Enzymes & Chemical Catalysis Flashcards
What is rate called?
Velocity (V)
What are reactants called?
Substrates (S)
Why should we care about enzymes?
1) lots of organic mechanism
2) lots of commercially available products
3) targets for drugs
What does aspirin inhibit?
Inhibitor of cycloygenase
What does Retrovir inhibit?
Inhibitor of reverse transcriptase (HIV)
What does roundup inhibit?
Inhibits an enzyme involved in biosynthesis of aromatic amino acids
What does tamiflu inhibits
Inhibitor of neuraminidade (flu)
What does penicillin inhibit?
Inihibits a transpeptidase in peptidoglycan synthesis ( bacteria cell wall synthesis)
Why are enzymes catalysts and why are they good catalysts?
They reduce the change in free energy- lower activation energy
1) reduce activation energy in mild conditions
2) immense catalytic power
3) exquist specificity
What catalysts are used in Haver process?
Chemical- Fe- needs stronger conditions
Biological- nitrogenase- milder conditions (pH, temperature, pressure)
What is the roll of glycosidase?
Cleaves sugars - add water, an alcohol leaves
Breaks the glycosidic bond (-O-R)
Why are enzymes specific ?
They only interact with proteins of a complementary shape/ e.g. If there is small change to glucose - enzyme no longer works as they are specific
Indentations, grooves and pockets on the surface of the enzyme provide the complementary bonding side for substrates-
Induced fit- strain towards TS
Lock and key hypothesis
What is the function of protease?
Hydrolysis of peptide bond (amide bond)
Protease and water react
( see mechanism)
Enzymes are active with certain R groups
Name catalytic strategies
1) proximity and orientation
2) covalent catalysis (Nu attack)
3) general acid/ base catalysis
4) electrostatics
5) strain
How does proximity and orientation increase rate?
Holding groups closer together- decreasing entropy
Holding the nucleophile closer to the electrophile and fix orientation increases the rate
- enzymes hold sugar in specific orientation and reduce rotation of side chain- hold close to active site
What are enzyme non covalent interactions?
Enzymes harness the full range of non covalent interactions
- electrostatics
- ion dipole
- dipole- dipole
- H bonding
- hydrophobic
What is covalent catalysis (Nu)
Enzyme intermediate in protein bonds to substrate and this drives the reaction forward as this increases the energy of the complex
ES is higher in energy then EP
- reaction via a short lived covalent intermediate
How do you form an imine?
Add a primary amine to a C=O bond
Water is the leaving group
See mechanism
How does retinal allow us to see?
Lysine acts a nucleophile and donates electrons from the nitrogen to the C=O bond on retinal
This causes imine formation
The imine can accept hv due to double bonds
This triggers a change in structure and allows us to see
How do you form a ketone and CO2?
Catalysed by acetoacetate decarboxylase
Lycine attacked
Water also attacks and Co2 is released
(See mechanism)
What is one or the best features of an enzymes ?
It can perform general acid and general base catalysis and at the same time
Describe glycoside hydrolysis
The amino residue in the enzyme is deprotonated
The acid is held in close proximity and the glycosidic bond is protonated
What pka do the enzyme residues need to have?
They need to have pka close to the pH you are working at so it can donate or accept a H
What is electrostatic catalysis?
The enzyme has the ability to change its pH environment to bind to the transition state rather than the substrate
This drives the reaction forwards
There is an attraction between the positive surface and the negative ester intermediate (charge-charge interactions)
What is the mechanism for Keto- enol tautomerisation?
See mechanism
How does strain and distortion catalyse the reaction?
Epoxides are more reactive than the other ethers, it wants to relieve its strain and drive reaction forwards
The strain makes the process go faster
Enzymes harness the binding energy of the substrate to distort them to make them more reactive (higher energy)
What do enzymes favour binding?
Enzymes favour binding to the transition state over the substrate
What is the evidence that enzymes stabilise the transition state?
1) enzymes are inhibited by transition state mimics
2) antibodies raise against transition state mimics have catalytic activity
What is the role of NAD+ coenzyme
From niacin
Oxidation or hydrogen transfer
What is the role of FAD coenzyme
From riboflavin
Oxidation or hydrogen transfer
What is the role of CoA coenzyme
From pantothenic acid
Acetyl group carrier
What is the role of coenzyme B-12
From vitamin B-12
Methyl group transfer
What is the role of TPP coenzyme
From thiamin (B-1)
Aldehyde group transfer
Describe hydride addition
See mechanism
