Overview of protein metabolism

Question 1

Ways to categorize amino acids

Answer 1

Chemical differences:
Acidic or basic: make aa more reactive with substrates or other molecules
Polar or non-polar: make the protein associate with a lipid mono/bilayer or with the aqueous portion of a cell or plasma

Body’s Ability to synthesize:
essential: can’t be synth by body
non-essential: can be synth from other aa
Conditionally essential: can be made by body but in limited capacity, deficiency may develop in critical illness/states of high consymption

Special classes of aa based on specific constituents/structures in side chain
Sulfur containing aa
AA w/ nitrogen in side chain (involved in nitrogen transport)
Branched chain aa
Aromatic aa (precursors for many NT and hormones)

AA can be broken down and carbon skeletons can be used for energy (after removing amino group)
Glucogenic: can be used as substrates for gluconeogenesis
Ketogenic: broken down and generate acetyl CoA, can go through TCA and get ATP or be used for ketone synth

Question 2

2 post-translationally modified aa that need Vitamin C for synthesis

Answer 2

Hydroxy-proline
Hydroxy-lysine

Vitamin C deficiency causes scurvy

Question 3

What does prothrombin use to target membranes?

Answer 3

gamma-carboxyglutamate

Question 4

Breakdown of protein in the diet

Answer 4

• broken down in GI tract by peptidases
• enzymes need to be activated in the gut lumen to be functional
• categorized by enzyme type and type of bond they cleave
• long peptide chains broken down into aa and absorbed and enter circulation

Question 5

Intracellular pathways for protein degradation

Answer 5

• ubiquination: targets proteins for degradation in the proteasome
• degradation in lysosomes

Question 6

Typical transamination rxn

Answer 6

• need to add NH2 to carbon skeleton to make aa
• need to remove NH2 from aa for carbon skeleton to be used in gluconeogenesis.
• usually bidirectional reactions
• in liver, lesser extent kidney, intestine, muscle
• Usually aa donates NH2 group to alpha ketoglutarate to produce L glutamate and alpha keto acid
• aminotransferase catalyzes rxn
• In reverse, NH3 can come off glutamate and alpha ketoglutarate is regenerated
• ammonia is toxic and needs to leave body (urea synthesis)

Question 7

Urea cycle first step

Answer 7

• ammonia that was produced from transamination rxn is converted to carbamoyl phosphate
• rxn catalyzed by carbamoyl phosphate synthase 1 (key regulated step in protein catabolism

Question 8

Where does nitrogen from carbamoyl phosphate go?

Answer 8

• enters urea cycle
• ultimately combined with NH3 from aspartate to form urea which contains 2 nitrogen atoms
• eventually leave body in urine as urine urea nitrogen

Question 9

Second key regulated step in prtein catabolism

Answer 9

• Glutamine has 2 Nitrogen atoms, carries nitrogen to liver and kidney and donates it to glutamate.
• ***Glutamate is converted to alpha ketoglutarate which is catalyzed by glutamate dehydrogenase

Question 10

Minor pathway for nitrogen removal

Answer 10

-involves arginine and the production of nitric oxide

Question 11

Why are sulfur containing aa cysteine and methionine important?

Answer 11

1. Cysteine can form disulfide bridges that change protein conformation
2. S-adenosylmethionine (SAM) is an energy source for imp biochem rxns; also a methyl donor
3. SAM is a precursor to homocysteine: imp in vascular disease, wound healing, involved in B12 and folate metabolism
4. Glutathione is a tri-peptide that contains cysteine, and serves as an important redox buffer, and protects against free radical injury

Question 12

AA with ring structures on side chains

Answer 12

tryptophan
phenylalanine
tyrosine

Precursors for serotonin, niacin, dopamine, epi, norepi, tetrahydrobiopterin, and thyroid hormone.