Properties of Enzymes and Catalysis

Question 1

How to name enzymes?

Answer 1

First describes the substrate

Second is the enzyme group that describes the reaction

Question 2

What are some features of enzymes?

Answer 2

High reaction rate - 10^6 to 10^12 times greater than uncatalysed

Works under mild conditions - neutral pH, temp below 100 & atmospheric pressure

Specificity - with respect to substrates (due to stereochemistry)

Can be regulated - allosteric control (bind somewhere other than active site), covalent modification & amount synthesised

Question 3

What are the enzyme groups?

Answer 3

Oxidoreductases 
Transferases
Hydrolases
Lyases
Isomerases
Ligases

These groups are 1-6 and that is the enzyme classification

Question 4

What is an oxidoreductase?

Answer 4

Redox reaction

Question 5

What is a transferase?

Answer 5

Transfer of functional groups

Question 6

What is a hydrolase?

Answer 6

Hydrolysis reactions

Question 7

What are lyases?

Answer 7

Group elimination to form double bonds

Question 8

What are ligases?

Answer 8

Bond formation coupled with ATP hydrolysis

Question 9

What are isomerases?

Answer 9

Isomerisation

Question 10

What is the active site? Types of complementarity?

Answer 10

An indentation or cleft on the surface of an enzyme that performs the catalysis

Geometric complementarity - the cleft is complementary in shape to the substrate

Electronic complementarity - amino acids in the cleft are arranged specifically to attract the substrate

Question 11

What are the proposed enzyme mechanisms?

Answer 11

Lock and key - enzyme and substrate are perfectly complementary

Induced fit - when the substrate binds the active site alters it shape to fit perfectly

Selected fit - the enzyme explores different structures and is most stable in the structure at the time of the substrate binding

Question 12

What forced are involved in induced fit?

Answer 12

Van der waals
Electrostatic attraction
Hydrogen bonding
Hydrophobic interactions

Question 13

Why are enzymes stereospecific?

Answer 13

They tend to be chiral due to the proteins consisting of L-amino acids
Therefore form asymmetric active sites
Therefore some enzymes are only specific for one compound

Question 14

What do some enzymes require? Why?

Answer 14

Cofactors (the enzymes “chemical teeth”)

Enzymes aren’t suitable alone for redox reactions and group transfer reactions

Question 15

Types of cofactors?

Answer 15

Metal ions
Eg Cu 2+, Fe 3+ or Zn 2+

Coenzymes:
Cosubstrates - transiently bound (loosely)
Eg NAD, NADP
Prosthetic group - permanently bound to the protein via covalent bonds

Coenzymes must be regenerated- to complete the catalytic cycle, it must return to original state

Question 16

What are the states of an enzyme?

Answer 16

Apoenzyme - inactive enzyme
Holoenzyme - active enzyme

Apoenzyme + cofactor ⇌ holoenzyme

Question 17

What is the transition state? Enzymes effect?

Answer 17

The point of highest free energy in a reaction

The enzyme doesn’t alter the ΔG but can decrease the ΔG++ (the difference in Gibbs free energy between the transition state and the reactants)
This allows the reaction to approach equilibrium faster than without a catalyst

So they reduce the free energy of the transition state and therefore stabilise the transition state

Question 18

What is the reaction coordinate?

Answer 18

Reactants proceeding along the path of minimum free energy

So a plot called a transition state diagram is the free energy v the reaction coordinate

Question 19

What can be produced in a multistep reaction?

Answer 19

The step with the highest transition state free energy acts as a ‘bottleneck’ and is called the rate determining step

Question 20

What are the types of catalytic mechnanisms enzymes employ?

Answer 20

Acid-base catalysis
Covalent catalysis
Metal ion catalysis
Proximity and orientation effects
Preferential binding of the transition state complex

Question 21

What is acid catalysis?

Answer 21

A process where a proton is transferred from an acid which lowers the free energy of a reaction’s transition state

Question 22

What is base catalysis?

Answer 22

A proton is abstracted by a base in order to increase the rate

Question 23

Give an example of acid-base catalysis?

Answer 23

Bovine pancreatic RNase A
It is secreted by the pancreas into the small intestine where it hydrolyses RNA to its component nucelotides
It has a His12 residue to act as a base and a His119 residue to act as an acid to first promote nucleophilic attack and bond cleavage
After this they swap roles and now promote hydrolysis

Question 24

Which amino acids are useful as acid/bases and why?

Answer 24

Asp, Glu, His, Cys, Tyr, and Lys

They have pK’s in/near the physiological pH range, allowing them to act as a acid/and or base

Question 25

What is covalent cataylsis?

Answer 25

Covalent catalysis accelerates reaction rates through the transient formation of a catalyst–substrate covalent bond

Usually requires a nucleophile on the catalyst and an electrophile on the substrate

Question 26

Describe a general outline of covalent cataylsis?

Answer 26

1. The nucleophilic reaction between the catalyst and the substrate to form a covalent bond.
2. The withdrawal of electrons from the reaction center by the now electrophilic catalyst.
3. The elimination of the catalyst, a reaction that is essentially the reverse of stage 1

Question 27

What is an nucleophile and an electrophile?

Answer 27

Nucleophile - negatively charged or contain unshared pair of electrons to form covalent bonds with electron-deficient centres (closely related to basicity)

Electrophile - positively charged and can contain an unfilled valence electron shell

Question 28

What makes a good covalent catalyst?

Answer 28

It can’t form a very stable covalent bond and it is harder to decompose
Therefore it needs contradictory properties of high nucleophilicity and ability to form a good leaving group
e.g. groups with high polarizability

Question 29

Examples of good covalent catalysts?

Answer 29

Unprotonated amino group of lysine
Imidazole group of histidine
Thiol group of cysteine
Carboxyl group of aspartic acid
Hydroxyl group of serine

Question 30

What is metal ion catalysis?

Answer 30

Using metal ions as cofactors called - metalloenzymes
They are tightly bound cofactors

Mainly transition state elements - they are directly involved
Na+, K+ and Ca2+ - used to stabilise the structure and hold its shape together
Mg2+ and Zn2+ - can stabilise and/or take part in the reaction directly

Question 31

How are metal ions used in catalytic processes?

Answer 31

1. By binding to substrates to orient them properly for reaction.
2. By mediating redox reactions through reversible changes in the metal ion’s oxidation state
3. By electrostatically stabilizing or shielding negative charges
4. They can bind water molecules and make them more acidic

Question 32

Example of metal ion catalysis?

Answer 32

Carbonic anhydrase and Zn2+ catalysing:
CO2 + H2O HCO3- + H+

Zn2+ binds to water polarizing and making it more acidic and allowing it to give up a proton more easily
His64 then assists in base catalysis

Question 33

How does proximity and orientation effects help catalysis?

Answer 33

The enzyme provides a surface to increase local concentration
Binding to the substrate brings the molecules closer together and they can then react
It stabilises the binding in the correct orientation
The enzymes freeze and rotational/translational movement

Question 34

What is another element to proximity and orientation effects?

Answer 34

Electrostatic catalysis is where charged groups can help stabilise the transition state
The expulsion of water enhances this
The charge distribution around the active sites of enzymes may also guide polar substrates toward their binding site

Question 35

Describe the effects of enzymes preferentially binding to the transition state?

Answer 35

An enzyme may bind the transition state of the reaction it catalyzes with greater affinity than its substrates or products

Enzymes that preferentially bind the transition state structure increase its concentration and therefore proportionally increase the reaction rate

Question 36

What can transition states act as?

Answer 36

Transition state analogs (similar structures) are enzyme inhibitors

Question 37

How can the transition state be achieved?

Answer 37

If there is stress/stain on surrounding groups it can push other groups together, distorting the bond angles making the molecule look like the transition state

Question 38

What has the understanding of transition states lead to?

Answer 38

The basis for drug design due to understanding specific enzyme reaction mechanisms