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Biochemistry > Chapter 7 > Flashcards

Chapter 7 Flashcards

1
Q

what are the 2 models to describe how enzymes and substrates fit together? what is the reality?

A
  1. lock and key
  2. induced fit
    in reality is likely a mixture of both
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2
Q

what is the lock and key model? what does it rely heavily upon?

A

there is a perfect substrate for every enzyme; relies heavily on conformational selection

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3
Q

what is the induced fit model? what is it dependent upon?

A

says that enzyme and substrate change a little bith to fit together; depends upon noncovalten interactions but allows more freedom

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3
Q

what is the active site?

A

the area inside the enzyme where the REACTION HAPPENS

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4
Q

give an example of a reaction site

A

where a ligand binds to a protein

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5
Q

does hemoglobin have an active site?

A

NO! although O2 binds, no reaction occurs

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6
Q

what is a substrate?

A

the reactant the enzyme binds (AKA the ligand)

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7
Q

what is rate?

A

reactions per unit time; bigger is better

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8
Q

what is rate enhancement?

A

catalyzed rate divided by uncatalyzed rate; bigger is better

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9
Q

what is rate enhancement used for?

A

to compare enzymes

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10
Q

what are the 3 ways to change the rate of a reaction? how do these ways do this?

A
  1. temperature: via conformational selection and diffusion
  2. concentrationn: shifts equilibrium
  3. catalysts: lower activation energy
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11
Q

what are the 2 types of catalysts?

A
  1. enzymatic: biological catalysts
  2. nonenzymatic
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12
Q

what allows enzymes to bind with high affinity and selectivity?

A

the creation of an active site environment that is optimal for substrate binding

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13
Q

what does susbtrate binding do to the enzymes conformation? how (2)

A

substrate binding changes the enzyme’s conformation by
1. nonbonded interactions broken and formed
2. new conformation favors product formation

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14
Q

in what 2 ways is enyzme activity heavily regulated in cells?

A
  1. bioavailability
  2. signaling
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15
Q

what is a transition state?

A

a high energy intermediate state formed during conversion of substrate to product

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16
Q

how many molecules are in the transition state simultaneously?

A

only a few

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17
Q

is the transition state easy to isolae through conventional methods?

A

nope

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18
Q

describe how transition state relates to the path from reactant to product

A

reactions have to take a certain path from reactants to products; the transition state is at the height of the path

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19
Q

describe the energy and stability of the transition state

A

high energy, low stability

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20
Q

what is delta G double dagger?

A

the activation energ, or the difference between reactant ground state energy and transition state energy

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21
Q

what do catalysts do to the transition state?

A

stabilize transition state to lower associated energy and make transition state more favorable

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22
Q

can a catalyst affect overall delta G? why or why not?

A

no; because cannot affect equilibrium

23
Q

give 4 things that help enzymes catalyze reactions

A
  1. amino acid side chains in active site
  2. cofactors
  3. coenzymes
  4. prosthetic groups
24
Q

what are cofactors?

A

small molecules that aid in catalysis (Fe2+, Cu2+, Mg2+)

25
Q

what are coenzymes?

A

cofcators that have organic components and include vitamin-derived species such as NAD+/NADH and FAD/FADH2

26
Q

what are prosthetic groups?

A

coenzymes that are permanently attached to enzymes like heme and biotin

27
Q

what are the 6 classes of enzymes?

A
  1. oxidoreductase
  2. transferase
  3. hydrolase
  4. lyase
  5. isomerase
  6. ligase
28
Q

what do oxidoreductases do?

A

oxidation-reduction; transfer of H or O atoms

29
Q

give 2 examples of oxidoreductases

A

oxidases, dehydrogenases

30
Q

what do transferases do?

A

trasnfer of functional groups like methyls, acyls, aminos, phosphoryls

31
Q

give 2 examples of transferases

A

kinases, transaminases

32
Q

what do hydrolases do?

A

formation of two products by hydrolyzin a substrate

33
Q

give two examples of hydrolases

A

peptidases, lipases

34
Q

what do lyases do?

A

cleavage of C-C, C-O, C-N, and other bonds by means other than hydrolysis or oxidation

35
Q

give two examples of lyases

A

decarboxylases, carboxylases

36
Q

what do isomerases do?

A

intramolecular rearrangements, transfer of groups within molecules

37
Q

give 2 examples of isomerases

A

mutases, isomerases

38
Q

what do ligases do?

A

formation of C-C, C-O, C-S, or C-N bonds using ATP cleavage

39
Q

give an example of a ligase

A

synthetases

40
Q

list and describe 3 methods of catalysis

A
  1. stabilize transition state: lower activation energy (barrier height) via interactions with involved molecules
  2. provide an alternate path for product formation via formation o stable intermediates (like base camp to rest before continue climb)
  3. orient substrates for reaction to occur and reduce entropy
41
Q

what is the active site microenvironment?

A

a small subenvironment away from other things for the reaction to occur

42
Q

what 3 things can an enzyme to in the active site microenvironment?

A
  1. induce geometric fit via altering protein conformation
  2. use cahrged residues on amino acid side chains
  3. exlusion of solvent via a hydrophobic core
43
Q

list the 3 enzyme mechanisms

A
  1. acid-base catalysis
  2. covalent catalysis
  3. metal ion catalysis
44
Q

describe the acid base catalysis enzyme mechanism (4)

A
  1. protons transferred between protein and substrate
  2. requires an ionizable aino acid
  3. enzyme always regenerated at the end
  4. pH dependent mechanism
45
Q

give an example and describe an amino acid involved in acid base catalysis enzyme mechanism

A

histidine, has a pKa of approximately 7, meaning it is readily found in either acid or base form at body pH; can act as proton donor or acceptor

46
Q

what is a nucleophile?

A

a reactant that donates an electron pair to form a bond

47
Q

what is an electrophile?

A

accepts an electron pair

48
Q

describe covalent catalysis as an enzyme mechanism

A

involves formation of a transient covalent bond between enzyme and substrate to form an unstable intermediate

49
Q

what 5 amino acids are typically involved in covalent catalysis enzyme mechanisms?

A
  1. serine
  2. tyrosine
  3. cysteine
  4. lysine
  5. histidine
50
Q

describe metal ion catalysis enzyme mechanism

A

positively charge metal ions stabilize negatively charged intermediated

51
Q

what are the 2 types of enzymes involved in metal ion catalysis? describe

A
  1. metal activated enzymes: loosely bound metal ions
  2. metalloenzymes: tightly bound metal ions
52
Q

what 2 amino acids are typically involved in metal ion catalysis?

A
  1. cysteine
  2. histidine
53
Q

describe enzyme binding affinity for the transition state

A

high

54
Q

why is the transition state so unstable?

A

free energy is high

55
Q

describe enzyme bindning affinity for products low and result of this

A

enzyme has low binding affinity for products, so products dissociate and enzyme regenerated

Biochemistry (20 decks)

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