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Basic Biochemistry > BB 9 10 11 Enyme Kinetics > Flashcards

BB 9 10 11 Enyme Kinetics Flashcards

0
Q

Trypsin

A

cleaves only after arginine and lysine residues

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1
Q

Enzymes

A
  • biological catalysts
  • accelerates rate of reactions
  • function by stabilizing transition states in reactions
  • don’t change equilibrium of reactions
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2
Q

Thrombin

A

cleaves between arginine and glycine in particular sequences

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3
Q

Papain

A

cleaves all peptide bonds irrespective of sequence

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4
Q

DNA Polymerase I

A

adds nucleotides in sequence determined by template strand

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5
Q

Cofactors

A

small molecules essential for enzyme catalysis

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6
Q

Apoenzyme

A

enzyme without its cofactor

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7
Q

Holoenzyme

A

enzyme with its cofactor

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8
Q

Free energy

A
  • the difference between its reactants and its products

* independent of reaction path

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9
Q

Negative delta G

A
  • reaction may occur spontaneously, doesn’t mean it will

* exergonic

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10
Q

Positive delta G

A
  • doesn’t occur spontaneously
  • requires energy input
  • endogonic
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11
Q

Delta G

A
  • energy of the endpoints

* tells nothing about rate of reaction

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12
Q

Equilibrium constant – Keq

A

defines rate of reaction

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13
Q

Activation energy

A
  • reactions go via a high energy intermediate
  • reduces the rate at which equilibrium is reached
  • larger activation energy = slower rate of reaction
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14
Q

Transition state theory

A
  • enzymes reduces the activation barrier
  • transition state energy becomes smaller
  • need to put energy in even though end up releasing energy
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15
Q

Active site

A
  • region that binds the substrate
  • a 3D structure formed by groups that can come from distant residues in the enzyme (tertiary structure)
  • take up a small volume of the enzyme
  • unique chemical environments, usually formed from a cleft or crevice in the enzyme
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16
Q

Active sites often exclude

A
  • water
  • non-polar, enhances binding of substrates, allow polar catalytic groups to acquire special properties required for catalysis
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17
Q

Active sites bind substrates with

A
  • weak interactions

* eg electrostatic, hydrogen bonds, Van der Waals, hydrophobic interactions

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18
Q

The specificity of an enzyme for its substrate(s) is critically dependent on

A

• the arrangement of amino acid residues at the active site

tertiary structure

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19
Q

Catalytic specificity depends on

A
  • binding specificity

* activity of enzymes regulated at this stage

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20
Q

Evidence for ES complexes

A
  • saturation effect
  • crystallography (structural data)
  • spectroscopic data
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21
Q

Saturation effect

A

• at constant enzyme concentration, reaction rate increases with substrate until Vmax is reached

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22
Q

Catalytic groups

A
  • amino acid side chains in the active site associated with the making and/or breaking of chemical bonds
  • make up the active site
23
Q

Induced fit model

A
  • Koschland, 1958
  • substrates and enzymes are flexible and dynamic
  • the enzyme changes shape in order to optimise its fit to the substrate only AFTER the substrate has bound
24
Q

First order reaction

uni-molecular

A

V = k [A]

k: s-1

25
Q

Second order reaction

bi-molecular

A

v = k [A][B]

k: M-1 s-1

26
Q

Michaelis-Menten Model

A
  • describes the kinetic property of enzymes
  • at a fixed concentration of enzyme, increasing substrate concentration increases reaction rate
  • maximal reaction velocity w/ saturating substrate for a fixed amount of enzyme implies a specific ES complex is a necessary intermediate in enzyme catalysis
  • add more substrate to point where it has no effect
27
Q

Michaelis-Menten Equation

A
  • relates the rate of catalysis to the concentration of the substrate
  • plotting initial velocity of a reaction against substrate concentration produces the Michaelis-Menten curve
28
Q

Km for any enzyme depends on

A
  • pH
  • temperature
  • ionic strength
29
Q

Km

A
  • substrate concentration required for the reaction velocity to be half the maximal value
  • Michaelis-Menten constant
  • tells us enzyme-substrate affinity
30
Q

Vmax

A
  • maximal velocity of the reaction
  • rate/velocity at which all enzyme active sites are filled
  • number of substrate molecules converted into product by an enzyme molecule per unit time when enzyme is fully saturated
31
Q

Catalytic power

A
  • enzyme’s turnover
  • maximum number of substrate molecules converted into product by an enzyme molecule un unit time
  • E fully saturated, equal to kinetic constant k2 = AKA kcat
32
Q

Diffusion limit

A

the max value of k2/Km

33
Q

The perfect enzyme is limited by

A

diffusion
• k+1 = how often the enzyme collides with its substrate
• only limited by the rate of collisions = diffusion limited

34
Q

Multiple substrate reactions can be classified into classes:

A
  • sequential reactions

* double displacement (ping-pong) reactions

35
Q

Sequential reactions

A
  • all substrates bind to enzyme, forming ternary complex

* can be ordered or random interactions

36
Q

Double-displacement reactions

A
  • AKA ping-pong reactions

* one or more products released before all substrates bind to enzyme

37
Q

Allosteric Enzymes consist of

A
  • multiple subunits
  • multiple active sites
  • sigmoidal
38
Q

Inhibitors

A

molecules that prevent enzymes from working
• may regulate enzymes
• can act as medicinal drugs or toxins

39
Q

2 main types of enzyme inhibition

A
  • irreversible

* reversible

40
Q

Irreversible inhibition

A

the inhibitor is tightly bound to the enzyme (sometimes covalently)

41
Q

Reversible inhibition

A

inhibitor can bind and dissociate from the enzyme

42
Q

Competitive inhibitors

A
  • bind to the active site of enzymes

* reduce the effective substrate concentration

43
Q

Non-competitive inhibitors

A
  • stop the enzyme from working by changing the conformation of the active site
  • reduce the effective enzyme concentration
  • don’t bind to active site
44
Q

Uncompetitive inhibitors

A
  • bind to the ES complex

* cannot be overcome by adding more substrate

45
Q

Methotrexate

A
  • reversible inhibitor
  • structural analog of substrate for DHFR
  • prevents nucleotide synthesis
  • used to treat cancer
  • biosynthesis of purines and pyrimidines
46
Q

Penicillin

A

• irreversible inhibitor
• covalently modifies transpeptidase
• inhibits bacterial cell wall synthesis, killing bacteria
(peptidoglycan)
• reacts with serine residue in active site

47
Q

Competitive inhibition

A
  • Km increases

* Vmax stays the same

48
Q

Non-competitive inhibition

A
  • Vmax lowered

* No change in Km

49
Q

Uncompetitive inhibition

A
  • binding to ES stops reaction

* both Vmax and Km are lowered

50
Q

Whether Km or Vmax change depends on

A

where the inhibitor binds to the enzyme (type of inhibition)

51
Q

Transition state analogs

A
  • mimic transition state = effective inhibitors
  • enzymes work by stabilizing transition state
  • TS analogs bind tightly to the active site
  • very good COMPETITIVE inhibitors
52
Q

Catalytic antibodies

A
  • stabilize transition state = catalyze reaction

* antibodies which recognize a transition state function as catalysts (bind and stabilize)

53
Q

Enzyme regulation can be

A
  • cooperative

* allosteric

54
Q

Cooperative regulation

A

• binding of substrate to one binding site helps binding to other active sites

55
Q

Allosteric regulation

A
  • involves product inhibition
  • product regulates work of first enzyme in pathway
  • used to control flux through metabolic pathways
  • feedback (negative) inhibition
  • DON’T SHOW MICHAELIS-MENTEN KINETICS (multiple subunits and multiple active sites = sigmoidal)

Basic Biochemistry (15 decks)

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