Chapter 4: Enzymes

What are enzymes?

Enzymes are biological catalysts. The speed up the rate of reactions by lowering the activation energy of the reaction and are chemically unaltered at the end of the reactions, and thus can be reused, and they are effective in small amounts.

Explain the mode of action of enzymes [8]

1. Enzymes have an specific active site which is complementary in shape and charge to the substrate

2. Effective collision between enzyme and substrate form a temporary enzyme-substrate complex

3. Based on the lock and key hypothesis, enzyme is the lock and substrate is the key

4. ESC held together by weak interactions eg. H, I, H/phobic ions

Catalysis

5. Enzyme lowers the activation energy barrier by:

   1. Aligning substrates next to each other in AS for rxn to occur

   2. Distorts the substrate and reducing activation energy to achieve transition state

   3. Orientates substrate such that bonds are exposed to attack

   4. Provides a favourable micro environment

   5. R-groups of amino acid residues in AS participate in direct catalysis (Eg. Acid-base catalysis)

Release

6. Products no longer fit active site and are released → enzyme is unchanged and can be used again

What are the 2 models that explain specificity of enzymes?

Lock and key hypothesis

• Enzyme is lock and substrate is key

• Enzyme active site has a conformation which is complementary in shape and charge to a specific substrate

• When enzyme and substrate molecules collide in the correct orientation the substrate will bind to the active site and form an enzyme-substrate complex

• Catalysis occurs

• Products no longer fit AS → leave AS, allowing other substrate molc to bind to AS

Induced fit hypothesis

• Binding of substrate to AS induces a conformational change in the AS such that it now provides a more precise fit for the substrate

• Enzyme can perform its catalytic function more effectively

Amino acid residues on enzymes

1. Contact residues

   1. Found in AS, helps to position substrate in the correct orientation via weak interactions eg…

2. Catalytic residues

   1. Found in AS, have specific R groups which act on bonds in the substrate, help to catalyse the conversion of substrate to product

3. Structural residues

   1. Interact with each other, maintain overall 3D conformation of protein

4. Non- essential residues

   1. Found on surface of protein, no specific function

How do enzymes lower activation energy?

1. Proximity effects

   1. Catalysed: Reactants next to each other temporarily bind in AS → incr chances of reaction

   2. Vs Uncatalysed: depend on random collisions

2. Strain effects

   1. Reactants slightly distort as they bind to enzyme → strain bonds which are to be broken → incr chance of breakage

3. Orientation effects

   1. Enzyme holds reactants so that bonds are exposed to chemical attack by catalytic R groups

4. Microenvironment effects

   1. Hydrophobic AA create water-free zone → non-polar reactants react more easily

5. Acid-base catalysis

   1. Acidic and basic AA in enzymes facilitate catalysis

Effect of desaturation on enzyme active site

1. Denaturation results when H bonds, ionic bonds and other weak interactions that stabilize 3D conformation are broken

2. Conformation of enzyme is altered including that of AS

3. AS no longer complementary in shape and charge to substrate

Enzyme cofactors

1. Inorganic ions

   1. Metal ions that change non-functioning AS into functioning one

   2. eg. Mg ions in PCR

   3. Mould enzyme or substrate and allows ESC to form more easily

2. Coenzymes

   1. Eg. NAD transfers electrons in certain redox runs in respiration

   2. Organic molcs required by certain enzymes to carry out catalysis

   3. Bind to AS of enzyme and participate in catalysis but are not considered substrates of the rxn 

   4. Function as intermediate carriers of electrons or specific atoms that are transferred in the overall rxn

3. Prosthetic group

   1. Eg. Haem group of cytochrome oxidase in ETC in inner mitochondrial membrane accepts electrons from cytochrome C and transfers them to oxygen to form water

   2. Permanently bound to enzyme

   3. transfers atoms/ chemical groups between AS of enzyme and another substance

Effect of temperature on enzyme-catalysed reactions

Effect of pH on enzyme-catalysed reactions

Effect on enzyme concentration on enzyme-catalysed reactions

Effect of substrate concentration on enzyme-catalysed reactions