Download Metabolism of amino acids, porphyrins

Metabolism of amino acids, porphyrins
PROTEIN TURNOVER
Protein turnover — the degradation and
resynthesis of proteins
Half-lives of proteins – from several minutes to many
years
Structural proteins – usually stable (lens protein
crystallin lives during the whole life of the organism)
Regulatory proteins - short lived (altering the amounts
of these proteins can rapidly change the rate of
metabolic processes)
How can a cell distinguish proteins that are meant
for degradation?
Ubiquitin - is the tag that
marks proteins for
destruction ("black spot" - the
signal for death)
Ubiquitin - a small (8.5-kd)
protein present in all
eukaryotic cells
Structure:
 extended carboxyl terminus
(glycine) that is linked to other
proteins;
 lysine residues for linking
additional ubiquitin molecules
Ubiquitin covalently
binds to -amino group
of lysine residue on a
protein destined to be
degraded.
Isopeptide bond is
formed.
Mechanism of the binding of ubiquitin to target protein
E1 - ubiquitin-activating enzyme (attachment of ubiquitin
to a sulfhydryl group of E1; ATP-driven reaction)
E2 - ubiquitin-conjugating enzyme (ubiquitin is shuttled
to a sulfhydryl group of E2)
E3 - ubiquitin-protein ligase (transfer of ubiquitin from
E2 to -amino group on the target protein)
Attachment of a single
molecule of ubiquitin - weak
signal for degradation.
Chains of ubiquitin are
generated.
Linkage – between -amino
group of lysine residue of
one ubiquitin to the terminal
carboxylate of another.
Chains of ubiquitin
molecules are more
effective in signaling
degradation.
What determines
ubiquitination of the
protein?
1. The half-life of a protein
is determined by its aminoterminal residue (Nterminal rule).
E3 enzymes are the readers
of N-terminal residues.
2. Cyclin destruction boxes
- specific amino acid
sequences (proline, glutamic
acid, serine, and threonine –
PEST)
Digestion of the Ubiquitin-Tagged Proteins
What is the executioner of the protein death?
A large protease complex proteasome or the
26S proteasome digests the ubiquitinated
proteins.
26S proteasome - ATP-driven multisubunit
protease.
26S proteasome consists of two components:
 20S - catalytic subunit
 19S - regulatory subunit
20S subunit
 resembles a barrel
 is constructed from 28 polipeptide chains which are
arranged in four rings (two  and two )
 active sites are located in  rings on the interior of the
barrel
 degrades proteins to peptides (seven-nine residues)
19S subunit
 made up of 20 polipeptide
chains
 controls the access to interior
of 20S barrel
 binds to both ends of the 20S
proteasome core
 binds to polyubiquitin chains
and cleaves them off
 possesses ATPase activity
 unfold the substrate
 induce conformational changes
in the 20S proteasome (the
substrate can be passed into the
center of the complex)
Fates of carbon
skeleton of
amino acids
Glucogenic vs ketogenic amino
acids
• Glucogenic amino acids (are degraded to
pyruvate or citric acid cycle intermediates) can supply gluconeogenesis pathway
• Ketogenic amino acids (are degraded to acetyl
CoA or acetoacetyl CoA) - can contribute to
synthesis of fatty acids or ketone bodies
• Some amino acids are both glucogenic and
ketogenic
Pyruvate as an Entry Point into Metabolism
Oxaloacetate as an Entry Point into Metabolism
Aspartate and asparagine are converted into oxaloacetate
aspartate + -ketoglutarate  oxaloacetate + glutamate
Asparagine is hydrolyzed to NH4+ and aspartate, which
is then transaminated.
-Ketoglutarate as an Entry Point into
Metabolism
Succinyl Coenzyme A Is a Point of Entry
for Several Nonpolar Amino Acids
Methionine Degradation
S-adenosylmethionine (SAM) - a common methyl donor in
the cell
Homocysteine promotes the development of vascular
diseases and atherosclerosis
The Conversion of Branched-Chain Amino Acids
branched-chain
dehydrogenase
The degradative pathways of valine and isoleucine resemble
that of leucine.
Isoleucine yields acetyl CoA and propionyl CoA
Valine yields CO2 and propionyl CoA.
Degradation of Aromatic Amino Acids
Acetoacetate, fumarate, and pyruvate — are common intermediates.
Molecular oxygen is used to break an aromatic ring.
homogentisate
oxidase
PA hydroxylase
+O2
tetrahydrobiopterin
Tryptophan degradation requires several oxygenases
Pyruvate
SYNTHESIS OF NITRIC OXIDE
(NO) FROM ARGININE
• Nitric oxide (.N=O) is a gas which can
diffuse rapidly into cells, and is a messenger
that activates guanylyl cyclase (GMP
synthesis)
• NO relaxes blood vessels, lowers blood
pressure, and is a neurotransmitter in the
brain
• Nitroglycerin is converted to NO and dilates
coronary arteries in treating angina pectoris
Conversion of arginine to NO via
nitric oxide synthase
•Plants and microorganisms can make all 20
amino acids
•Humans can make only 11 of the 20 amino acids
(“nonessential” amino acids)
•Nonessential amino acids for mammals are
usually derived from intermediates of
glycolysis or the citric acid cycle
•The others are classed as "essential" amino
acids and must be obtained in the diet
A deficiency of
even one amino
acid results in a
negative
nitrogen
balance.
In this state,
more protein is
degraded than
is synthesized.
The nonessential amino acids are synthesized by quite
simple reactions.
The pathways for the formation of the essential amino
acids are quite complex.
The pathways for the biosynthesis of amino acids are
diverse
Common feature: carbon skeletons come from
intermediates of
 glycolysis,
 pentose phosphate pathway,
 citric acid cycle.
All amino acids
are grouped
into families
according to the
intermediates
that they are
made from