Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

MCB 3010 > EXAM 1 > Flashcards

EXAM 1 Flashcards

1
Q

phi

A

nitrogen carbon

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

psi

A

carbon carbon

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

ramachandron plot

A

distribution of phi and psi dihedral angles

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

alpha helix stabilized by

A

H bonds between nearby residues

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

b sheet stablized by

A

H bonds between segments of peptide chain

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

alpha helix residues per turn

A

3.6

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

helical backbone

A

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

parallel to helical axis

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

helical side chains

A

point out, perpendicular with axis (CO down)

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

average AA in helix

A

12

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

proline (helix)

A

helical breaker, because rotation is impossible (kink)

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

glycine (helix)

A

helical breaker, tiny R group is flexible for other conformations

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

what affects formation of helix

A

interactions bw side chains 3-4 AA apart

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

glycine and proline (beta)

A

break it

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

common in sheets

A

aromatic (more space) and branched

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

branched AA

A

thr, val, ile

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

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

antiparallel b sheets

A 
H bonds in opposite directions
linear H bonds (stronger)
fewer strands for stable
B turns
1 repeat = 7
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

strand length

A

6 AA

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

sheet length

A

2-22 strands

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

b turns

A

antiparallel, short turnaround

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

AA in a b turn

A

4 AA

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

what stabilized b turns

A

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

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

proline position in b turn

A

2 OR glycine in 3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
proline isomers
peptide bond not with proline are trans with proline? 6% cis conformation in beta turns
26
proline isomerases
catalyze proline isomerization for righter turn than trans
27
Circular dichroism (CD) analysis
measures difference in molar absorption of left and right circularly polarized light signals depend on chain conformation
28
tertiary structure
stabilized by weak interactions bw AA side chains hydrophobic and polar disulfide and ionic
29
2 classes tertiary structure
globular | fibrous
30
globular proteins
combo of helices and b sheets w beta turns or loops water soluble hydrophobic interactions drive folding
31
fibrous proteins
collagen helix alpha keratin silk fibroin
32
collagen helix
3 left handed helical strands w a right handed twist
33
alpha keratin
2 alpha helices twist together nonpolar AA at interface of 2 helices disulfide bonds link pp to pack together
34
permanent weaving
reduce disulfide bonds to sulfhydryl gropus, then durl, then oxidize
35
silk fibroin
antiparallel b sheet | small side chains for close packing (ala, gly)
36
silk fibroin is stabilized by
h bonding within sheets | van der waals between sheets
37
motifs
subset of tert specific arrangements of several secondary structure elements
38
b-a-b loop
1st b sheet linked by alpha helix to another parallel b sheet
39
a/b barrel
formed with b-a-b loops inside; alpha helices on outside
40
a/b
alpha helix and b sheet together and alternate
41
a + b
separate regions of protein
42
protein domain
region of protein that folds independently and can be stable if separated diff parts of pp diff functionalities in 1 protein
43
4 structure
assembly of pp | subunits with same or diff function
44
intrinsically disordered proteins
segments that lack definable structure some AA condusive to this (Lys, Arg, Glu, Pro) promiscuous
45
XRAY crystallography
``` purify crystalize diffraction data calculate electron density fit residues into density ```
46
XRAY C: pros
no size limits, well established
47
XRAY C: cons
difficult for membrane proteins , cannot see H (no e-), cannot see flexible regions, inhibit crystal formation how close to native structure is crystal?
48
Biomolecular NMR
purify collect NMR data, protein in solution assign signals calculate structure
49
NMR pros
no need to crystallize protein, see hydrogens, see flexibility
50
NMR cons
needs to be soluble protein, best with small proteins, diff possibilities leads to diff structures
51
denaturation methods
heat or cold pH organic solvents or detergents chaotropic agents (urea, guanidine hydrochloride)
52
ribonuclease
small protein with 8 cysteines linked w 4 disulfide bonds
53
ribonuclease denaturation
urea and 2-mercaptoethanol (reductant) | sequence alone determines conformation
54
speed of protein folding
proteins fold to the lowest energy fold in second time scales direction toward the native structure is thermodynamically most favorable
55
functions of globular proteins
``` storage transport defense against pathogens muscle contraction biological catalysis ```
56
how do ligands bind
noncovalent forces (hydrophobic, ionic, van der waals) allow transience
57
equillibrium constant
Ka
58
dissociation constant
Kd
59
Kd
P*L / PL
60
lower Kd?
greater affinity for ligand
61
Y =
binding sites occupied / total binding sites
62
Y = [PL]
[PL]/[PL] + [P]
63
Y = [L]
L/ L + Kd
64
when does [L] = Kd
when half of all binding sites are occupied Y=½
65
P50 =
Y
66
Kd is the
concentration of ligand which causes half the binding sites to be filled
67
induced fit model
conformational changes occur upon binding tighter binding high affinity for diff ligands both can change conformations
68
can AA bind O2?
no
69
why can't transition metals bind O2?
generate free radicals
70
myoglobin
storage 1 pp chain tissues binds o2 w high affinity 1 O2 on 1 heme
71
hemoglobin
transport 4 pp chains (2 a/b dimers) RBC high affinity, cooperativity 4 O2 on 4 heme
72
how many coordination sites does iron have
6 4 for porphyrin nitrogens (heme itself) 1 proximal histidine 1 oxygen binding
73
distal histidine in heme
H bonds with oxygen bound to heme group, promotes O2 binding not on heme itself
74
why is CO toxic
competes with oxygen, blocks function of myo, hemo, mitochondrial cytochromes
75
proximal histidine
on iron in heme
76
allosteric regulation
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
cooperativity
case of allosteric binding multiple sites for same ligand binding of one ligand influences binding of others
78
cooperativity sequential model
o2 on one site goes from T to R and then another shifts
79
concerted model
all subunits in low or high affinity state
80
T state
tense lower affinity for O2 more interactions (salt bridges) therefore mores table cavity from salt bridges
81
r state
relaxed higher affinity for O2 fewer interactions, more flexible
82
conf change from T to R
``` oxygen binds, iron pulls into heme group heme straightens out iron pulls forward pulls proximal histidine pulls f helix ```
83
3 ways hemoglobin binding is affected
pH CO2 2,3-BPG
84
pH and bohr effect
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
CO2 bohr effect
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
2,3,-BPG
binds to central cavity of hemoglobin on T state, stabilizes binds + amino acids (has many -) --> ionic interactions
87
2,3BPG and altitude
at high altitudes: more 23BPG made to increase offloading of 02 at tissues, compensates for low pO2 in atomosphere rightward shift, decreased affinity
88
sickle cell anemia
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
most enzymes are
globular proteins
90
enzymes
increase reaction rates without being used up, does not affect equilibrium or dG
91
rRNA catalyzes...
formation of peptide bond
92
some RNA can..
catalyze reactions
93
why are enzymes selective?
protein structure only allows sufficient noncovalent interactions with its substrate for catalysis to proceed
94
phenylalanine hydroxylase
puts OH group on phenylalanine opposite chirality? interactions not sufficient
95
cofactor
inorganic ion or complex organic or metalorganic molecule needed for enzyme function
96
cofactorS
coenzyme | prosthetic group
97
coenzymes
organic or metallorganic cofactor permanently bound or leaves to be recycled often changed in catalysis and must be changed back to original state
98
prosthetic group
cofactor that is covalently bound to protein must be recycled within the protein
99
enzyme commission number (EC)
refers to catalytic activities regardless of source of enzyme
100
pre steady state
substrate binding all enzyme, making ES complex
101
steady state
ES complex stays the same; as product leaves, new substrate immediately binds
102
transition state
unstable chemical species formed during enzyme reaction
103
what is the rate limiting step
transition state formation | highest free energy and may decay to substrate or product
104
transition state of catalyzed reaction
Not ES or EP --> in between
105
activation energy
energy to reach TS required to convert S to P
106
catalysis produces
intermediates with lower activation energies
107
ways to catalyze reactions
desolvate the substrate alignment of 2 or more substrates break one reaction up into several with lower activation energies
108
how does desolving the substrate by binding to an enzyme catalyze reactions?
adds strains in covalent bonds that leads to a similar structure to TS --> induced fit changes shape
109
how does alignment of 2 or more substrates catalyze a reaction?
binding to enzyme betters orientation
110
how does an enzyme bind a substrate
noncovalent interactions of interactions b/w E and S increase until transition state is reached
111
dGb
binding energy difference between the AE of uncatalyzed and catalyzed reaction
112
acid base catalysis
give and take protons amino acids involved might have changed pKas because H+ may come off between interactions with different groups
113
covalent catalysis
change reaction path through formation of transient covalent bonds requires a nucleophile A/B + X --> A/X + B --> A + X + B
114
metal ion catalysis
metal ion in enzymes acts as a redox cofactor can interact with substrate (stabilize -) or participate in redox reactions (bind/release e)
115
catalytic mechanisms
acid base covalent metal ion
116
nucleophiles for covalent catalysis
OH in serine Sulfhydryl amine carboxylate
117
kinetics is affected by
``` enzyme substrate effectors temperature pH ```
118
enzyme kinetics
presence, concentration, effectiveness
119
substrate kinetics
concentration, match for active site
120
temperature kinetics
increase temp = better
121
ph kinetics
all are pH dependent
122
catalytic perfection
specificity constant close to diffusion controlled upper limit (10^8 or 9)
123
specificity constant
Kcat/Km
124
Kcat
Vmax/[Et]
125
random sequential
each substrate binds but both must be bound to form a ternary complex before catalysis can occur
126
ordered sequential
substrate 1 must bind before substrate 2 can bind and then catalysis occurs intersect before y axis
127
ping pong mechanism
only one substrate bound at a time, intrinsically ordered parallel lines
128
enzyme inhibitors
compounds that decrease an enzyme's activity ``` irreversible inhibitors (inactivators) reversible inhibitors ```
129
irreversible inhibitors
``` 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
reversible inhibitors
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
competitive inhibition
competes with substrate for binding on active site does not affect catalysis (can outcompete with high [s])
132
graph of competitive inhibition
no change in Vmax, increase in Km lines intersect at y axis
133
uncompetitive inhibition
inhibitor binds to ES complex not active site inhibits catalysis, usually with 2 or more substrates
134
graph of uncompetitive inhibition
decrease in Vmax, decrease in Km parallel lines
135
mixed inhibition
binds enzyme with or without substrate binds to regulatory site decreases rate of catalysis 2 or more S
136
graph of mixed inhibition
decreased Vmax, inc or dec Km | lines intersect to left of y axis
137
regulation of enzyme activity
can allow some enzymes to be active only in certain locations in the cell
138
types of enzyme activity regulation
allosteric regulation reversible covalent modifications irreversible covalent modifications
139
allosteric regulation
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
reversible covalent modifications
functional group covalently added or removed from enzyme can change: properties of AA conformation of protein location of protein in cell
141
types of reversible covalent modifications
phosphorylation acetylation myristoylation
142
phosphorylation
phosphate on serine, threonine, histidine, tyrosine
143
acetylation
acetyl on Nterm of lysine or whole polypeptide chain
144
myristoylation
hydrophobic chain to relocation proteins to membrane
145
irreversible covalent modification
removal of portion of enzyme zymogen --> enzyme proprotien --> protein active until degraded
146
dispersion kJ/mol
24
147
in vivo buffer
phosphate bicarbonate histidine
148
in vitro buffer
phosphate acetate tris base sulfonic acids of cyclic amines (HEPES, PIPES)
149
buffer additives
SaH EDTA dithriothreitol / b-mercaptoethanol detergents
150
SaH
controls ionic strength (too high or low, p precipitates)
151
EDTA
binds metal ions
152
dithriothreitol / b-mercaptoethanol
maintains sulfhydryl groups in reduced state
153
thioester
know it
154
inorganic phospahte
know it
155
gibbs free energy
max amount of energy used for "work" that can be extracted from a thermodynamic system at constant temp and pressure
156
heat is a ____ of reactions
common byproduct
157
most useful energy
chemical | light
158
DH
total E in a thermodynamic system reflects bonds
159
broken bonds
absorb energy
160
formed bonds
releases energy
161
relative free energy
dG'* maximum of free energy available or needed constant; reflects relative free energy of the reactants to products dependent on intrinsic energy
162
when [reactants] = [products] = 1
dG'* = -RTlnKeq
163
actual free energy change
dG = dG'* + RTlnKeq
164
functions of protein
catalysis transport structure motion
165
aliphatic nonpolar R groups
``` glycine alanine proline valine leucine isoleucine methionine ```
166
aromatic R groups
phenylalanine tyrosine tryptophan
167
polar uncharged R groups
``` serine threonine cysteine asparagine glutamine ```
168
negatively charged R gropus
aspartate | gluatamate
169
positively charged R groups
lysine arganine histidine
170
how do uncommon AA arise
post translational modifications of AA reversible phosphorylation
171
hydrophathy index
how phobic (+) or philic (-) a molcule is free energy when AA goes from an organic solvent to water
172
how do chemical environments affect pKas?
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)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions