Ch. 6 How enzymes work

Question 1

Enzymes

Answer 1

-Enzymes are living systems catalysts
-Most enzymes are proteins, but few are made of RNA
-Most exhibit a high degree of specificity and greater catalytic power than non-biologic catalysts that are specific for that reactant

Question 2

Ribozymes

Answer 2

-made up of RNA

Question 3

Catalytic power

Answer 3

-rate enhancement/catalytic efficiency 10^8-10^12
- Enzymes have a higher catalytic power
-Ratio of catalyzed rate: uncatalyzed rate

Question 4

Specificity of enzymes

Answer 4

• Enzymes are specific to their substrates
  -Functional groups on enzymes are arranged so that enzyme can distinguish its substrates from others

Question 5

Chymotrypsin and its specifity

Answer 5

• Has a reacting binding site and has 3 amino acids bonded to the substrate. Histidine, Serine, and carboxylate.
  -Chymotrypsin uses hydrolysis to cleave the polypeptide bond following large aromatic residues
  -catalyzed hydrolysis of amide and ester bonds

Question 6

Role of artificial substrates to study proteases

Answer 6

-Artificial substrates (p-nitrophenyl acetate) mimic the actual substrate of chymotrypsin–> p-nitrophenolate. ( allows the substrate to have color)
Role: to monitor activity of the specific enzyme

• look at study guide

Question 7

The 6 classes of enzymes and the reactions they catalyze

Answer 7

1. Oxidoreductases: Oxidative reduction reactions
2. Transferases: Transfer of functional groups
3. Hydrolases: Hydrolysis reactions
   4.Lyases: Group elimination to form double bonds
4. Isomerases: Isomerization reactions
5. Ligases: bond formation coupled with ATP hydrolysis

Question 8

How are enzymes named

Answer 8

• Enzymes are usually named after the substrate name and the reaction they catalyze and their names end in -Ase

Question 9

The meaning of the values of the free energy change of a reaction, the free energy of activation, and the concept of the transition state

Answer 9

Transition state: is the point of the highest energy and is the midway between the reactants and the products
-Free energy activation is the energy-requiring step of the reaction as the energy barrier and is symbolized as ΔG.

Question 10

Effect of enzyme on activation energy and on free energy change of a reaction

Answer 10

-Enzymes lower the activation energy for a reaction but do not affect its free energy change. The sign of ΔG indicates if the reaction is spontaneous or favorable.

Question 11

Cofactors

Answer 11

-non A A substrates required for catalytic/enzymatic activity

Question 12

Coenzyme

Answer 12

-Type of cofactor, it may be derived from vitamins

Question 13

Cosubstrate

Answer 13

-Type of coenzyme, it enters and exits active site (substrate def.) ( not recycled)

Question 14

Prosthetic group

Answer 14

• Is permanently attached to the enzyme that remains in the active site between reactions(recycled)

Question 15

The 3 major chemical catalytic mechanisms

Answer 15

-Acid-base catalysis: A proton is transferred between the enzyme and the substrate
-Covalent catalysis: Involves the use of a nucleophile
-Metal ion catalysis: mediate redox reactions/promote reactivity of active site

Question 16

The role of an acid and base on the tautomerization of a ketone to an enol

Answer 16

(look at the study guide)
-An acid catalyst (H-A) donates an H+ to the ketones oxygen atom. This lowers the energy of the transition state, therefore, lowering the activation energy for the reaction.
-A base catalyst accepts an H+ lowering the energy of the transition state’

Question 17

Amino acids involved in acid-base catalysis

Answer 17

• Asp
  -Glu
  -His
  -Lys
  -Cys
  -Tyr

Question 18

The reaction coordinate of a reaction involving covalent catalysis

Answer 18

Look at the study guide for the diagram

Question 19

Amino acids involved in covalent catalysis

Answer 19

• Ser,Tyr
  -Cys
  -Lys
  -His

Question 20

The role of a metal ion on the alcohol dehydrogenase reaction

Answer 20

-Zn2+ stabilizes the (-) charge on the O atom of the transition state

Question 21

Types of catalysis used by chymotrypsin

Answer 21

-Uses acid-base catalysis and covalent catalysis and has 3 essential amino acid residues at the active site. It has a serine protease. The reaction occurs in 2 phases that correspond to the formation of a covalent intermediate and its breakdown.

Question 22

What is the catalytic triad of chymotrypsin

Answer 22

-It promotes peptide bond hydrolysis
-Chymotrypsin uses Acid-Base and covalent catalysis
-It also has a serine protease
-3 essential amino acid residues @ the active site known as the catalytic triad Asp102, His 57, Ser 195.

Question 23

Roles of each of the catalytic triad amino acid residues

Answer 23

-His 57 acts as a base catalyst and Ser 195 acts as a nucleophile

Question 24

Understand the steps of the mechanism of peptide hydrolysis by chymotrypsin

Answer 24

1. His 57 acts as a base catalyst and accepts H+ from ser 195 hydroxyl group. This results in nucleophilic O-(covalent catalyst) attacking carbonyl C of the substrate. The n-terminal portion of the substrate remains covalently linked to an enzyme
2. His 57 acts as an acid catalyst and donates H to N of the scissile peptide bond. This cleaves the bond and Asp promotes the reaction by stabilizing His 57 through hydrogen bonding
3. Water then enters the active site and donates a proton to His 57, leaving a hydroxyl group that attacks the carbonyl group of the remaining substrate.
4. In the 2nd tetrahedral transition state: His 57 acts as an acid catalyst and donates H+ to ser oxygen and breaks down the transition step(similar to step 2)
5. N-terminal portion of the original substrate w/new C-terminus diffuses and the enzyme is regenerated

Question 25

The role of the oxyanion hole

Answer 25

-is within the active site of chymotrypsin and the transition state stabilized. Forms 3 new H bonds

Question 26

proximity and orientation effects

Answer 26

increase of reactants and increase of frequency of collisions by bringing reacting groups into close proximity of the active site
-Substrates rotational motions freeze for proper orientation to bind to the enzyme

Question 27

The induced fit model

Answer 27

-Is the binding of a substrate to enzyme that triggers a conformational change at the active site enhancing catalysis and fully enclosing substrates.
-Glucose + ATP -(hetokinase) glucose-6-phosphate + ADP

Question 28

How similar are the sequences and structures of the three serine proteases are

Answer 28

-Chymotrypsin,Trypsin, and elastase positions of their catalytic residues in their active sites are identical and have very similar secondary + tertiary structures

Question 29

How different the active sites of the three serine proteases are and how these determine their specificity

Answer 29

-Chymotrypsin binding site= Ser and binds to large hydrophobic aromatic rings (Phe,Trg,Tyr)
-Trypsin binding site=Asp and binds to basic residues (Arg,Lys)
-Elastase binding site= Val +Thr on walls and binds to small hydrophobic residues(Ala,Gly)

Question 30

How the activity of proteases can be limited

Answer 30

-By their synthesis as inactive precursors are known as zymogens
-The action of small proteins that pose as substrates but are not hydrolyzed

Question 31

How zymogens of proteases are activated

Answer 31

-Trypsinogen is activated by the hydrolysis of the peptide bond between Lys 6 and Ile7. Trypsin then cleaves other zymogens including its own leading to auto-activation.

Question 32

How protease inhibitors limit the activity of proteases

Answer 32

-Protease inhibitors are small proteins that pose as substrates but are not hydrolyzed.
-BPTI is the protease inhibitor of trypsin and poses as the substrate
- Ser 195 of trypsin attacks peptide bind of Lys 15 of BPTI but the bond is not hydrolyzed and halts the formation of the 1st transition state.