aminolevulinate

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 32: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Synthesis of Heme from -Aminolevulinate

bull Two molecules of -aminolevulinate condense to form porphobilinogen

bull Four molecules of porphobilinogen combine to form protoporphyrin

bull Fe ion is inserted into protoporphyrin with the enzyme ferrochelatase

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 33: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Defects in Heme Biosynthesis

bull Most animals synthesize their own heme

bull Mutations or misregulaton of enzymes in heme biosynthesis pathway lead to porphyrias

ndash Precursors accumulate in red blood cells body fluids and liver

ndash Homozygous individuals also suffer intermittent neurological impairment abdominal pain

ndash King George III may have been affected

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 34: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Enzymes Inhibited in Heme Synthesis Defects

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 35: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Heme is the source of bile pigments

bull Heme from dying erythrocytes is degraded to bilirubin in two steps antioxidant

1 Heme oxygenase linearizes heme to create biliverdin a green compound (seen in a bruise)

2 Biliverdin reductase converts biliverdin to bilirubin a yellow compound that travels bound to serum albumin in the bloodstream

bull HO-1 stress-sensitive HO-2 constitutive

뇌고환 존재

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 36: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

bull In liver bilirubin diglucouronide is made from bilirubin

ndash Secreted with rest of bile into small intestine

ndash Microbial enzymes break it down to urobilinogen and other compounds

ndash Some urobilinogen is transported to the kidney and converted to urobilin

bull Gives urine its yellow color

bull Remaining intestinal urobilinogen is microbially digested to stercobilin of feces

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 37: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Formation and Breakdown of Bilirubin

CO

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 38: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Jaundice is caused by bilirubin accumulation

bull Jaundice (yellowish pigmentation of skin whites of eyes etc) can result from

ndash Impaired liver (in liver cancer hepatitis)

ndash Blocked bile secretion (due to gallstones pancreatic cancer)

ndash Insufficient glucouronyl bilirubin transferase to process bilirubin (occurs in infants)

bull Treated with UV to cause photochemical breakdown of bilirubin

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 39: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Gly and Arg are precursors of creatine and phosphocreatine

bull Phosphocreatine is hydrolyzed for energy in muscle

bull Gly and Arg combine then Adomet acts as a methyl donor

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 40: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of Creatine and Phosphocreatine

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 41: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Glutathione (GSH) derives from Glu Cys and Gly

bull GSH is present in most cells at high amounts

bull Reducing agentantioxidant

ndash Keeps proteins metal cations reduced

ndash Keeps redox enzymes in reduced state

ndash Removes toxic peroxides

bull Oxidized to a dimer (GSSG)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 42: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis and Oxidation of Glutathione

1)Redox status 유지 Glutaredoxin환원 항산화

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 43: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

D-amino acids in bacteria arise from racemases

bull Bacterial peptidoglycans contain D-Ala and D-Glu

bull Racemases act on D-amino acids use PLP as cofactor

bull Racemase inhibitors are usedstudied as antibiotic targets

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 44: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Amino acid racemase inhibitors antibacterial drug

결핵치료제

세균 D-form

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 45: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Aromatic amino acids are precursors to plant lignins hormones and natural

products

bull Lignin (rigid polymer in plants) from Phe and Tyr

bull Auxin (growth hormone indole-3-acetate) from Trp

bull Other extracts spices (nutmeg vanilla) alkaloids (morphine) etc

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 46: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of Auxin from Trp and Cinnamate from Phe

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 47: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

5) Neurotransmitter (싞경전달물질)의 생합성

① Tyr rarr DOPA Dopamine rarr Norepinephrine rarr Epinephrine

② Glutamate GABA 억제성 싞경전달물질 rArr 간질 고혈압증의 치료

③ Trp rarr 5-hydroxytryptophan serotonin (rarrrarrmelatonin)

④ His histamine 혈관확장제 cf) cimetidine antagonist 위산분비 억제

polyamines ⅰ) putrescine spermidine spermine

ⅱ) 역할 - 세포의 성장인자

- (+)charge로 핵산 안정화

- tumor marker 암 진행시 putrescine을 생합성시키는

ornithine decarboxylase 활성

PLP

부족 (파킨슨씨병) VS 과잉 (정싞분열증)

PLP

PLP

PLP

간질발작

Phe

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 48: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Amino acid decarboxylation yields neurotransmitters inhibitors

bull Decarboxylations often require PLP

bull Trp yields catecholamines such as dopamine norepinephrine and epinephrine

bull Glu yields neurotransmitters -aminobutyrate (GABA진정) and serotonin(기분)

bull His yields the vasodilator and stomach acid secretion stimulant Histamine

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 49: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of Some Neurotransmitters

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 50: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

H2 antagonist cimetidine(tagamet)

위산 분비억제

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 51: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

6) NO의 생합성

① NO의 역할 신경전달물질 혈액응고 혈압조절

② 생합성과정 Arg [Hydroxy Arg] Cit + NO

rArr NADPH의 의존적 반응

③ NOS의 종류 a) iNOS inducible (염증)

b) bNOS brain (기억력)

c) eNOS endothelial (혈관확장)

Nucleotide의 생합성과 분해

nucleotide의 역할

ⅰ) DNA RNA의 전구체

ⅱ) 화학E의 운반체 ATP GTP

ⅲ) Coenzyme의 구성성분(NAD FAD S-adenosyl Met Coenzyme A) amp 활성화된 생합성 중간체의 성분(UDP-Glucose CDP-diacyl glycerol)

ⅳ) 세포의 2nd messenger cAMP cGMP

NADPH O2

NADP+ H2O

frac12NADPH O2

frac12NADP+ H2O

NO synthase(NOS)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 52: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Arg is precursor for nitric oxide (NO)

bull Mid-80rsquos discovery that pollutant NO played important role in blood pressure regulation blood clotting etc

bull Synthesized from Arg via nitric oxide synthase using NADPH

ndash Enz similar to cyt P450 reductase

ndash Stimulated by interaction with Ca2+ and calmodulin

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 53: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of Nitric Oxide

NOS

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 54: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

22-30 Biosynthesis of spermidine and spermine

From Arg

DNA packaging

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 55: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Nucleotide Biosynthesis

bull Nucleotides can be synthesized de novo from amino acids ribose-5-phosphate CO2 and NH3

bull Nucleotides can be salvaged from nucleobases

bull Many parasites (eg malaria) lack de novo biosynthesis pathways and rely exclusively on salvage

ndash Compounds that inhibit salvage pathways are promising anti-parasite drugs

1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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1) Nucleotide 생합성의 경로

① De novo pathway amino acid Ribose-5 phosphate CO2 NH3를 전구

체로 합성

② Salvage pathway 유리염기 nucleotide를 재이용

2) Purine nucleotide의 생합성

① 전구체 PRPP (Phosphoribosyl Pyrophosphate)

ltpurinegt

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 57: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

3) Ribonucleotide의 deoxyribonucleotide 환원

전자전달

deoxy의 nucleotide

RNA의 nucleotide

Ribonucleotide reductase

Glutaredoxin Thioredoxin

2GSH

NADPH + H+

FADH2

Glutaredoxin reductase

thioredoxin reductase

Ribonucleotide reductase

HS

HS

S

S

S

S

S

S

SH

SH

SH

SH

dNDP NDP

NADP+ NADP+ NADPH + H+

FAD

- Ribonucleotide Reductase 억제 DNA 합성억제 rArr 항암효과

GSSG

Thioredoxin Glutaredoxin

DNA RNA

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 58: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

4) dUMP rarr dTMP

① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)

NADPH + H+

NADP+

ldquoDHFRrdquo

Glycine

Serine

PLP

78-Dihydrofolate

DHFR(dihydrofolate reductase)

rArr DNA 합성조절 可 rArr 항암치료

Tetrahydro

folate

dTMP

N5N10-methylene

tetrahydrofolate

dUMP

dTMP

dCTP dUTP

Thymidylate

synthase

dUMP

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 59: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Origin of Ring Atoms in Purines

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 60: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

De novo synthesis of purine nucleotides construction of the purine ring of inosinate (IMP)

C

N

N

N

N Asp

formic acid

CO2

Gln

Gly

formic acid

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 61: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Synthesis of AMP and GMP from IMP

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 62: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Regulation of Adenine and Guanine Biosynthesis in E coli

22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate

Asp

N

N

O

O

Asp

CO2

Gln

ltpyrimidinegt

Carbamoyl phosphate synthetase II (cytosol)

Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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Reduction of Ribonucleotides to Deoxyribonucleotides

by Ribonucleotide Reductase

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 65: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Structure of Ribonucleotide Reductase

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 66: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Proposed ribonucleotide reductase mechanism involves free radicals

bull Most forms of enzyme have two catalyticregulatory subunits and two radical-generating subunits

ndash Contain Fe3+ and dithiol groups

ndash Enz creates stable Tyr radical to abstract H from sugar

bull A 3rsquo-ribonucleotide radical forms

bull 2rsquo-OH is protonated to help eliminate H2O and form a radical-stabilized carbocation

bull Electrons are transferred to the 2rsquo-C

Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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Proposed mechanism for ribonucleotide reductase

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 68: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Ribonucleotide reductase has two types of regulatory sites

bull One type affects activity

ndash ATP activates dATP inhibits

bull Other type affects substrate specificity in order to maintain balanced pools of nucleotides

ndash If ATP or dATP high less specificity for adenine and MORE specificity for UDP and CDP etc

ndash Enzyme oligomerizes to accomplish this change

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 69: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Oligomerization of Ribonucleotide Reductase when dATP Binds

dATP

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 70: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Regulation of Ribonucleotide Reductase by dNTPs

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 71: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Biosynthesis of dTMP

dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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dTMP is made from dUTP

bull Roundabout pathwayhellip

1 dUTP is made (via deamination of dCTP or by phosphorylaton of dUDP)

2 dUTP to dUMP by dUTPase

3 dUMP dTMP by thymidylate synthase

- adds a methyl group from tetrahydrofolate

Thymidylate synthase is a target for some anticancer drugs

Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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Conversion of dUMP to dTMP by Thymidylate Synthase

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 74: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

thymidylate synthase 저해제

Dihydrofolate reductase 저해제

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 75: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Folic acid deficiency leads to reduced thymidylate synthesis

bull Folic acid deficiency is widespread especially in nutritionally poor populations

bull Reduced thymidylate synthesis causes uracil to be incorporated into DNA

bull Repair mechanisms remove the uracil by creating strand breaks that affect the structure and function of DNA

ndash Associated with cancer heart disease neurological impairment

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 76: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Catabolism of Purines Formation of Uric Acid

bull Degradation of purines proceeds through dephosphorylation (via 5rsquo-nucleotidase)

bull Adenosine is deaminated to inosine and then hydrolyzed to hypoxanthine and ribose

bull Guanosine yields xanthine via these hydrolysis and deamination reactions

bull Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase

bull Spiders and other arachnids lack xanthine oxidase

Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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Catabolism of Purines

Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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Conversion of Uric Acid to Allantoin Allantoate and Urea

Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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Catabolism of Purines Degradation of Urate to Allantoin

bull Urate is oxidized into a 5-hydroxy-isourate by urate oxidase

bull Hydrolysis and the subsequent decarboxylation of 5-hydroxy-isourate yields allantoin

bull Most mammals excrete nitrogen from purines as allantoin

bull Urate oxidase is inactive in humans and other great apes we excrete urate

bull Birds most reptiles some amphibians and most insects also excrete urate

NH

N NH

NH

O

O

O

NH

N N

NH

O

O

O OH

NH2

NH

NH

NH

O

O

O

H

H+

-

-

O2 + H2O

H2O2

CO2

H2O

urate oxidase

spontaneous or catalyzed

urate

5-hydroxyisourate

allantoin

Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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Catabolism of Purines Degradation of Allantoin

bull Most mammals do not degrade allantoin

bull Amphibians and fishes hydrolyze allantoin into allantoate bony fishes excrete allantoate

bull Amphibians and cartilaginous fishes hydrolyze allantoate into glyoxylate and urea many excrete urea

bull Some marine invertebrates break urea down into ammonia

NH2

NH

NH

NH

O

O

O

H

NH2

NH

NH

NH2

O O

O

H

O

H+

OH

OO

NH2

NH2

ONH2

NH2

O

NH4+

H2O

H2O

2 H2O + 4 H+

2 CO2

4

allantoinase

allantoicase

urease

allantoin

allantoate

urea

ammonium cation

Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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Catabolism of Thymine a Pyrimdine

gtgtgtSuccinyl CoA

Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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Purine and pyrimidine bases are recycled by salvage pathways

bull Free bases released in metabolism are reused

ndash Example Adenine reacts with PRPP to form the adenine nucleotide AMP

bull Catalyzed by adenosine phosphoribosyltransferase

bull Brain is especially dependent on salvage pathways

bull Lack of hypoxanthine-guanine phosphoribosyltransferase leads to Lesch-Nyhan Syndrome with neurological impairment finger-and-toe-biting behavior

Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

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Purine nucleotide 합성의 salvage pathway (재이용 경로)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 84: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Excess uric acid seen in gout

bull Painful joints (often in toes) due to deposits of sodium urate crystals

bull Primarily affects males

bull May involve genetic under-excretion of urate andor may involve over-consumption of fructose

bull Treated with avoidance of purine-rich foods (seafood liver) or avoidance of fructose

bull Also treated with xanthine oxidase inhibitor allopurinol

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 85: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Allopurinol inhibits xanthine oxidase

Competitive inhibitor

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 86: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Many chemotherapeutic agents target nucleotide biosynthesis

bull Glutamine analogs azaserine acivicin

ndash Inhibit glutamine amidotransferases

bull Fluorouracil

ndash Converted by salvage pathway into FdUMP which inhibits thymidylate synthase

bull Methotrexate and aminopterin

ndash Inhibit dihydrofolate reductase (competitive inhibitors)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 87: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Antibiotics also target nucleotide biosynthesis

bull Allopurinol etc

ndash Studied against African sleeping sickness (trypanosomiasis) because the trypanosomes lack enzymes for de novo nucleotide synthesis

bull Trimethoprim ndash

ndash Inhibits bacterial dihydrofolate reductase but binds human enzyme several orders of magnitude less strongly

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 88: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Azaserine and Acivicin Inhibitors of Glutamine Amidotransferases

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 89: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Proposed mechanism for glutamine amidotransferases

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 90: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Chemotherapy Targets―Thymidylate Synthesis and Folate Metabolism

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 91: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Thymidylate synthesis and folate metabolism as targets of chemotherapy

요로감염 (antibiotics)

Anticancer agent

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 92: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

fdUMP Inhibition of dUMPdTMP Conversion

Fluorouracil

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 93: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Chapter Summary

bull Some prokaryotes are able to reduce molecular nitrogen into ammonia understanding details of the nitrogen fixation is one of the holy grails in biochemistry

bull The 20 common amino acids are synthesized via difficult-to-remember pathways from -ketoglutarate 3-phosphoglycerate oxaloacetate pyruvate phosphoenolpyruvate erythrose 4-phosphate and ribose-5-phosphate

bull Nucleotides can be synthesized either de novo from simple precursors or reassembled from scavenged nucleobases

bull Purine degradation pathway in most organisms leads to uric acid but the fate of uric acid is species-specific

In this chapter we learned

Nucleotide metabolism 대사의 주요 개념도

Page 94: Nitrogen Assimilation, Biosynthetic Use, and Excretionmrca.or.kr/board/files/fff pr 17 SL_8 ch22-aa na syns.pdf · –Precursors accumulate in red blood cells, ... (e.g., malaria)

Nucleotide metabolism 대사의 주요 개념도