Chapter 6 - Enzyme Flashcards

(50 cards)

1
Q

Nature of chemical rxn in biology world?

A

thermodynamic favorable but kinetics controlls (very slow without catalyst)

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2
Q

How to change the rate of reaction?

A

increase temperature, concentration of reactants, add catalyst

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3
Q

What are enzyme characteristics?

A

enhance rxn rate

mild condition

reaction speicificty

regulation activity

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4
Q

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

A

Vander Waals interactions

H-bond

hydrophobic interactions

electrostatic interactions

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5
Q

Factor contributes to substrate binding

A

geometric complimentarity

electronic complimentarity (lock and key)

induced fit

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6
Q

induced fit

A

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

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7
Q

Type of enzyme

A

Oxidoreductase

Transferase

Hydrolase

Lyases

Isomerases

Ligases

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8
Q

Oxidoreductase

transferase

hydrolase

A

redox reaction

transfer of funcional groups

hydrolysis reactions

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9
Q

Lyase

Isomerase

Ligase

A

Group elimination to form double bonds

isomerization rxn

bond formation coupled with ATP hydrolysis

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10
Q

How does enzyme distinguish the substrates?

A

through enzyme’s functional groups in active site

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11
Q

Mild condition of enzyme

A

enzyme-rxn can occur at normal temp and pressure

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12
Q

Regulation activity of enzyme

A

allosteric regulation

post-translational modification of enzyme

up and down regulation for concentration of enzyme

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13
Q

What doe enzyme do to the delta G++?

A

It lower the activation energy by lowering the transition state energy

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14
Q

What are 3 chemical catalytic mechanism of enzymes?

A

acid-base catalysis

transient covalent catalysis

metal ions catalysis (charge-charge interaction)

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15
Q

What do 3 chemical catalytic mechanisms need?

A

amino acid side chains

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16
Q

cofactor

Type of cofactos

A

required for functional group transfer or redox reaction

metal ions and coenzymes (cosubstrate and prosthetic group)

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17
Q

cosubstrate

prosthetic group

A

transient association with enzyme - leave/enter with substrate

permanent association with active site of enzyme

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18
Q

Common metal ions in cofactors

A

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

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19
Q

Apoenzyme

Holoenzyme

A

enzymes after removing cofactors

enzyme-cofactor complex

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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

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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
Formula for calculate the increase rxn rate by decreasing delta G++?
V = e^(delta-G++ /RT)
26
What does enzyme have when at the transition state? What is downside of this?
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
acid catalysis
the process in which the transfer of proton from acid lower the free energy of reactant's transition state
28
base catalysis
the process in which the abstraction of proton by a base lower the free energy of reactant's transition state
29
Covalent catalysis what is the other name for covalent catalysis
the process in which the covalent bonds form between enzyme and substrate nucleophilic catalysis
30
nucleophilic catalysis
the process in which nucleophiles of enzyme attack the electrophile on substrates
31
nucleophilic groups characteristics
negatively charge or have lone pair electrons they are deprotonated
32
What is a good covalent catalysis?
It is the balance between nucleophilicity and the ability as a good leaving group
33
Nucleophicility need for? good leaving group need for?
starting the rxn release the product
34
How many process does covalent catalysis have?
two-part rxn process thus two activation energy
35
What are the metal ions role in metal ion catalysis?
orientate the substrate in enzyme active site mediate oxidation-reduction rxn electrostatically stabilizing
36
How does enzyme maximize the enhancing rxn rate?
by confining the substrate
37
Confine the substrate in enzyme
bring the substrate close to the catalytic site (proximity) proper orientation charge groups (electrostatic catalysis) freeze the translational and rotational motions
38
factors contribute to rate acceleration in catalysis
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
group specificity
an enzyme is specific to a typical bond and groups around that bond (peptide bond)
40
What type of enzyme is chymotrypsin? What catalysis mechanism does this type of enzyme use?
serine protease acid-base and covalent catalysis
41
What are amino acids made of active sites in serine protease? Function of each AA in active site?
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
scissile bond
bond to be cleaved by hydrolysis
43
Chymotrepsin catalyzed peptide bond process
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
Ultimately, why do we want His abstract proton from Ser?
To make oxygen of Ser more negatively charged and become nucleophilic attack on carbonyl group (electrophile) of the substrate
45
What are the two uniques properties of chymotrepsin-peptide catalysis?
oxyanion hole the shorter length bond between Asp and His
46
Oxyanion hole
the stabilized anchor for substrate oxygen ion with two new hydrogen bonds with backbone NH groups of Ser and Gly
47
What step has to occur for oxyanion hole happen?
the nucleophilic attacks of Ser oxygen to carbonyl group of substrate, causing the anion oxygen
48
enzymes with similar mechanisms dont exhibit different substrate specificty? T/F
False
49
specificity pocket
a cavity on the enzyme active site that accomodate the residue on the N-terminus of scissile bond
50
Chymotrepsin (Ser) trepsin (Asp) elatase
large hydrophic residue basic residues (Lys/ Arg) small uncharged molecules (Gly, Val, Ala)