Midterm 1 Flashcards
(101 cards)
1
Q
very non-polar side chains
A
hydrocarbon dominated, alanine, valine, leucine, isoleucine, phenylalanine, methionine
2
Q
moderately non-polar side chains
A
glycine, cysteine, proline, tryptophan, tyrosine
3
Q
polar but uncharged side chains
A
good hydrogen bond donors or acceptors, serine, threonine, asparagine, glutamine
4
Q
positively charged side chains, very polar
A
weak bases that gain H+, histidine, lysine, arginine
5
Q
negatively charged side chains, very polar
A
aspartate, glutamate
6
Q
Alanine
A
Ala, A
7
Q
Valine
A
Val, V
8
Q
Leucine
A
Leu, L
9
Q
Isoleucine
A
Ile, I
10
Q
Phenylalanine
A
Phe, F
11
Q
Methionine
A
Met, M
12
Q
Glycine
A
Gly, G
13
Q
Cysteine
A
Cys, C
14
Q
Proline
A
Pro, P
15
Q
Tryptophan
A
Trp, W
16
Q
Tyrosine
A
Tyr, Y
17
Q
Serine
A
Ser, S
18
Q
Threonine
A
Thr, T
19
Q
Asparagine
A
Asn, N
20
Q
Glutamine
A
Gln, Q
21
Q
Histidine
A
His, H
22
Q
Lysine
A
Lys, K
23
Q
Arginine
A
Arg, R
24
Q
Aspartate
A
Asp, D
25
Glutamate
Glu, E
26
neutral when protonated, -1 when deprotonated
aspartate, glutamate, tyrosine, cysteine, C-terminus
27
+1 when protonated, neutral when deprotonated
arginine, histidine, lysine, N-terminus
28
specific enzyme activity formula
specific activity=enzyme activity/total protein
29
enzyme activity
moles of substrate or product converted per unit time, rate of reaction x volume
30
enzyme units
amount of enzyme needed to convert 1 micro mol of substrate to product per minute
31
specific activity
enzyme activity per mass of protein/enzyme
32
trypsin
cuts after arginine or lysine but not if followed by proline
33
alpha helix
AA have same orientation and turn in same direction, 3.6 AA per turn, distance between each turn is 5.4 A
34
amino acids that prefer alpha helix
ala, arg, gln, glu, his, leu, lys, met
35
amino acids that prefer beta sheets
trp, tyr, val, ile, thr, cys
36
secondary structure breakers
gly, pro, asn, asp, ser, 2 breakers in a group of 4 AA break structure and forms turn or loop
37
hydrophobic effect
folding encloses most non-polar AA in core, polar on outside
38
michaelis and menten equation
Vo=Vmax[s]/km+[s]
39
Km
concentration of substrate where rate = 50% of max rate, low km means enzyme uses substrate well
40
if [s]=km then
Vo = 0.5
41
y-intercept for straight line graph
1/Vmax
42
x-intercept for straight line graph
-1/Km
43
slope of straight line graph
Km/Vmax
44
inactivators
react with enzymes irreversibly, uses up enzyme
45
inhibitors
decreases enzyme activity without destroying functions
46
competitive inhibition
binds to enzyme, increases Km, Vmax stays constant
47
non competitive inhibition
binds to enzyme/substrate, Km stays constant, decreases Vmax
48
partition chromatography
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
thin layer chromatography
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
ninhydrin
reacts with primary and secondary amines to give purple color, yellow for proline, used with TLC plate
51
fluorescamine
gives yellow fluorescence under UV light, amino acid detection
52
ion exchange chromatography
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
affinity chromatography
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
Tag
peptide or protein that binds to ligand with high affinity
55
immobilized metal affinity chromatography (IMAC)
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
gel filtration/molecular exclusion
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
electrophoresis
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
polyacrylamide gel
electrophoresis carries out here, proteins visualized by adding dye
59
SDS-polyacrylamide gel electrophoresis (SDS-PAGE)
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
isoelectric focusing
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
two dimensional gels
separation of complex proteins, combines isoelectric focusing and SDS electrophoresis
62
kiloDaltons
protein size, 1 dalton =1g/mol
63
stereoisomers
central carbon of all AA is chiral (except glycine), so 2 possible stereoisomers, AA in proteins are L configuration
64
condensation
removal of H2O from units being linked
65
hydrolysis
regenerates original carboxylic acid and amino groups using water
66
residues
amino acids in protein chains due to water being removed
67
average molecular weight of amino acid
128-18=110
68
number of amino acids residues in protein
molecular weight of protein/110
69
henderson-hasselbalch equation
pH=pKa + log deprotonated/protonated
70
dep/pro
x/1-x
71
nucleophilic substitution
X: + C-Y ---> X-C + Y:
72
nucleophilic addition
X: + C=Y ---> X-C-Y
73
fluorodinitrobenzene, fred sagner
tags first AA in protein at N-terminus, turns bright yellow, can only identify first AA and hydrolysis destroys rest of chain
74
edman degradation
allows N-terminus to be reacted removed and identified without destroying, can be repeated up to 50 times, coupling and cyclization
75
coupling
PITC reacted with N terminal in basic conditions
76
cyclization
under acidic conditions the N terminus amino acid is extracted, shortened peptide remains
77
cyanogen bromide
cuts chain after methionine, met is converted into homoserine (Hse, serine with extra CH2), only C terminus is without Hse
78
conformations
states of a molecule that can be interconverted by bond rotations without breaking covalent bonds
79
configurations
can only be interchanged by breaking covalent bonds
80
angstrom unit
1A = 1x10^-10 meter
81
alpha helix C=O will bond with
N+4
82
extended beta strand and beta sheet
amino acids alternate orientation
antiparallel- strands in opposite directions, more stable
parallel- strands in same directions
83
beta sheets maximum space for
WYF
VIT
C
84
antiparallel barrel
polar sheet on outside non polar sheet on inside
85
alpha beta barrel
mostly no polar AA
86
hydrogen bonding
forms between donors and acceptors that line up in folded protein, secondary structure
87
disulfide bonds
hold together tertiary structure
88
proximity effect
enzyme holds substrate close together long enough for reaction to proceed, increases Z
89
orientation effect
enzyme binds so reactive groups are ideally aligned, increases p
90
nucleophilic catalysis
enzymes speed up reaction by providing better nucleophile
91
electrophilic catalysis
initiates reaction by withdrawing electrons from substrate
92
general acid catalysis
catalysis by amino acid side chain that donates H+ to rxn
93
general base catalysis
catalysis by an amino acid side chain that removes H+ from reaction
94
transition state
less Ea is needed if enzyme active site is complementary to transition state
95
chymotrypsin
phe, tyr, trp, but not if followed by P
96
catalytic triad
asp, his and ser line up side by side in chymotrypsin to increase effectiveness
97
absorbance formula
A=log Intensity initial/intensity final
98
beers law
A= c x l x Ɛ
99
molar activity
activity per mole of enzyme, specific activity x molar mass of enzyme
100
rate of reaction
change in conc. of substrate or product per unit time
101
