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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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)
②
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
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)
②
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
4) dUMP rarr dTMP
① dTMP의 생성 Ribonucleotide reductase에 의해 촉매 (CDPrarrdCDP UDPrarrdUDP)
②
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Nucleotide metabolism 대사의 주요 개념도