1. Metabolism of amino acids, porphyrins

2. 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? 2

3. Ubiquitin - a small (8.5-kd) protein present in all eukaryotic cells
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 3

4. Isopeptide bond is formed.
Ubiquitin covalently binds to -amino group of lysine residue on a protein destined to be degraded.
Isopeptide bond is formed. 4

5. 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) 5

6. Chains of ubiquitin are generated.
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. 6

7. What determines ubiquitination of the protein?
1. The half-life of a protein is determined by its amino-terminal residue (N-terminal 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) 7

8. Digestion of the Ubiquitin-Tagged Proteins
What is the executioner of the protein death?
A large protease complex proteasome or the S proteasome digests the ubiquitinated proteins.
26S proteasome - ATP-driven multisubunit protease.
26S proteasome consists of two components:
20S - catalytic subunit
19S - regulatory subunit 8

9. active sites are located in  rings on the interior of the barrel
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) 9

10. made up of 20 polipeptide chains
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) 10

11. Fates of carbon skeleton of amino acids

12. 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

13. Pyruvate as an Entry Point into Metabolism

14. 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.

15. -Ketoglutarate as an Entry Point into Metabolism

16. Succinyl Coenzyme A Is a Point of Entry for Several Nonpolar Amino Acids

17. Methionine Degradation
S-adenosylmethionine (SAM) - a common methyl donor in the cell
Homocysteine promotes the development of vascular diseases and atherosclerosis

18. 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.

19. Degradation of Aromatic Amino Acids
Acetoacetate, fumarate, and pyruvate — are common intermediates.
Molecular oxygen is used to break an aromatic ring.
homogentisate oxidase
+O2
tetrahydro-biopterin
PA hydro-xylase

20. Tryptophan degradation requires several oxygenases
Pyruvate

21. 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

22. Conversion of arginine to NO via nitric oxide synthase

23. 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

24. A deficiency of even one amino acid results in a negative nitrogen balance.
In this state, more protein is degraded than is synthesized.

25. The nonessential amino acids are synthesized by quite simple reactions.
The pathways for the formation of the essential amino acids are quite complex.

26. 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