1.3 Proteins

Question 1

What are the monomers of proteins?

Answer 1

Amino acids

Question 2

Describe amino acid structure

Answer 2

Each amino acid has a central carbon atom (alpha carbon).
There are four atoms or groups of atoms bonded to the central carbon atom:
NH2 (an amine group).
COOH (a carboxyl group).
H (a hydrogen atom).
R (a side group).

Question 3

What are the bonds between amino acids?

Answer 3

Peptide bonds

Question 4

What are the two end terminals of a polypeptide?

Answer 4

The N-terminal (amine terminal).
The C-terminal (carboxyl terminal).

Question 5

How do peptide bonds form?

Answer 5

When two amino acids react together, a bond forms between the carboxyl group of one amino acid and the amine group of a second amino acid.
One water molecule is released as a by-product.
The bond formed between two amino acids is a covalent bond called a peptide bond.

Question 6

How to test for presence of proteins?

Answer 6

• Add distilled water and biuret solution
• Shake then leave
• Blue to violet if protein present (only positive if peptide bonds present, not present with free floating amino acids)

Question 7

What is the primary structure of a protein?

Answer 7

Amino acids in a polypeptide chain are arranged in a specific sequence.
The sequence of amino acids is the primary structure.

Question 8

What determines the primary structure of a protein?

Answer 8

Genes in the DNA which encode the amino acid sequence.

Question 9

What is the secondary structure of proteins? Give examples

Answer 9

Folding of the polypeptide with multiple hydrogen bonds. E.g. beta pleated sheet and alpha helix.

Question 10

How is the secondary structure stable?

Answer 10

Individual hydrogen bonds are quite weak, but there are many bonds throughout the molecule which leads to overall high stability.

Question 11

What is the tertiary structure of a protein?

Answer 11

Complex 3D structure usually coiled or folded made with ionic bonds, hydrogen bonds and disulfide bridges.

Question 12

What is the quaternary structure of a protein?

Answer 12

More than one polypeptide coming together E.g. insulin, collagen, haemoglobin.

Question 13

How do enzymes work?

Answer 13

Enzymes lower the activation energies of chemical reactions inside the cell to increase the rate of reactions.
Enzymes lower the activation energy by binding to the reactant molecules (substrate) and allowing chemical bond-breaking and bond-forming processes to happen more easily.

Question 14

What is the shape of the active site determined by?

Answer 14

Tertiary structure of the polypeptide

Question 15

Describe the lock and key model

Answer 15

The model proposes that the enzyme and substrate fit together perfectly.

Question 16

Describe the induced fit model

Answer 16

The induced fit model states that as an enzyme and substrate come together, their interaction causes a small shift in the enzyme’s structure.
The shift means that the enzyme and substrate can bind to form an enzyme-substrate complex and catalyse a reaction.
As it changes shape it puts strain on the substrate. The strain distorts bonds in the substrate which lowers the activation energy needed to break the bonds.

Question 17

What two environmental factors affect the rate of enzyme action

Answer 17

Temperature:
- Increasing the temperature will increase the kinetic energy of the molecules.
- This increases the chance of a collision between the enzyme and substrate and so more collisions are likely in a set period of time. In other words, the rate of reaction is faster.

pH:
- Changing the pH changes the number of hydroxide ions and hydrogen ions (OH− and H+) surrounding the enzyme.
- These interact with the charges on the enzyme’s amino acids, affecting hydrogen bonding and ionic bonding, so resulting in changes to the tertiary structure.

Question 18

What happen if temperature or pH goes outside of optimal range?

Answer 18

Denatures the enzyme because chemical bonds in the active site are affected.

Question 19

What two non environmental factors affect enzyme activity?

Answer 19

• Enzyme concentration
• Substrate concentration

Question 20

Name the two types of enzyme inhibitors

Answer 20

• Competitive
• Non competitive

Question 21

How do competitive inhibitors work?

Answer 21

Competitive inhibitors are similar in shape to the usual substrate and affect the active site directly, blocking access for the formation of ES complexes.

Question 22

How do you decrease the effect of competitive inhibitors?

Answer 22

Increase substrate concentration

Question 23

How do non-competitive inhibitors work?

Answer 23

Non-competitive inhibitors bind to another part of the enzyme molecule (not active site) causing a change to the shape of the active site.
The active site is no longer complementary to the substrate molecules.

Question 24

How can rates of reaction be calculated?

Answer 24

By measuring the increase in products or decrease in reactants over time. (Calculate gradient if on a graph)