Enzymes

Question 1

What are enzymes?

Answer 1

Proteins that catalyse specific chemical reactions

Question 2

What functions are enzymes involved in?

Answer 2

Digestion, blood clotting, defence, movement, nerve conduction

Question 3

List 5 properties of allosteric enzymes

Answer 3

They’re multisubunit complexes.
They have regulatory sites and catalytic sites on different subunits.
Regulation occurs via conformational changes.
They exhibit non-Michaelis-Menten kinetics- V vs S plots are sigmoidal.
They’re involved in feedback inhibition of metabolic pathways

Question 4

Give an example of how an enzyme can be a drug target for antibiotic treatment

Answer 4

Penicillins inhibit cell wall synthesis by inhibiting the enzymes that make pentapeptide links

Question 5

Give an example of how an enzyme can be a drug target for anti-inflammatory agents?

Answer 5

Aspirin blocks prostaglandin

Question 6

Give an example of how an enzyme can be a drug target for anticancer drugs

Answer 6

Methotrexate is a folate analogue which interferes with synthesis of DNA precursors

Question 7

Give the general 5 properties of enzymes

Answer 7

Increase reaction rate by up to 10 billion times
Enzymes show specificity
They remain unchanged at the end of the reaction
They do not alter reaction equilibrium
They facilitate reactions by decreasing free energy of activation of the reaction

Question 8

What’s the name of the point of the reaction where free energy is highest?

Answer 8

The transition state

Question 9

What are active sites?

Answer 9

3D cavities that bind substrates using electrostatic, hydrophobic, and hydrogen bonding and van Der Waal’s interactions.

Question 10

What are 4 ways in which enzyme activity is regulated?

Answer 10

Control of gene expression
Compartmentation
Allosteric regulation
Covalent modification

Question 11

What’s allosteric regulation of enzymes?

Answer 11

The regulation of an enzyme by binding an effector molecule at a site other than the active site, termed an allosteric site

Question 12

What are the 2 types of allosteric regulators?

Answer 12

Allosteric inhibitors and allosteric activators

Question 13

What is Michaelis constant?

Answer 13

KM is the substrate concentration where the rate is Vmax divided by 2, hence being where half the active sites are bound by substrate

Question 14

What enzyme cleaves fructose 1,6-bisphosphate in glycolysis and what into?

Answer 14

Aldolase cleaves fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate

Question 15

What converts dihydroxyacetone phosphate into glyceraldehyde 3-phosphate?

Answer 15

Triosephosphate isomerase (TIM)

Question 16

Give a definition for a perfect enzyme

Answer 16

One for which the rate of the reaction it catalyses is limited by diffusion rate, not by the enzymes activity

Question 17

What are the 4 categories of proteases?

Answer 17

Serine proteases, cysteine proteases, aspartyl proteases and metalloproteases

Question 18

What allows serine proteases to function?

Answer 18

They have a very reactive serine amino acid which is able to directly participate in peptide bond hydrolysis

Question 19

What are 3 important serine proteases?

Answer 19

Chymotrypsin, trypsin (pancreas) and elastase (lungs)

Question 20

How does chymotrypsin affect peptide hydrolysis?

Answer 20

The very reactive serine attacks peptide bonds to form acyl-enzyme intermediates, which are much more prone to hydrolysis

Question 21

What makes the serine amino acid so reactive in serine proteases?

Answer 21

There’s a catalytic triad of serine, histidine and aspartic acid in sequence. A proton is removed from the serine onto the histidine side chain, and then a proton on a nitrogen of the histidine can be moved away onto the negatively charged aspartic acid carboxyl group. This makes the serine oxygen very nucleophilic.

Question 22

What amino acids does trypsin work specifically on?

Answer 22

Lysine and arginine

Question 23

Why does trypsin work specifically on lysine and arginine?

Answer 23

Trypsin has a negatively charged pocket which accommodates the positive side chain of lysine and arginine, which gives tighter binding

Question 24

What amino acids is chymotrypsin specific to?

Answer 24

Phenylalanine, tryptophan and tyrosine

Question 25

Why is chymotrypsin specific to phenylalanine, tryptophan and tyrosine?

Answer 25

Chymotrypsin has a hydrophobic pocket that accommodates the aromatic, hydrophobic side chains of these amino acids

Question 26

What amino acids is elastase specific to?

Answer 26

Amino acids with small side chains

Question 27

Why is elastase specific to amino acids with small side chains?

Answer 27

Elastase has a narrow pocket

Question 28

How are serine proteases structurally similar and different?

Answer 28

They have a conserved 3D structure with a charged-relay system, but their primary structures are very different, apart from the catalytic triad

Question 29

How many active sites does rotary ATP synthase have?

Answer 29

3 active sites activated by a rotating spindle

Question 30

How does ATP catalysis in mitochondria start?

Answer 30

ATP catalysis begins when protons pass through the part of the ATP synthase that lies in the cell membrane, causing it to turn. The central core of ATP synthase then rotates inside the top half of the enzyme. This region holds an ATP molecule and pulls in ADP and Pi. As the core rotates, the subunit with ATP loosens and the section holding ADP closes. The original ATP molecule is released, and a new one is formed from ADP. This cycle repeats.

Question 31

What is topoisomerase II?

Answer 31

An enzyme that untangles chromosomes before they’re pulled to opposite poles of the cell in mitosis. It takes 2 interlocked DNAs and can make a transient double-stranded break in one of them to allow the other DNA chromosome to go through in an active process

Question 32

Describe the mechanism of action of topoisomerase II in detail

Answer 32

Topoisomerase II is a dimeric clamp that binds the DNA from one of the chromosomes, called the gate (G-segment). Then in the presence of ATP, the clamp closes to capture the DNA from the other fragment, which is called the transported segment (T segment). This is an active trapping process. Once it’s trapped the DNA from the second chromosome, it passes it through a double-stranded break and out through the other side. The break is then resealed before another gate opens in the enzyme to free the chromosome out through the other side