Exam 1

Question 1

Where will trypsin cut?

Answer 1

After positive residues (R or K); Not after P

Question 2

Where will chymotrypsin cut?

Answer 2

After bulky/aromatic residues (F, Y, W, L); Not after P

Question 3

Where is the phi angle?

Answer 3

Between the central carbon and carbonyl group

Question 4

Where is the psi angle?

Answer 4

Between the central carbon and NH group

Question 5

Handedness of alpha helicies?

Answer 5

right

Question 6

What’s the pseudo-repeat sequence of alpha-keratin?

Answer 6

heptad: np, p, p, np, p, p, p

Question 6

Handedness of alpha keratin (2 helicies)

Answer 6

left

Question 7

Handedness of individual collagen fiber

Answer 7

left

Question 8

Handedness of whole collagen triple helix

Answer 8

right

Question 9

Repeat pattern of collagen

Answer 9

Gly-X-Y (X, Y often Pro-Hyp)

Question 10

Triose Phosphate Isomerase (TIM)

Answer 10

Beta barrel in the middle surrounded by alpha helices; 8 fold repeated beta-alpha repeat

Question 11

Myoglobin

Answer 11

stores oxygen, contains 1 heme group, oxygen coordinated by heme and histidine

Question 12

Hemoglobin

Answer 12

transports/ delivers oxygen, 4 subunits with C2 symmetry; two alpha chains and two beta chains

Question 13

Neuraminidase

Answer 13

C4 tetramer; active site puts carbon 2 in a strained confirmation, changing the structure from tetrahedral to planar

Question 14

Pyruvate dehydrogenase core

Answer 14

Octahedral symmetry; 32 subunits

Question 14

Cholera toxin

Answer 14

one A-subunit with enzymatic activity and five B-subunits with sugar binding capability that form a ring with C5 cyclic symmetry; pore in B where A binds

Question 15

Hemocyanin

Answer 15

hexamer with dihedral D3 symmetry; oxygen bound by two Cu(I) ions and 6 histidines

Question 16

F-actin

Question 17

GroES symmetry?

Answer 17

C7 symmetry

Question 18

GroEL symmetry?

Answer 18

D7 (14 subunits): trans and cis rings

Question 18

GroEL/GroES

Answer 18

C7 symmetry with 21 subunits; hydrolyzes 7 ATP per single protein

Question 18

ATCase

Answer 18

multimer with six Catalytic (C - substrate) and six Regulatory (R - ATP/CTP) subunits

Question 19

Hemagglutinin

Question 20

Km

Answer 20

amount of substrate that gives 1/2 Vmax; coefficient of break down of ES (k-1 + k2) divided by coefficient of build up (k1)

Question 21

Michaelis-Menten equation

Answer 21

v0 = Vmax [S] / Km + [S]

Question 22

reaction mechanisms of RNase A

Answer 22

Acid-base catalysis involving two histidine residues, one as a general acid and the other as a general base (and then switched)

Question 23

reaction mechanism of carbonic anhydrase

Answer 23

metal ion catalysis using zinc ion -- Zn polarizes water making it more likely to donate it's proton to histidine

Question 24

reaction mechanism of serine protease

Answer 24

covalent catalysis (Ser forms covalent bond with peptide to be cleaved --> transiently creates tetrahedral C), concerted acid-base catalysis (His as a general acid and base), transition state stabilization (oxyanion hole); acyl-enzyme intermediate formed

Question 25

Competitive inhibition

Answer 25

inhibitor binds to the active site; increases Km by a factor alpha and Vmax is unchanged

Question 26

Uncompetitive inhibition

Answer 26

inhibitor binds to the enzyme-substrate complex; divde Vmax and Km by a factor alpha prime (same factor for both), slope unchanged

Question 27

Mixed inhibition

Answer 27

inhibitor binds to both the enzyme substrate complex and free enzyme; divide Vmax by factor alpha prime and scale Km by a alpha/alpha prime (sslope and intercept changed

Question 28

noncompetitive (mixed) inhibition

Answer 28

Inhibitor binds both E and ES with equal affinity --> alpha = alpha prime; no change to Km and decreased Vmax

Question 29

K'i

Answer 29

[ES][I]/ [ESI]; the smaller the Ki' the better the inhibitor

Question 30

Oxidation state of PDI for improperly connected disulfides

Answer 30

reduced PDI, stays reduced

Question 31

oxidation state of PDI for protein without disulfides that need it

Answer 31

oxidized PDI, ends reduced