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KCU Comprehensive Exam > Ford Review > Flashcards

Ford Review Flashcards

1
Q

What are the four types of noncovalent interactions?

A

charge-charge
dipole interactions
van der waals
hydrogen

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2
Q

Example of charge-charge interaction

A

salt bridges

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3
Q

Example of dipole interaction

A

selectivity filter of K+ channgel

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4
Q

Example of van Der Waals interactions

A

nucleotide stacking

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5
Q

Example of hydrogen interactions

A

nuclei acid and base pairing/protein secondary structure

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6
Q

If pH< pKa what does that mean?

A

protonated

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7
Q

If pH> pKa what does that mean

A

deprotonated

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8
Q

If pH=pKa what does that mean?

A

just as likely to be protonated as deprotonated

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9
Q

what is the equation for pKa?

A

pKa= -logKa = [H+] [A-] / [HA]

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10
Q

What does Ka mean?

A

dissociation constant, predicts how likely an acid will donate a proton

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11
Q

What is the Henderson-Hasselbalch equation?

A

pH= pKa + log [A-] / [HA]

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12
Q

What happens when something is reduced?

A

gains electrons (H)

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13
Q

What happens when something is oxidized?

A

loses electrons

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14
Q

What amino acid preforms redox?

A

cystein (disulfide linkages are reductions)

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15
Q

What are the 3 important electron carriers in cellular metabolism and their reduced and oxidized forms?

A

NAD+/NADH
FAD/FADH2
FMN/FMNH2

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16
Q

What is equilibrium?

A

forward rate = reverse rate, no net formation or destruction

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17
Q

How does Le Chatlier fit into cellular metabolism?

A

it’s how to drive an unfavorable reaction forward

  • make pathway/use up products
  • couple it to a favorable reaction like ATP hydrolysis
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18
Q

What is the gibs free energy equation?

A

deltaG= deltaH- TdeltaS

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19
Q

how does thermodynamics relate to protein folding?

A

change of entropy–protein folds, loses entropy

aqueous environment has more disorder

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20
Q

negative delta H

A

energy released

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21
Q

postive delta H

A

energy added

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22
Q

zero delta H

A

closed system

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23
Q

negative delta S

A

decrease disorder

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24
Q

positive delta S

A

increase disorder

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25
Q

zero delta S

A

no net change in disorder

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26
Q

negative delta G

A

free energy released
exergonic, favorable
spontaneous reaction

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27
Q

positive delta G

A

free energy required
endergonic, unfavorable
driven reaction

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28
Q

zero delta G

A

equilibrium

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29
Q

Give example of cooperative binding

A

hemoglobin binds oxygen cooperatively

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30
Q

Positive cooperativity definition

A

binding site affinity for ligand increases with every subsequent binding

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31
Q

negative cooperativity definition

A

binding site affinity for ligand decreases with every subsequent binding

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32
Q

no cooperativity definition

A

binding sites are independent, situation can be Michaelis menten enzyme

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33
Q

Km definition

A

Michaelis constat, [S] where reaction rate is half maximal OR half of the active sites are full

Km= [E] [S] / [ES]

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34
Q

Vmax definiton

A

maximum rate possible for a give concentration of enzyme

Vmax= Kcat [E]T

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35
Q

Kcat definition

A

number of substrate molecules concerted per active site per time (first order rate constant)

kcat= K2

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36
Q

Kcat/Km definition

A

measure of enzyme performance by predicting the fate of E*S, how good an enzyme is

Kcat/Km= Kcat/ k-1 +Kcat

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37
Q

VIEW DIFFERENT TYPES OF INHIBITORS

A

pictures on slides

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38
Q

similarities between substate level control and feedback control

A

alters ability of reaction to proceed

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39
Q

differences between substate level control and feedback control

A

substrate: acts on single reaction
feedback: acts on different reaction pathway

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40
Q

example of substrate level control

A

G6P and hexokinase

Acetyl-CoA inhibits PDH

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41
Q

example of feedback control

A

nucleotide de novo synthesis

aa biosynthesis

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42
Q

similarities between activation and inhibition

A

alters ability of reaction to proceed, can be substrate or feedback

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43
Q

differences between activation and inhibition

A

activation: adds new or increases existing function
inhibition: decreases or stops existing function

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44
Q

example of activation

A

dephosphorylation of pyruvate kinase

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45
Q

example of inhibition

A

phosphorylation of pyruvate kinase

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46
Q

description of reversible covalent modification

A

+/- small molecule

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47
Q

description of irreversible covalent modification

A

proteolytic activation

48
Q

similarities between reversible covalent modification and irreversible covalent modification

A

reversible: may be activating
irreversible: activating mechanism only

49
Q

differences between reversible covalent modification and irreversible covalent modification

A

reversible: may be inhibiting, reversible
irreversible: never inhibiting, irreversible

50
Q

examples of reversible covalent modification

A

histone modification
adenylation/uridylation
and glutamine synthetase
phosphorylation

51
Q

examples of irreversible covalent modification

A

protease cascade/digestive enzyme
blood clotting factors
insulin

52
Q

allosteric effector description

A

binds at unique locations and alters the proteins functionality

53
Q

competitive effector description

A

competes with intended substate to bind the active site

54
Q

allosteric effector and competitive effector similarities

A

allosteric: may inhibit function
competitive: always inhibits function

55
Q

allosteric effector and competitive effector differences

A

allosteric: does not bind active site, may be activating
competitive: binds at active site, can never be activating

56
Q

allosteric effector examples

A

ATCase
ribonucleotide reductase
phosphofructokinase

57
Q

competitive effector examples

A

methotrexate vs dihydrofolate for dihydrofolate reductase

58
Q

What does covalent catalysis do?

A

share electrons

59
Q

What does acid base catalysis do?

A

share protons

60
Q

What does approximation do in catalysis?

A

orientation and proximity

61
Q

What does electrostatic catalysis do?

A

non covalent interactions

62
Q

oxidoreductases description and example

A

description: redox, move elections
example: dehydrogenase (oxidizers)
reductases (reducers)

63
Q

transferases description and example

A

move a functional group
kinases add phosphate
phosphotases remove phosphate

64
Q

hydrolases description and example

A

break a bond by adding water

citrate synthase, lactose

65
Q

lyases description and example

A

break a bond without water

aldolase in glycolysis

66
Q

isomerases description and example

A

rearrange order of atoms

TPI

67
Q

ligases description and example

A

make a covalent bond

aldolase in gluconeogenesis

68
Q

Describe active transport

A

requires energy

moves something against/creates a concentration gradient

69
Q

Describe the P-type ATPase

A

phosphorylates itself
transports ions
4 domains: transmembrane, actuator, nucleotide, binding, phosphorylation
example: Na/K pump

70
Q

Describe the ABC transporter

A

no phosphorylation of self
transport small molecules
dimeric, contains 2 copies of transmembrane domain and aTP binding cassette (ABC)

example: multidrug resistance protein

71
Q

describe the secondary transport

A

uses gradient established by primary active transport
moves ion or molecule against its gradient without using energy

example: Na-glucose cotransport

72
Q

describe passive transport

A

no energy needed

73
Q

describe the ion channel

A

selectivity filter

gate: voltage gated, ligand gated

74
Q

describe the aquaporin

A

selectivity filter

no gate

75
Q

describe the gap junction

A

no selectivity filter

no gate

76
Q

review glycolysis, TCA and ox-phos

A

look at notes

77
Q

location of glycolysis

A

cytoplasm

78
Q

rate limiting enzyme of glycolysis

A

phosphofructokinase

79
Q

how does hexokinase regulate in glycolysis

A

G6P inhibits

80
Q

how is phosphofructokinase regulated in glycolysis

A

citrate inhibits

low ATP is activating

81
Q

how is pyruvate kinase regulated in glycolysis

A

high ATP is inhibitory

F16BP activates

82
Q

location of TCA cycle

A

mitochondrial matrix

83
Q

rate limiting enzyme of TCA cycle

A

isocitrate dehydrogenase

84
Q

how is the pyruvate dehydrogenase complex regulated in the TCA cycle

A

ATP, acetyl CoA, NADH are inhibitory (kinase/+PO4)

ADP and pyruvate are activating (phosphatase/-PO4)

85
Q

how is isocitrate dehydrogenase regulated in the TCA cycle

A

ATP and NADH inhibit

ADP activates

86
Q

how is alpha-ketoglutarate dehydrogenase complex regulated in TCA cycle

A

ATP, succinyl CoA and NADH inhibit

87
Q

location of ox phos

A

mitochondrial inner membrane and inter membrane space

88
Q

glycogenolysis location

A

cytoplasm

89
Q

glycogenolysis rate limiting enzyme

A

glycogen phosphorylase

90
Q

glycogenolysis regulated enzyme

A

glyogen phosphorylase

  • dephosphorylation inhibits
  • phosphorylation activates
91
Q

amino acid catabolism location

A

cytoplasm and mitochondrial matrix

urea cycle only in liver

92
Q

beta oxidation location

A 
cytoplasm (activation)
mitochondrial matrix (beta oxidation)
93
Q

rate limiting enzyme of beta oxidation

A

perilipins

94
Q

how is perilipins regulated in beta oxidation

A

phosphorylation promotes TAG release by inhibiting perilipin

95
Q

location of ketone bodies

A

only produced in liver, but broken down in non liver cells though

96
Q

location of gluconeogenesis

A

cytoplasm (ER in liver and kidney only)

97
Q

rate limiting enzyme of gluconeogenesis

A

fructose- 1,6- bisphophate

98
Q

How is pyruvate carboxylase regulated in gluconeogenesis

A

ADP inhibits

acetyl CoA is activating

99
Q

how is PEP carboxykinase regulated in gluconeogenesis

A

ADP inhibits

100
Q

how is fructose 1,6 bisphoate regulated in gluconeogenesis

A

low ATP is inhibitory

citrate activates

101
Q

location of PPP

A

cytoplasm

102
Q

rate limiting enzyme of PPP

A

glucose 6 phosphate dehydrogenase

103
Q

how is G6P dehydrogenase regulated in the PPP

A

monomers inactive, dimers activate
dephosphorylated inactive, phosphorylation activates
insulin activates

104
Q

location of nucleotide de novo synthesis

A

cytoplasm (except dihydroorotate dehydrogenase in mitochondria)

105
Q

what are the regulated in enzymes in nucleotide de novo synthesis

A

general theme: feedback regulation

ribonucleotide reductase: activity site and specificity site

106
Q

amino acid biosynthesis location

A

cytoplasm and mitochondrial matrix

107
Q

amino acid biosynthesis regulated enzymes

A

general theme: feedback regulation

glutamine synthetase:

  • adenylylation inhibits/deadenylylation actives
  • PII is inactivating/ PII-UMP is activating
  • feed back inhibition is glutamine
  • feed forward activation is alpha ketoglutarate, ATP
108
Q

fatty acid synthesis location

A

cytoplasm and mitochondrial matrix

109
Q

rate limiting enzyme of fatty acid synthesis

A

acetyl coA carboxylase

110
Q

how is ATP citrate lyase regulated in fatty acid synthesis

A

activated by phosphorylation and glucose/insulin

inhibited by PUFAs and leptin

111
Q

how is acetyl coA carboxylase regulated in fatty acid synthesis

A

active by citrate, -PO4/ insulin, high carb diet

inhibited by palmitate, +PO4/epinephrine/glucagon/AMP

112
Q

how is fatty acid synthase regulated in fatty acid synthesis

A

activated by sugar-PO4, insulin, high carb diet

inhibited by high fat diet, starvation and PUFAs

113
Q

glycogenesis location

A

cytoplasm

114
Q

glycogenesis rate limiting enzyme

A

glycogen synthase

115
Q

how is glycogen synthase regulated in glycogenesis

A

phosphorylation inhibits

dephosphorylation activates

116
Q

where does TAG synthesis occur

A

hepatocytes and adipocytes

KCU Comprehensive Exam (13 decks)

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