Enzymes

Question 1

What are the effects of pH on enzyme activity?

Answer 1

Activity is dependent upon pH of medium

Enzymes are only active over a narrow pH range: Essential groups are either protonated or unprotonated in order to react with substrate.

Question 2

Maintenance of correct conformation for catalysis dependent on?

Answer 2

on ionisation of amino acids side chains

Question 3

Catalytic amino acids residues often have?

Answer 3

ionisable functional groups: charged (unprotonated) acids, protonated bases (Thiol, imidazole, etc)

Question 4

Effect of pH on kinetic constants:

Possible to identify active site amino acids by?

Answer 4

Examining effect of pH and Km and Vmax

Question 5

Effect of pH on kinetic constants: Ionsiable groups in the active site will produce?

Answer 5

Titration curves for Km and Vmax

Amino acid side chains essential for catalysis alter Vmax

Amino acid side chains essential for binding alter Km

Question 6

Effect of pH on kinetic constants: Amino acid side chains essential for?

Answer 6

catalysis alter Vmax

binding alter Km

Question 7

Effect of pH on kinetic constants: Identification is only?

Answer 7

Tentative

Question 8

Effect of pH on kinetic constants:Tentative meaning?

Answer 8

pH effects on the formation of the enzyme

pKa of side chains in proteins is often different to that in free solution

Example: pKa of Arg and Glu side chains can be increased in proximity to hydrophobic residues

Glu35 in lysozyme is protonated at pH 5

Question 9

Enzymes catalysed reactions are highly specific meaning?

Answer 9

A given enzyme will always catalyse the same reaction

Specificity is normally absolute

Some enzymes work on classes of compounds

Substrates can be one of many hexose sugars

Specificity and mode of catalysis are determined by active site

Question 10

What is the active site of an enzyme?

Answer 10

Region of the protein essential for catalysis

Composition determined by whole protein

Comprises a small fraction of total protein: Typically, a fold/cleft between domains or sub-units.

Question 11

What are the molecular features of the active site?

Answer 11

The surface is lined with amino acid residues responsible for substrate binding and catalysis

Comprised mainly of hydrophobic residues:

Several polar and charged species also present

These are frequently catalytic residues

Question 12

What constitutes the catalytic centre of the enzyme?

Answer 12

Polar residues (and coenzymes) which undergo chemical changes during catalysis constitute the catalytic centre of the enzyme

Question 13

What are the type of reactions the residues participate in are nucleophilic or electrophilic substitutions?

Answer 13

Nucleophile: Molecular species is electron rich

Negatively charged, or has an unshared electron pairs

Electrophile: Electron poor

Positively charged or has a slight positive dipole

Question 14

What are the ionic intermediates?

Answer 14

Acyl group transfer

Direct displacement reactions

Question 15

Explain lock and key hypothesis

Answer 15

Enzymes are rigid locks to which the substrate is a precisely fitting key

3-D shape of the active site is complementary to 3-D shape of the substrates

Question 16

Explain Induced fit hypothesis

Answer 16

Enzymes are flexible molecules

Binding of substrate causes conformational change in enzyme resulting in catalysis

Question 17

Explain increasing local concentration of substrates

Answer 17

Enzymes act as entropy traps by collecting highly mobile reagents from dilute solution

Decreases entropy

Increases probability that reaction will occur

Question 18

Explain correctly orientating substrates for reaction to occur

Answer 18

Reducing degrees of freedom of interaction

Reduces entropy

Increases likelihood of reaction occurring

Question 19

Explain Exertion of strain on covalent bonds

Answer 19

Lowering activation energy for bond cleavage

Physical distortion (bond strain)

Changes to charge distribution within substrate

Question 20

Define transition state hypothesis

Answer 20

Enzymes are flexible molecules, the shape of which is precisely complementary to the 3-D structure of substrate(s) in the activated “transition state” geometry

Question 21

Rate reaction is dependent upon?

Answer 21

Reactant interactions: Both concentration and free energy of reactants are important in this

Question 22

Transition state hypothesis: When do products form?

Answer 22

Products form when reactant collision reaches a configuration resembling the transition state of a reaction

Question 23

How do enzymes catalyse reactions?

Answer 23

By stabilizing the transition state:

Catalysts provide reaction pathways which have lower activation energies (Delta G) compared to uncatalysed reactions (Delta G).

Question 24

What are intermediates?

Answer 24

Reactions often proceeds via formation of intermediates

They are products formed between the final product

Question 25

Define Acid-Base catalysis

Answer 25

Acceleration of reaction rate achieved by catalytic proton transfer

Commonly found mechanism of enzymatic catalysis

Amino acids which are can donate or accept protons at near neutral pH are important in this type of mechanism.

Proton acceptors are bases (B:) or ionised acids (A-)

Proton donors are the conjugate acid of a base (BH+) or protonated (uni-ionised) acids (AH).

Question 26

What are the two ways Proton acceptors can assist in catalysis?

Answer 26

Direct cleavage of O-H, N-H or 9some) C-H bonds

Cleavage of other carbon-containing bonds (e.g C-N) by generating OH- equivalents from water in neutral solutions

Question 27

How can proton donors assist in catalysis?

Answer 27

Proton donors (BH+ or AH) can also assist in bond cleavage

Covalent bonds may break more easily if one of the atoms is protonated by a general acid.

BH+ or AH can catalyse bond cleavage by donating a proton to an atom more labile

Question 28

Define Covalent catalysis

Answer 28

A substrate, or a part of a substrate is bound covalently to an enzyme to form a reactive intermediate

Subsequent steps in the catalytic mechanism transfer reactive intermediate to a second substrate