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MCB 3010 > EXAM 1 > Flashcards

EXAM 1 Flashcards

1
Q

phi

A

nitrogen carbon

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2
Q

psi

A

carbon carbon

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3
Q

ramachandron plot

A

distribution of phi and psi dihedral angles

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4
Q

alpha helix stabilized by

A

H bonds between nearby residues

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5
Q

b sheet stablized by

A

H bonds between segments of peptide chain

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6
Q

alpha helix residues per turn

A

3.6

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7
Q

helical backbone

A

H bonds of NH and CO of an n and N+4 bond

parallel to helical axis

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8
Q

helical side chains

A

point out, perpendicular with axis (CO down)

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9
Q

average AA in helix

A

12

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10
Q

proline (helix)

A

helical breaker, because rotation is impossible (kink)

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11
Q

glycine (helix)

A

helical breaker, tiny R group is flexible for other conformations

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12
Q

what affects formation of helix

A

interactions bw side chains 3-4 AA apart

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13
Q

helix dipole

A 
peptide bonds similar orientatino
large macrosocpic dipole moment
- residues near N term
\+ residues near C term
2 helices in antiparallel
might point into active site to stabilize catalysis
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14
Q

glycine and proline (beta)

A

break it

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15
Q

common in sheets

A

aromatic (more space) and branched

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16
Q

branched AA

A

thr, val, ile

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17
Q

parallel b sheets

A

H bonds in same direction
angled H bonds (weaker)
1 repeat = 6.5
more strands to be stable

never less than 5 strands

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18
Q

antiparallel b sheets

A 
H bonds in opposite directions
linear H bonds (stronger)
fewer strands for stable
B turns
1 repeat = 7
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19
Q

strand length

A

6 AA

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20
Q

sheet length

A

2-22 strands

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21
Q

b turns

A

antiparallel, short turnaround

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22
Q

AA in a b turn

A

4 AA

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23
Q

what stabilized b turns

A

H bond from carbonyl oxygen to amide hydrogen bw 1 and 4 residues

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24
Q

proline position in b turn

A

2 OR glycine in 3

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25
Q

proline isomers

A

peptide bond not with proline are trans

with proline? 6% cis conformation in beta turns

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26
Q

proline isomerases

A

catalyze proline isomerization for righter turn than trans

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27
Q

Circular dichroism (CD) analysis

A

measures difference in molar absorption of left and right circularly polarized light

signals depend on chain conformation

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28
Q

tertiary structure

A

stabilized by weak interactions bw AA side chains

hydrophobic and polar
disulfide and ionic

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29
Q

2 classes tertiary structure

A

globular

fibrous

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30
Q

globular proteins

A

combo of helices and b sheets w beta turns or loops

water soluble
hydrophobic interactions drive folding

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31
Q

fibrous proteins

A

collagen helix
alpha keratin
silk fibroin

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32
Q

collagen helix

A

3 left handed helical strands w a right handed twist

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33
Q

alpha keratin

A

2 alpha helices twist together
nonpolar AA at interface of 2 helices
disulfide bonds link pp to pack together

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34
Q

permanent weaving

A

reduce disulfide bonds to sulfhydryl gropus, then durl, then oxidize

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35
Q

silk fibroin

A

antiparallel b sheet

small side chains for close packing (ala, gly)

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36
Q

silk fibroin is stabilized by

A

h bonding within sheets

van der waals between sheets

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37
Q

motifs

A

subset of tert

specific arrangements of several secondary structure elements

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38
Q

b-a-b loop

A

1st b sheet linked by alpha helix to another parallel b sheet

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39
Q

a/b barrel

A

formed with b-a-b loops inside; alpha helices on outside

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40
Q

a/b

A

alpha helix and b sheet together and alternate

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41
Q

a + b

A

separate regions of protein

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42
Q

protein domain

A

region of protein that folds independently and can be stable if separated
diff parts of pp
diff functionalities in 1 protein

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43
Q

4 structure

A

assembly of pp

subunits with same or diff function

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44
Q

intrinsically disordered proteins

A

segments that lack definable structure
some AA condusive to this (Lys, Arg, Glu, Pro)
promiscuous

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45
Q

XRAY crystallography

A 
purify
crystalize
diffraction data
calculate electron density
fit residues into density
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46
Q

XRAY C: pros

A

no size limits, well established

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47
Q

XRAY C: cons

A

difficult for membrane proteins , cannot see H (no e-), cannot see flexible regions, inhibit crystal formation

how close to native structure is crystal?

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48
Q

Biomolecular NMR

A

purify
collect NMR data, protein in solution
assign signals
calculate structure

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49
Q

NMR pros

A

no need to crystallize protein, see hydrogens, see flexibility

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50
Q

NMR cons

A

needs to be soluble protein,
best with small proteins,
diff possibilities leads to diff structures

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51
Q

denaturation methods

A

heat or cold
pH
organic solvents or detergents
chaotropic agents (urea, guanidine hydrochloride)

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52
Q

ribonuclease

A

small protein with 8 cysteines linked w 4 disulfide bonds

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53
Q

ribonuclease denaturation

A

urea and 2-mercaptoethanol (reductant)

sequence alone determines conformation

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54
Q

speed of protein folding

A

proteins fold to the lowest energy fold in second time scales
direction toward the native structure is thermodynamically most favorable

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55
Q

functions of globular proteins

A 
storage 
transport
defense against pathogens
muscle contraction
biological catalysis
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56
Q

how do ligands bind

A

noncovalent forces (hydrophobic, ionic, van der waals)

allow transience

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57
Q

equillibrium constant

A

Ka

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58
Q

dissociation constant

A

Kd

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59
Q

Kd

A

P*L / PL

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60
Q

lower Kd?

A

greater affinity for ligand

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61
Q

Y =

A

binding sites occupied / total binding sites

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62
Q

Y = [PL]

A

[PL]/[PL] + [P]

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63
Q

Y = [L]

A

L/ L + Kd

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64
Q

when does [L] = Kd

A

when half of all binding sites are occupied

Y=½

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65
Q

P50 =

A

Y

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66
Q

Kd is the

A

concentration of ligand which causes half the binding sites to be filled

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67
Q

induced fit model

A

conformational changes occur upon binding

tighter binding
high affinity for diff ligands
both can change conformations

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68
Q

can AA bind O2?

A

no

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69
Q

why can’t transition metals bind O2?

A

generate free radicals

70
Q

myoglobin

A

storage

1 pp chain

tissues

binds o2 w high affinity

1 O2 on 1 heme

71
Q

hemoglobin

A

transport

4 pp chains (2 a/b dimers)

RBC

high affinity, cooperativity

4 O2 on 4 heme

72
Q

how many coordination sites does iron have

A

6

4 for porphyrin nitrogens (heme itself)
1 proximal histidine
1 oxygen binding

73
Q

distal histidine in heme

A

H bonds with oxygen bound to heme group, promotes O2 binding

not on heme itself

74
Q

why is CO toxic

A

competes with oxygen, blocks function of myo, hemo, mitochondrial cytochromes

75
Q

proximal histidine

A

on iron in heme

76
Q

allosteric regulation

A

binding of ligand to one site affects binding properties of a different site on same protein

ligands can be positive or negative and same/different

77
Q

cooperativity

A

case of allosteric binding
multiple sites for same ligand
binding of one ligand influences binding of others

78
Q

cooperativity sequential model

A

o2 on one site goes from T to R and then another shifts

79
Q

concerted model

A

all subunits in low or high affinity state

80
Q

T state

A

tense

lower affinity for O2
more interactions (salt bridges) therefore mores table
cavity from salt bridges

81
Q

r state

A

relaxed

higher affinity for O2
fewer interactions, more flexible

82
Q

conf change from T to R

A 
oxygen binds, iron pulls into heme group
heme straightens out
iron pulls forward
pulls proximal histidine
pulls f helix
83
Q

3 ways hemoglobin binding is affected

A

pH
CO2
2,3-BPG

84
Q

pH and bohr effect

A

H+ stabilizes T state
protonates 3rd histidine which forms salt bridge, leads to release of O2 in tissues

DECREASED AFFINITY

pH difference between lungs and metabolic tissues increase efficiency of O2 transport

85
Q

CO2 bohr effect

A

15-20% Co2 exported in carbamate on N-term residues of subunits in hemoglobin
carbamate forms additional salt bridges, stabilizing T state

yields proton, contributes to Bohr effect

86
Q

2,3,-BPG

A

binds to central cavity of hemoglobin on T state, stabilizes

binds + amino acids (has many -) –> ionic interactions

87
Q

2,3BPG and altitude

A

at high altitudes: more 23BPG made to increase offloading of 02 at tissues, compensates for low pO2 in atomosphere
rightward shift, decreased affinity

88
Q

sickle cell anemia

A

mutation: glutamate 6 binds to valine in beta chain

new valine side chain binds to a hydrophobic patch on a different side chain during deoxy state

causes chains to form, sickling cells, which blocks vessels

89
Q

most enzymes are

A

globular proteins

90
Q

enzymes

A

increase reaction rates without being used up, does not affect equilibrium or dG

91
Q

rRNA catalyzes…

A

formation of peptide bond

92
Q

some RNA can..

A

catalyze reactions

93
Q

why are enzymes selective?

A

protein structure only allows sufficient noncovalent interactions with its substrate for catalysis to proceed

94
Q

phenylalanine hydroxylase

A

puts OH group on phenylalanine

opposite chirality? interactions not sufficient

95
Q

cofactor

A

inorganic ion or
complex organic or
metalorganic molecule needed for enzyme function

96
Q

cofactorS

A

coenzyme

prosthetic group

97
Q

coenzymes

A

organic or metallorganic cofactor

permanently bound or leaves to be recycled

often changed in catalysis and must be changed back to original state

98
Q

prosthetic group

A

cofactor that is covalently bound to protein

must be recycled within the protein

99
Q

enzyme commission number (EC)

A

refers to catalytic activities regardless of source of enzyme

100
Q

pre steady state

A

substrate binding all enzyme, making ES complex

101
Q

steady state

A

ES complex stays the same; as product leaves, new substrate immediately binds

102
Q

transition state

A

unstable chemical species formed during enzyme reaction

103
Q

what is the rate limiting step

A

transition state formation

highest free energy and may decay to substrate or product

104
Q

transition state of catalyzed reaction

A

Not ES or EP –> in between

105
Q

activation energy

A

energy to reach TS required to convert S to P

106
Q

catalysis produces

A

intermediates with lower activation energies

107
Q

ways to catalyze reactions

A

desolvate the substrate

alignment of 2 or more substrates

break one reaction up into several with lower activation energies

108
Q

how does desolving the substrate by binding to an enzyme catalyze reactions?

A

adds strains in covalent bonds that leads to a similar structure to TS –> induced fit changes shape

109
Q

how does alignment of 2 or more substrates catalyze a reaction?

A

binding to enzyme betters orientation

110
Q

how does an enzyme bind a substrate

A

noncovalent interactions

of interactions b/w E and S increase until transition state is reached

111
Q

dGb

A

binding energy

difference between the AE of uncatalyzed and catalyzed reaction

112
Q

acid base catalysis

A

give and take protons

amino acids involved might have changed pKas because H+ may come off between interactions with different groups

113
Q

covalent catalysis

A

change reaction path through formation of transient covalent bonds

requires a nucleophile

A/B + X –> A/X + B –> A + X + B

114
Q

metal ion catalysis

A

metal ion in enzymes acts as a redox cofactor

can interact with substrate (stabilize -) or participate in redox reactions (bind/release e)

115
Q

catalytic mechanisms

A

acid base
covalent
metal ion

116
Q

nucleophiles for covalent catalysis

A

OH in serine
Sulfhydryl
amine
carboxylate

117
Q

kinetics is affected by

A 
enzyme
substrate
effectors
temperature
pH
118
Q

enzyme kinetics

A

presence, concentration, effectiveness

119
Q

substrate kinetics

A

concentration, match for active site

120
Q

temperature kinetics

A

increase temp = better

121
Q

ph kinetics

A

all are pH dependent

122
Q

catalytic perfection

A

specificity constant close to diffusion controlled upper limit (10^8 or 9)

123
Q

specificity constant

A

Kcat/Km

124
Q

Kcat

A

Vmax/[Et]

125
Q

random sequential

A

each substrate binds but both must be bound to form a ternary complex before catalysis can occur

126
Q

ordered sequential

A

substrate 1 must bind before substrate 2 can bind and then catalysis occurs

intersect before y axis

127
Q

ping pong mechanism

A

only one substrate bound at a time, intrinsically ordered

parallel lines

128
Q

enzyme inhibitors

A

compounds that decrease an enzyme’s activity

irreversible inhibitors (inactivators)
reversible inhibitors
129
Q

irreversible inhibitors

A 
react with enzyme
bind covalently
or
destroy functional group
or form stable noncovalent interactions
1 can shut off 1 enzyme molecule
will not dissociate
130
Q

reversible inhibitors

A

bind to and then dissociate from enzyme (temporary inhibit)

can be structural analogs of substrates or products

can bind to free enzyme and prevent S binding

can bind to ES and prevent catalysis

131
Q

competitive inhibition

A

competes with substrate for binding on active site

does not affect catalysis (can outcompete with high [s])

132
Q

graph of competitive inhibition

A

no change in Vmax, increase in Km

lines intersect at y axis

133
Q

uncompetitive inhibition

A

inhibitor binds to ES complex not active site

inhibits catalysis, usually with 2 or more substrates

134
Q

graph of uncompetitive inhibition

A

decrease in Vmax, decrease in Km

parallel lines

135
Q

mixed inhibition

A

binds enzyme with or without substrate

binds to regulatory site

decreases rate of catalysis

2 or more S

136
Q

graph of mixed inhibition

A

decreased Vmax, inc or dec Km

lines intersect to left of y axis

137
Q

regulation of enzyme activity

A

can allow some enzymes to be active only in certain locations in the cell

138
Q

types of enzyme activity regulation

A

allosteric regulation

reversible covalent modifications

irreversible covalent modifications

139
Q

allosteric regulation

A

binding of small molecule (effector/modulator)

noncovalent NOT active site

almost always reversible

structural change; affect Km or Vmax

allosteric enzymes often have many subunits (catalytic or regulatory AND catalytic)

140
Q

reversible covalent modifications

A

functional group covalently added or removed from enzyme

can change:
properties of AA
conformation of protein
location of protein in cell

141
Q

types of reversible covalent modifications

A

phosphorylation

acetylation

myristoylation

142
Q

phosphorylation

A

phosphate on serine, threonine, histidine, tyrosine

143
Q

acetylation

A

acetyl on Nterm of lysine or whole polypeptide chain

144
Q

myristoylation

A

hydrophobic chain to relocation proteins to membrane

145
Q

irreversible covalent modification

A

removal of portion of enzyme
zymogen –> enzyme
proprotien –> protein

active until degraded

146
Q

dispersion kJ/mol

A

24

147
Q

in vivo buffer

A

phosphate
bicarbonate
histidine

148
Q

in vitro buffer

A

phosphate
acetate
tris base
sulfonic acids of cyclic amines (HEPES, PIPES)

149
Q

buffer additives

A

SaH
EDTA
dithriothreitol / b-mercaptoethanol
detergents

150
Q

SaH

A

controls ionic strength (too high or low, p precipitates)

151
Q

EDTA

A

binds metal ions

152
Q

dithriothreitol / b-mercaptoethanol

A

maintains sulfhydryl groups in reduced state

153
Q

thioester

A

know it

154
Q

inorganic phospahte

A

know it

155
Q

gibbs free energy

A

max amount of energy used for “work” that can be extracted from a thermodynamic system at constant temp and pressure

156
Q

heat is a ____ of reactions

A

common byproduct

157
Q

most useful energy

A

chemical

light

158
Q

DH

A

total E in a thermodynamic system

reflects bonds

159
Q

broken bonds

A

absorb energy

160
Q

formed bonds

A

releases energy

161
Q

relative free energy

A

dG’*

maximum of free energy available or needed

constant; reflects relative free energy of the reactants to products dependent on intrinsic energy

162
Q

when [reactants] = [products] = 1

A

dG’* = -RTlnKeq

163
Q

actual free energy change

A

dG = dG’* + RTlnKeq

164
Q

functions of protein

A

catalysis
transport
structure
motion

165
Q

aliphatic nonpolar R groups

A 
glycine
alanine
proline
valine
leucine
isoleucine
methionine
166
Q

aromatic R groups

A

phenylalanine
tyrosine
tryptophan

167
Q

polar uncharged R groups

A 
serine
threonine
cysteine
asparagine
glutamine
168
Q

negatively charged R gropus

A

aspartate

gluatamate

169
Q

positively charged R groups

A

lysine
arganine
histidine

170
Q

how do uncommon AA arise

A

post translational modifications of AA

reversible

phosphorylation

171
Q

hydrophathy index

A

how phobic (+) or philic (-) a molcule is

free energy when AA goes from an organic solvent to water

172
Q

how do chemical environments affect pKas?

A

interaction of alpha amino group and alpha carboxyl group lowers pkas of both

  • stabilization of zwitterion from opposite charges
  • O- oxygen atoms pull electrons from the alpha amino group, lowering its pKa

MCB 3010 (12 decks)

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