1.
Biochemistry
Sixth Edition
Chapter 23:
Protein Turnover and
Amino Acid Catabolism
Copyright © 2007 by W. H. Freeman and Company
Berg • Tymoczko • Stryer

2.
Protein turnover and
amino acid catabolism
 Protein turnover
 Removal of nitrogen(UREA CYCLE)
 Fates of carbon skeletons of amino acids

3.
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

4.
Ubi attaches
defective
proteins
by isopeptide
bonds (ATP)

5.
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!

6.
 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

7.
Proteasome: Executioner

8.
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.

9.
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 a-
ketoacid.
 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.

10.
Amino Acid Degradation
C 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.

11.
The sum of the reactions catalyzed by
aminotransferases and glutamate dehydrogenase :

12.
Substrate specificity of transaminases:
 Alanine transaminase
– also called glutamate pyruvate transaminase, GPT
Ala + 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)

13.
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

14.
PLP–amino acid Schiff-base
Lys of the enzyme

15.
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 + pyruvate
NH3 is transferred from Ala to Glu!!!

16.
Ser and Thr can be directly deaminated.
• Ser dehydratase and Thr dehydratase
deaminate them.

17.
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.

18.
 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..

19.
Oxidative deamination

20.
Glutamine
transports
ammonia to
the liver

21.
Glucose-Alanine
Cylcle (alanine
cycle)

22.
Step 1: Formation of carbamoyl phosphate
• Enzyme: carbamoyl phosphate synthetase
• Place: mitochondria
• 2 ATP are used.

23.
Step 2: Formation of citrulline
• Enzyme: ornithine transcarbamoylase
• Place: mitochondria
• No ATP is used.

24.
Step 3: Synthesis of argininosuccinate
• Enzyme: argininosuccinate synthetase
• Place: Cytosol
• 1 ATP is used.

25.
Step 4: Cleavage of argininosuccinate
• Enzyme: argininosuccinase
• Place: cytosol
• No ATP is used.

26.
Step 5: Cleavage of arginine to ornithine and urea
• Enzyme: arginase
• Place: cytosol
• No ATP is used.

27.
Krebs Cycle
a bicycle

28.
Regulation of
the urea cycle Accumulates
when urea cyle
slows down!

29.
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!