Lecture 10- How do enzymes catalyse reactions?

Question 1

What is the active site and what is it’s function?
Also what does it have facing towards it giving it specificity?

Answer 1

The specific site on an enzyme where the substrates interact with to create products
Side chains of amino acids facing towards it.

Question 2

Why do we need optimal bonding, e.g. not too tightly bound?

Answer 2

Because we need optimal binding so effective catalysis can occur, however the product needs to be able to leave.

Question 3

What is the enzyme-substrate complex?

Answer 3

A complex formed between the enzyme and a substrate

Question 4

Why are weak bonds advantageous and how many bonds are required for substrate bonding?

Answer 4

They can only form if the relevant atoms are positioned correctly(specificity) and easier to break weak bond(reversible)

Question 5

What is critical to the relationship between a substrate and enzyme?

Answer 5

Molecular compatibility

Question 6

What two properties do weak bonds infer?

Answer 6

Reversibility and specificity

Question 7

What are the types of enzyme-substrate bonds?

Answer 7

Ionic bonds, Hydrogen bonds, Van de vaals interaction, Covalent bonds

Question 8

What are the three features of the active site?

Answer 8

Amino acid sidechains projecting into it, binds to substrate via several weak interactions and determines specificity of reaction

Question 9

How do ionic bonds occur in terms of enzymes?

Answer 9

Between the charged side chains

Question 10

How do hydrogen bonds occur in terms of enzymes?

Answer 10

Side chain or backchain O and N can act as hydrogen bond donators and acceptors

Question 11

How do van de vaals occur in terms of enzymes?

Answer 11

Between any protein and substrate in close proximity(Weakest)

Question 12

What are covalent bonds(Simple)

Answer 12

Shared electrons(Stronger and rarer than other types of bonds)

Question 13

What does the active site of enzymes show in terms of shape?

Answer 13

Asymmetric binding sites, need correct shape and stereospecificity to bind properly

Question 14

Explain the lock and key model?

Answer 14

The shape of the substrate and the active site are complementary to one another

Question 15

Explain the induced fit model?

Answer 15

A conformation change occurs to the enzyme upon binding to the substrate. Becomes complementary to substrate after binding

Question 16

Are enzymes dynamic or static?

Answer 16

Dynamic, they will change their configuration

Question 17

What are the three ways activation energy can lowered?

Answer 17

Transition state stabilization, Ground state destabilization, and alternative reaction pathways

Question 18

How can Transition state stabilization and Ground state destabilization both be achieved?

Answer 18

Having a active site that has a shape/charge that is closer to the transition state rather than the substrate

Question 19

What is transition state stabilization?

Answer 19

Reducing the energy of the transition state by stabalizing it at the active site

Question 20

What is ground state destabilizing?

Answer 20

Increasing the energy of the substrate by destabilizing it when it binds to the active site

Question 21

What are the five catalytic mechanisms?

Answer 21

Preferential binding of TS, proximal and orientational effects, Acid-base catalysis, Metal ion catalysis and covalent catalysis

Question 22

What is preferential binding of TS?

Answer 22

Where an enzyme favours binding the transition state more tightly compared to the substrate

Question 23

What makes using transition states a problem with enzyme reactions?

Answer 23

They are transient and cannot be isolated hence analogues of the transition state must be used

Question 24

What is an example of a drug that limits cholesterol and how does it do this?

Answer 24

Lipitor, inhibits HMG CoA reductase so synthesis pathway of cholesterol cannot happen

Question 25

What usually targets enzymes and what are some examples?

Answer 25

Transition state analogues(E.g. protease inhibitors, Tamiflu, Aliskiren)

Question 26

What are the proximal and oriental effects?

Answer 26

Bring molecules closer together and ensure they are in the right configuration

Question 27

What is acid-base catalysis?

Answer 27

Proton transfer(e.g side chains accepting or donating protons)

Question 28

What type of reaction is histidine most suited for and why is its Pka important?

Answer 28

Suited for acid-base and the PKA is important as around biological PH allowing for His to either be a donator or acceptor of protons

Question 29

What do metal ion catalysis provide?

Answer 29

Correct substrate orientation, act as Lewis acids polarizing group and site of electron transfer

Question 30

What does hexokinase use as its cofactor?

Answer 30

Mg2+

Question 31

What is covalent catalysis?

Answer 31

Formation of short lived intermediate which is covalently attached to enzyme