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MAMS BCH > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

Heme pathway mnemonic

A

Graduate Students Are Perfect - BU Consistently Picks Proper Humans

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2
Q

Glycine + Succinyl CoA –> ALA
Enzyme and byproducts?

A

ALA Synthase, CoA-SH and CO2

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3
Q

ALA –> PBG
enzyme and byproducts?

A

ALA Dehydrase, 2H2O

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4
Q

PBG –> Bilane
enzyme

A

PBG Deaminase

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5
Q

Bilane –> Uro’gen III
Enzyme

A

Uro’gen III cosynthase

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6
Q

Uro’gen III –> Copro’gen III
Enzyme and byproducts?

A

Uro’gen III decarboxylase, 4CO2

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7
Q

Copro’gen III –> Proto’gen IX
Enzyme and byproducts?

A

Copro’gen III decarboxylase, 2CO2

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8
Q

Proto’gen IX –> Protoporphyrin IX
enzyme and byproducts?

A

Proto’gen IX dehydrogenase, 6H+

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9
Q

Protoporphyrin IX –> Heme
enzyme and byproducts?

A

Ferrocheletase, 2H+, adds Fe2+

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10
Q

From 1-8, which intermediates in the heme synthesis pathway are the most hydrophobic

A

1 - least hydrophobic
8 - most hydrophobic

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11
Q

4 ways of ALA synthase inhibition by heme

A

1) Heme binds to ALA synthase
2) Heme binds repressor in nucleus (inhibits transcription of ALA synthase)
3) Heme blocks translation of ALA synthase
4) Heme blocks ALA synthase import into mitochondria

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12
Q

Heme oxygenase pathway enzymes

A

1) Heme Oxygenase
2) Biliverdin reductase

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13
Q

What are the notable cofactors and byproducts in the heme oxygenase pathway and at what step are they used?

A

It uses O2 and produces CO in the production of Heme to Biliverdin IXa

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14
Q

3 acute porphyrias

A

AIP - Acute Intermittent Porphyria
HC - Hereditary Coproporphyria
VP - Variegate Porphyria

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15
Q

Chronic porphyria

A

Porphyria Cutanea Tarda

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16
Q

3 photosensitive porphyrias

A

HC, PCT, VP

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17
Q

What intermediates build up as a result of PCT?

A

Only Uro’gen III

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18
Q

PCT enzyme

A

Uro’gen III Decarboxylase

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19
Q

HC enzyme

A

Copro’gen III Decarboxylase

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20
Q

VP enzyme

A

Proto’gen IX Dehydrogenase

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21
Q

AIP enzyme

A

PBG Deaminase

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22
Q

Gilbert’s Syndrome

A

Inhibition of BRGT/UGT promoter, results in increased BR-Albumin

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23
Q

What is a stasis

A

Defect in liver secretion

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24
Q

Crigler-Najjar (two types)

A

Mutation in BRGT/UGT coding regions, results in increased BR-Albumin
Type I is homozygous = fatal
Type II is heterozygous

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25
Q

Conjugated Hyperbilirubinemia

A

Liver stasis, BRDG leaks back into the blood, eliminated in dark orange urine

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26
Q

Neonatal Jaundice

A

Lack of BRGT/UGT expression in first 5-14 days, since BR is unconjugated, it is not transported into liver and BR-Albumin builds up in the blood. Treated by using light to break down BR-Albumin

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27
Q

Kernicterus

A

BR-Albumin buildup due to lack of BRGT/UGT expression. Since blood-brain barrier not complete, becomes toxic to nervous system, build-up in basal ganglia

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27
Q

Porphyria Cutanea Tarda illness course

A

1) Found in Hep C patients where Iron is deposited in the liver, leading to inflammation and production of ROS.
2) ROS then causes Uro’gen III to become inhibitor of Uro’gen III decarboxylase.
3)Uro’gen III becomes Uroporphyrin, creating an immune response (rash, lesions, etc.)

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28
Q

Prolyl and Lysyl Hydroxylase

A

Hydroxylate Proline and Lysine using Ascorbate (Vitamin C) on alpha chains of pre-pro collagen in ER

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28
Q

Lysosomal storage disease is characterized by:

A

accumulation of sphingolipids in the lysosome

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29
Q

Galactosyl and Glucosyl transferase

A

Glycosylate hydroxyLYSINE in ER, first Galactose, and then sometimes Glucose gets added

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30
Q

collagen alpha chains amino acids

A

33% Glycine, 17% Proline

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31
Q

What cleaves procollagen and where does it happen?

A

Procollagen peptidase, outside the cell

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32
Q

Ehlers-Danlos syndrome is a result of:

A

Lack of Lysyl Hydroxylase, resulting in fragile collagen and stretchy skin

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33
Q

Lysyl Oxidase (LOX)

A

1) Cross-links collagen fibers using Copper, creating aldehydes on Lysines and Hydroxylysines
2) cross-links tropoelastins to create insoluble elastin fiber

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34
Q

Osteogenesis Imperfect is a result of:

A

mutations in the alpha1 and alpha2 chains used to create the procollagen triple helix

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35
Q

Elastin turnover is catalyzed by:

A

Elastase

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36
Q

Alpha1 Antitrypsin role

A

Inhibits Elastase, otherwise Elastin would be destroyed and skin would become stiff

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37
Q

Rac1/PIP2

A

Activate WASP/WAVE complex in response to extracellular signals to begin reorganization of actin

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38
Q

WASP/WAVE complex

A

Stimulate actin nucleation via activation of Arp2/3 complex

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39
Q

Arp2/3 complex

A

stimulate actin nucleation and creation of new filaments

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40
Q

Formin proteins

A

Cap + ends of growing actin filaments to prevent further extension

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41
Q

Rac1

A

Regulates extension of the leading edge
Rho GTPase

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42
Q

RhoA

A

Regulates detachment of trailing edge, inhibits Rac1
Rho GTPase

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43
Q

Does NMII move towards the + or - end

A

+ end of action filament via hydrolysis of one ATP

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44
Q

Proteolysis by MMPs can generate

A

signalling molecules

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45
Q

Proteoglycan functions

A

1) serve as a reservoir for growth factors
2) facilitate contact between proteins and cell-surface receptors
3) protect proteins from proteolytic degradation

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46
Q

Fibronectin

A

1) Used by cells to migrate
2) Remodeling of fibronectin can send a signal for integrity to remodel and vice versa
3) 2 monomers linked by disulfide bonds

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47
Q

Tay-Sachs

A

An inherited form of lysosomal storage disease which progressively destroys neurons in the brain and spinal cord. characterized by a cherry-red spot.

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48
Q

Peroxisomes

A

responsible for beta-oxidation and synthesis of certain glycerolipids.

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49
Q

X-linked adrenoleukodystrophy

A

Peroxisomal disorder: FAs can’t get to the peroxisome for breakdown

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50
Q

Zellweger syndrome

A

biogenesis disorder

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51
Q

Glycerophospholipid structure

A

Polar head (choline, serine), phosphate and glycerol group connection, 2 fatty acid tails

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52
Q

Intermediate filaments function

A

mechanical integrity, and providing a scaffold for signaling molecules

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53
Q

IF assembly

A

two monomers form a coiled-coil dimer, two coiled-coil dimers form a staggered tetramer, two tetramers pack together, eight tetramers twist together into a ropelike filament

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54
Q

Actin filament function

A

Important for cell shape, locomotion

55
Q

microtubule assembly

A

hollow cylinders of 13 protofilaments made up of alpha/beta dimers

56
Q

Can ATP be a co-substrate?

A

Only if it provides energy. If Pi is part of the end product, then it is a regular substrate

57
Q

Cofactors are:

A

small, nonprotein molecules

58
Q

Holoenzyme

A

Enzyme with a cofactor

59
Q

Apoenzyme

A

Enzyme without a cofactor

60
Q

Organic cofactors are called:

A

coenzymes

61
Q

Does ∆G provide information about the rate of the reaction?

A

No

62
Q

∆G equation

A

∆G = ∆Gº’+RTln([Products]/[Reactants])

63
Q

Relatively small changes in ∆G‡ lead to

A

relatively large changes in overall reaction rate

64
Q

What does the Induced Fit theory explain that the Lock and Key theory does not?

A

Transition state stabilization, they both explain enzyme specificity but experimental data supports induced fit

65
Q

Four strategies besides binding energy (major pathway) to form and stabilize the transition state

A

1) Covalent catalysis: covalent bond forms between substrate and enzyme
2) General acid-base catalysis: molecule (not H2O) becomes a proton donor/acceptor
3) Catalysis by approximation: reactants are aligned and held close together
4) Metal ion catalysis

66
Q

First order

A

The rate of product formation is directly proportional to concentration of reactant

67
Q

Second order

A

The rate of product formation is directly proportional to the product of the concentration of two reactants

68
Q

Michaelis-Menten equation

A

Vo = Vm[S]/Km+[S]

69
Q

equation for fraction of active sites filled

A

Vo/Vmax = [S]/Km+[S] = fraction of active sites filled

70
Q

5 assumptions of the Michaelis Menten equation

A

1) ES complex exists
2) no back reaction
3) initial velocities at t=0
4) steady state for [ES]
5) oversaturation of substrate

71
Q

catalytic efficiency equation

A

Kcat/Km
- perfect enzymes have the highest ratio
- if substrates have a similar ration, the one with the highest Kcat is usuallly the best

72
Q

2 types of sequential reactions

A

1) ordered sequential: A, then B, then P then Q
2) random sequential: B then A, then P then Q

73
Q

ping-pong reaction

A

A binds, then P releases, then B binds, then Q releases

74
Q

What are transition-state analogs

A

A form of competitive inhibitor that represent the transition state and bind the enzyme more tightly (more potent inhibitors)

75
Q

effect of uncompetitive inhibitor on kcat/km

A

stays the same

76
Q

effect of competitive and noncompetitive on kcat/km

A

Decreases

77
Q

Inhibitor if the relative rate decreases with increasing [S]

A

Uncompetitive Inhibitor

78
Q

Inhibitor if the relative rate increases with increases [S]

A

Competitive Inhibitor

79
Q

Inhibitor if the relative rate stays the same with increasing [S]

A

Noncompetitive Inhibitor

80
Q

Equation for % inhibition

A

(1-relative rate)*100
Relative rate: Vo,i/Vo
Vo,i = initial reaction rate with inhibitor
Vo = initial reaction rate without inhibitor

81
Q

Equation for relative rate

A

Relative rate: Vo,i/Vo
Vo,i = initial reaction rate with inhibitor
Vo = initial reaction rate without inhibitor

82
Q

3 types of irreversible inhibitors

A

1) Group-specific reagents
2) Affinity labels
3) Suicide inhibitors

1 - least specific
3 - most specific

83
Q

Group-specific reagents

A

Type of irreversible inhibitor: covalently interact with a specific enzyme side chain to inactivate the enzyme

84
Q

Affinity labels

A

Type of irreversible inhibitor: Structurally similar to the substrate and bind active-site residues

85
Q

Suicide Inhibitors

A

Type of irreversible inhibitor: substrate analog that binds the active site and tricks the enzyme into catalysis, creating an intermediate which results in permanent inactivation. MOST SPECIFIC

86
Q

4 methods of enzymatic regulation

A

1) Allosteric control: sigmoidal
2) Regulatory proteins
3) Reversible covalent modifications
4) Proteolytic activation

87
Q

Homotropic effector

A

Type of allosteric enzymatic control where the effector is the same as the substrate and binds near the active site, almost always increasing activity

88
Q

Heterotropic effector

A

Type of allosteric enzymatic control, effector is different from the substrate, “true” allosteric site and interaction increases or decreases activity

89
Q

What occurs when a positive effector binds to an allosteric site?

A

Activity is increased

90
Q

What occurs when a negative effector binds to an allosteric site?

A

Activity is decreased

91
Q

Explain the ATCase example

A

similar to Hgb, R state allows for more substrate binding. CTP is negative effector and stabilizes T, ATP is positive effector and stabilizes R, Aspartate is the substrate and stabilizes R

92
Q

PKA example

A

Inhibitory: Needs cAMP to bind to allow PKA to leave, allowing the enzyme active site to be open and active

93
Q

Reversible covalent modifications

A

Kinases and Phosphatases: overall cycle (phosphorylation+dephosphorylation) hydrolyzes one ATP and the overall ∆G is negative

94
Q

Proteolytic activation

A

1) IRREVERSIBLE
2) OUTSIDE of the cell
3) NO ATP

95
Q

VIIIa

A

Antihemophillic factor: lack of this leads to classic hemophilia
ACTIVATED BY THROMBIN, leading to positive feedback

96
Q

Intrinsic pathway

A

activated by damage of vasculature, involves anti hemophilic factor (lack of this is classic hemophilia)

97
Q

Extrinsic pathway

A

Activated by external trauma
VII is activated by THROMBIN
Contains tissue factor X

98
Q

Thrombin

A
  • Most important enzyme, cleaved from prothrombin,
  • can act on VIIIa and VII as positive feedback to upregulate intrinsic and extrinsic pathways respectively
  • can activate factor C to shut down the pathway
  • can act on transglutaminase to promote cross-linking of fibrin into hard clot
99
Q

How is the soft clot formed?

A

fibrinogen is cleaved to fibrin

100
Q

How is the hard clot formed?

A

Fibrin is catalyzed by transglutaminase to form a cross-linked hard fibrin clot

101
Q

Characteristics of the blood clotting cascade

A

1) Signal amplification at each step
2) rapid response to trauma
3) cascade of zymogen activations

102
Q

Heparin mechanism

A

Anticoagulant, Irreversible inactivation of Thrombin

(via antithrombin III)

103
Q

tPA

A

Clot Buster

degrades fibrin clots via activation of plasminogen (serine protease)

104
Q

Tyrosin Kinase Inhibitor

A

Imitates ATP and binds the ATP-binding pocket to prevent phosphorylation of substrate

105
Q

TKI resistance

A

mutations can develop in proteins locking tyrosine kinase into active conformation

106
Q

Branched chain amino acids

A

Valine, Leucine, Isoleucine, sometimes Alanine included
Cluster together for stability, hydrophobic

107
Q

Mnemonic for uncharged polar amino acids

A

CYST NQ

108
Q

Which three amino acids favor alpha helix formation?

A

Methionine, Alanine, Leucine

109
Q

Each turn of the Alpha helix is about how many residues?

A

3.6

110
Q

Peptide bonds H-bond with residues how many away?

A

4

111
Q

Why are disordered protein regions notable?

A

They allow for interactions with multiple other proteins, such as p53 which can bind four different proteins with this region

112
Q

Hsp70 functions:

A

co-translationally

113
Q

Hsp60 functions:

A

post-translationally

114
Q

Ubiquitination steps

A

1) E1 picks up Ub
2) E1 primes E2/3 with Ub
3) E2/3 binds target protein and attaches Ub
4) cycles through

115
Q

How does E1 pick up Ub

A

Ub is bound to a cysteine via a thioester bond using the hydrolysis of ATP to AMP

116
Q

How does E1 transfer Ub to E2/3

A

Moves from E1 cysteine to E2/3 cysteine

117
Q

How does E2/3 transfer Ub onto the target protein

A

Target protein contains a lysine side chain degradation signal. Ub is transferred to the epsilon amino group via an iso-peptide bond

118
Q

How many Ub for protein to go to proteasome

A

4

119
Q

BiP

A

Binding protein: Hsp70 chaperone
- hydrolyzes ATP as proteins brought into ER
- recognizes misfolded proteins by binding amino acids usually found on the interior

120
Q

PDI

A

promotes formation of disulfide bonds

121
Q

PPI

A

facilitates interconversion of proline from cis to trans to facilitate protein folding

122
Q

Calnexin and Calreticulin

A

Play a role in glucose tagged proteins attempting to exit ER to Golgi

123
Q

UPR (Unfolded Protein Response)

A

1) increased ER protein folding
2) up regulation of chaperone and protein degrading genes
3) apoptosis

124
Q

PrP-c

A

3 alpha helices
2 beta strands
one unstructured region

125
Q

PrP-sc

A

multiple stacked beta strands
protease resistant core
amyloid fibril

126
Q

Increased pH shifts curve to ___ and stabilizes ___ state

A

Left, stabilizes R state

127
Q

Increased CO2 shifts curve to ___ and stabilizes ___ state

A

Right, stabilizes T state

128
Q

Why does fetal Hb have a higher affinity for O2?

A

Less bound 2,3-BPG

129
Q

Sickle cell disease

A

substitution on the beta chain, causing HbS to self-associate and cell to sickle

130
Q

Alpha Thalassemia (HbH) mechanism and effects

A

Defect in alpha chain genes, binds O2 with high affinity and no cooperatively

131
Q

Beta Thalassemia mechanism and effects

A

Defect in beta chain, lack of O2 cooperativity, tetramers tend to be insoluble and precipitate

132
Q

Methemeglobinemia

A

Fe2+ oxidized to Fe3+ leading to high O2 affinity

133
Q

Glutathione

A

Sacrificial molecule to keep ROS low and prevent inactivation of methemoglobin reductase

134
Q

Methemglobin reductase

A

Uses NADH to reduce Fe3+

135
Q

Actin filament structure

A
  • 2 stranded helical polymers of actin subunits form each filament
  • 3 types: alpha, beta, gamma
  • each filament is made from one type
136
Q
A

MAMS BCH (19 decks)

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