Proteins and Enzymes

Question 1

What are the functions of proteins?

Answer 1

• Enzymes
• Defensive proteins (e.g. antibodies).
• Hormonal and regulatory proteins (control physiological processes).
• Receptor proteins (receive and respond to molecules signals).
• Storage proteins (store amino acids).
• Structural proteins.
• Transport proteins (e.g. haemoglobin).
• Genetic regulatory proteins (regulate when/how/to what extent a gene is expressed).

Question 2

What is the definition of a polypeptide chain?

Answer 2

A single, unbranched chain of amino acids.

Question 3

What functional groups fo amino acids have?

Answer 3

A carboxyl and an amino group so they function as both an acid and a base.

Question 4

What are the two isometric forms that amino acids can exist in?

Answer 4

1. D-amino acids

2. L-amino acids (found in organisms).

Question 5

What are the special functions of the amino acids methionine, proline and cysteine?

Answer 5

Methionine - Initiates chains of amino acids (in translation).
Proline - Causes kinks in chains of amino acids.
Cysteine - Links amino acid chais together and can form disulphide bridges.

Question 6

How are disulphide bridges formed and what are they important for?

Answer 6

They are formed by the terminal -SH group of cysteine reacting with another cysteine side chain to form a disulphide bridge/bond (-S-S). Important in protein folding.

Question 7

How are amino acids bonded together?

Answer 7

They are covalently bonded together in a condensation reaction by peptide bonds. The amino group of one amino acid reacts with the carboxyl group fo another to for the peptide bond. A molecule of water is lost as each linkage forms.

Question 8

What is the primary structure of a protein?

Answer 8

The sequence of amino acids in the polypeptide which determines the secondary and tertiary structure (how the protein is folded).

Question 9

What are the 2 types of secondary structure?

Answer 9

1. Alpha helix - resulting from hydrogen bonding between N-H groups on one amino acids and C=O groups on another.
2. Beta pleated sheet - 2 or more polypeptide chains are aligned and hydrogen bonds form between them.

Question 10

What is the tertiary structure of proteins?

Answer 10

Bending and folding of the polypeptide which results in a macromolecules with specific 3D shape. The outer surfaces present functional groups that can interact with other molecules.

Question 11

What types of interactions between R groups determine tertiary structure?

Answer 11

• Disulphide bridges.
• Hydrogen bonds.
• Aggregation of hydrophobic side chains.
  Van der Waals forces.
• Ionic bonds.

Question 12

What happens when a protein is heated or treated with chemicals?

Answer 12

The secondary and tertiary structure is broken down and the protein is said to be denatured. When cooled the protein returns to its normal tertiary structure which shows the information to specify protein shape is contained in the primary structure.

Question 13

What is quaternary structure?

Answer 13

Results from the interaction of subunits by hydrophobic interactions, van Der Waals forces, ionic and hydrogen bonds. Each subunit has its own unique tertiary structure. Not all proteins have quaternary structure. E.g. haemoglobin.

Question 14

What is the specificity of proteins to non-covalently bind with specific molecules determined by?

Answer 14

1. Protein shape

2. Chemistry

Question 15

What are the main conditions that affect secondary or tertiary structure?

Answer 15

1. High temperature
2. pH changes
3. High concentration of polar molecules.
4. Non-polar substances.

Question 16

What is energy and what are the 2 categories?

Answer 16

The capacity to do work or the capacity for change. Can be potential energy (stored energy) and kinetic energy (energy of movement).

Question 17

What does ‘metabolism’ mean?

Answer 17

The sum total of all chemical reactions in an organism.

Question 18

What is an anabolic reaction?

Answer 18

Where complex molecules are made from simple molecules. Energy input required.

Question 19

What is a catabolic reaction?

Answer 19

Where complex molecules are broken down into simpler ones. Energy is released.

Question 20

What is the first law of thermodynamics?

Answer 20

Energy is neither created or destroyed. When energy is converted from one form to another, the total energy before and after is the same.

Question 21

What is the second law of thermodynamics?

Answer 21

No energy transformation is 100% efficient.
Disorder tends to increase because of energy transformations. Living organisms must have a constant supply of energy to maintain order.

Question 22

What is entropy?

Answer 22

The measure of disorder in a system. It takes energy to impose order on a system so with no energy, a system will be randomly arranged or disordered.

Question 23

What is an exergonic and endergonic reaction?

Answer 23

Exergonic - Releases free energy (catabolism).

Endergonic - Consumes free energy (Anabolism).

Question 24

What is the free energy at chemical equilibrium?

Answer 24

0. Forward and reverse reactions are balanced.

Question 25

What is the activation energy (Ea)?

Answer 25

The amount of energy required to start a reaction. It changes the reactants into unstable forms with higher free energy called transition state intermediates.

Question 26

What do enzymes do to the activation energy of a reaction?

Answer 26

Lower the barrier by bringing the reactants together. The final equilibrium and the free energy does not change.

Question 27

What is the enzyme-substrate complex (ES) held together by?

Answer 27

Hydrogen bonds, electrical attraction or covalent bonds.

Question 28

What 3 mechanisms might an enzyme use when catalysing a reaction?

Answer 28

1. Orientation of the substrate molecule.
2. Physical strain of the substrate.
3. Chemical change of the substrate.

Question 29

What is the meaning of induced fit?

Answer 29

The changing shape of an enzyme when binding to a substrate.

Question 30

What is lysozyme?

Answer 30

An enzyme found in egg white, saliva and tears that acts as an antibiotic by catalysing the cutting of polysaccharide chains in bacterial cell walls causing them to rupture. Catalyses a hydrolysis reaction that is spontaneous but not instantaneous.

Question 31

What is feedback inhibition/end-product inhibition?

Answer 31

The final product of a metabolic pathway acts as a non-competitive inhibitor of the first enzyme, shutting down the pathway.

Question 32

What are ribozymes?

Answer 32

Biological catalysts made from RNA (not protein).