Enzyme Mechanisms

Question 1

Chemical species with an affinity for a positive charge

Answer 1

Nucleophile

Question 2

Chemical Species with an affinity for a negative charge

Answer 2

Electrophile

Question 3

Species referred to as an electron donor

Answer 3

Nucleophile

Question 4

Species referred to a as an electron acceptor

Answer 4

Electrophile

Question 5

Term given when an electron rich nucleophile attacks a positve or partially positive electrophile

Answer 5

Nucleophilic Attack

Question 6

What is released when a large # of weak interactions are formed between E &S

Answer 6

Binding Energy

Question 7

Which orbital forms most/all of the needed interactions, hence promoting specifity.

Answer 7

S orbital

Question 8

3 ways in which Binding energy promotes Catalytic efficiency

Answer 8

Lowers Ea, Stabilizes transitional state( full complement of interactions only form with the transition state)

Question 9

Type of enzyme that has the active Enzyme + non-protein component, required for activity

Answer 9

Holoenzyme

Question 10

Type of enzyme that has the inactive enzyme but lacks the non-protein component.

Answer 10

Apoenzyme

Question 11

Metal ion required for enzyme activity

Answer 11

Cofactor

Question 12

Small organic molecule required for enzyme activity. (Many are seen in vitamins)

Answer 12

Coenzyme

Question 13

Term given when the ligand that binds to the allosteric site is the substrate (usually positive)

Answer 13

Homotrophic Effector

Question 14

Term given when the ligand that binds to the allosteric site is different from the substrate (can be either negative and positive)

Answer 14

Heterotrophic Effector

Question 15

Term given when the coenzyme only temporarily associates with the enzyme (NAD+)

Answer 15

Cosubstrate

Question 16

True or false, the prosthetic group only temporarily associates itself with an enzyme.

Answer 16

False,

Question 17

An example of a prosthetic group

Answer 17

FAD+

Question 18

True or False, Covalent Catalysis is when neutrophils form temporary covalent bond with substrate

Answer 18

False, Covalent Catalysis is when neutrophils form temporary covalent bond with substrate

Question 19

What is usually the active site in covalent catalysis.

Give an example

Answer 19

Powerful Nucleophile, Serine Proteases

Question 20

What class do proteases fall under and what is their function?

Answer 20

Class III- Hydrolases-Hydrolyse peptide bonds

Question 21

What is the normal half life of Proteases?

Answer 21

20-2,000 years

Question 22

What is the MOA used by the protease Chymotrypsin to catalyse a reaction.

Answer 22

Nucleophillic attack of oxygen 
Unstable tetrahedral intermediate form
HIS donates proton to cleave amine portion
This forms a acyl-enzyme 
intermediate
Water takes amine's place
His pulls proton, thus creating OH-
OH attacks Carbonyl C
Unstable tetrahedral intermediate forms
Carboxylc acid portion is released

Question 23

What are the three amino acids involved in the Chymotrypsin mechanism for catalytic reacrions

Answer 23

Asp 102, His 57, Ser 195

Question 24

Examples of Protease inhibitors

Answer 24

Captopril, Retrovir

Question 25

What drug inhibits Angiotensin-converting enzyme (metalloprotease)

Answer 25

Captopril

Question 26

What does Retrovir inhibit

Answer 26

HIV protease

Question 27

True or false an Acid-Base Catalysis is when H20 acts as a proton donor/acceptor

Answer 27

False, it is other than H20 that acts as a proton donor/acceptor

Question 28

HC0'3 is dehydrated to CO2 for what process

Answer 28

exhalation

Question 29

What class is carbonic anhydrase under

Answer 29

Class IV- lyase

Question 30

Explain the mechanism for carbonic anhydrase used in Acid-base catalysis

Answer 30

Central Zn2+ + 3 imidazole His rings + H20 Zn2+ lowers H20's pKa from 15.7 to 7 (promotes dissociation) CO2 binds to the active site OH- attacks the CO2, forming HCO-3 HCO-3 is released (H20 binds Zn2+, active site regenerated)

Question 31

What metal ion is used in carbonic anhydrase for acid-base reactions

Answer 31

Zn

Question 32

Which enzyme is found in RBC for acid-base reaction

Answer 32

Carbonic Anhydrase II

Question 33

How is carbonic anhydrase II an evolved proton shuttle

Answer 33

HIS 64 moves proton from H20 to protein surface to buffer

Question 34

What is another name for proximity effect?

Answer 34

Catalysis by Approximation

Question 35

True or False, Involves bringing two substrates close together

Answer 35

True

Question 36

An enzyme that undergoes the proximity effect

Answer 36

Nucleoside Monophosphate Kinase

Question 37

What class are Nucleoside monophosphates kinases

Answer 37

Class II- transferases

Question 38

What Challenge is involved in nucleoside monophosphate kinase reactions

Answer 38

Catalysing the correct reaction out of the two competing reactions

Question 39

What are the two competing reactions in nucleoside monophosphate reactions

Answer 39

Transfering phosphoryl from NTP to NMP | Transfer phsphoryl to H2O

Question 40

What constitutes a well defined conformation for specific binding for NMP kinase

Answer 40

Nucleotide+ Metal ion

Question 41

What are the two substrates in NMP kinase

Answer 41

NMP and NTP

Question 42

Outline the steps in Proximity in Action enzyme reactions

Answer 42

NTP Binds P-loop closes on top of polyphosphate chain P-loop triggers lid domain γ- phosphoryl is next to NMP binding site Catalytic conformation only exists when NTP & NMP are present Keeps water from receiving the phosphoryl

Question 43

What are the true substrates involved in NMP kinase enzyme reactions

Answer 43

Divalent ion Mg2+, Mn2+

Question 44

True or false, Metal ions help with nucleophile formation in metal ion catalysis If true, state examples

Answer 44

True Zn2+, carbonic anhydrase

Question 45

What can the metal ion in metal ion catalyisis act as.

Answer 45

Electrophile stabilising intermediate

Question 46

What challenge is present in Metal ion catalysis

Answer 46

Restriction endonucleases protect bacterial host from invading DNA Host is protected by methylation Specifity is critical

Question 47

Outline the steps in Metal ion catalysis for ECORV

Answer 47

H20 attacks the bond between 3' O and P Mg2+ is bound to 2 Asp + O of the phosphoryl Ion positions and activates the water for its attack

Question 48

What in ECORV can be describe as twofold rotational symmetry

Answer 48

Palindrome of the recognition sequence

Question 49

What is created around the recognition sequence when an enzyme surrounds it

Answer 49

kink

Question 50

What is the term given to molecules with no kink, that aren't able to bind to the Mg2+ site

Answer 50

Non-cognate molecules

Question 51

What process interferes with the binding to Asn, thus preventing the kink

Answer 51

Methylation

Question 52

What are three roles of cofactors

Answer 52

Promote nucleophilic attack Stabilise transition state Induce the formation of the active site

Question 53

Give an example of how cofactors promote nucleophilic attack

Answer 53

Zn2+ & carbonic anhydrase | Mg+ & EcoRV

Question 54

Give an example of how cofactors stabilise transition state

Answer 54

Zn2+ & carboxypeptidase

Question 55

Give an example of how cofactors induce the formation of the active site

Answer 55

Pyruvate kinase & K+ | Induces two conformational changes

Question 56

How do enzymes exhibit enzyme control in covalent modification

Answer 56

PO4- addition/ removal | Pyruvate decarboxylase inactivated