L10 - Introduction to enzymes

Question 1

What are enzymes? What are they usually like?

Answer 1

• proteins that catalyse the conversion of substrates to products without being chemically changed
• stereospecific (chiral environment)

Question 2

What do enzymes do to the eq?

Answer 2

nothing

Question 3

What is important for activity regarding enzymes?

Answer 3

folding into a specific 3D conformation

Question 4

What are the 2 models of catalysis?

Answer 4

• lock and key
• induced fit

Question 5

what is induced fit particularly important for?

Answer 5

multi-substrate enzymes

Question 6

How do most enzymes work?

Answer 6

by lowering the activation energy of the reaction

Question 7

What type of interactions are there on enzymes?

Answer 7

• hydrophobic
• ionic
• hydrogen bond
• hydrogen bond to charged group
• hydrogen bond to main chain

Question 8

what are substrates and reacting groups like in chemical catalysis of enzyme reactions?

Answer 8

substrates and reacting groups held together

Question 8

what are reacting groups orientated like in chemical catalysis of enzyme reactions?

Answer 8

with respect to each other

Question 9

what happens to the hydrogen bonds in chemical catalysis of enzyme reactions?

Answer 9

typically stretched or bent
(resembles transition state)

Question 10

what are active sites usually rich in in chemical catalysis of enzyme reactions? and so what?

Answer 10

hydrophobic residues
- can change pKa of charged amino-acid-side-chains and substrate groups

Question 11

what is excluded from enzyme active sites?

Answer 11

the bulk solvent
- charged groups are not masked

Question 12

what often participates in the reaction?

Answer 12

ordered water molecules within active sites

Question 13

what can happen by active site groups?

Answer 13

protons can be donated or accepted
- acid (adds H+)/ base (remove H+) catalysis

Question 14

what intermediates are there in nucleophilic catalysis?

Answer 14

acyl-enzyme intermediates

Question 15

What do enzymes often use?

Answer 15

• cofactors (metal ions)
• cosubstrates (nucleotides)

derived from vitamins and minerals

Question 16

what are enzyme active sites often complementary to?

Answer 16

transition states
- distortion of bond lengths and bond angles

Question 17

When is the rate higher?

Answer 17

when the degrees of freedom are smaller

Question 18

how do enzymes substantially mediate catalysis?

Answer 18

by locking substrate into a fixed position in the active site

Question 19

what is important in enzyme reactions?

Answer 19

• carbonyl chemistry
• control of stereochemistry

Question 20

what are the number of reactions like?

Answer 20

there’s a large number of them
- but there’s only a small number of types of reactions

Question 21

what should small molecules have?

Answer 21

the correct bond angles

Question 22

What is ‘R’?

Answer 22

non-reacting parts of the molecule

Question 23

when is it necessary to draw enzyme residue side-chains?

Answer 23

when covalent intermediates are formed when explicitly asked for

Question 24

what are the steps in acyl-substitution reactions?

Answer 24

1. activation of active site nucleophile by deprotonation
2. acyl substitution using active site nucleophile
3. acyl substitution by water to regenerate enzyme

Question 25

What enzymes are typically used in acyl substitution reactions?

Answer 25

• serine proteases
• cysteine proteases
• penicillinases and other b-lactamases
• lipases
• esterases and thioesterases

Question 26

what type of leaving groups often require protonation?

Answer 26

poor leaving groups
RO-, RHN-

Question 27

when does an acyl-substitution reaction often not occur? and why?

Answer 27

for aldehydes and ketones
- as H atoms, alkyl groups and aryl groups cannot leave