Protein Biochemistry I

Question 1

What two post-translational modifications of AA lead to collagen?

Answer 1

Hydroxyproline and Hydroxylysine

Question 2

What mediates interstrand H-bonds formed by Hyp

Answer 2

Water molecules; increases strength of fibrils

Question 3

What enzyme creates interstrand x-links between lys & hyl

Answer 3

lysyl oxidase

• schiff base (covalent interaction)

Question 4

Hyp vs. Hyl interactions

Answer 4

Hyp: electrostatic interstrand H-bonds
Hyl: covalent interstrand X-links

Question 5

Prolyl Hydroxylase

Lysl Hydroxylase

Answer 5

Prolyl hydroxylase converts Pro to Hyp
Lysyl hydroxylase converts Lys to Hyl

Both require ascorbate (lack of Vit C leads to Scurvy - reduced strength of collagen fibrils)

Question 6

Scurvy patho

Answer 6

Reduced vascular endothelium –> hemorrhages –> loss of RBCs –> swollen gums, bruising, anemia

Question 7

Gamma-carboxyglutamate

Answer 7

Glu –(Gamma-glutamyl carboxylase) –> gamma carboxyglutamate

• Vit K dependent
• Important because negative charge at terminus and chelation of heavy metal = bury the negative charge
• Charge normally on outside of protein except membrane proteins

Question 8

Prothrombin uses Gla to target membranes

Answer 8

• N-terminal domain of prothrombin is “Gla domain”
• Gla domain contains 10 Gla residues that bind Ca
• Partially embeds into membrane (yellow)

Question 9

2 ways to degrade proteins

Answer 9

1. Ubiquination pathway targets enzymes to the proteasome and is ATP-dependent
2. The lysosome engulfs extracellular proteins to mix with digestive enzymes

Question 10

Ubiquitin-proteasome mechanism

Answer 10

To get to the proteasome, have to go through a shuttle of 3 enzymes (E1, E2, and E3)

• 1st step is ATP-dependent: conjugates E1 to Ubiquitin; done through a cysteine thioester bond
• Shuttled from there and is not ATP-dependent
• At the end, the E3-E2 complex dictate which substrate gets marked with ubiquitin for degradation
• Proteasome cuts protein into pieces and recycles ubiquitin

Question 11

Do all ubiquitinated things go to the garbage?

Answer 11

No– some are involved in signaling

Question 12

Lysosome

Answer 12

• engulfs extracellular proteins to mix with digestive enzymes
• engulf larger material such as bacteria as well
• contains hydrolytic enzymes that include aspartic proteases

Question 13

Enzymatic degradation in stomach and small intestine

Answer 13

Stomach: pepsin (aspartic protease)

Intestine: trypsin, chymotrypsin, (serine proteases) carboxypeptidase A and B (metalloproteases)

Acidically activated from zymogen form at low pH

Question 14

Enteropeptidase

Answer 14

Activates trypsinogen –> trypsin

Activates procarboxypeptidsase-A &B–> carboxypeptidase A&B

Question 15

Aminotransferases

Answer 15

Transfer amino groups

L-amino acid –> alpha keto acid

Question 16

Transamination reactions

Answer 16

• Reversible reaction Keq = 1
• Major goal is to produce Asp and NH3 for Urea cycle
• 100s of aminotransferases that are selective for a few AA
• Mostly in cytosol
• Increased levels indicate liver damage/disease

Question 17

2 most important aminotransferases

Answer 17

1. ALT –> pyruvate

2. AST –> oxaloacetate

Question 18

Glutamate acts as a shuttle for which products?

Answer 18

1. Free ammonia for urea cycle

2. Aspartic acid for urea cycle

Question 19

Pyridoxal Phosphate (PLP)

Answer 19

• Vitamin B6
• A required coenzyme for aminotransferases
• “holds” the amino group and waits for another reaction to occur
• active form is the phosphorylated form of B6

Question 20

Schiff base

Answer 20

This is when PLP kept around, held in place by the aminotransferase so that it can do another reaction

Question 21

Control points for protein catabolism

Answer 21

1. Directionality of transamination is regulated by relative concentrations of substrates and products (regulating nitrogen entry into urea cycle)
2. N-acetylgutamate is required activator of carbamoyl phosphate synthetase I that kick starts the urea cycle
3. The directionality of oxidative deamination by Glu dehydrogenase depends on the relative concentrations of GLU, alpha-ketoglutarate, NH3
4. ATP & GTP are allosteric inhibitors of Glu dhydroenase while ADP & GDP are activators

Question 22

Purpose of the Urea Cycle

Answer 22

Get rid of ammonia because there is no storage

Ammonia is toxic in the blood - can cause cerebral edema, coma, and death

Question 23

Overall sum of Urea Cycle Reactions

Answer 23

• Need 3 ATP to go through the cycle once

- 2 Entry points of nitrogen (free ammonia, and aspartate)