Protein Metabolism Denotes the various biochemical processes
responsible for the synthesis of proteins and amino acids the
breakdown of proteins (and other large molecules, too) by
catabolism The Digestion and Absorption of Dietary Proteins
Pepsin nonspecific maximally active at low pH of the stomach.
Proteolytic enzymes of the pancreas in the intestinal lumen display
a wide array of specificity. Aminopeptidases digest proteins from
the amino-terminal end. Cellular Proteins Are Degraded at Different
Rates
Some proteins are very stable, while others are short lived.
Altering the amounts of proteins important in metabolic regulation
can rapidly change metabolic patterns. Cells have mechanisms for
detecting and removing damaged proteins. A significant proportion
of newly synthesized protein molecules are defective because of
errors in translation. Other proteins may undergo oxidative damage
or be altered in other ways with the passage of time. Ubiquitin
Tags Proteins for Destruction
How can a cell distinguish proteins that are meant for degradation?
Ubiquitin, a small (8.5-kd) protein present in all eukaryotic
cells, is the tag that marks proteins for destruction. The
c-terminal glycine residue of ubiquitin (Ub) becomes covalently
attached to the e-amino groups of several lysine residues on a
protein destined to be degraded. The energy for the formation of
these isopeptide bonds (iso because e- rather than a-amino groups
are targeted) comes from ATP hydrolysis. Three enzymes participate
in the attachment of ubiquitin to each protein:
ubiquitin-activating enzyme, or E1 ubiquitin-conjugating enzyme, or
E2 ubiquitin-protein ligase, or E3. Chains of ubiquitin can be
generated by the linkage of the e-amino group of lysine residue 48
of one ubiquitin molecule to the terminal carboxylate of another.
Chains of four or more ubiquitin molecules are particularly
effective in signaling degradation What determines whether a
protein becomes ubiquitinated?
The half-life of a cytosolic protein is determined to a large
extent by its amino-terminal residue the N-terminal rule. In yeast:
if N terminus is methionine half-life > 20 hours, whereas if N
terminus is arginine half-life 2 minutes. A highly destabilizing
N-terminal residue such as arginine or leucine favors rapid
ubiquitination, whereas a stabilizing residue such as methionine or
proline does not. E3 enzymes are the readers of N-terminal
residues. Cyclin destruction boxes are amino acid sequences that
mark cell-cycle proteins for destruction. Proteins rich in proline,
glutamic acid, serine, and threonine (PEST sequences). The
Proteasome Digests the Ubiquitin-Tagged Proteins
A large protease complex called the proteasome or the 26S
proteasome digests the ubiquitinated proteins. In eukaryotes, they
are located in the nucleus and the cytoplasm. The degradation
process yields peptides of about 7-8 amino acids long, then further
degraded into amino acids and used in synthesizing new proteins.
This ATP-driven multisubunit protease spares ubiquitin, which is
then recycled. Protein Degradation Can Be Used to Regulate
Biological Function
Example: E3 P P E3 NF-kB I-kB P Inflammation Ub initiates the
expression of a number of the genes that take part in this response
P Ub NF-kB proteosome What is the fate of amino acids released on
protein digestion?
Nitrogen Removal is the first step in the degradation of amino
acids. Any amino acids not needed as building blocks are degraded
to various compounds, depending on the type of amino acid and the
tissue from which it originates. The major site of amino acid
degradation in mammals is the liver. The resulting -ketoacids are
then metabolized so that the carbon skeletons can: 1. enter the
metabolic mainstream as precursors of glucose 2. or as citric acid
cycle intermediates. Degradation in the liver
Digested proteins Amino Acids Degradation in the liver NH4+
a-ketoacids The amino group must be removed, as there are no
nitrogenous compounds in energy-transduction pathways enter the
metabolic mainstream as precursors to glucose or citric acid cycle
intermediates The fate of the a-amino group
The a-amino group of many aas is transferred to a-ketoglutarate to
form glutamate. Glutamate is then oxidatively deaminated to yield
ammonium ion (NH4+). Aminotransferases (transaminases) catalyze the
transfer of an a-amino group from an a-amino acid to an a-keto
acid. Example: Aspartate aminotransferase: Alanine
aminotransferase:
These transamination reactions are reversible and can thus be used
to synthesize amino acids from a-ketoacids, The nitrogen atom that
is transferred to a-ketoglutarate in the transamination reaction is
converted into free ammonium ion by oxidative deamination. This
reaction is catalyzed by glutamate dehydrogenase. This enzyme is
unusual in being able to utilize either NAD+ or NADP+ at least in
some species. The reaction proceeds by dehydrogenation of the C-N
bond, followed by hydrolysis of the resulting Schiff base.
Exception the -amino groups of serine and threonine can be directly
converted into NH4+ . These direct deaminations are catalyzed by
serine dehydratase and threonine dehydratase, in which pyridoxal
phosphate (PLP) is the prosthetic group. Glutamate dehydrogenase
and other enzymes required for the production of urea are located
in mitochondria. This compartmentalization sequesters free ammonia,
which is toxic. In most terrestrial vertebrates, NH4+ is converted
into urea, which is excreted. Pyridoxal Phosphate Forms Schiff-Base
Intermediates in Aminotransferases
All aminotransferases contain the prosthetic group pyridoxal
phosphate (PLP), which is derived from pyridoxine (vitamin B6).
Pyridoxal phosphate derivatives can form stable tautomeric
forms
The most important functional group allows PLP to form covalent
Schiff-base intermediates with amino acid substrates a pyridine
ring that is slightly basic A phenolic hydroxyl group that is
slightly acidic The aldehyde group of PLP usually forms a
Schiff-base linkage with the e-amino group of a specific lysine
residue of the enzyme. The a-amino group of the amino acid
substrate displaces the e-amino group of the active-site lysine
residue. Peripheral Tissues Transport Nitrogen to the Liver
Muscle uses branched-chain amino acids: - leucine, - Valine, -
Isoleucine as a source of fuel during prolonged exercise and
fasting. How is the nitrogen processed in these other
tissues?
As in the liver - the first step is removal of nitrogen from the
amino acid. - However, muscle lacks the enzymes of the urea cycle
(the set of reactions that prepares nitrogen for excretion). in
muscle, the nitrogen must be released in a form that can be
absorbed by the liver and converted into urea. Nitrogen is
transported from muscle to the liver in two principal transport
forms:
Alanine and glutamine. Glutamate is formed by transamination
reactions, - Nitrogen is then transferred to pyruvate to form
alanine, which is released into the blood. The liver takes up the
alanine and converts it back into pyruvate by transamination.
The pyruvate can be used for gluconeogenesis, and the amino group
eventually appears as urea. This transport is referred to as the
glucosealanine cycle. It is reminiscent of the Cori cycle
It is reminiscent of the Cori cycle. However, in contrast with the
Cori cycle, pyruvate is not reduced to lactate, Thus more
high-energy electrons are available for oxidative phosphorylation
in muscle. Glutamine synthase catalyzes the synthesis of glutamine
from glutamate and NH4+ in an
ATP-dependent reaction: The nitrogen atoms of glutamine can be
converted into urea in the liver The Urea Cycle Some of the NH4+
formed in the breakdown of amino acids is consumed in the
biosynthesis of nitrogen compounds. In most terrestrial
vertebrates, the excess NH4+ is converted into urea and then
excreted. The urea: One nitrogen atom is transferred from
aspartate. The other nitrogen atom is derived directly from free
NH4+ . The carbon atom comes from HCO3-. The Urea Cycle
Reactions
Formation of Carbamoyl Phosphate: catalyzed by carbamoyl phosphate
synthetase. The consumption of two molecules of ATP makes the
synthesis essentially irreversible. The carbamoyl group of
carbamoyl phosphate has a high transfer potential because of its
anhydride bond. Carbamoyl is transferred to ornithine to form
citrulline.
The reaction is catalyzed by ornithine transcarbamoylase. Ornithine
and citrulline are amino acids, but they are not used as building
blocks of proteins. Citrulline is transported to the cytoplasm
where it condenses with aspartate to form argininosuccinate The
reaction is catalyzed by argininosuccinate synthetase. The reaction
is driven by the cleavage of ATP into AMP and PPi, and by the
subsequent hydrolysis of PPi. Argininosuccinase cleaves
argininosuccinate into arginine and fumarate.
Thus, the carbon skeleton of aspartate is preserved in the form of
fumarate. Arginine is hydrolyzed to generate urea and ornithine in
a reaction catalyzed by arginase.
Ornithine is then transported back into the mitochondrion to begin
another cycle. Mitochondrial reactions:
The formation of NH4+ by glutamate dehydrogenase. Its incorporation
into carbamoyl phosphate Synthesis of citrulline Cytosolic
reactions: The next three reactions of the urea cycle, which lead
to the formation of urea, take place in the cytosol. THE END