lecture 10

Question 1

describe the active site of an enzyme, 3 attributes

Answer 1

1: has amino acids projecting into it
2:binds the substrate via several weak interactions
3:determines the specificity of the reaction

Question 2

what are the types of enzyme substrate bonds

Answer 2

ionic bonds, hydrogen bonds, van der waals interactions, covalent bonds

Question 3

describe the ionic bonds between enzymes and substrates

Answer 3

interactions between the charged side chains of the amino acids

Question 4

describe the hydrogen bonds between enzymes and substrates

Answer 4

-the side chains or backbone O and N atoms can act as sites of hydrogen bonds. These hydrogen bonds can also be good at positioning atoms to exactly where they need to be.

Question 5

describe the van der waals interactions between enzyme and substrate

Answer 5

Interactions between any protein and substrate atoms in close proximity, this is the weakest of the interactions.

Question 6

why dont we want lots of covalent bonds in the enzyme substrate complex

Answer 6

The reason they are rare is the fact they are strong and harder to make reversible.

Question 7

what specificities does the active site have

Answer 7

shows geometric specificity as the active site must be a similar shape to the substrate. also stereospecificity, if the aacitve site is asymetric, the enzyme can distinguish between the R&S forms

Question 8

what are the two enzyme substrate bonding theories

Answer 8

lock and key, and induced fit

Question 9

how does an enzyme lower the gibbs free energy of a transition state

Answer 9

through ground state destabilisation, transition state stabilisation, and providing an alternate reaction pathway with a different lower energy transition state

Question 10

how can ground state destabilisation and transition state stabilisation occur

Answer 10

by having an active site that has a shape which is complementary to the TS, and not the substrate.

Question 11

what are the 5 catalytic mechanisms

Answer 11

acid-base catalysis, metal ion catalysis, covalent catalysis, preferential binding of the transition state, proximity and orientation effects

Question 12

what happens to get from ES complex to the transition state

Answer 12

the substrate is rearranged in the active site until the enzyme and substrate fit perfectly together, this point is the transition state.

Question 13

explain acid base catlaysis

Answer 13

amino acid residues in the acitve site transfer protons,

Question 14

what amino acid residue is common for the active site involving acid-base catalysis

Answer 14

histidine. as it has a pka close to 7. so depending on the PH of the environment it can act as either an acid or base, accepting or donating H+

Question 15

expalin metal ion catalysis

Answer 15

really common, about a third of enzymes use metal ions for enzyme activity. metal ion cofactors are used for redox reactions.

Question 16

how does Mg2+ metal ion work on hexokinase for metal ion catalysis

Answer 16

the Mg2+ balances the negative charges on the transition state, there by lowering activation energy.

Question 17

if we are making a drug what sort of state do we want it to be

Answer 17

we want it being a transition state analogue

Question 18

what was the transition state analogue we talked about in the lecture and discuss how they work

Answer 18

it was lipitor, This acts as a transition state, reducing the abilities if HMG-CoA reductase.

Question 19

how do transition state analouges work

Answer 19

Drugs are not substrate analouges as the drug would form a complex in the enzyme and the enzyme would just turn over. For this reason drugs mimic the transition state so the enzyme cannot further react.

Question 20

how does covalent catalysis work

Answer 20

we have a substrate with two halves that we want broken, a nucleophilic enzyme attacks the substrate covalently bonding to it. this frees one half of substrate. then the covalent bond is hydrolysed with water removing the other half substrate. this makes the substrate in half and the enzyme back to being able to re function.