Lecture 3.1: Intro to Enzymes

Question 1

Enzymes [ ] the rate of the reaction

Answer 1

increase

they do not permentanty change

Question 2

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

Answer 2

transition

Question 3

Transition State

Answer 3

activated form of moelcule that has undergone a partial chemical reaction

Question 4

Activation Energy

Answer 4

energy required to reach the transition state

Question 5

Free energy

Answer 5

G_product - G_reactant

Question 6

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

Answer 6

orientation
sufficent energy

Question 7

What do productive collisions require?

Answer 7

proximity orientation
orientation
collision energy

Question 8

Enzymes increase reaction rates by lowering?

Answer 8

activation energy

Question 9

Enzymes can provide?

Answer 9

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

Question 10

Enzymes have [ ] effect on ∆G or Keq

Answer 10

No effect!

Question 11

Enzyme [ ] provide chemical environments that facilitate catalytic reactions

Answer 11

active sites

Question 12

Substrate

Answer 12

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

Question 13

Holoenzyme

Answer 13

enzyme with cofactor
catalytically active enzyme-cofactor complex

Question 14

Apopenzyme

Answer 14

enzyme without cofactor (inactive form)

Question 15

Cofactors

Answer 15

• 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

Question 16

Coenzyme

Answer 16

organic cofactor
ex) vitamins, derivative, etc.

Question 17

Metal Ions

Answer 17

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

Question 18

Prosthetic Groups

Answer 18

tight association coenzyme
Ex) heme

Question 19

Co-Substrate

Answer 19

loose association coenzyme
Ex) NAD+

Question 20

Metal-Ion Cofactor in Enzymes Roles:

Which ones do oxidation reduction?

Answer 20

Fe2+
Mn2+
Cu2+
Se
Mo

Question 21

Metal-Ion Cofactor in Enzymes Roles:

Help bind ATP

Answer 21

Mg2+

Question 22

Metal-Ion Cofactor in Enzymes Roles:

Help bind the substrate

Answer 22

Zn2+

Question 23

Metal-Ion Cofactor in Enzymes Roles:

Required in the catalytic site

Answer 23

Ni2+

Question 24

Metal-Ion Cofactor in Enzymes Roles:

Increases enzyme activity

Answer 24

K+

Question 25

# Types of enzyme: oxioreductase

Answer 25

* oxidation-reduction * transfer of H or O atoms * Generic Enzymes: oxidase, dehydrogenases

Question 26

# Types of Enzymes Transferase

Answer 26

* transfer functional groups * Ex) methyl, acyl, amino, phosphoryl * Generic Enzymes: kinases, transaminases

Question 27

# Types of Enzymes Hydrolase

Answer 27

* Formation of two products hydrolyzing a substrate * Generic Enzymes: Ppeptidases, lipases

Question 28

# Types of Enzymes Lyase

Answer 28

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

Question 29

# Types of enzymes: Isomerase

Answer 29

* Intramolecular rearrangements * transfer of groups within molecules * Generic enzymes: mutases, isomerases

Question 30

# Types of enzymes Ligases

Answer 30

* formation of C-C, C-O, C-S, or C-N bonds using ATP cleavage * Generic Enzymes: synthetases

Question 31

What happens when glucose binds to free hexokinase?

Answer 31

conformational changes block water from the active site and promote phosphorylation

Question 32

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

Answer 32

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

Question 33

Transition State Stabilization Model/Induced fit model

Answer 33

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

Question 34

What contributes to lowered activation energy?

Answer 34

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

Question 35

Acid-Base Catalysis

Answer 35

* proton transfer * general acid = H+ donor * general base = H+ acceptor

Question 36

His12 = acid or base?

Answer 36

step 1 = base step 2 = acid

Question 37

His119 = acid or base

Answer 37

step 1 = acid step 2 = base

Question 38

His12 and His119 acid base catalysis steps

Answer 38

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

Question 39

Covalent Catalysis

Answer 39

* 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

Question 40

Covalent Catalysis Steps

Answer 40

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

Question 41

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

Answer 41

a covalent enzyme substrate intermediate

Question 42

Nucleophile

Answer 42

* electron rich group * loves nucleus * negatively charged * O, N, S

Question 43

Electrophile

Answer 43

* electron poor group * electron loving * positively charged

Question 44

Metal Ion Catalysis

Answer 44

* 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)

Question 45

Carbonic Anhydrase Steps

Answer 45

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