chapter 3 Flashcards

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1
Q

what are enzymes?

A
  • biological catalysts
    • speed up the rate of a reaction by reducing the activation energy
    • sensitive to temperature and pH
    • specific for certain reactions or classes of reactions
    • do not affect the equilibrium of a reaction or the thermodynamic paramters of the reaction
    • also speed up the reverse reaction in order to avoid affecting the equilibrium
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2
Q

the substance that an enzyme operates on is known as?

A
  • a substrate and they interact at the active site of an enzyme, which can be divided into a binding site and a catalytic site
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3
Q

what is a catalytic and binding site?

A
  • the catalytic site is the very specific place where a reaction is catalyzed
  • the binding site is a larger area where the substrate interacts with the enzyme through intermolecular interactions in a way that positions the substrate properly relative to the catalytic site
    • when the substrate interacts with the active site of an enzyme it forms the enzyme-substrate complex
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4
Q

regulatory elements that interact with an enzyme at its active site are known as?

regulatory molecules that bind at some other site of an enzyme are known as?

the substance that an enzyme interacts with can be reffered to as?

A
  • orthosteric
  • allosteric
  • ligand
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5
Q

what are the 2 important models proposed to describe how enzymes interact with substrates?

A
  • lock and key- proposes that the active site of an enzyme and the substrate fit together like puzzle pieces, with no change in tertiary or quaternary structure
  • induced fit model- the enzyme and substrate are seen as affecting each otehr; the initial stages of binding induce conformational shifts that allow closer binding and more efficient catalysis
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6
Q

what are oxidoreductases?

A
  • catalyze redox reactions
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7
Q

what are transferases?

A
  • transfer a functional group between molecules
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8
Q

what are hydrolases?

A
  • catalyze hydrolysis
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9
Q

what are lyases?

A
  • cleave bonds through non-hydrolysis mechanisms
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10
Q

what are isomerases?

A
  • catalyze isomerization
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11
Q

what are ligases?

A
  • join moelcules together with covalent bonds
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12
Q

enzymes in a metabolic pathway are commonly regulated by downstream products of the pathway, which is a process known as?

A
  • feedback regulation
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13
Q

what is negative feedback/feedback inhibition?

A
  • the downstream product of a pathway acts to inhibit the pathway itself
    • when we have enough of a product, then we don’t need to produce more of it
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14
Q

what is positive feedback?

A
  • ex. blood clotting
    • positive feedback allows a quick response, while negative feedback ensures that the process doesn’t spiral out of control
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15
Q

what is feed-forward regulation

A

control of a metabolic pathway by a metabolite of the pathway that acts in the same direction as the metabolic flux, i.e. downstream or ‘later’ in the pathway, e.g. the activation of pyruvate kinase by fructose 1,6-bisphosphate.

an enzyme is regualted by an upstream product of the pathway

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16
Q

what is cooperativity?

A
  • when an enzyme has multiple active sites and binding at one active site facilitates or makes the second binding easier or harder
    • positive = easier
    • negative = harder
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17
Q

the degree of cooperativity in an enzyme or protein can be expressed using?

A
  • the Hill coefficient
    • a Hill coefficint > 1 results from positive cooperativity
    • equal to 1 indicates non-cooperativity
    • < 1 negative cooperativity
18
Q

what is the Michaelis-Menten model of enzyme kinetics?

A
  • The Michaelis-Menten model (1) is the one of the simplest and best-known approaches to enzyme kinetics. It takes the form of an equation relating reaction velocity to substrate concentration for a system where a substrate S binds reversibly to an enzyme E to form an enzyme-substrate complex ES, which then reacts irreversibly to generate a product P and to regenerate the free enzyme E.
19
Q

what is teh definition of Km?

A
  • the concentration of substrate that corresponds to half of vmax
    • can be used as a measure of the affinity that an enzyme has for its substrate
    • Km is not affected if you change the concentration of the substrate or enzyme, but can be affected by inhibitors
20
Q

what is the Michaelis-Menten equation?

A

v = vmax[S]/Km + [S]

21
Q

what are lineweaver-Burk plots?

A
  • double-reciprocal transformation of Michaelis-Menten plots
22
Q

parameters of Km abd Vmax on a linweaver burke plot?

A
  • increase Km = increase in intercept (became less negative) so moved towards origin
  • decrease Km = decrease in intercept (became mroe negative) so moved away from origin
  • increase vmax = decrease (become less positive) so moved towards origin
  • decrease vmax = increase (became more negative) so moved away from origin
23
Q

what are inhibitors?

A
  • substances that reduce the effective activity of enzymes
    • can be reversible or irreversible
24
Q

how do non reversible inhibitors interact with enzymes?

A
  • through non-covalent interactions
25
Q

what are competitive inhibitors?

A
  • an inhibitor competes with substrate binding to the active site, resulting in an unchanged vmax and an increased Km
26
Q

what are noncompetitive inhibitors?

A
  • a subclass of mixed inhibition in which an inhibitor binds to the enzyme alone 50% of the time and the enzyme-substrate complex 50% of the time, resulting in a decreased vmax and an unchanged Km
27
Q

what is uncompetitive inhibition?

A
  • an inhibitor binds to the enzyme-substrate complex, resulting in a decreased vmax and a decreased Km
28
Q

what is mixed inhibiton?

A
  • an inhibitor binds to both the enzyme alone and the enzyme-substrate complex, resulting in a decreased vmax and an increased or decreased Km
  • Vmax decreases and Km varies
29
Q

summary of enzyme inhibitors?

A
30
Q

enzyme inhibitors effects on MM plot?

A
31
Q

enzyme inhibitors on LWB plot?

A
32
Q

what does phosphorylation refer to?

A
  • attaching a phosphate group to a protein and dephosphorylation refers to removing it
    • affects enzyme activity
33
Q

phosphorylation most often targets?

A
  • serine, threonine, and tyrosine which all have -OH groups that a phosphate can be attached to
34
Q

what catalyses phosphorylation and what catalyses dephosphorylation?

A
  • kinases
  • phosphatases
35
Q

what does glycosylation refer to?

A
  • the modification of enzymes by carbohydrate moieties with a broad range of effects
36
Q

what are zymogens?

A
  • aka proenzymes are inactive forms of enzymes that must be cleaved to become active
37
Q

what are cofactors?

A

A cofactor is a non-protein chemical that assists with a biological chemical reaction. Co-factors may be metal ions, organic compounds, or other chemicals that have helpful properties not usually found in amino acids. Some cofactors can be made inside the body, such as ATP, while others must be consumed in food (organic = coenzymes like vitamins- ex. coenzyme A which transfers acyl groups from one place to another).

38
Q

coenzymes that are tightly bonded to their enzyme are known as?

A
  • prosthetic groups
    • ex. heme which contains an iron ion in the center of a porphyrin ring, and is attached to oxygen-transport proteins
39
Q

what is a holoenzyme?

A
  • an enzyme together with the coenzyme(s) and/or metal ions it needs to carry out its catalytic activity
40
Q

what is an apoenzyme?

A
  • refers to an enzyme without the coenzymes/cofactors it needs to function correctly