Protein Biochem 1

Question 1

number of aa

Answer 1

20 (have specific tRNAs

about 300 overall

Question 2

2 aa into collagen

Answer 2

hydroxyproline (Hyp)
hydroxylysine (Hyl)

Hyp: used in collagen for H-bonding that increases collagen strength. Prolyl hydroxylase converts Pro to Hyp.

Hyl: use in collagen for interchain crosslinks. Lysyl hydroxylase converts Lys to Hyl
-interstrand cross links between Lys and Hyl–covalent interaction (lysyl oxidase)

collagen is most abundant protein in human body

• triple helix
• tensile strength

Question 3

What to prolyl hydroxylases and lysyl hydroxylase need?

Answer 3

Vit C (ascorbate) as coenzyme
-Lack of Vit C leads to scurvy (reduced collagen strength)

Question 4

Scurvy

Answer 4

• reduced strength of collagen fibrils due to deficiency in Vitamin C
• reduced vascular strength
• hemorrhages
• loss of red blood cells
• bruising
• anemia
• swollen gums

Question 5

Gamma carboxyglutamate (Gla)

Answer 5

• Glutamic acid modified by gamma glutamylcarboxylase (a transmembrane protein)
• makes gamma carboxyglutmate (Gla) which has 2 negative charges
• Vit K dependent

Effect: chelate Ca2+ leads to conformational changes

• Prothrobin uses Gla to target membranes.
• N-terminal domain of prothrombin is “Gla domain”
• Gla domain contains 10 Gla residues that bind Ca
• Partially embeds into membrane

Question 6

2 ways for protein degrdations

Answer 6

Ubiquination pathway: ATP dependent
-targets enzyme to proteasome after cross linking protein to ubiquitin

Lysosome engulfs extracellular proteins to mix with digestive enzymes

Question 7

Ubiquitin proteasome mechanism

Answer 7

-Shuttling mech:
E1, E2, E3
-Allows covalent bond b/t ubiquitin and substrate
-Step 1: ATP dependent: Conjugate E1 to ubiquitin, through cysteine
-Pass from one enzyme to next (E1 to E2)
-E2 and E3 complex decide which substrate will get marked for degradation
-E2 modulates how active E3 is by binding to it

Know E1 to E2 to E3
-can get one or many ubiquitins

Question 8

Ubiquitin structure

Answer 8

7 lysine residues

• C terminus has glycine
• Gly Gly will be bound to chain

Ubiquitin put on protein thru lysines and protein gets cut up in proteasome
-Ub recycled

Question 9

Lysosome

Answer 9

-engulfs extracellular proteins to mix with digestive enzymes
-Can engulf larger material like bacteria
-Contains hydrolytic enzymes that include aspartic proteases
Ex: mac and granulocytes

Question 10

Enzymatic degradation of proteins

Answer 10

-In stomach: pepsin (pepsinogen cleaved by HCl)
-In intestine:
enteropeptidase (cleaves trypsinogen to trypsin)
-trypsin produced in pancreas, goes to small intestine: cleaves all other zymogens in SI (chymotrypsinogen, procarboxypeptidase)

Question 11

Trypsin cleaves after

Answer 11

arginine or lysine

Question 12

Chymotrypsin cleaves after

Answer 12

aromatic residue

Question 13

Aspartic Protease

Answer 13

Pepsin: hydrolyzes N terminal of aromatic residues (phe, trp, tyr)

Question 14

Serine proteases

Answer 14

Trypsin: hydrolyzes C terminal side of basic amino acids (arg, lys)

Chymotrypsin: hydrolyzes C terminal side of aromatic and some hydrophobic residues (phe, trp, typr and leu, met)

Question 15

Metallocarboxypeptidases

Answer 15

Carboxypeptidase A: hydrolyzes C terminal of hydrophic aa (Ala, Ile, Leu, Val)

Carboxypeptidase B: hydrolyzes C terminal of basic residues aa ( arg, lys)

Question 16

Aminotransferases

Answer 16

(transaminases) transfer amino groups
- point is to get rid of nitrogen
- catalyze rxn of an alpha keto acid and an amino acid to another alpha keto acid and amino acid

• reversible rxn & Keq 1
• goal: produce Asp, NH3 for urea cycle
• hundreds of aminotransferases within our genome
• mostly in cytosol of cells and especially abundant in liver, kidney, intestine, muscle
• **increased lvls in blood indicate liver damage/disease

Question 17

Alanine aminotransferase (ALT)

Answer 17

alanine + alpha ketoglutarate pyruvate + glutamate

Question 18

Aspartate aminotransferase (AST)

Answer 18

aspartate + alpha ketoglutarate oxaloacetate + glutamate

Question 19

Glutamate from AST and ALT rxns

Answer 19

• ALT path: glutamate turned into NH3+ that is incorporated into urea cycle by Glu dehydrogenase
• AST path: use bidirectionality to make aspartate that feeds into urea cycle

Question 20

Transamination requires

Answer 20

Vitamin B6 (derivative is pyridoxal phosphate PLP)

• holds amino group during transfer
• waits for other ketoacid to transfer it to

Question 21

Schiff base

Answer 21

In the resting state, PLP forms a Schiff Base with the aminotransferase.
-Covalent linkage holds PLP in resting enzyme

Question 22

Control points for protein catabolism

Answer 22

1. The directionality of transamination (by ALT and AST) is regulated by the relative concentrations of “substrates and products”
2. N-acetylglutamate is a required activator of carbamoyl phosphate synthetase I that kick starts the urea cycle (ie protein degradation)
3. The directionality of oxidative deamination by Glu dehydrogenase depends on the relative conc of GLU, alpha-ketoglutarate, NH3
4. ATP and GTP are allosteric inhibitors of Glu dehydrogenase while ADP and GDP are activators

Question 23

Urea Cycle

Answer 23

purpose:
get rid of ammonia by forming something less toxic (urea)

Why? ammonia is toxic, body cannot store aa (hyperammonemia)

-cerbral edema, coma, death can come from hyperammonemia

Question 24

Entry points for nitrogen in urea cycle

Answer 24

1. aspartic acid (aspartate)

2. free ammonia

Question 25

Overall sum of urea cycle

Answer 25

3ATP + HCO3- + NH4+ + aspartate –>

2ADP + AMP + 2Pi + PPi + fumarate +urea