Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry > Midterm 1 > Flashcards

Midterm 1 Flashcards

1
Q

very non-polar side chains

A

hydrocarbon dominated, alanine, valine, leucine, isoleucine, phenylalanine, methionine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

moderately non-polar side chains

A

glycine, cysteine, proline, tryptophan, tyrosine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

polar but uncharged side chains

A

good hydrogen bond donors or acceptors, serine, threonine, asparagine, glutamine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

positively charged side chains, very polar

A

weak bases that gain H+, histidine, lysine, arginine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

negatively charged side chains, very polar

A

aspartate, glutamate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Alanine

A

Ala, A

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Valine

A

Val, V

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Leucine

A

Leu, L

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Isoleucine

A

Ile, I

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Phenylalanine

A

Phe, F

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Methionine

A

Met, M

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Glycine

A

Gly, G

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Cysteine

A

Cys, C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Proline

A

Pro, P

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Tryptophan

A

Trp, W

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Tyrosine

A

Tyr, Y

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Serine

A

Ser, S

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Threonine

A

Thr, T

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Asparagine

A

Asn, N

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Glutamine

A

Gln, Q

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Histidine

A

His, H

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Lysine

A

Lys, K

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Arginine

A

Arg, R

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Aspartate

A

Asp, D

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Glutamate

A

Glu, E

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

neutral when protonated, -1 when deprotonated

A

aspartate, glutamate, tyrosine, cysteine, C-terminus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

+1 when protonated, neutral when deprotonated

A

arginine, histidine, lysine, N-terminus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

specific enzyme activity formula

A

specific activity=enzyme activity/total protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

enzyme activity

A

moles of substrate or product converted per unit time, rate of reaction x volume

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

enzyme units

A

amount of enzyme needed to convert 1 micro mol of substrate to product per minute

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

specific activity

A

enzyme activity per mass of protein/enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

trypsin

A

cuts after arginine or lysine but not if followed by proline

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

alpha helix

A

AA have same orientation and turn in same direction, 3.6 AA per turn, distance between each turn is 5.4 A

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

amino acids that prefer alpha helix

A

ala, arg, gln, glu, his, leu, lys, met

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

amino acids that prefer beta sheets

A

trp, tyr, val, ile, thr, cys

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

secondary structure breakers

A

gly, pro, asn, asp, ser, 2 breakers in a group of 4 AA break structure and forms turn or loop

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

hydrophobic effect

A

folding encloses most non-polar AA in core, polar on outside

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

michaelis and menten equation

A

Vo=Vmax[s]/km+[s]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Km

A

concentration of substrate where rate = 50% of max rate, low km means enzyme uses substrate well

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

if [s]=km then

A

Vo = 0.5

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

y-intercept for straight line graph

A

1/Vmax

42
Q

x-intercept for straight line graph

A

-1/Km

43
Q

slope of straight line graph

A

Km/Vmax

44
Q

inactivators

A

react with enzymes irreversibly, uses up enzyme

45
Q

inhibitors

A

decreases enzyme activity without destroying functions

46
Q

competitive inhibition

A

binds to enzyme, increases Km, Vmax stays constant

47
Q

non competitive inhibition

A

binds to enzyme/substrate, Km stays constant, decreases Vmax

48
Q

partition chromatography

A

stationary phase: solid particles chosen with specific properties, mobile phase: liquid buffer flows past particles and is non polar, polar AA spend more time bonded to silica and move slowly

49
Q

thin layer chromatography

A

silica gel spread thin on plastic sheet, samples applied on lower edge, lower edge placed in solvent, as sheet soaks up solvent different samples move at different rate, highest point reached is solvent front, polar AA have low Rf non polar have high Rf

50
Q

ninhydrin

A

reacts with primary and secondary amines to give purple color, yellow for proline, used with TLC plate

51
Q

fluorescamine

A

gives yellow fluorescence under UV light, amino acid detection

52
Q

ion exchange chromatography

A

separates based on charge, uses charged resins as stationary phase, cation exchanger contains negative groups which bind to cations, anion exchanged contains positive groups which bind to anions, elution completed by adding high ion concentration (NaCl) which changes the pH and alters charge on amino acid so it no longer binds

53
Q

affinity chromatography

A

chemical group ligand is attached to beads in column, proteins with affinity to ligand bind tightly, others eluted quickly, bound proteins are eluted after adding high salt concentration that weakens bond

54
Q

Tag

A

peptide or protein that binds to ligand with high affinity

55
Q

immobilized metal affinity chromatography (IMAC)

A

His in protein bind to Ni2+ or Co2+, his residues are fused to target protein at N or C terminus (his tag), column of chelating resin with Ni2+, his tagged proteins bind tightly to resin, bound protein is eluted by adding imidazole, high degree of purification

56
Q

gel filtration/molecular exclusion

A

separation based on size, polymeric beads have water filled pores that small protein molecules can fit into and travel through, larger proteins cannot fit and elude first

57
Q

electrophoresis

A

doesn’t contribute to purification as structure is often affected, can determine number of different proteins and degree of purity, rate of movement depends on size shape and charge, smaller and more charge move faster

58
Q

polyacrylamide gel

A

electrophoresis carries out here, proteins visualized by adding dye

59
Q

SDS-polyacrylamide gel electrophoresis (SDS-PAGE)

A

protein pre treated with detergent sodium dodecyl sulfate which binds to proteins and partially unfolds them, gives protein a large negative charge, proteins have charge per unit size, separation on size small proteins travel faster

60
Q

isoelectric focusing

A

separation based isoelectric point of proteins (pH at which net charge on protein is 0), at high pH protein is deprotonated moves toward + electrode, as it passes through gradient of decreasing pH it becomes protonated, when net charge=0 protein stops moving

61
Q

two dimensional gels

A

separation of complex proteins, combines isoelectric focusing and SDS electrophoresis

62
Q

kiloDaltons

A

protein size, 1 dalton =1g/mol

63
Q

stereoisomers

A

central carbon of all AA is chiral (except glycine), so 2 possible stereoisomers, AA in proteins are L configuration

64
Q

condensation

A

removal of H2O from units being linked

65
Q

hydrolysis

A

regenerates original carboxylic acid and amino groups using water

66
Q

residues

A

amino acids in protein chains due to water being removed

67
Q

average molecular weight of amino acid

A

128-18=110

68
Q

number of amino acids residues in protein

A

molecular weight of protein/110

69
Q

henderson-hasselbalch equation

A

pH=pKa + log deprotonated/protonated

70
Q

dep/pro

A

x/1-x

71
Q

nucleophilic substitution

A

X: + C-Y —> X-C + Y:

72
Q

nucleophilic addition

A

X: + C=Y —> X-C-Y

73
Q

fluorodinitrobenzene, fred sagner

A

tags first AA in protein at N-terminus, turns bright yellow, can only identify first AA and hydrolysis destroys rest of chain

74
Q

edman degradation

A

allows N-terminus to be reacted removed and identified without destroying, can be repeated up to 50 times, coupling and cyclization

75
Q

coupling

A

PITC reacted with N terminal in basic conditions

76
Q

cyclization

A

under acidic conditions the N terminus amino acid is extracted, shortened peptide remains

77
Q

cyanogen bromide

A

cuts chain after methionine, met is converted into homoserine (Hse, serine with extra CH2), only C terminus is without Hse

78
Q

conformations

A

states of a molecule that can be interconverted by bond rotations without breaking covalent bonds

79
Q

configurations

A

can only be interchanged by breaking covalent bonds

80
Q

angstrom unit

A

1A = 1x10^-10 meter

81
Q

alpha helix C=O will bond with

A

N+4

82
Q

extended beta strand and beta sheet

A

amino acids alternate orientation
antiparallel- strands in opposite directions, more stable
parallel- strands in same directions

83
Q

beta sheets maximum space for

A

WYF
VIT
C

84
Q

antiparallel barrel

A

polar sheet on outside non polar sheet on inside

85
Q

alpha beta barrel

A

mostly no polar AA

86
Q

hydrogen bonding

A

forms between donors and acceptors that line up in folded protein, secondary structure

87
Q

disulfide bonds

A

hold together tertiary structure

88
Q

proximity effect

A

enzyme holds substrate close together long enough for reaction to proceed, increases Z

89
Q

orientation effect

A

enzyme binds so reactive groups are ideally aligned, increases p

90
Q

nucleophilic catalysis

A

enzymes speed up reaction by providing better nucleophile

91
Q

electrophilic catalysis

A

initiates reaction by withdrawing electrons from substrate

92
Q

general acid catalysis

A

catalysis by amino acid side chain that donates H+ to rxn

93
Q

general base catalysis

A

catalysis by an amino acid side chain that removes H+ from reaction

94
Q

transition state

A

less Ea is needed if enzyme active site is complementary to transition state

95
Q

chymotrypsin

A

phe, tyr, trp, but not if followed by P

96
Q

catalytic triad

A

asp, his and ser line up side by side in chymotrypsin to increase effectiveness

97
Q

absorbance formula

A

A=log Intensity initial/intensity final

98
Q

beers law

A

A= c x l x Ɛ

99
Q

molar activity

A

activity per mole of enzyme, specific activity x molar mass of enzyme

100
Q

rate of reaction

A

change in conc. of substrate or product per unit time

101
Q
A

Biochemistry (1 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions