Amino Acids, Peptides, and Protein I

Question 1

Hydrophobic and non-polar amino acids

Answer 1

Valine
Isoleucine
Leucine
Methionine
Phenylalanine
Tryptophan
Cystine
(LIMP- TV Channel)

Question 2

hydrophilic and polar amino acids

Answer 2

argenine
lysine
aspartate
glutamate
asparagine
glutamine

Question 3

acidic amino acids

Answer 3

aspartate

glutamate

Question 4

basic amino acids

Answer 4

lysine
arginine
histidine

Question 5

what may interactions between positive and negative R groups form?

Answer 5

salt bridge important for stabilization in proteins

Question 6

what is a disulfide bond?

Answer 6

covalent linkage between two sulfer atoms specifically between cystine residues (thiol groups)

Question 7

which amino acid has a sulfur bond but cannot participate in a disulfide bond?

Answer 7

methionine

Question 8

where are disulfide bonds usually found within a folded protein?

Answer 8

on the inside because they are hydrophobic

Question 9

what are the 6 major post-translational modifications that we need to know?

Answer 9

1. hydroxylation of proline
2. carboxylation of glutamate
3. modification by acetylation or methylation
4. glycosylation
5. reversible phosphorylation/dephosphorylation
6. ubiquination

Question 10

what adds a hydroxyl group to proline residue?

Answer 10

prolyl hydroxylase

Question 11

what is the predominate secondary structure in collagen and how is it formed?

Answer 11

proline helix

formed by multiple prolines and hydroxyprolines in a row

Question 12

what is the cofactor of prolyl hydroxylase?

Answer 12

vitamin C

Question 13

what disease results as a lack of vitamin C and which structure is affected?

Answer 13

scurvy, loss of integrity in connective tissues becase lack of proline hydroxylation

Question 14

which enzyme adds a carboxyl group to the side chain of glutamate?

Answer 14

Gamma-glutamyl carboxylase

Question 15

what is the co-factor of carboxylation of glutamate?

Answer 15

vitamin K

Question 16

where is carboxylation of glutamate mostly found?

Answer 16

within clotting factors

Question 17

what will a lack of vitamin K cause in regards to carboxylation of glutamate?

Answer 17

hemorrhage

Question 18

how does waafarin work?

Answer 18

blood thinner that prevents clotting by inhibiting activity of gamma-glutamyl carboxylase

Question 19

where does acetylation by HATs usually occur?

Answer 19

lysine residues of free tails of histones

Question 20

where does methylation usually occur and by which enzyme?

Answer 20

lysine and arginine residues on histones by methyltransferases

Question 21

what type of inhibitor is Vorinostat?

Answer 21

HDAC inhibitor

Question 22

what is the mechanism of Vorinostat?

Answer 22

prevents removal of acetyl groups from histones. Tumors usually use deacetylation to repress tumor suppresor genes.

Question 23

what is glycosylation?

Answer 23

attaching glycans (sugars) to proteins

Question 24

what are the 4 types of glycans?

Answer 24

1. N-linked glycans
2. O-linked glycans
3. phospho-glycans
4. C-linked glycans

Question 25

what amino acids to N-linked glycans attach to?

Answer 25

asparagine and arginine side chains

Question 26

what amino acids to O-linked glycans attach to?

Answer 26

serine, threonine, tyrosine, hydroxylysine, hydroxyproline side chains

Question 27

where do phospho-glycans attach?

Answer 27

phosphate of phospho-serine

Question 28

where do C linked glycans attach?

Answer 28

carbon on tryptophan side chain

Question 29

True of False

Glycosylation makes protein more polar

Answer 29

true

Question 30

what is the purpose of glycosylation?

Answer 30

• proper protein folding
• increased stability of secreted glycoproteins
• cell to cell adhesion
• role in recognition

Question 31

what genetic disease does disruption in N-glycosylation lead to?

Answer 31

Congenital disorder of glycosylation (CDG)

Question 32

what is the presentation of congenital disorder of glycosylation (CDG)?

Answer 32

developmental delay and hypertonia

Question 33

what mutation causes congenital disorder of glycosylation (CDG)?

Answer 33

PMM2 gene, autosomal recessive

Question 34

which amino acids does phosphorylation usually occur?

Answer 34

serine, threonine, tyrosine

phosphate group added to OH

Question 35

what does phosphorylation do?

Answer 35

activates or deactivates proteins and does reverse with dephosphorylation

Question 36

what is the target of Gleevac?

Answer 36

bcr-abl tyrosine kinase

Question 37

what disease is Gleevac used to treat?

Answer 37

Chronic myelogenous leukemia (CML)

Question 38

what is the mechanism of action of Gleevac?

Answer 38

kinase inhibitor: prevents bcr-abl tyrosine kinase from phosphoyrlating tyrosine by competitively binding to active site

Question 39

what is the most common type of modification of amino acids in cells?

Answer 39

ubiquination

Question 40

what is the function of ubiquination?

Answer 40

targets protein for destruction from the proteosome

Question 41

what is the process of ubiquination?

Answer 41

adds ubiquitin to lysine residues, addition of one recruits several more

Question 42

what disease does bortezomib treat?

Answer 42

multiple myeloma

Question 43

what kind of drug is bortezomib classified as?

Answer 43

proteasome inhibitor

Question 44

what is the mechanism of bortezomib?

Answer 44

boron atom in bortezomib binds to catalytic site of 26S proteasome with high affinity and specificity

Question 45

what is the theory of proteasome inhibition?

Answer 45

prevents degredation of pro-apoptotic factors permitting programmed cell death in cells dependent on suppression of pro-apoptotic pathways