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QUIZ 3 > Enzymes > Flashcards

Enzymes Flashcards

1
Q

competitive inhibition

A

increases Km, no effect on Vmax

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2
Q

uncompetitive inhibition

A

reduces both Km and Vmax

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3
Q

noncompetitive inhibition

A

no effect on Km, reduces Vmax

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4
Q

sarin (diisopropylphosphofluoridate)

A

irreversible inhibitor; permanently inactivates acetylcholinesterase by forming a covalent bond with serine on active site

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5
Q

acetylsalicylic acid (aspirin)

A

irreversible inhibitor; acetylates an active site serine in the enzyme prostaglandin endoperoxide synthase

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6
Q

malathion (organophosphate insecticide)

A

irreversible inhibitor; Irreversibly inactivates acetylcholinesterase by forming a covalent bond with the active site serine

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7
Q

penicillin

A

suicide inhibitor

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8
Q

sulfanilamide

A

competitive inhibitor of p-aminobenzoic acid

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9
Q

example of control of substrate availabilty

A

if no lactate, liver can not convert it into glucose

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10
Q

How do enzymes stabilize transition state of a reaction?

A

acid-base catalysis, electrostatic catalysis, metal catalysis, covalent catalysis, substrate strain

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11
Q

general acid catalysis

A

catalyst is an acidic group on the enzyme that donates a proton to the substrate, allowing easier cleavage

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12
Q

general base catalysis

A

catalyst is a basic group on the enzyme that takes a proton from the substrate

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13
Q

example of acid-base catalysis

A

Glu35 in lysozyme is a proton donor to the O in the polysaccharide chain, allowing cleavage

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14
Q

How can an enzyme alter pKa?

A

can surround it by hydrophobic molecules –> Glu35 in lysozyme is allowed to be protonated

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15
Q

electrostatic catalysis

A

enzyme uses charged amino acid to neutralize charges that develop during formation of a transition state

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16
Q

example of electrostatic catalysis

A

upon cleavage of the polysaccharide by lysozyme, a positive charge will develop on one of the carbons –> Asp52 is surrounding by hydrophilic molecules, retaining its negative charge –> can neutralize that positive carbon

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17
Q

substrate strain

A

active site of enzyme only recognizes transition state, not regular unbound substrate

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18
Q

example of substrate strain

A

preferred conformation for polysaccharide is the chair conformation –> lysozyme binds in half chair formation –> an-acetyl group on C2 sterically clashes with proton on C1 –> unfavorable
–> so in transition state it will increase angle of C2 from 109 to 120, moving proton away

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19
Q

metals as lewis acids

A

Zn in carbonic anhydrase accepts protons

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20
Q

metals as chelates

A

iron in heme group

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21
Q

chelates

A

metal is covalently bound to enzyme or coenzyme

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22
Q

metals as charge stabilizers

A

Mg+2 stabilizes negative oxygens on ATPs

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23
Q

metals in oxi-red reactions

A

during respiration, oxygen is converted to water by the addition of protons and electrons, supplied by cytochrome a3 –> if cyanide inhaled, it reacts with the Fe3+ in the heme of cytochrome a3, preventing cytochrome a3 from transferring electrons to oxygen –> no energy production –> cell death

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24
Q

antidote for cyanide poisoning

A

have the patient inhale nitrites –> will convert the Fe2+ in hemoglobin to Fe3+ (this converts hemoglobin into methemoglobin) –> Fe3+ in methemoglobin removes the cyanide from the Fe3+ in cytochrome a3 –> reactivates cytochrome a3 and restores mitochondrial respiration

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25
Q

metals for enzyme structure

A

K+ in pyruvate kinase needed for active formation

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26
Q

covalent catalysis

A

enzyme forms a transient covalent intermediate with substrates of reaction

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27
Q

example of covalent catalysis

A

chymotrypsin catalyzing hydrolysis of peptide bonds

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28
Q

chymotrypsin covalent catalysis

A

serine will attack carbonyl carbon to form covalent bond putting negative charge on that oxygen –> water comes in to cleave

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29
Q

How does serine have negative charge for chymotrypsin cleavage?

A

charge relay system in serine proteases

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30
Q

charge relay system

A

charge relay system includes ser, his, and asp –> his will pull of proton from serine because asp pulls off proton from his –> asp is surrounded by hydrophobic residues to raise pKa to allow it to do this

31
Q

oxyanion hole

A

stabilize negative charge that develops in transition state –> serine and glycine spread out negative charge

32
Q

specificity pocket

A

designed to recognize side chain of amino acid on amino terminus that is going to be cleaved

33
Q

transition state analogs

A

enzyme inhibitors must mimic transition state

34
Q

example of transition state analog

A

tetrahydrouridine is a transition state analogue of cytidine deaminase –> target for anticancer drugs

35
Q

How do cells control specific reactions?

A

control of enzyme activity, control of enzyme levels, control of enzyme location, control of substrate availability, removal or conversion of reaction products

36
Q

control of substrate availability

A

if substrates of a reaction are not available, the enzyme can’t catalyze their conversion into product

37
Q

removal of reaction products

A

can remove or convert products to keep reaction moving in the forward direction

38
Q

example of product removal

A

taking away fructose-6-phosphate and making it into pyruvate will stimulate phosphoglucose isomerase to convert more G6P to F6P

39
Q

product inhibition

A

occurs when product of reaction builds up and competes with the substrate for binding to active site of enzyme

40
Q

how to prevent product inhibition

A

reaction products are either rapidly removed or converted into other products

41
Q

enzyme activity regulation

A

allosteric control, covalent modification, proteolytic activation, stimulation/inhibition by control proteins

42
Q

allosteric regulators

A

do not bind active site

43
Q

feedback inhibition

A

end product will go back and allosterically inhibit an upstream enzyme

44
Q

feed-forward regulation

A

product upstream will go activate/inhibit downstream enzyme

45
Q

covalent modification

A

regulates catalytic activity of some enzymes by adding a modifying group

46
Q

biotin

A

covalently attached to pyruvate carboxylase and serves as CO2 carrier for carboxylation of pyruvate to oxaloacetate

47
Q

biotin is found in _

A

red meat, eggs, nuts, seed, broccoli, sweet potatoes, spinach

48
Q

biotin deficiency symptoms

A

nausea, hair loss, dermatitis, depression, pale skin, muscle pain, fatigue

49
Q

phosphorylation as reversible covalent modification

A

protein kinases and tyrosine kinases; can only be done inside cell not extracellularly

50
Q

phosphorylation effects

A

rapidly amplified via kinase cascade

51
Q

oncogene gain of function

A

will always be phosphorylated, leading to it always being on and cell cycle always going

52
Q

tumor suppressor loss of function

A

usually phosphorylated to be activated so if a mutation causes it to be de-phosphorylated, it will not turn off the cell cycle when needed

53
Q

tumor suppressor mutations are _

A

recessive (loss of function)

54
Q

oncogene mutations are _

A

dominant (gain of function)

55
Q

proteolytic activation

A

keeps enzymes in inactive form –> will be proteolytically cleaved when it needs to be activated (not reversible, enzyme is permanently activated); can be done extracellularly

56
Q

pepsinogen cleavage

A

propeptide forms salt bridges with active site –> at pH >5 it will be binded and inactive –> once in stomach, the low pH will break salt bridges allowing activation

57
Q

blood clot formation

A

zymogen activations –> prothrombin –> thrombin –> thrombin cleaves fibrinogen to fibrin –> cross-linked fibrin blood clot

58
Q

BPTI

A

binds to trypsin active site, inactivating it

59
Q

serine protease inhibitors (serpins)

A

serine proteases will bind the serpin reactive center loop, thinking it is a substrate –> forms acyl-enzyme intermediate with serine –> reactive center loop is cleaved and serpin undergoes conformational change that reduces functionality of serine protease

60
Q

serpinopathies

A

mutations in hinge domains of serpins that cause inactivation –> leads to death of cells producing serpin

61
Q

alpha-1-antitrypsin

A

inhibits elastase, a serine protease that is secreted by leukocytes in response to bacteria cell

62
Q

AAT mutation

A

glu is replaced for lys, resulting in mutant cells –> uncontrolled elastase activity which breaks down alveolar walls

63
Q

cigarette smoking

A

oxidizes Met358 of AAT, which prevents it from binding active site of elastase –> emphysema

64
Q

factors that increase PMN elastases secretion

A

bacterial infection, smoking (irritates lung and stimulates PMN cells)

65
Q

Which of the following systems is established by the International Union of Biochemistry and Molecular Biology (IUBMB) in naming an enzyme?

A

The substrate is stated first, followed by the reaction type suffixed with –ase

66
Q

examples of hydrolases

A

lipases, proteases

67
Q

examples of lyases

A

decarboxylases, aldolases

68
Q

examples of oxidoreducatases

A

anything with an H, dehydrogenases

69
Q

enzymes can _

A

distinguish between both isomers and stereoisomers, distinguish between two substrates that differ by a single methyl group, catalyze the formation of a stereospecific product from an achiral (non-stereospecific)
substrate

70
Q

enzymes can NOT _

A

stabilize products of a reaction

71
Q

the transition state is _

A

the least stable species in reaction diagram

72
Q

enzymes catalyze reactions by _

A

lowering activation energy and stabilizing transition state

73
Q

in electrostatic catalysis _

A

negatively charged amino acid side chains in the enzyme are positioned near positive charges that develop in the transition state of the reaction, and vice versa

QUIZ 3 (12 decks)

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