Enzyme Mechanisms Flashcards
Chemical species with an affinity for a positive charge
Nucleophile
Chemical Species with an affinity for a negative charge
Electrophile
Species referred to as an electron donor
Nucleophile
Species referred to a as an electron acceptor
Electrophile
Term given when an electron rich nucleophile attacks a positve or partially positive electrophile
Nucleophilic Attack
What is released when a large # of weak interactions are formed between E &S
Binding Energy
Which orbital forms most/all of the needed interactions, hence promoting specifity.
S orbital
3 ways in which Binding energy promotes Catalytic efficiency
Lowers Ea, Stabilizes transitional state( full complement of interactions only form with the transition state)
Type of enzyme that has the active Enzyme + non-protein component, required for activity
Holoenzyme
Type of enzyme that has the inactive enzyme but lacks the non-protein component.
Apoenzyme
Metal ion required for enzyme activity
Cofactor
Small organic molecule required for enzyme activity. (Many are seen in vitamins)
Coenzyme
Term given when the ligand that binds to the allosteric site is the substrate (usually positive)
Homotrophic Effector
Term given when the ligand that binds to the allosteric site is different from the substrate (can be either negative and positive)
Heterotrophic Effector
Term given when the coenzyme only temporarily associates with the enzyme (NAD+)
Cosubstrate
True or false, the prosthetic group only temporarily associates itself with an enzyme.
False,
An example of a prosthetic group
FAD+
True or False, Covalent Catalysis is when neutrophils form temporary covalent bond with substrate
False, Covalent Catalysis is when neutrophils form temporary covalent bond with substrate
What is usually the active site in covalent catalysis.
Give an example
Powerful Nucleophile, Serine Proteases
What class do proteases fall under and what is their function?
Class III- Hydrolases-Hydrolyse peptide bonds
What is the normal half life of Proteases?
20-2,000 years
What is the MOA used by the protease Chymotrypsin to catalyse a reaction.
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
What are the three amino acids involved in the Chymotrypsin mechanism for catalytic reacrions
Asp 102, His 57, Ser 195
Examples of Protease inhibitors
Captopril, Retrovir
What drug inhibits Angiotensin-converting enzyme (metalloprotease)
Captopril
What does Retrovir inhibit
HIV protease
True or false an Acid-Base Catalysis is when H20 acts as a proton donor/acceptor
False, it is other than H20 that acts as a proton donor/acceptor
HC0’3 is dehydrated to CO2 for what process
exhalation
What class is carbonic anhydrase under
Class IV- lyase
Explain the mechanism for carbonic anhydrase used in Acid-base catalysis
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)
What metal ion is used in carbonic anhydrase for acid-base reactions
Zn
Which enzyme is found in RBC for acid-base reaction
Carbonic Anhydrase II
How is carbonic anhydrase II an evolved proton shuttle
HIS 64 moves proton from H20 to protein surface to buffer
What is another name for proximity effect?
Catalysis by Approximation
True or False, Involves bringing two substrates close together
True
An enzyme that undergoes the proximity effect
Nucleoside Monophosphate Kinase
What class are Nucleoside monophosphates kinases
Class II- transferases
What Challenge is involved in nucleoside monophosphate kinase reactions
Catalysing the correct reaction out of the two competing reactions
What are the two competing reactions in nucleoside monophosphate reactions
Transfering phosphoryl from NTP to NMP
Transfer phsphoryl to H2O
What constitutes a well defined conformation for specific binding for NMP kinase
Nucleotide+ Metal ion
What are the two substrates in NMP kinase
NMP and NTP
Outline the steps in Proximity in Action enzyme reactions
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
What are the true substrates involved in NMP kinase enzyme reactions
Divalent ion Mg2+, Mn2+
True or false, Metal ions help with nucleophile formation in metal ion catalysis
If true, state examples
True Zn2+, carbonic anhydrase
What can the metal ion in metal ion catalyisis act as.
Electrophile stabilising intermediate
What challenge is present in Metal ion catalysis
Restriction endonucleases protect bacterial host from invading DNA
Host is protected by methylation
Specifity is critical
Outline the steps in Metal ion catalysis for ECORV
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
What in ECORV can be describe as twofold rotational symmetry
Palindrome of the recognition sequence
What is created around the recognition sequence when an enzyme surrounds it
kink
What is the term given to molecules with no kink, that aren’t able to bind to the Mg2+ site
Non-cognate molecules
What process interferes with the binding to Asn, thus preventing the kink
Methylation
What are three roles of cofactors
Promote nucleophilic attack
Stabilise transition state
Induce the formation of the active site
Give an example of how cofactors promote nucleophilic attack
Zn2+ & carbonic anhydrase
Mg+ & EcoRV
Give an example of how cofactors stabilise transition state
Zn2+ & carboxypeptidase
Give an example of how cofactors induce the formation of the active site
Pyruvate kinase & K+
Induces two conformational changes
How do enzymes exhibit enzyme control in covalent modification
PO4- addition/ removal
Pyruvate decarboxylase inactivated
