Enzymes

Question 1

What are the different amino acid residues that make up the enzymes and their functions?

Answer 1

Contact residues
-found in the active site - help to position the substrate in the correct orientation via weak interactions such as hydrogen bonds, ionic bonds and hydrophobic interactions

Catalyctic residues
-found in the active site - have specific R groups which act on bonds in the substrate and help to catalyse the conversion of substrate to product

Structural residues
-interact with each other to maintain the overall 3D conformation of protein

Non-essential residues
-found on surface of protein, no function

Question 2

How do enzymes lower activation energy?

Answer 2

1. Proximity effects
   -temporary binding of substrates in close proximity in active site, increasing chance of reaction
2. Orientation effects
   -substrates are held by enzymes in their active sites in an orientation, enable bonds in substrated to be exposed to chemical attack
3. Strain effect
   -slight distortion of substrates when they bind to the enzyme active site, strains bonds in substrates that need to be broken
4. Microenvironment effects
   -provide a favourable environment for catalysis e.g. hydrophobic amino acids create water-free zone for non-polar reactants to react more easily
5. Acid-base catalysis
   -R groups of acidic and basic amino acids in enzyme facilitate catalysis

Question 3

Explain effect of increasing temperature on rate of reaction.

Answer 3

As temperature increases,
-kinetic energy of enzyme and substrate molecules increase
-frequency of effective collisions between enzyme and substrate molecules increase
-rate of enzyme-substrate complex formation increases
-number of substrate molecules with sufficient energy to overcome the activation energy barrier and form products increases
-rate of reaction increases until optimum temperature

Question 4

Explain effect of increasing temperature on rate of reaction, beyond optimum temperature of enzyme.

Answer 4

Beyond optimum temperature,
-kinetic energy of enzyme and substrate molecules increase
-intramolecular vibrations increase
-H bonds, ionic bonds and hydrophobic interactions between R groups that maintain the 3D conformation of the enzyme are disrupted.
-specific conformation of active site is lost, enzyme denatures
-substrate no longer complementary to shape and charge of active site and cannot bind to it
-rate of enzyme-substrate complex formation decreases and rate of reaction decreases

Question 5

Explain the effect of pH on rate of enzyme-catalysed reaction

Answer 5

At optimum pH,
-conformation of enzyme active site is most ideal for substrate binding and rate of reaction is highest

As pH deviates from optimum,
-excess H+ or OH- ions affect the ionisation of the R-groups of the amino acids residues; excess H+ results in COO- groups becoming COOH and excess OH- results in NH3+ becoming NH2
-thus ionic bonds and H bonds that maintain the conformation of the enzyme active site is disrupted and the enzyme denatures
-thus interaction between substrate and catalytic residues in the active site of enzyme is disrupted
-rate of enzyme-substrate complex formation decreases, rate reaction decreases

Question 6

Explain the effect of [enzyme] in rate of reaction.

Answer 6

Initially, when [enzyme] is low, as concentration increases,
-frequency of effective collisions between enzyme and substrate molecule increases
-rate of enzyme-substrate complex formation increases and rate of reaction increases

Question 7

Describe function of non-competitive inhibitor and its effect on rate of reaction.

Answer 7

-Non-competitive inhibitor bears no structural similarity to substrate, binds to a site other than the enzyme active site
-Alters the conformation of the active site, substrate cannot bind in correct orientation
-Non-competitive inhibitors effectively decrease the availability of enzymes as it forms inactive enzyme-inhibitor complexes.
-Effects cannot be overcome by high concentration of substrates

Question 8

Describe the effect of allosteric enzyme on rate of enzyme-catalysed reaction, and effect of increasing substrate on inhibition.

Answer 8

1.

-Inhibitor/activator binds to allosteric site of the enzyme, resulting in conformational change in enzyme.
-Binding of inhibitor/activator stabilises enzyme in an inactive/active state –> shifts curve to right/left

2.

-Substrate binding stabilises the enzyme in the active conformation and opposes the effect of the inhibitor, allowing Vmax to be reached at higher [S].
-binding of substrate in allosteric enzymes exhibits cooperativity: binding of first substrate to first subunit, changes the conformation of other subunits, easier to accept subsequent substrates. Hence rate against substrate concentration plot is sigmoidal.