Chapter 6 - Enzyme

Question 1

Nature of chemical rxn in biology world?

Answer 1

thermodynamic favorable but kinetics controlls (very slow without catalyst)

Question 2

How to change the rate of reaction?

Answer 2

increase temperature, concentration of reactants, add catalyst

Question 3

What are enzyme characteristics?

Answer 3

enhance rxn rate

mild condition

reaction speicificty

regulation activity

Question 4

What are the forces that are used in enzyme/substrate interactions?

Answer 4

Vander Waals interactions

H-bond

hydrophobic interactions

electrostatic interactions

Question 5

Factor contributes to substrate binding

Answer 5

geometric complimentarity

electronic complimentarity (lock and key)

induced fit

Question 6

induced fit

Answer 6

the binding of substrate can induce conformational change in enzyme to accomodate both geometric and electronic complementarity

Question 7

Type of enzyme

Answer 7

Oxidoreductase

Transferase

Hydrolase

Lyases

Isomerases

Ligases

Question 8

Oxidoreductase

transferase

hydrolase

Answer 8

redox reaction

transfer of funcional groups

hydrolysis reactions

Question 9

Lyase

Isomerase

Ligase

Answer 9

Group elimination to form double bonds

isomerization rxn

bond formation coupled with ATP hydrolysis

Question 10

How does enzyme distinguish the substrates?

Answer 10

through enzyme’s functional groups in active site

Question 11

Mild condition of enzyme

Answer 11

enzyme-rxn can occur at normal temp and pressure

Question 12

Regulation activity of enzyme

Answer 12

allosteric regulation

post-translational modification of enzyme

up and down regulation for concentration of enzyme

Question 13

What doe enzyme do to the delta G++?

Answer 13

It lower the activation energy by lowering the transition state energy

Question 14

What are 3 chemical catalytic mechanism of enzymes?

Answer 14

acid-base catalysis

transient covalent catalysis

metal ions catalysis (charge-charge interaction)

Question 15

What do 3 chemical catalytic mechanisms need?

Answer 15

amino acid side chains

Question 16

cofactor

Type of cofactos

Answer 16

required for functional group transfer or redox reaction

metal ions and coenzymes (cosubstrate and prosthetic group)

Question 17

cosubstrate

prosthetic group

Answer 17

transient association with enzyme - leave/enter with substrate

permanent association with active site of enzyme

Question 18

Common metal ions in cofactors

Answer 18

Ca2+, Mg2+, Fe3+, Cu2+, Zn2+

Question 19

Apoenzyme

Holoenzyme

Answer 19

enzymes after removing cofactors

enzyme-cofactor complex

Question 20

vitamin

Where does vitamin exist? Can it be synthesized by our body?

Answer 20

the compounds are used as precursors for coenzyme biosynthesis

No, it exists only in diet

Question 21

Type of vitamin

which one is used for biosynthesis?

Answer 21

water soluble and water insoluble

water soluble

Question 22

transition state

Delta G++

Answer 22

the state where bonds are broken and formed (A- - B - -C)

activation energy - energy required for reactants to reach the transition state

Question 23

The higher delta G++

The lower delta G++

Answer 23

the longer the rxn will take

the shorter the rxn will take

Question 24

How much delta-G++ have to decrease to increase rxn by 10-fold?

Answer 24

1.36 kcal/mol (5.71 kJ/mol)

Question 25

Formula for calculate the increase rxn rate by decreasing delta G++?

Answer 25

V = e^(delta-G++ /RT)

Question 26

What does enzyme have when at the transition state? What is downside of this?

Answer 26

higher affinity to the substrate for compounds mimics the transition state, it can have very high affinity to bind with enzyme and can be great inhibitors

Question 27

acid catalysis

Answer 27

the process in which the transfer of proton from acid lower the free energy of reactant's transition state

Question 28

base catalysis

Answer 28

the process in which the abstraction of proton by a base lower the free energy of reactant's transition state

Question 29

Covalent catalysis what is the other name for covalent catalysis

Answer 29

the process in which the covalent bonds form between enzyme and substrate nucleophilic catalysis

Question 30

nucleophilic catalysis

Answer 30

the process in which nucleophiles of enzyme attack the electrophile on substrates

Question 31

nucleophilic groups characteristics

Answer 31

negatively charge or have lone pair electrons they are deprotonated

Question 32

What is a good covalent catalysis?

Answer 32

It is the balance between nucleophilicity and the ability as a good leaving group

Question 33

Nucleophicility need for? good leaving group need for?

Answer 33

starting the rxn release the product

Question 34

How many process does covalent catalysis have?

Answer 34

two-part rxn process thus two activation energy

Question 35

What are the metal ions role in metal ion catalysis?

Answer 35

orientate the substrate in enzyme active site mediate oxidation-reduction rxn electrostatically stabilizing

Question 36

How does enzyme maximize the enhancing rxn rate?

Answer 36

by confining the substrate

Question 37

Confine the substrate in enzyme

Answer 37

bring the substrate close to the catalytic site (proximity) proper orientation charge groups (electrostatic catalysis) freeze the translational and rotational motions

Question 38

factors contribute to rate acceleration in catalysis

Answer 38

proximity orientation of the substrate strains that generated in binding desolvation after binding to the enzyme active site the preferential binding of enzyme to transition state

Question 39

group specificity

Answer 39

an enzyme is specific to a typical bond and groups around that bond (peptide bond)

Question 40

What type of enzyme is chymotrypsin? What catalysis mechanism does this type of enzyme use?

Answer 40

serine protease acid-base and covalent catalysis

Question 41

What are amino acids made of active sites in serine protease? Function of each AA in active site?

Answer 41

Asp-His-Ser (catalytic triad) Asp: stabilizing the positively charged imidazole of His His: abstracts proton from Ser so oxygen of Ser can covalently bind with substrate Ser: binding site of substrate

Question 42

scissile bond

Answer 42

bond to be cleaved by hydrolysis

Question 43

Chymotrepsin catalyzed peptide bond process

Answer 43

His catalyzes the removal of H from Ser hydroxyl Ser 195's nucleophilic O attacks on carbonyl group of substrate His 57 acts as acid catalyst and donates proton H to nitrogen of scissile peptide bond, causing the cleave of bond The C-terminus portion of original substrate with the new N-terminus diffuses away Water donates H to His 57, resulting OH attack carbonyl group of remaining substrate His 57 donates back proton H to Ser 195 leading to the realease of remaining substrate (N-terminus portion with the new C-terminus)

Question 44

Ultimately, why do we want His abstract proton from Ser?

Answer 44

To make oxygen of Ser more negatively charged and become nucleophilic attack on carbonyl group (electrophile) of the substrate

Question 45

What are the two uniques properties of chymotrepsin-peptide catalysis?

Answer 45

oxyanion hole the shorter length bond between Asp and His

Question 46

Oxyanion hole

Answer 46

the stabilized anchor for substrate oxygen ion with two new hydrogen bonds with backbone NH groups of Ser and Gly

Question 47

What step has to occur for oxyanion hole happen?

Answer 47

the nucleophilic attacks of Ser oxygen to carbonyl group of substrate, causing the anion oxygen

Question 48

enzymes with similar mechanisms dont exhibit different substrate specificty? T/F

Answer 48

False

Question 49

specificity pocket

Answer 49

a cavity on the enzyme active site that accomodate the residue on the N-terminus of scissile bond

Question 50

Chymotrepsin (Ser) trepsin (Asp) elatase

Answer 50

large hydrophic residue basic residues (Lys/ Arg) small uncharged molecules (Gly, Val, Ala)