TA Review 1 Flashcards
Exam 2
1
Q
when enzymes stabilize the transition state, what do they do?
A
reduce activation energy
2
Q
chymotrypsin pocket is
A
large and hydrophobic
3
Q
Trypsin pocket is
A
contains aspartate (- charged)
4
Q
Elastase pocket is
A
size constrained
5
Q
binds to small aa like glycine, alanine, valine
A
Elastase
6
Q
binds to positively charged aa residues like argenine and lysine
A
trypsin
7
Q
binds more hydrophobic aa residues, such as tryptophan and phenylalaline
A
chymotrypsin
8
Q
pancreatic enzymes are
A
serine proteases
9
Q
catalytic machinery is composed of
A
catalytic triad and oxyanion hole
10
Q
serine 195 acts as an
A
alkoxide
11
Q
asp 102, ser 57 and ser 195 form a network of hydrogen bonds that forces ser 195 to be
A
very active
12
Q
what does the oxyanion hole does?
A
stabilizes the transition state via hydrogen bonding
13
Q
catalyze redox reactions
A
oxidoreductase
14
Q
catalyze transfer of chemical group
A
transferase
15
Q
catalyzes cleavage with water
A
hydrolases
16
Q
catalyzes cleavage reaction without water
A
lyases
17
Q
catalyzes change of molecular configuration
A
isomerases
18
Q
catalyzes joining of two compounds
A
ligases
19
Q
process of serine protease (3)
A
(1) attack by serine
(2) stabilization of transition state
(3) release of products
20
Q
release of products in serine protease
A
attack by water causes release of products and regeneration of enzyme
21
Q
delta G = -
A
spontaneous reaction
22
Q
delta G= 0
A
reaction at equilibrium
23
Q
delta G= +
A
non-spontaneous reaction
24
Q
delta G is sensitive to concentration of
A
reactants, products, temperature, pH
25
removal of products drives
forward reaction
26
delta D not can derive
Keq (delta G= -RT ln Keq)
27
catalysts speed up the reaction by
lowering delta G
28
serves as the main source of energy in biosynthetic processes
ATP
29
Sum the delta Gs
coupling unfavorable reactions
30
process of burning ATP for biosynthetic work, active transport, and creation of complex molecules
anabolism
31
process of burning fuel to make ATP
catabolism
32
reaction velocity is dependent on
substrate concentration
33
high Km
weak affinity
34
what does low Km reflects
high affinity and you need less substrate to achieve 1/2 Vmax
35
substrate concentration at which the reaction velocity has achieved 1/2 Vmax
km
36
what will allow you to measure by saturating amounts of substrate
measure Vmax which is proportional to amount of enzyme present
37
how can you measure amount of substrate?
low substrate levels has a linear relationship to enzyme and substrate. Velocity will be directly proportional to amount of substrate present--> good to measure Km
38
increasing enzyme concentration increases?
Vmax but Km is contant
39
coenzymes in nature tend to be
vitamins
40
increased enzymatic activity with vitamin means
enzyme must bind vitamin
41
high or altered levels of enzyme in tissues indicates
diseased state
42
high level of alanine transminase in the blood that balances aa levels in the liver indicates
diseased liver
43
alpha-1 antritrypcin is also made in the liver but is found in blood, meaning that low level of it in blood indicates
diseased liver
44
zymogens
inactive enzymes
45
proteolytic cleavage of zymogen forms
final active form
46
what activates the blood clotting cascade
trauma/endothelial damage activates the cascade
47
prothrombin is made in the
liver
48
after secretion of liver prothrombin associates
on membranes
49
prothrombin is cleaved
at aa 274 to release it from membrane
50
thrombin is a
serine protease
51
cleave of prothrombin at aa 323 will
activate enzyme
52
cleavage of 323 activates
Asp 102, Ser 195 and His 57
53
activated thrombin cleaves
fibrinogen to fibrin
54
what will fibrin do to form clots?
cross link
55
protein inhibitor that binds strongly to thrombin
antithrombin
56
heparin
an anticoagulant that promotes antithrombin binding
57
lung neutrophils release _________ to degrade foreign material
elastase
58
elastase also
breaks down elastin of lungs
59
elastase is inhibited by
alpha 1-antitrypsin
60
what happens to elastase by smoking?
oxidation of alpha-antritrypsin leading to emphysema
61
what can drastically change enzyme activity?
phosphorylation and dephosphorylation
62
competitive inhibitors
compete with the substrate by binding directly to substrate site
63
same Vmax, increased Km (decreased affinity)
competitive inhibitors
64
noncompetitive inhibitor
binds to other location
65
same Km, reduced Vmax
noncompetitive inhibitor
66
irreversible inhibitor
binds like noncompetitive inhibitor but are irreversible
67
covalently modify enzyme
irreversible inhibitor
68
lower Ki
tighter inhibitor binding
69
measure of inhibitor affinity for enzyme
Ki
70
can changes in substrate levels change enzyme activity?
yes
71
S-shape curve on Michaelis-Menten curve
allosteric enzyme
72
Feedback ihibitions =/=
product inhibition
73
regulates committed step of glycolysis
PFK1
74
```
PFK1:
high AMP(low energy state)
```
R-state of PFK1 favored
75
```
PFK1:
low AMP (high energy state)
```
T-state of PFK1 favored
76
only one mutation is needed
for alteration of function
77
encode for growth promoting proteins such as growth factors, receptors, signal transduction molecules, transcription factors
proto-oncogenes
78
mutated and always active
oncogenes
79
enhancer for gene replication proteins in S-phase
E2F
80
has anti-proliferative signals and exerts its effect by binding to E2F and freezing it
pRB
81
Cyclin D/E with kinase and use of ATP will
phosphorylate pRB, causing E2F liberation and binding to gene replication proteins
82
will bind to response elements and inactivate transcription at the G1/S checkpoint
p53
83
Once p53 acts as a trnascription factor and turns on transcription of p21 what happens?
p21 inhibits Cyclin/CDK complex through binding to PCNA and Stops progression of replication fork
84
p53 causes apoptosis via
gene induction of molecules involved in reactive oxygen species
85
Gene:Tumor
pRB
retinoblastoma
86
Gene:Tumor
p53
Sarcomas, Carcinomas
87
Gene:Tumor
NF1
Neuroblastoma
88
Gene:Tumor
APC
Colon, Stomach
89
Gene:Tumor
BRCA 1
Breast Cancer
90
create and respond to their own growth signals
tumor cells
91
how does signal transduction relay signals?
outside the cell to the inside
92
what is PGDF?
Platelet Growth Derived factor is a receptor and tyrosine kinase
93
what so special about the plasma membrane receptors involved in signal transduction?
they penetrate the membrane and have intracellular domain with enzymatic activity
94
tyrosine kinase special something
autophosphorylation
95
what encodes for PDGF?
simian Sarcoma Oncogene
96
Simian Sarcoma causes
excess PDGF production
97
what can growth factor receptors so?
remain active in absence of growth factor
98
mutant EGF Receptor (ErbB/HER2) is a
tyrosine kinase that remains active
99
cancer is caused by an
accumulation of mutations
100
Colon Cancer is caused by (3)
(1) loss of APC
(2) Ras Activation
(3) p53 loss
101
tumor viruses target
tumor supressors
102
SV40 T-antigen stops
pRB binding to E2F and p53 binding to DNA
103
transforms DNA to induce cancer, E6 and E7 work together
HPV
104
E6 stops
p53 binding and proteolysis it
105
E7 binds to
pRB
106
what controls progression through the cell cycle?
cyclins
107
transcription factors that promote transient growth
Fos and Jun
108
transcription factor that regulates expression of 15% of all genes
MyC
109
what happens when MyC is mutated?
there is an upregulation of proliferative genes and proliferation & Cancer
110
involves translocation of Chromosome 8 that encodes for MyC to Chromosome 2, 14, or 22; where there are promoters for antibody molecules
Burkitt's lymphoma
111
In Burkitt's lymphoma constitutive activation of MyC leads to
cancer
112
type of cancer beginning in the immune cells
Burkitt's lymphoma
113
involved in signal transduction
Ras protein
114
inactive Ras is bound to
GDP
115
active Ras has
GTP bound
116
Activated Ras needs
a helper protein or GTPase Activating Protein
117
what happens with Mutant Ras has GTPase Activity affected?
always active and thus excess signal transduction
118
NF1 gene encodes
neurofibromin protein
119
neurofibromin protein
GTPase Activating Protein
120
associated with Cafe-au-lait spots & benign neurofibroma due to faulty Neurofibromin protein
Nuerofibromatosis
121
helper proteins helps Ras
hydrolyze GTP--> GDP
