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Cell Biology (1201) > Enzyme Mechanisms > Flashcards

Enzyme Mechanisms Flashcards

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1
Q

Chemical species with an affinity for a positive charge

A

Nucleophile

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2
Q

Chemical Species with an affinity for a negative charge

A

Electrophile

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3
Q

Species referred to as an electron donor

A

Nucleophile

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4
Q

Species referred to a as an electron acceptor

A

Electrophile

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5
Q

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

A

Nucleophilic Attack

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6
Q

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

A

Binding Energy

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7
Q

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

A

S orbital

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8
Q

3 ways in which Binding energy promotes Catalytic efficiency

A

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

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9
Q

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

A

Holoenzyme

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10
Q

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

A

Apoenzyme

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11
Q

Metal ion required for enzyme activity

A

Cofactor

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12
Q

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

A

Coenzyme

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13
Q

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

A

Homotrophic Effector

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14
Q

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

A

Heterotrophic Effector

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15
Q

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

A

Cosubstrate

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16
Q

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

A

False,

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17
Q

An example of a prosthetic group

A

FAD+

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18
Q

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

A

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

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19
Q

What is usually the active site in covalent catalysis.

Give an example

A

Powerful Nucleophile, Serine Proteases

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20
Q

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

A

Class III- Hydrolases-Hydrolyse peptide bonds

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21
Q

What is the normal half life of Proteases?

A

20-2,000 years

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22
Q

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

A 
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
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23
Q

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

A

Asp 102, His 57, Ser 195

24
Q

Examples of Protease inhibitors

A

Captopril, Retrovir

25
Q

What drug inhibits Angiotensin-converting enzyme (metalloprotease)

A

Captopril

26
Q

What does Retrovir inhibit

A

HIV protease

27
Q

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

A

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

28
Q

HC0’3 is dehydrated to CO2 for what process

A

exhalation

29
Q

What class is carbonic anhydrase under

A

Class IV- lyase

30
Q

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

A

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)

31
Q

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

A

Zn

32
Q

Which enzyme is found in RBC for acid-base reaction

A

Carbonic Anhydrase II

33
Q

How is carbonic anhydrase II an evolved proton shuttle

A

HIS 64 moves proton from H20 to protein surface to buffer

34
Q

What is another name for proximity effect?

A

Catalysis by Approximation

35
Q

True or False, Involves bringing two substrates close together

A

True

36
Q

An enzyme that undergoes the proximity effect

A

Nucleoside Monophosphate Kinase

37
Q

What class are Nucleoside monophosphates kinases

A

Class II- transferases

38
Q

What Challenge is involved in nucleoside monophosphate kinase reactions

A

Catalysing the correct reaction out of the two competing reactions

39
Q

What are the two competing reactions in nucleoside monophosphate reactions

A

Transfering phosphoryl from NTP to NMP

Transfer phsphoryl to H2O

40
Q

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

A

Nucleotide+ Metal ion

41
Q

What are the two substrates in NMP kinase

A

NMP and NTP

42
Q

Outline the steps in Proximity in Action enzyme reactions

A

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

43
Q

What are the true substrates involved in NMP kinase enzyme reactions

A

Divalent ion Mg2+, Mn2+

44
Q

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

A

True Zn2+, carbonic anhydrase

45
Q

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

A

Electrophile stabilising intermediate

46
Q

What challenge is present in Metal ion catalysis

A

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

47
Q

Outline the steps in Metal ion catalysis for ECORV

A

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

48
Q

What in ECORV can be describe as twofold rotational symmetry

A

Palindrome of the recognition sequence

49
Q

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

A

kink

50
Q

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

A

Non-cognate molecules

51
Q

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

A

Methylation

52
Q

What are three roles of cofactors

A

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

53
Q

Give an example of how cofactors promote nucleophilic attack

A

Zn2+ & carbonic anhydrase

Mg+ & EcoRV

54
Q

Give an example of how cofactors stabilise transition state

A

Zn2+ & carboxypeptidase

55
Q

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

A

Pyruvate kinase & K+

Induces two conformational changes

56
Q

How do enzymes exhibit enzyme control in covalent modification

A

PO4- addition/ removal

Pyruvate decarboxylase inactivated

Cell Biology (1201) (5 decks)

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