bi/ch 422/622 outline

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BI/CH 422/622OUTLINE:Protein Degradation (Catabolism)

DigestionInside of cellsProtein turnover

UbiquitinActivation-E1Conjugation-E2Ligation-E3

Proteosome

Amino-Acid DegradationAmmonia

freetransamination-mechanism to know

Urea Cycle – dealing with the nitrogen5 Steps

Carbamoyl-phosphate synthetaseOrnithine transcarbamylaseArginino-succinate synthetaseArginino-succinaseArginase

EnergeticsUrea Bi-cycleUrea Cycle – dealing with the nitrogenFeeding the Urea Cycle

Glucose-Alanine CycleFree Ammonia

GlutamineGlutamate dehydrogenase

Overall energetics

OUTLINE:Amino-Acid Degradation

Dealing with the carbonSeven Families

1. ADENQ2. RPH

oxidaseone-carbon metabolism

THFSAM

3. GSCPLP uses

4. MT – one carbon metabolism5. FY – oxidase vs oxygenase6. KW –7. BCAA – VIL

Convergence with Fatty acid-odd chainOverview

Fates of the 29 nitrogen atoms in 20 AA:

9 ammonia18 transamination2 urea

Amino Acid DegradationA. Concepts

1. Convergent2. ketogenic/glucogenic3. Reactions seen before

B. Transaminase (A,D,E) / Deaminase (Q,N) FamilyC. Related to biosynthesis (R,P,H; C,G,S; M,T)

1.Glu Familya. Introduce oxidases/oxygenasesb. Introduce one-carbon metabolism (1C)

2.Pyruvate Familya. PLP reactions

3. a-Ketobutyric Family (M,T)a. 1-C metabolism

D. Dedicated1. Aromatic Family (F,Y)

a. oxidases/oxygenases2. a-Ketoadipic Family (K,W)3. Branched-chain Family (V,I,L)

E. Convergence with Fatty Acids: propionyl-CoA

29 N

The SEVEN (7) Families

2

• Intermediates of the central metabolic pathway• Some amino acids result in more than one intermediate.• Ketogenic amino acids can be converted to ketone bodies.

• Glucogenic amino acids can be converted to glucose.Six to pyruvate1 Ala, Cys, Gly, Ser, Thr, Trp

Five to a-ketoglutarate2 Arg, Glu, Gln, His, Pro

Four to succinyl-CoA Ile, Met, Thr, Val

Two to fumarate3 Phe, Tyr

Two to oxaloacetate4 Asp, Asn

Seven to Acetyl-CoA Leu, Ile, Thr, Lys, Phe, Tyr, Trp

Amino Acid Degradation

2Glu family3Aromatic family4Trans-/de-aminase family

1Pyruvate family

a-ketobutyric

✓

✓

✓

a-keto butyrate family

a-keto adipate family

✓Branched-chain family

Amino Acid DegradationAromatic Family

NIH-shift

–OH

–OH

_

Ferryl-peroxylOO

O

O

Acetoacetate

2,4-shift

Phenylalanine hydroxylase

Tyrosine aminotransferase

p-hydroxyphenylpyruvate dioxygenase

Homogentisate 1,2-dioxygenase

Maleylacetoacetate isomerase

Fumarylacetoacetase

123

56

7

8

124 35 6 7 8

F,Y

O2

H2O

O2

CO2NIH-shiftOxidative decarboxylation alpha to a carbonyl

4

carbo-cation

2

4

O2

H2O

Acetoacetyl-CoA3-ketoacyl-CoA transferase

Succinyl-CoASuccinate

⊕

3

Amino Acid DegradationAromatic Family

NIH-shift

–OH

–OH

_

Ferryl-peroxylOO

O

O

Acetoacetate

2,4-shift


Tyrosine aminotransferase

p-hydroxyphenylpyruvate dioxygenase

Homogentisate 1,2-dioxygenase

Maleylacetoacetate isomerase

Fumarylacetoacetase

123

56

7

8

124 35 6 7 8

F,Y

O2

H2O

O2

CO2NIH-shiftOxidative decarboxylation alpha to a carbonyl

4

carbocation

2

4

O2

H2O

Acetoacetyl-CoA3-ketoacyl-CoA transferase

Succinyl-CoASuccinate

⊕


• In phenylketonuria (PKU) there is a buildup of Pheand phenylpyruvate

– Impairs neurological development leading to severe intellectual deficits

– Controlled by limiting dietary intake of Phe• In Alkatonuria there is a buildup of homogentisate,

which turns black on oxidation

Genetic Defects in Aromatic Family Degradation Lead to Disease

Aromatic Family

⊕⇀Alkaptonuria

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• In phenylketonuria (PKU) there is a buildup of Pheand phenylpyruvate

– Impairs neurological development leading to severe intellectual deficits

– Controlled by limiting dietary intake of Phe• In Alkatonuria there is a buildup of homogentisate,

which turns black on oxidation

Genetic Defects in Aromatic Family Degradation Lead to Disease

Aromatic Family

⊕⇀Alkaptonuria

Oxidases – use molecular oxygen as an electron acceptor, but no atoms into substrate

– e.g., cytochrome oxidase, proline oxidase – usually have water or hydrogen peroxide as product

Oxygenase* – use of molecular oxygen to put into the substrate– dioxygenases – use both atoms; e.g., cysteine dioxygenase

– mono-oxygenases – one atom in substrate, one atom as water

Amino Acid Degradation: Oxidases

*a.k.a.: hydroxylase, mixed-function oxygenase, “mixed-function oxidase”

Nomenclature

AH + BH2 + O2 à AOH + B + H2O

A(red) + O2 + 4H+ à A(ox) + 2H2O

RH + BH2 + O2 à ROH + B + H2O

A + O2 à AO2

• The enzyme is a cytochrome called P-450• The co-substrate electrons are from NADPH• There is Cytochrome P-450 reductase to funnel electrons from co-substrate

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Amino Acid Degradation: OxidasesRH + BH2 + O2 à ROH + B + H2O

Example of P-450 reactions in adrenal gland:

1) Source of reducing electrons are most often NADPH (the co-substrate)

2) Other co-substratesa) FAD, FeS clusters, a-ketoglutarate (oxidative

decarboxylation to succinate)b) Others: tetrahydrobiopterin (Phe

hydroxylase)3) Major class are the P-450 heme hydroxlases

a) Expressed in liver and adrenal glandsb) Steroids & fatty acidsc) Xenobiotics (drugs)

i. Specificii. Non-specificiii. Inducibleiv. Drug-drug interactions

Hydroxylases










1Pyruvate family

F,Y

a-keto butyrate family

a-keto adipate family

Branched-chain family

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Amino Acid Degradation K,W

a-Ketoadipic Family

2-Amino muconate e-semialdehyde

N-formyl-L-kynurenine

O

O

O

O

O

Alanine

O

OO

3-Hydroxyanthranilic acid 3,4-dioxygenase

Tryptophan 2,3-dioxygenase

Kynurenine formamidase

Kynurenine hydroxylase

Kynureninase

2-Amino 3-carboxyl-

muconate e-semialdehydedecarboxylase

Muconicacid

a-Amino muconate e-

semialdehyde dehydrogenase

a-Aminomuconate reductase

Amino Acid Degradation K,W

a-Ketoadipic Family

2-Amino muconate e-semialdehyde

N-formyl-L-kynurenine

O

O

O

O

O

Alanine

O

OO

Tryptophan 2,3-dioxygenase

Kynurenine formamidase

Kynurenine hydroxylase

Kynureninase

3-Hydroxyanthranilic acid 3,4-dioxygenase

2-Amino 3-carboxyl-

muconate e-semialdehydedecarboxylase

Muconicacid

a-Amino muconate e-

semialdehydedehydrogenase

a-Aminomuconate reductase

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Saccharopinedehydrogenase

a-Ketoadipic Family -removal of e-amino-oxidation of e-carbon

Lysine:a-ketoglutaratereductase

a-aminoadipate-d-semialdehydedehydrogenase

2-aminoadipate aminotransferase

PLPa-ketoglutarate

glutamate


Saccharopinedehydrogenase

a-Ketoadipic Family -removal of e-amino-oxidation of e-carbon

Lysine:a-ketoglutaratereductase

a-aminoadipate-d-semialdehydedehydrogenase

2-aminoadipate aminotransferase

PLPa-ketoglutarate

glutamate

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1Pyruvate family

K,W

1.Transaminase/Deaminase Family2.Glu Family3.Pyruvate Family4.a-ketobutyric Family5.Aromatic Family6.a-ketoadipic Family7.Branched-chain Family

V,I,LAmino Acid Degradation•Degradation of branched-chain amino acids does

not occur in the liver• Leucine, isoleucine, and valine are oxidized for fuel

in muscle, adipose tissue, the kidneys, and the brain• Branched-chain amino acids are degraded to

succinyl-CoA, an important citric acid cycle intermediate.

3 steps

7 steps

CO2

5 steps

CO2

HMG-CoA Ketone Bodies

1234b-Hydroxy-methyl-glutaryl-CoA

(OMSGAP)

5

6

9

2

MethionineThreonine

a-Ketobutyrate

2

|COO –

2

LysineTryptophan

a-Ketoadipate

AlanineCysteineGlycineSerine

Pyruvate Acetyl-CoA


GlutamateGlutamineHistidineProlineArginine

a-Ketoglutarate Succinyl-CoA

2Propionyl-CoA

|COO –

2

2

Glutaryl-CoA

a-Ketoisovalerate

a-Keto b-methylvalerate

a-Keto isocaproate

Isobutryl-CoA

a-Methybutryl-CoA

Isovaleryl-CoA

PLP

OH

OH

OH

|| O|| O

Dehydrogenase (FAD)

Hydrolase (CoASH)

Carboxylase (biotin)

HMG-CoA

Propionyl-CoAAcetyl-CoA +

a-methyl-acetoacetyl-CoA

Glutaconcyl-CoA Crotonyl-CoA

CO2

biotin

Hydratase (H2O)

Dehydrogenase (NAD+)

Thiolase (CoASH)

2Acetyl-CoACrotonyl-CoA

CH2

Methylmalonyl-CoA

CoASHCoASH

TPP

Lipoicacid

FAD

pyruvate dehydrogenase complex

a-ketoglutarate dehydrogenase complex

CO2

V,I,L

||O

biotin

OXIDATIVE DECARBOXYLATION


2Propionyl-CoA

|COO –

2

2

Glutaryl-CoA

a-Ketoisovalerate

a-Keto b-methylvalerate

a-Keto isocaproate

Isobutryl-CoA

a-Methybutryl-CoA

Isovaleryl-CoA

PLP

TPP

Lipoicacid

AlanineCysteineGlycineSerine

Pyruvate Acetyl-CoA

GlutamateGlutamineHistidineProlineArginine

a-Ketoglutarate Succinyl-CoA

2

MethionineThreonine

a-Ketobutyrate

2

|COO –

2

LysineTryptophan

a-Ketoadipate

OH

OH

OH

|| O|| O

Dehydrogenase (FAD)

Dehydrogenase (NAD+)

Hydratase (H2O)

Hydrolase (CoASH)

Carboxylase (biotin)

CO2

HMG-CoA

a-methyl-acetoacetyl-CoA

Methylmalonyl-CoA

Propionyl-CoAAcetyl-CoA +

Glutaconcyl-CoA Crotonyl-CoA

CO2

biotin

Thiolase (CoASH)

2Acetyl-CoACrotonyl-CoA

CH2

CoASHCoASH

FAD

pyruvate dehydrogenase complex

a-ketoglutarate dehydrogenase complex

V,I,LOXIDATIVE DECARBOXYLATION

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1Pyruvate family

V,I,L

Amino Acid Degradation Meets Fatty Acid DegradationOxidation of Propionyl-CoA

( R )

( R )

L–

Threonine Valine

Odd-Chain Fatty Acids

thymidines

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Amino Acid Degradation Meets Fatty Acid DegradationOxidation of Propionyl-CoA

( R )

( R )

L–

Threonine Valine

Odd-Chain Fatty Acids

thymidines

Only a handful of enzymes require Coenzyme B12(cobalamin)

Amino Acid Degradation Meets Fatty Acid Degradation

Vitamin B12(OH-Cbl)

TC-1(OH-Cbl)

IF-1(OH-Cbl)

Plasma

Saliva

Stomach

Diet

H2O

(Co3+)

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Complex Cobalt-Containing Compound: Coenzyme B12


Dr. Kornberg: Lecture 16 02.27.17 (28:19-29:33) VitB-12 1.3 min

19641957

Nobel Prize


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Amino Acid Degradation: OverviewGlutamine

a-ketoadipic

a-ketobutyricPropionyl-CoA

Histidine Proline

Glu-semialdehyde

Arginine

Asparagine

Methionine

Threonine3 Steps

4 Steps 2 Steps2 Steps

5 Steps

SAMcycle

5/6 Steps

ValineIsoleucineLeucine2 Steps

5 Steps4 Steps

HMG-CoA3 Steps

Lysine

Tryptophan Alanine

Serine

Glycine

Cysteine

2 Steps 2 Steps

5 Steps

3 Steps

5 Steps

4 Steps3 Steps

glutaryl-CoA

THFcycle

1.Transaminase/Deaminase Family2.Glu Family3.Pyruvate Family4.a-ketobutyric Family5.Aromatic Family6.a-ketoadipic Family7.Branched-chain Family

Oxidative decarboxylation by a complex yielding NADHCO2 + NH4+

THF

TABLE 18-2 Some Human Genetic Disorders Affecting Amino Acid Catabolism

Medical condition

Approximate incidence (per 100,000 births) Defective process Defective enzyme Symptoms and effects

Albinism <3 Melanin synthesis from tyrosine

Tyrosine 3-monooxygenase(tyrosinase)

Lack of pigmentation; white hair, pink skin

Alkaptonuria <0.4 Tyrosine degradation Homogentisate 1,2-dioxygenase

Dark pigment in urine; late-developing arthritis

Argininemia <0.5 Urea synthesis Arginase Mental retardation

Argininosuccinic acidemia <1.5 Urea synthesis Argininosuccinase Vomiting; convulsions

Carbamoyl phosphate synthetase I deficiency

<0.5 Urea synthesis Carbamoyl phosphate synthetase I

Lethargy; convulsions; early death

Homocystinuria <0.5 Methionine degradation Cystathionine β-synthase

Faulty bone development; mental retardation

Maple syrup urine disease (branchedchain ketoaciduria)

<0.4 Isoleucine, leucine, and valine degradation

Branched-chain α-keto acid dehydrogenase complex

Vomiting; convulsions; mental retardation; early death

Methylmalonic acidemia <0.5 Conversion of propionyl-CoA to succinyl-CoA

Methylmalonyl-CoA mutase

Vomiting; convulsions; mental retardation; early death

Phenylketonuria <8 Conversion of phenylalanine to tyrosine


Neonatal vomiting; mental retardation

Amino Acid Degradation: Overview

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• amino acids from protein are an important energy source in carnivorous animals

• the first step of AA catabolism is transfer of the NH3 via PLP-dependent aminotransferase usually to a-ketoglutarateto yield L-glutamate

• in most mammals, toxic ammonia is quickly recaptured into carbamoyl phosphate and passed into the urea cycle

• amino acids are degraded to pyruvate, acetyl-CoA, α-ketoglutarate, succinyl-CoA, and/or oxaloacetate

• amino acids yielding acetyl-CoA are ketogenic• amino acids yielding other end products are glucogenic• genetic defects in amino degradation pathways result in a

number of human diseases• amino acid catabolism is dependent on a variety of cofactors,

including THF, ado-Met (SAM), Cbl, biotin, and PLP

We learned that:Amino Acid Degradation: Overview

End of Material for Exam 3

bi/ch 422/622 outline

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