Biochem Chap 1

Question 1

What is zwitterion?

Answer 1

At pH ~ 7 - amino group is positive and carboxylic acid is negative

Question 2

What configuration are amino acids found in body?

Answer 2

L

Question 3

What catalyzes peptide bonds?

Answer 3

Ribosomes

Question 4

What type of reaction is a peptide bond?

Answer 4

Nucleophilic substitution reaction - carbonyl is electrophile - nucleophile is nitrogen.

Then electrons reform a second bond - dehydration reaction.

Question 5

What type of bond is a peptide bond and what character does it have?

Answer 5

Peptide bond - amide bond - partial double bond character

Question 6

What type of reaction results in breakage of peptide bonds?

Answer 6

Hydrolysis

Question 7

What is a parallel vs. antiparallel beta sheet?

Answer 7

parallel - both strands of polypep run in same direction - antiparallel - opposite directions.

Question 8

What are some post-translation modifications?

Answer 8

include phosphorylation at certain amino acid residues, formation of disulfide bonds, glycosylation or linkage of short carb polymers to protein, ubiquitination (attaching of protein ubiquitin that marks protein as target for degredation)

Question 9

What are some features of glycine?

Answer 9

single hydrogen side chain - least sterically hindered amino acid - rotate and move more easily - found in areas of protein which need high amount of flexibility and rotation

Question 10

What are some features of cysteine?

Answer 10

as thiol (SH) at side chain - ability to bind other cysteines through formation of disulfide bond (S-S). Important to tertiary and quaternary structures of many proteins

Question 11

What are some features of proline?

Answer 11

most sterically hindered - not a lot of rotational ability and creates kind in protein - found where bend is needed.

Question 12

What is the hydrophobic effect?

Answer 12

Consequence of nonpolar and polar interactions - hydrophobic amino acids found in inside. Also has to do with entropy - measure of disorder in system. When outer residues are polar, water in solvation layer can form hydrogen bonds. Increases entropy

Question 13

What can disrupt protein folding?

Answer 13

pH, salt concentration (including molecules like urea), temperature. Can also cause denaturation

Question 14

What facilitates protein folding

Answer 14

Chaperones assist in folding denatured proteins back into native state

Question 15

What amino acids have S vs. R config?

Answer 15

All 19 amino acids are S-config except cysteine because the thiol side chain has higher priority making it R.