M114 MT stuff I don't know

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Last updated 9:31 AM on 10/30/25
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108 Terms

1
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Enzyme that turns milk into cheese
rennet
2
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Side chain of ___ & center of benzene is what interaction
Arg, charge-polar
3
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Peptide-peptide is ____-____ interaction
polar-polar
4
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Protein interior has high or low epsilon
low
5
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NPPN
alpha helix
6
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NPNP
antiparallel beta
7
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NNNN
parallel beta
8
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Structure papers generate _____
hypotheses
9
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Tertiary structure is stabilized by
interior packing
10
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3 stabilization strategies
metal coordination, cofactor binding, disulfide bonds
11
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How many AAs does smallest motif contain
3
12
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Where does helix-turn-helix bind to DNA ____ groove
major, C-term
13
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What motif does homeo-domain contain
helix-turn-helix
14
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Active site of four-helix bundle
top or bottom
15
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Active site of globin fold
where heme is
16
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Active site of up-and-down
top or bottom or sides
17
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Active site of beta barrel
center
18
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Active site of Greek Key
top or bottom
19
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Active site of Jelly Roll
top or bottom
20
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Where does saddle bind DNA ____ groove
minor, middle
21
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What part of zinc-finger binds DNA ____ groove
major, alpha helix
22
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Right handed is…, left handed is…
right is counterclockwise, left is clockwise
23
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Active site of TIM barrel
top where arrows point
24
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Active site of beta twist
top where arrows point
25
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Valine loves alpha or beta
beta
26
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What is mutated in sickle cell anemia
beta subunit
27
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3 types of protein movement
fluctuations, collective motions, triggered conformational changes
28
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Who conducted electron microscopy
Joachim Frank
29
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Usual method to set up crystallization is
sitting drop vapor diffusion
30
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Why are crystals cooled in liquid nitrogen
to prevent radiation damage
31
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3 components for structure-based drug design
protein structure, small molecule database, reliable software
32
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Example of protein homology server and what can it conduct
Alpha Fold 3, can conduct protein structure prediction, protein-protein docking, protein-ligand docking
33
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3 criteria for druggable pockets
large, concave, hydrophobic
34
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Isozymes are important for…
producing personalized medicine
35
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Examples of fragment-based softwares
FlexX, LUDI, DOCK
36
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HIV protease structure
dimer
37
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HIV protease active site, conformational change site, drug-binding site
2 red Asp, flaps, above active site
38
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Mechanism of HIV protease
tetrahedral intermediate is transition state analog
39
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P1 and P1’ for HIV protease
P1: Phe, P1’: Pro
40
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_____ are needed to fool HIV protease from mutating
41
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Structure of Mpro
homodimer
42
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P1 and P1’ for Mpro
P1: Gln, P1’: Ser
43
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Mpro strategy is…
suicide inhibitor
44
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What is the method used to quantify coronavirus RNA
qRT-PCR
45
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Where does digitoxigenin bind and inhibit and how
Na-K ATPase by raising [Ca2+]
46
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Order of domains in Ca2+ ATPase
transmembrane above, then left → A, P, N
47
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Where is active site in Ca2+ ATPase
transmembrane domain
48
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Where does ATP bind in Ca2+ ATPase
N domain
49
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Where does foxglove bind
transmembrane domain of E2-P state of Ca2+ ATPase
50
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Potassium channel structure
homotetramer
51
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Mechanism that forms a homodimer
tyrosine kinase
52
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Mechanism that produces cGMP as cyclic messenger
guanylyl cyclase
53
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Mechanism that alters cytoskeleton
integrin
54
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2 strategies to design kinase inhibitor
ATP mimic, lock kinase in inactive conformation
55
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SH3 binds…
proline
56
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SH2 binds…
P-Tyr
57
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PTB binds…
P-Tyr
58
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PH binds…
IP3 (in membrane)
59
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IP: what binds insulin
alpha subunit
60
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IP: what gets phosphorylated
beta subunit
61
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IP: what undergoes conformational change
activation loop
62
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IP: what domain(s) does IRS-1 have and what does it do
PTB, binds P-Tyr on beta subunit
63
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IP: what domain(s) does Grb2 have and what does it do
SH2 binds IRS-1 (P-Tyr), SH3 binds SOS (proline-rich)
64
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IP: what does REM domain of SOS bind
Switch 2 of RAS
65
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IP: what does Cdc25 domain of SOS bind
Switch 1 of RAS
66
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IP: what conformation do Switch 1 and 2 need to be in to interact with Raf1
”in”
67
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IP: what does Ras target
Raf1
68
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IP: what is kicked off Raf-1
14-3-3
69
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IP: what does Raf-1 target
MEK
70
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IP: what are the 3 proteins in phosphorylation cascade
Raf-1, MEK, ERK
71
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IP: what is the only protein that enters the nucleus
phosphorylated ERK
72
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Ras is a drug target against…
cancer
73
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What is the intermediate formed by RNase
5-mem ring
74
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Why are vanadates good RNase inhibitors
they mimic 5-mem ring
75
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3 possible RNase mechanisms
general acid-base, lewis acids, electrophilic catalysis
76
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Hammerhead ribozyme cleavage mechanism is _____
acid-base catalysis
77
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Angiozyme inhibits…
cancer
78
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Hepatozyme inhibits…
Hepatitis C
79
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Herzyme inhibits…
cancer
80
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Prof. Luptak used _____ to conduct in vitro evolution of ribozyme
transition state analog
81
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What are the 4 ribosome binding sites and where are they located
E,P,A on larger subunit, mRNA on smaller subunit
82
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Why do proteins in ribosome have an unusual shape
because they only play a supporting role
83
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First tRNA connected to Met binds to __ site
P
84
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Incoming tRNA binds to __ site
A
85
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Peptide bond forms at __ site
P
86
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Release factor binds to __ site
A
87
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What is the quaternary structure of the release factor
homotrimer
88
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What is the AA in active site for ribosome
adenine
89
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Puromycin binds to __ site
A
90
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Two other antibiotics that target ribosome are…
tetracycline and erythromycin
91
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3 stages of CRISPR-CAS
adaptation, expression, interference
92
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3 strategies for bacteria to protect themselves against phage
restriction enzymes, biofilm, CRISPR-CAS
93
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2 types of CRISPR-CAS
cascade complex, Cas9 complex
94
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RNAi: ____ binds ____
siRNA binds mRNA
95
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CRISPR-i: ____ binds ____
crRNA binds DNA
96
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Type I seahorse complex is called ____
CASCADE
97
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How many copies of C in type I seahorse complex
6
98
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Why was the E subunit assigned wrong
because of low resolution
99
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What forms the groove to bind crRNA
6 CasC
100
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What CASCADE subunit(s) bind 3’
CasE