BiochemistrySixth Edition

Chapter 23:Protein Turnover andAmino Acid Catabolism

Copyright © 2007 by W. H. Freeman and Company

Berg • Tymoczko • Stryer

Protein turnover and amino acid catabolism

Protein turnover Removal of nitrogen(UREA CYCLE) Fates of carbon skeletons of amino acids

Protein turnover tightly regulated

Question: How can a cell distinguish proteins that are meant for degradation?

Ubiquitin– Tags proteins for destruction

• Black spot / Death signal• The -COOH terminal Gly residue in Ubi covalently attaches

epsilon-amino groups of Lys on a protein destined to be destroyed.

• The energy for the formation of isopeptide bonds comes from ATP hydrolysis.

– Is highly conserved in eukaryotes• Yeast and human ubi differ at only 3 of 76 residues

Ubi attaches defective proteinsby isopeptide bonds (ATP)

What determines whether a protein becomes ubiquitinated?

Simple: The half life of a cytosolic protein is determined to a large extend by its amino-terminal residue.

N-terminal rule E3 enzymes are the readers of N-terminal residues!

HPV encodes a protein that activates a specific E3 enzyme.

The enzyme ubiquitinates the tumor suppressor p53 and other proteins that control DNA repair, which are then destroyed!

The activation of this E3 enzyme is observed in more than 90% of cervical carcinomas.

Importance of E3 Proteins

Proteasome: Executioner

Amino Acid Degradation

Amino acids in excess cannot be stored or excreted. Surplus amino acids are used as metabolic fuel.

Amino Acid Degradation The -a amino group is transferred to -a ketoglutarate to form

glutamate. The remaining C skeletons are transformed into major

metabolic intermediates.

The major site of amino acid degradation in mammals is the liver, although muscles readily degrade the branched-chain amino acids.

Amino Acid Degradation

-a amino group The -a amino group is transferred to -a ketoglutarate to

form glutamate.• Aminotransferases (also called transaminases) catalyze the

tranfer of an -a amino group from an -a amino acid to an -aketoacid.

Which is then oxidatively deaminated to yield ammonium ion (NH4

+).• Some of the ammonium ions are consumed in the biosynthesis

of nitrogen compounds.• Most of the ammonium ions are converted into urea (by the urea

cycle) and then excreted.

Amino Acid DegradationC skeletons The C skeletons are transformed into major

metabolic intermediates Acetyl CoA Acetoacetyl CoA Pyruvate α-ketoglutarate Succinyl CoA Fumarate Oxaloacetate

The intermediates are converted into glucose oxidized by the citric acid cycle

Therefore, fatty acids, KBs, and glucose can be formed from amino acids.

The sum of the reactions catalyzed by aminotransferases and glutamate dehydrogenase :

Substrate specificity of transaminases: Alanine transaminase

– also called glutamate pyruvate transaminase, GPTAla + a-KG pyruvate + Glu

Aspartate transaminase – also called glutamate oxaloacetate transaminase, GOT

Asp + a-KG Oxaloacetate + Glu

Mechanism of action of transaminases: All require the cofactor pyridoxal phosphate (a derivative of vitamine

B6)

Diagnostic values of transaminases: Transaminases are normally intracellular enzymes. Thus, the presence

of elevated levels of transaminase in the serum indicated damage to cells rich in the enzyme.– Serum glutamate:oxaloacetate transaminase (SGOT)– Serum glutamate;pyruvate transaminase (SGPT)

Role of Pyridoxal phosphate(PLP)

All aminotransferases contain PLP– derived from Vit B6

The most important functional group on PLP is the aldehyde.– This group allows PLP to form covalent Schiff-base

intermediates with amino acid substrates.

Steps in transamination reactions:

Amino acid1 + E-PLP a-ketoacid1 + E-PMP

a-ketoacid2 + E-PMP amino acid2 + E-PLP

– The sum of these reactions

Amino acid1 + a-ketoacid2 amino acid2 + a-ketoacid1

PLP–amino acid Schiff-base

Lys of the enzyme

Transamination mechanism

The second half takes place by the reverse of the above pathway.a-ketoacid2 + E-PMP amino acid2 + E-PLP

The sum of these reactions:Amino acid1 + a-ketoacid2 amino acid2 + a-ketoacid1

Ala + a-ketoglutarate Glu + pyruvateNH3 is transferred from Ala to Glu!!!

Ser and Thr can be directly deaminated.

• Ser dehydratase and Thr dehydratase deaminate them.

Oxidative deamination results in the release of free ammonia.

The amino groups of most amino acids are ultimately funneled to glutamate by means of transamination with a-ketoglutarate.

How are amino acid groups removed from glutamate to prepare them for excretion?

By oxidative deamination.

α-amino groups are converted into ammonium ions by the oxidative deamination of glutamate.

NH4+ is very toxic.

The liver, where most of the amino acid degradation takes place, uses the urea cycle to convert NH4

+ into urea which is then excreted from the body.

How is NH4 carried to liver?1. Gln carries ammonia to the liver!

2. Ala carries ammonia from muscles to the liver by Alanine (glucose-alanine) cycle..

Oxidative deamination

Glutamine transports ammonia to the liver

Glucose-Alanine Cylcle (alanine cycle)

Step 1: Formation of carbamoyl phosphate• Enzyme: carbamoyl phosphate synthetase• Place: mitochondria• 2 ATP are used.

Step 2: Formation of citrulline• Enzyme: ornithine transcarbamoylase• Place: mitochondria• No ATP is used.

Step 3: Synthesis of argininosuccinate• Enzyme: argininosuccinate synthetase• Place: Cytosol• 1 ATP is used.

Step 4: Cleavage of argininosuccinate• Enzyme: argininosuccinase• Place: cytosol• No ATP is used.

Step 5: Cleavage of arginine to ornithine and urea• Enzyme: arginase• Place: cytosol• No ATP is used.

Krebs Cyclea bicycle

Regulation of the urea cycle Accumulates

when urea cyleslows down!

Genetic defects in urea cycle

Argininosuccinase deficiency: this could be partially treated by providing a surplus of Arg in the diet and restricting the total protein intake.

• Arg is the product of this reaction. Arg will provide ornithine. Carbomyl P and ornithine will provide citrulline and then arginosuccinate.

• So, argininosuccinate will be excreted. The problem is NOT due to the accumulation of argininosuccinate but the lack of one of the products, Arginine. Nitrogen atoms are eliminated in the form of argininosuccinate!