Exam 1

Question 1

hydrophobic effect

Answer 1

increases entropy by freeing water molecules
number of unordered water molecules increases

Question 2

peptide bond formation

Answer 2

dehydration/condensation, water removed

Question 3

peptide bond breaking

Answer 3

hydrolysis, water is added

Question 4

omega bond can either be ___ or ____ and is usually

Answer 4

180, 0, 180

Question 5

which bond can rotate freely

Answer 5

phi and psi

Question 6

phi

Answer 6

n - ca

Question 7

psi

Answer 7

ca-c

Question 8

which aa has more areas on rp

Answer 8

glycine

Question 9

which aa has less areas on rp

Answer 9

proline

Question 10

pka is what for protons

Answer 10

when pka=ph, 50% of protons are lost

Question 11

what is the best buffering for a weak acid

Answer 11

+/- 1 ph from the pka

Question 12

pka 1 for amino acids with neutral side chains

Answer 12

2

Question 13

pka2 for amino acids with neutral side chains

Answer 13

9

Question 14

if given a peptide with lots of rkh, what does this mean about pi

Answer 14

high pi

Question 15

is pi is 2,3,4 what does this mean abt side chains

Answer 15

acidic side chains present

Question 16

pi is the point where

Answer 16

the net charge on the protein is 0

Question 17

at a pH below the pi

Answer 17

more protons available, side chains protonated, will have + charge

Question 18

at pH above the pI

Answer 18

protons LEAVE, side chains are DEPROTONATED, there will be - charge

Question 19

lower pI =

Answer 19

more acidic side chains (ED), easily deprotonated at physiological pH

Question 20

higher pI

Answer 20

more basic side chains (RKH), harder to deprotonate at physiological pH

Question 21

primary protein structure

Answer 21

linear arrangement of amino acids from n to c

Question 22

secondary protein structure

Answer 22

regularly repearting pattern of H bonding from backbone chain

Question 23

tertiary protein structure

Answer 23

many interactions between side chain to form 3d shape

Question 24

quant protein structure

Answer 24

multiple tertiary structures associate w each other

Question 25

h bond in alpha helix between

Answer 25

i and i+4

Question 26

residues/turn for alpha helix

Answer 26

3.6

Question 27

rise/residue for alpha helix

Answer 27

1.5 a

Question 28

rise/turn for alpha helix

Answer 28

5.4

Question 29

what aa in not common in alpha helix

Answer 29

proline

Question 30

why are h bonds stronger in antiparallel

Answer 30

h bonds are strongest at 18- degrees

Question 31

how many a between strands in bs

Answer 31

4

Question 32

how many a between r groups on same bs face

Answer 32

7

Question 33

which two aa are common in beta turns

Answer 33

proline and glycine

Question 34

keratin coils are held together by

Answer 34

hydrophobic interactions

Question 35

collegen is made up of

Answer 35

3 left hand helixes (gly-x-y, glycine proline hydroxyproline)

Question 36

silk is

Answer 36

stacked antiparallel beta sheets

Question 37

if u sub a hydrophobic aa for a hydrophilic aa would keratin form

Answer 37

no

Question 38

pH

Answer 38

protein is positive (binds cation exchanger)

Question 39

pH>pI in ion exchange

Answer 39

protein is negative (binds anion exchanger)

Question 40

elution for ion exchange

Answer 40

increase salt to disrupt binding, adjust pH to change protein charge and reduce binding ability

Question 41

diethylaminoethyl

Answer 41

weak anion exchanger

Question 42

carboxymethyl

Answer 42

weak cation exchanger

Question 43

which proteins elute first is sec

Answer 43

large

Question 44

elution in affinity chromatography

Answer 44

high concentration of ligand solution

Question 45

disfavorable entropy in protein folding

Answer 45

exteended chain to one folded conformation

Question 46

favorable entropy change in pf

Answer 46

water molecules freeed

Question 47

favorable enthalpy changes

Answer 47

stronger h-h bonds, salt bridges, dipole, and vdw

Question 48

pI

Answer 48

point where net charge on protein is 0

Question 49

lysine pkr

Answer 49

10.5

Question 50

arginine pkr

Answer 50

12.5

Question 51

histidine pkr

Answer 51

6

Question 52

glutamic acid pkr

Answer 52

4

Question 53

aspartate pkr

Answer 53

3.5

Question 54

cysteine pkr

Answer 54

8

Question 55

tyrosine pkr

Answer 55

10

Question 56

carboxylic acid pkr

Answer 56

2-3

Question 57

amine group pkr

Answer 57

8.5-9.5

Question 58

hydrophobic aa

Answer 58

GAV LIMP

Question 59

polar uncharged

Answer 59

stncq

Question 60

basic aa

Answer 60

rkh

Question 61

acidic aa

Answer 61

ed

Question 62

aromatic aa

Answer 62

fwy