Module 5: V1 - V4

Question 1

How do enzymes lower ΔG?

Answer 1

enzyme active sites are complementary to the transition state of the reaction
stronger/additional interactions with the transition state as compared with the ground state lower the activation barrier

Question 2

What are enzymes?

Answer 2

enzymes are biomolecules (not necessarily proteins) that have a distinctive 3-D structure and employ catalytic mechanisms

Question 3

What is the structure of enzymes?

Answer 3

the active sites of enzymes are lined with functional groups (usually from amino acids) that bind the substrate(s) and catalyze the chemical transformation to product(s)

Question 4

Do enzymes affect the equilibrium of a reaction?

Answer 4

no, they only affect the reaction rate

Question 5

What is enzyme catalysis formally described as?

Answer 5

the stabilization of the transition state through tight binding to the enzyme

Question 6

What are three common catalytic mechanisms and what are they involved in?

Answer 6

acid-base catalysis: give and take protons
covalent catalysis: change reaction paths
metal ion catalysis: use redox cofactors, pKa shifters

Question 7

Why are enzymes important?

Answer 7

living organisms must be able to catalyse the conversion of carbon fuel sources into cellular energy (e.g. ATP) in an appropriate timescale
some diseases are caused by excessive / too little enzymatic activity
many drugs target enzymes either by inhibiting or activating the enzyme target

Question 8

What are cofactors?

Answer 8

small inorganic molecules which are used by enzymes for activity

Question 9

What are coenzymes?

Answer 9

more complex molecules used by enzymes that transiently carry functional groups during catalysis of a reaction

Question 10

What are kinases?

Answer 10

enzymes which catalyse the phosphoryl transfer from one molecule (usually ATP) to another e.g. hexokinase

Question 11

What are phosphorylases?

Answer 11

enzymes which catalyse the covalent addition of inorganic phosphate (Pi) to a molecule; e.g. glycogen phosphorylase

Question 12

What are phosphatases?

Answer 12

enzymes which catalyse the cleavage of a phosphate to yield the dephosphorylated product and Pi; e.g. glucose-6-phosphatase

Question 13

What are dehydrogenases?

Answer 13

enzymes which catalyse an oxidation/reduction reaction commonly using NADH/NAD+, NADPH/NADP+ or FADH2/FAD as cofactors; e.g. glyceraldehyde-3-phosphate dehydrogenase

Question 14

What are mutases?

Answer 14

enzymes which catalyse the shift of a phosphoryl group from one atom to another within the same molecule; e.g. phosphoglycerate mutase

Question 15

What are isomerases?

Answer 15

enzymes which catalyse the conversion of one isomer to another; e.g. triose phosphate isomerase

Question 16

What are hydratases?

Answer 16

enzymes which catalyse the addition/removal of water e.g. enolase

Question 17

What are synthases?

Answer 17

enzymes which catalyse the synthesis of a product e.g. citrate synthase

Question 18

What does the activation of an enzyme affect?

Answer 18

the rate of the forward and backward reactions

Question 19

Where are intermediates located on a free energy plot?

Answer 19

found at local minima as they are ‘stable’ states

Question 20

What are transition states?

Answer 20

transient species (maxima on a free energy plot)

Question 21

Why are energy barriers to reactions important?

Answer 21

prevent complex molecules from reverting spontaneously to their simpler precursors

Question 22

What is the binding free energy?

Answer 22

the difference between the activation energies of the uncatalysed and catalysed reactions caused by the enzyme binding the transition state

Question 23

What are the different ways in which enzymes reduce the activation energy and accelerate rates of reaction?

Answer 23

binding substrates in the correct orientation relative to the active groups
providing catalytically active groups (side chains, acids, bases, metal ions)
polarizing bonds, stabilising charged species
stabilising the transition state

Question 24

Why does rate decrease with time?

Answer 24

(main reason) S is depleted by conversion to product
the reaction is reversible, so as [P] increases the rate of the reverse reaction increases
the enzyme may be unstable under the reaction conditions

Question 25

What is the rate of an enzyme catalysed reaction proportional to?

Answer 25

enzyme concentration

Question 26

What is a Michaelis-Menten plot?

Answer 26

a graph which shows initial velocity (µm/min) vs. substrate concentration (mM)

Question 27

Does the reverse reaction get faster, or only the forward reaction?

Answer 27

both sides of the reaction get faster

Question 28

Why is the transition state more stable when an enzyme is involved? How is that helpful?

Answer 28

because enzymes are complementary to the transition state of the reaction and therefore, form stronger/additional interactions with the transition state