Enzymes I

Question 1

What are enzymes?

Answer 1

Enzymes are proteins that speed up (catalyse) specific chemical reactions by lowering the activation energy required for the reaction to take place.

Question 2

What are some functions of proteins?

Answer 2

Their functions are:-

a. Digestion in gut: carbohydrates, fats, proteins
b. Blood clotting: fibrin clot catalysed by thrombin
c. Defence: immune system - activation of complement
d. Movement: muscle actomyosin is an ATPase (enables the conversion of ATP into movement)
e. Nerve conduction: membrane ion pumps for Na+, Ca2+ to control concentration gradient

Question 3

What are the two diseases caused by enzyme defects?

Answer 3

1. Phenylketonuria - it is an inherited disease where a child cannot convert phenylalanine to tyrosine.
2. Tay-Sachs disease - the body is unable to make a membrane lipi called cerebroside.

Question 4

Give examples of how bacterial enzymes are drug targets.

Answer 4

• Antibiotics: e.g. penicillin inhibits cell wall synthesis.
• Anti-inflammatory agents: Inflammation involves a messenger molecule called prostaglandin. And aspirin works to block the synthesis of prostaglandins. [Prostaglandin is a hormone like substance that participates in a wide range of bodily functions such as the contraction / relaxation of smooth muscles, dilation / constriction of blood vessels, etc.]
• Anti cancer drugs: methotrexate is a folate analogue that interferes with synthesis of DNA precursors.

Question 5

How does an enzyme reduce the free energy of activation?

Answer 5

• The enzymes have active sites that is a 3-D cavity or cleft that binds substrates using electrostatic, hydrophobic, hydrogen bonding and van der Waals interactions.
• The enzyme uses the binding energy to reduce the free energy.

Question 6

What evidence do we have for enzyme active sites?

Answer 6

1. X-ray crystallography
2. Kinetic studies of enzyme activity

Question 7

What is the lock and key model?

Answer 7

This model postulates that the enzymes active site is directly complementary in shape to that of the substrate.

Question 8

What is the induced fit model entail?

Answer 8

• The free enzymes active site isn’t directly complementary to the substrate.
• As the substrate starts to bind the enzyme has a conformational change and the active sit changes its shape to become complementary to the substrate.

Question 9

What is the enzyme-substrate binding energy used for?

Answer 9

The enzyme-substrate binding energy is used:
◦ To bring molecules together in the active site-
A + B = C + D
◦ To constrain substrate moment.
◦ Stabilise positive and negative charges in t-state
◦ Provide a reaction pathway of lower energy: e.g. Involving covalent enzyme-substrate intermediates.
◦ To strain particular bonds in the substrate-making breaking easier. Substrate distorted on binding to resemble transition state.
◦ Use cofactors: they bring new chemistry to active site.

Question 10

What is Km?

Answer 10

• Km is called the Michaelis constant.
• Km is the concentration of substrate which permits the enzyme to achieve half Vmax.
• A small Km indicates that the enzyme requires only a small amount of substrate to become saturated. Hence, the maximum velocity is reached at relatively low substrate concentrations.
• A large Km indicates the need for high substrate concentrations to achieve maximum reaction velocity.

Question 11

What are the two versions of the equation we need to know for Km?

Answer 11

Question 12

What is turnover number? What is the equation for turnover number?

Answer 12

• Turnover number (also termed k_cat) is defined as the maximum number of chemical conversions of substrate molecules per second that a single catalytic site will execute for a given enzyme concentration [E_T ].
• It can be calculated from the maximum reaction rate V_max and catalyst site concentration [E_T] as follows:

Question 13

What is Vmax?

Answer 13

The rate of reaction when the enzyme is saturated with substrate is the maximum rate of reaction is the Vmax.

Question 14

How is the Km and Vmax altered with competitive inhibition?

Answer 14

• The Vmax is unaltered.
• The Km is increased.

Question 15

How is Km and Vmax altered with non-competitive inhibition?

Answer 15

• The Vmax decreases.
• The Km is unaltered.

Question 16

In what ways is enzyme activity regulated?

Answer 16

1. Control of gene expression-enzyme amount.
2. Compartmentation: sequences in enzyme polypeptide chain target enzyme to ER, mitochondrion, nucleus etc.
3. Allosteric regulation: regulatory molecules control protein shape-increase (or decrease activity).
4. Covalent modification of enzyme which changes the enzymes shape and activity-
   e. g. phosphorylation

Question 17

What is feedback inhibition?

Answer 17

• In a metabolic reaction, substance A is converted through a number of steps to Z.
• If we want to regulate this pathway, we can do this through feedback inhibition, which is as the product builds up, this inhibits the reaction of A, so this is done by allosteric regulation.

Question 18

What are some properties of allosteric enzymes?

Answer 18

• Allosteric enzymes are an exception to the Michaelis-Menten model.
• Because they have more than two subunits and active sites, they do not obey the Michaelis-Menten kinetics but instead have sigmoidal kinetics.
• Thus, allosteric enzymes show the sigmodial curve shown below.

Question 19

What is ATCase (Aspartate carbamoyltransferase) regulated by?

Answer 19

It is regulated by CTP (Cytidine triphosphate).