Chapter 6 - Enzyme Flashcards Preview

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Flashcards in Chapter 6 - Enzyme Deck (50)
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1
Q

Nature of chemical rxn in biology world?

A

thermodynamic favorable but kinetics controlls (very slow without catalyst)

2
Q

How to change the rate of reaction?

A

increase temperature, concentration of reactants, add catalyst

3
Q

What are enzyme characteristics?

A

enhance rxn rate

mild condition

reaction speicificty

regulation activity

4
Q

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

A

Vander Waals interactions

H-bond

hydrophobic interactions

electrostatic interactions

5
Q

Factor contributes to substrate binding

A

geometric complimentarity

electronic complimentarity (lock and key)

induced fit

6
Q

induced fit

A

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

7
Q

Type of enzyme

A

Oxidoreductase

Transferase

Hydrolase

Lyases

Isomerases

Ligases

8
Q

Oxidoreductase

transferase

hydrolase

A

redox reaction

transfer of funcional groups

hydrolysis reactions

9
Q

Lyase

Isomerase

Ligase

A

Group elimination to form double bonds

isomerization rxn

bond formation coupled with ATP hydrolysis

10
Q

How does enzyme distinguish the substrates?

A

through enzyme’s functional groups in active site

11
Q

Mild condition of enzyme

A

enzyme-rxn can occur at normal temp and pressure

12
Q

Regulation activity of enzyme

A

allosteric regulation

post-translational modification of enzyme

up and down regulation for concentration of enzyme

13
Q

What doe enzyme do to the delta G++?

A

It lower the activation energy by lowering the transition state energy

14
Q

What are 3 chemical catalytic mechanism of enzymes?

A

acid-base catalysis

transient covalent catalysis

metal ions catalysis (charge-charge interaction)

15
Q

What do 3 chemical catalytic mechanisms need?

A

amino acid side chains

16
Q

cofactor

Type of cofactos

A

required for functional group transfer or redox reaction

metal ions and coenzymes (cosubstrate and prosthetic group)

17
Q

cosubstrate

prosthetic group

A

transient association with enzyme - leave/enter with substrate

permanent association with active site of enzyme

18
Q

Common metal ions in cofactors

A

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

19
Q

Apoenzyme

Holoenzyme

A

enzymes after removing cofactors

enzyme-cofactor complex

20
Q

vitamin

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

A

the compounds are used as precursors for coenzyme biosynthesis

No, it exists only in diet

21
Q

Type of vitamin

which one is used for biosynthesis?

A

water soluble and water insoluble

water soluble

22
Q

transition state

Delta G++

A

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

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

23
Q

The higher delta G++

The lower delta G++

A

the longer the rxn will take

the shorter the rxn will take

24
Q

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

A

1.36 kcal/mol (5.71 kJ/mol)

25
Q

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

A

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

26
Q

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

A

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

27
Q

acid catalysis

A

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

28
Q

base catalysis

A

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

29
Q

Covalent catalysis

what is the other name for covalent catalysis

A

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

nucleophilic catalysis

30
Q

nucleophilic catalysis

A

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

31
Q

nucleophilic groups characteristics

A

negatively charge or have lone pair electrons

they are deprotonated

32
Q

What is a good covalent catalysis?

A

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

33
Q

Nucleophicility need for?

good leaving group need for?

A

starting the rxn

release the product

34
Q

How many process does covalent catalysis have?

A

two-part rxn process thus two activation energy

35
Q

What are the metal ions role in metal ion catalysis?

A

orientate the substrate in enzyme active site

mediate oxidation-reduction rxn

electrostatically stabilizing

36
Q

How does enzyme maximize the enhancing rxn rate?

A

by confining the substrate

37
Q

Confine the substrate in enzyme

A

bring the substrate close to the catalytic site (proximity)

proper orientation

charge groups (electrostatic catalysis)

freeze the translational and rotational motions

38
Q

factors contribute to rate acceleration in catalysis

A

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

39
Q

group specificity

A

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

40
Q

What type of enzyme is chymotrypsin?

What catalysis mechanism does this type of enzyme use?

A

serine protease

acid-base and covalent catalysis

41
Q

What are amino acids made of active sites in serine protease?

Function of each AA in active site?

A

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

42
Q

scissile bond

A

bond to be cleaved by hydrolysis

43
Q

Chymotrepsin catalyzed peptide bond process

A

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)

44
Q

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

A

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

45
Q

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

A

oxyanion hole

the shorter length bond between Asp and His

46
Q

Oxyanion hole

A

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

47
Q

What step has to occur for oxyanion hole happen?

A

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

48
Q

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

A

False

49
Q

specificity pocket

A

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

50
Q

Chymotrepsin (Ser)

trepsin (Asp)

elatase

A

large hydrophic residue

basic residues (Lys/ Arg)

small uncharged molecules (Gly, Val, Ala)