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Biochemistry > Lecture 3.1: Intro to Enzymes > Flashcards

Lecture 3.1: Intro to Enzymes Flashcards

1
Q

Enzymes [ ] the rate of the reaction

A

increase

they do not permentanty change

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2
Q

For the reaction to occur the reaction must first reach the [ ] state

A

transition

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3
Q

Transition State

A

activated form of moelcule that has undergone a partial chemical reaction

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4
Q

Activation Energy

A

energy required to reach the transition state

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5
Q

Free energy

A

G_product - G_reactant

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6
Q

Molecules need to collied in the appropriate [ ] and with [ ] energy in order to react to produce product

A

orientation
sufficent energy

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7
Q

What do productive collisions require?

A

proximity orientation
orientation
collision energy

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8
Q

Enzymes increase reaction rates by lowering?

A

activation energy

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9
Q

Enzymes can provide?

A

alternate path
stabilize transition state
more favorable conditions for the reaction to occur

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10
Q

Enzymes have [ ] effect on ∆G or Keq

A

No effect!

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11
Q

Enzyme [ ] provide chemical environments that facilitate catalytic reactions

A

active sites

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12
Q

Substrate

A

the chemical substance on which the enzyme acts
binds to active site where chemical rxn occurs

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13
Q

Holoenzyme

A

enzyme with cofactor
catalytically active enzyme-cofactor complex

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14
Q

Apopenzyme

A

enzyme without cofactor (inactive form)

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15
Q

Cofactors

A
  • non-amino acids
  • non-protein compounds or metallic ions that are required for the catalytic activity of an enzyme
  • provide additional chemical felxibility for facilitating the catalytic reaction
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16
Q

Coenzyme

A

organic cofactor
ex) vitamins, derivative, etc.

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17
Q

Metal Ions

A

inorganic cofactor
Ex) Cu2+, Zn2+, K+, Mg2+

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18
Q

Prosthetic Groups

A

tight association coenzyme
Ex) heme

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19
Q

Co-Substrate

A

loose association coenzyme
Ex) NAD+

20
Q

Metal-Ion Cofactor in Enzymes Roles:

Which ones do oxidation reduction?

A

Fe2+
Mn2+
Cu2+
Se
Mo

21
Q

Metal-Ion Cofactor in Enzymes Roles:

Help bind ATP

A

Mg2+

22
Q

Metal-Ion Cofactor in Enzymes Roles:

Help bind the substrate

A

Zn2+

23
Q

Metal-Ion Cofactor in Enzymes Roles:

Required in the catalytic site

A

Ni2+

24
Q

Metal-Ion Cofactor in Enzymes Roles:

Increases enzyme activity

A

K+

25
Q

Types of enzyme:

oxioreductase

A
  • oxidation-reduction
  • transfer of H or O atoms
  • Generic Enzymes: oxidase, dehydrogenases
26
Q

Types of Enzymes

Transferase

A
  • transfer functional groups
  • Ex) methyl, acyl, amino, phosphoryl
  • Generic Enzymes: kinases, transaminases
27
Q

Types of Enzymes

Hydrolase

A
  • Formation of two products hydrolyzing a substrate
  • Generic Enzymes: Ppeptidases, lipases
28
Q

Types of Enzymes

Lyase

A
  • Cleavage of C-C, C-O, C-N, and other bonds by means other than hydrolysis or oxidation
  • Generic Enzymes: decarboxylases, carboxylases
29
Q

Types of enzymes:

Isomerase

A
  • Intramolecular rearrangements
  • transfer of groups within molecules
  • Generic enzymes: mutases, isomerases
30
Q

Types of enzymes

Ligases

A
  • formation of C-C, C-O, C-S, or C-N bonds using ATP cleavage
  • Generic Enzymes: synthetases
31
Q

What happens when glucose binds to free hexokinase?

A

conformational changes block water from the active site and promote phosphorylation

32
Q

What happens when glucose does not bind free (unbound) hexokinase?

A

Glucose replaces water in the active site: similar volume & interactions

33
Q

Transition State Stabilization Model/Induced fit model

A

transition state is complementary to active site
best contact is during the transition state

34
Q

What contributes to lowered activation energy?

A
  • formation of many noncovalent interactions between enzyme and substrate
  • the combo of + activation energy plus - binding energy results in lowered net activation energy
35
Q

Acid-Base Catalysis

A
  • proton transfer
  • general acid = H+ donor
  • general base = H+ acceptor
36
Q

His12 = acid or base?

A

step 1 = base
step 2 = acid

37
Q

His119 = acid or base

A

step 1 = acid
step 2 = base

38
Q

His12 and His119 acid base catalysis steps

A
  1. His12 acts as a general base to abstract a proton from the RNA molecule
  2. His119 acts as a general acid to donate a proton to the RNA molecule -> the RNA product leaves the active site
  3. His12 now acts as gneral acid donating a proton to the remaining part of the RNA molecule
  4. His119 now acts as a general base, accepting a proton from water, forming a hydroxyl group that attacks at the phosphoryl grouo of the remaining RNA
  5. His residues are back in their initial state
39
Q

Covalent Catalysis

A
  • formation of enzyme substrate complex
  • transient covalent bond is formed between the enzyme and substrate to create an unstable intermediate
  • the formation of an unstable covalent intermediate promotes the catalytic reaction
40
Q

Covalent Catalysis Steps

A
  1. Acylation
  2. Enzyme-Substrate intermediate
  3. Deacylation
  4. enzyme regenerated
41
Q

Nucleophillic attack by R-groups in the enzyme on the substrate forms?

A

a covalent enzyme substrate intermediate

42
Q

Nucleophile

A
  • electron rich group
  • loves nucleus
  • negatively charged
  • O, N, S
43
Q

Electrophile

A
  • electron poor group
  • electron loving
  • positively charged
44
Q

Metal Ion Catalysis

A
  • facilitate the formation of a reactive nucleophile
  • act as electrophile to stabilize the negative charge on a reaction intermediate
  • Hold the substrate in a favorable position for catalysis
  • mediate redox reactions through reversible changes in oxidation state (transfer or accept electrons readily)
45
Q

Carbonic Anhydrase Steps

A
  1. Zn2+ binds a water molecule lowering its pKa to facilitate deprotonation
  2. The hydroxide anion bound to the Zn2+ acts as a nucleophile
  3. Bicarb product is coordinated to Zn2+. The buildup of positve charge makes displacement of bicarb by a neutral water molecule favorable
  4. Zn2+ interacts with a second water molecule, resulting in release of the bicarb product and regeneration of the enzyme
  1. lower pKa –> deprotonation
  2. nucleophilic attack by hydroxide anion
  3. buildup of + charge = displacement of bicarb
  4. release of bicarb product + regeneration of enezyme

Biochemistry (10 decks)

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