Chapter 11 - Enzymatic Catalysts

Question 1

Why enzymes?

Answer 1

speciic for substrates (enzyme reactant)

single product

practice and “green” (no wasteful byproducts)

regulated

Question 2

Enzymes act on specific substarates at the active site

3D site where enzyme rxns take place

(details)

Answer 2

protein surface crevice -> favored rxn environment

complimentar, non-covalent interactions bind substrate

geometric and electronic (manipulated): 3D specificity

Possible induced fit triggered by binding

Question 3

Oxidoreductases

Answer 3

oxidation-reduction reactions

(electron transfer)

ex: NAD, FAD (require dehydrogenases)

Question 4

Transerases

Answer 4

Catalyze group transfer reactions “group carrier”

Question 5

Hydrolases

Answer 5

break bonds via group transfer to water (hydrolysis reactions)

Question 6

Lyases

Answer 6

breaks substrate into parts via nonhydrolytic or oxidative elimination resulting in double bond (whereas synthases catalyze reverse reaction -> adds to double bond)

(group elimination to form double bonds)

Question 7

Isomerases

Answer 7

aid compound rearrangment

(isomerization)

Question 8

Ligases (synthases)

Answer 8

ligate or join two substrates; requires energy (e.g. ATP)

(Bond formation coupled with ATP hydrolysis)

Question 9

Cofactors

Answer 9

coenzymes and ions (usually metals)

Apoenzyme (inactive) + cofactor -> holoenzyme (active enzyme)

essential ions (activator ions, loosely bound) & metal ions of metalloenzymes (tightly bound)

coenzymes (cosubstrates, loosely bound) & prosthetic groups (tightly bound)

Question 10

Range of Cofactor Activities

Answer 10

Metals -> electrophilic, electron transfer, coordination of compounds

Specific group transfer agents -> protons, electrons, carboxyl groups, methyl, etc.

Role: participate in rxn, aid substrate binding, stabilize intermediates

Question 11

Types of cofactors and their functions

Answer 11

Metals: Activation or catalytic; 1 mM Mg biochem std. state (F consistent charge, multiple oxidation states)

Coenzymes: organic compounds (often vitamin derivatives)

Coenzymes include cosubstrates and prosthetic group

Cosubstrates: reversible binding; altered in rxn but regenerated - cellular pools with various forms (NAD+, NADH, ATP, ADP, etc); concentrations can be regulatory; compartmentalized in cell

Prostethic groups: permanently bound to enzyme: heme, thiamine

*functional ATP has Mg+ bound, changes conformation a bit

Question 12

Enzyme catalyzed reactions

Answer 12

reduced activation energy due to a lower energy path thru transition state (Transition State Theory)

Question 13

Enzyme mechanisms designed reduce activation energy

Answer 13

1) Chemical catalysts: enzyme groups act as acids/bases, nucleophiles, etc
2) Substrate binding: position (facilitates transition state formation; reduces freedom); catalytic group organization; envrionment
3) Transition state stabilization: stable transition state more probable to form product
4) Multistep reactions: reactions split to reduce activation energy; intermediates are semi-stable compounds between two transition states

Question 14

Classes of chemical catalysis

Answer 14

acid-base; covalent; metal ions

Question 15

Amino acids typically found in active sites

Answer 15

Hydrophobic: surrounds active site and excludes solvent (water)

Hydrophilic: active participants in reactions and polar interactions

Coenzymes present: chemistry over and above amino acid capabilities

Question 16

Proximity, orientation, and binding effects: enzyme-substrate complex

Answer 16

cavity volume small so concentration of substrates increased

specific binding of the transition state

limited rotational/translational freedom of substrates and catalytic groups

Question 17

catalytic function depends on residue protonation state and polarity

Solution pH-drastically affects enzyme activity

Histidine?

Answer 17

imidazole participates in proton transfer

common in active sties since it can donate or accept protons

1. Accepts proton in first step (or “abstract” proton)
2. Donates it back to another group to finish off reaction
3. Enzyme is regenerated for another reaction

Question 18

Effects of pH on Enzyme Activity

Answer 18

*recall pKa’s may change with environment

enzymes have a pH profile specific to essential active site acidic or basic residues

Question 19

Acid-Base Catalysis

Answer 19

Active site catlytic proton transfer

General acid or base involves OH, NH, CH, or similar groups (usually aided by other active site groups)

Enzyme regenerated by accepting/donating protons from water or other groups

Question 20

Base

Answer 20

proton abstraction forms stronger nucleophile to stimulate reactions

(ex. indirect base catalysis reaction via water)

Question 21

Acid

Answer 21

proton donation makes other groups into good leaving group

Donation of a proton lowers free energy of transition state

(acid donates prton in transfer, while bases accept protons)