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Biochem 2 > TA Review 1 > Flashcards

TA Review 1 Flashcards

Exam 2

1
Q

when enzymes stabilize the transition state, what do they do?

A

reduce activation energy

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2
Q

chymotrypsin pocket is

A

large and hydrophobic

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3
Q

Trypsin pocket is

A

contains aspartate (- charged)

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4
Q

Elastase pocket is

A

size constrained

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5
Q

binds to small aa like glycine, alanine, valine

A

Elastase

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6
Q

binds to positively charged aa residues like argenine and lysine

A

trypsin

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7
Q

binds more hydrophobic aa residues, such as tryptophan and phenylalaline

A

chymotrypsin

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8
Q

pancreatic enzymes are

A

serine proteases

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9
Q

catalytic machinery is composed of

A

catalytic triad and oxyanion hole

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10
Q

serine 195 acts as an

A

alkoxide

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11
Q

asp 102, ser 57 and ser 195 form a network of hydrogen bonds that forces ser 195 to be

A

very active

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12
Q

what does the oxyanion hole does?

A

stabilizes the transition state via hydrogen bonding

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13
Q

catalyze redox reactions

A

oxidoreductase

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14
Q

catalyze transfer of chemical group

A

transferase

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15
Q

catalyzes cleavage with water

A

hydrolases

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16
Q

catalyzes cleavage reaction without water

A

lyases

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17
Q

catalyzes change of molecular configuration

A

isomerases

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18
Q

catalyzes joining of two compounds

A

ligases

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19
Q

process of serine protease (3)

A

(1) attack by serine
(2) stabilization of transition state
(3) release of products

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20
Q

release of products in serine protease

A

attack by water causes release of products and regeneration of enzyme

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21
Q

delta G = -

A

spontaneous reaction

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22
Q

delta G= 0

A

reaction at equilibrium

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23
Q

delta G= +

A

non-spontaneous reaction

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24
Q

delta G is sensitive to concentration of

A

reactants, products, temperature, pH

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25
Q

removal of products drives

A

forward reaction

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26
Q

delta D not can derive

A

Keq (delta G= -RT ln Keq)

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27
Q

catalysts speed up the reaction by

A

lowering delta G

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28
Q

serves as the main source of energy in biosynthetic processes

A

ATP

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29
Q

Sum the delta Gs

A

coupling unfavorable reactions

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30
Q

process of burning ATP for biosynthetic work, active transport, and creation of complex molecules

A

anabolism

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31
Q

process of burning fuel to make ATP

A

catabolism

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32
Q

reaction velocity is dependent on

A

substrate concentration

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33
Q

high Km

A

weak affinity

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34
Q

what does low Km reflects

A

high affinity and you need less substrate to achieve 1/2 Vmax

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35
Q

substrate concentration at which the reaction velocity has achieved 1/2 Vmax

A

km

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36
Q

what will allow you to measure by saturating amounts of substrate

A

measure Vmax which is proportional to amount of enzyme present

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37
Q

how can you measure amount of substrate?

A

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

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38
Q

increasing enzyme concentration increases?

A

Vmax but Km is contant

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39
Q

coenzymes in nature tend to be

A

vitamins

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40
Q

increased enzymatic activity with vitamin means

A

enzyme must bind vitamin

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41
Q

high or altered levels of enzyme in tissues indicates

A

diseased state

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42
Q

high level of alanine transminase in the blood that balances aa levels in the liver indicates

A

diseased liver

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43
Q

alpha-1 antritrypcin is also made in the liver but is found in blood, meaning that low level of it in blood indicates

A

diseased liver

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44
Q

zymogens

A

inactive enzymes

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45
Q

proteolytic cleavage of zymogen forms

A

final active form

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46
Q

what activates the blood clotting cascade

A

trauma/endothelial damage activates the cascade

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47
Q

prothrombin is made in the

A

liver

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48
Q

after secretion of liver prothrombin associates

A

on membranes

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49
Q

prothrombin is cleaved

A

at aa 274 to release it from membrane

50
Q

thrombin is a

A

serine protease

51
Q

cleave of prothrombin at aa 323 will

A

activate enzyme

52
Q

cleavage of 323 activates

A

Asp 102, Ser 195 and His 57

53
Q

activated thrombin cleaves

A

fibrinogen to fibrin

54
Q

what will fibrin do to form clots?

A

cross link

55
Q

protein inhibitor that binds strongly to thrombin

A

antithrombin

56
Q

heparin

A

an anticoagulant that promotes antithrombin binding

57
Q

lung neutrophils release _________ to degrade foreign material

A

elastase

58
Q

elastase also

A

breaks down elastin of lungs

59
Q

elastase is inhibited by

A

alpha 1-antitrypsin

60
Q

what happens to elastase by smoking?

A

oxidation of alpha-antritrypsin leading to emphysema

61
Q

what can drastically change enzyme activity?

A

phosphorylation and dephosphorylation

62
Q

competitive inhibitors

A

compete with the substrate by binding directly to substrate site

63
Q

same Vmax, increased Km (decreased affinity)

A

competitive inhibitors

64
Q

noncompetitive inhibitor

A

binds to other location

65
Q

same Km, reduced Vmax

A

noncompetitive inhibitor

66
Q

irreversible inhibitor

A

binds like noncompetitive inhibitor but are irreversible

67
Q

covalently modify enzyme

A

irreversible inhibitor

68
Q

lower Ki

A

tighter inhibitor binding

69
Q

measure of inhibitor affinity for enzyme

A

Ki

70
Q

can changes in substrate levels change enzyme activity?

A

yes

71
Q

S-shape curve on Michaelis-Menten curve

A

allosteric enzyme

72
Q

Feedback ihibitions =/=

A

product inhibition

73
Q

regulates committed step of glycolysis

A

PFK1

74
Q 
PFK1: 
high AMP(low energy state)
A

R-state of PFK1 favored

75
Q 
PFK1: 
low AMP (high energy state)
A

T-state of PFK1 favored

76
Q

only one mutation is needed

A

for alteration of function

77
Q

encode for growth promoting proteins such as growth factors, receptors, signal transduction molecules, transcription factors

A

proto-oncogenes

78
Q

mutated and always active

A

oncogenes

79
Q

enhancer for gene replication proteins in S-phase

A

E2F

80
Q

has anti-proliferative signals and exerts its effect by binding to E2F and freezing it

A

pRB

81
Q

Cyclin D/E with kinase and use of ATP will

A

phosphorylate pRB, causing E2F liberation and binding to gene replication proteins

82
Q

will bind to response elements and inactivate transcription at the G1/S checkpoint

A

p53

83
Q

Once p53 acts as a trnascription factor and turns on transcription of p21 what happens?

A

p21 inhibits Cyclin/CDK complex through binding to PCNA and Stops progression of replication fork

84
Q

p53 causes apoptosis via

A

gene induction of molecules involved in reactive oxygen species

85
Q

Gene:Tumor

pRB

A

retinoblastoma

86
Q

Gene:Tumor

p53

A

Sarcomas, Carcinomas

87
Q

Gene:Tumor

NF1

A

Neuroblastoma

88
Q

Gene:Tumor

APC

A

Colon, Stomach

89
Q

Gene:Tumor

BRCA 1

A

Breast Cancer

90
Q

create and respond to their own growth signals

A

tumor cells

91
Q

how does signal transduction relay signals?

A

outside the cell to the inside

92
Q

what is PGDF?

A

Platelet Growth Derived factor is a receptor and tyrosine kinase

93
Q

what so special about the plasma membrane receptors involved in signal transduction?

A

they penetrate the membrane and have intracellular domain with enzymatic activity

94
Q

tyrosine kinase special something

A

autophosphorylation

95
Q

what encodes for PDGF?

A

simian Sarcoma Oncogene

96
Q

Simian Sarcoma causes

A

excess PDGF production

97
Q

what can growth factor receptors so?

A

remain active in absence of growth factor

98
Q

mutant EGF Receptor (ErbB/HER2) is a

A

tyrosine kinase that remains active

99
Q

cancer is caused by an

A

accumulation of mutations

100
Q

Colon Cancer is caused by (3)

A

(1) loss of APC
(2) Ras Activation
(3) p53 loss

101
Q

tumor viruses target

A

tumor supressors

102
Q

SV40 T-antigen stops

A

pRB binding to E2F and p53 binding to DNA

103
Q

transforms DNA to induce cancer, E6 and E7 work together

A

HPV

104
Q

E6 stops

A

p53 binding and proteolysis it

105
Q

E7 binds to

A

pRB

106
Q

what controls progression through the cell cycle?

A

cyclins

107
Q

transcription factors that promote transient growth

A

Fos and Jun

108
Q

transcription factor that regulates expression of 15% of all genes

A

MyC

109
Q

what happens when MyC is mutated?

A

there is an upregulation of proliferative genes and proliferation & Cancer

110
Q

involves translocation of Chromosome 8 that encodes for MyC to Chromosome 2, 14, or 22; where there are promoters for antibody molecules

A

Burkitt’s lymphoma

111
Q

In Burkitt’s lymphoma constitutive activation of MyC leads to

A

cancer

112
Q

type of cancer beginning in the immune cells

A

Burkitt’s lymphoma

113
Q

involved in signal transduction

A

Ras protein

114
Q

inactive Ras is bound to

A

GDP

115
Q

active Ras has

A

GTP bound

116
Q

Activated Ras needs

A

a helper protein or GTPase Activating Protein

117
Q

what happens with Mutant Ras has GTPase Activity affected?

A

always active and thus excess signal transduction

118
Q

NF1 gene encodes

A

neurofibromin protein

119
Q

neurofibromin protein

A

GTPase Activating Protein

120
Q

associated with Cafe-au-lait spots & benign neurofibroma due to faulty Neurofibromin protein

A

Nuerofibromatosis

121
Q

helper proteins helps Ras

A

hydrolyze GTP–> GDP

Biochem 2 (14 decks)

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