Proteins

Question 1

What is the structure of an amino acid?

Answer 1

One carbon atom connected to a R group and hydrogen atom, one carboxyl group and a NH2 (amino group)

Question 2

How are polypeptides formed?

Answer 2

When amino acids join together in condensation reactions, forming a peptide bond and eliminating H2O.

Question 3

What is meant by primary, secondary and tertiary structures?

Answer 3

Primary, basic amino acid sequence with peptide bonds
Secondary, whether the polypeptide chain is arranged into a helix or pleated sheet with hydrogen bonds
Tertiary, folding of the secondary structure into a complex shape with chemical bonds

Question 4

How does the primary structure affect the tertiary structure?

Answer 4

R group variations produce different bonds. The sequence of amino acids in a primary structure determines its three-dimensional shape.

Question 5

What is meant by a ‘specific’ active site?

Answer 5

• The 3D structure of each enzyme is unique due to the side chains and branches that are present
• This also makes the active site unique and therefore only the substrates that match each active site can bind there

Question 6

How many amino acids are there and how do they differ from one another?

Answer 6

20, differ only by ‘R’ groups.

Question 7

How do dipeptides and polypeptides form?

Answer 7

Condensation reaction forms peptide bonds and eliminates molecules of water. Dipeptide, 2 amino acids. Polypeptide, 3 or more amino acids.

Question 8

Define quaternary structure of a protein.

Answer 8

May consist of more than one polypeptide. Precise 3D structure held together by the same bonds as tertiary structure. May contain addition of prosthetic groups.

Question 9

What is the significance of the structure of the R group?

Answer 9

Affects the way an amino acid bonds with others in a protein, depending largely on whether the R group is polar or not.

Question 10

What’s a peptide bond?

Answer 10

The bond formed by condensation reactions between amino acids

Question 11

What is an alpha helix?

Answer 11

When the chain of amino acids coil with the presence of hydrogen bonds for stability

Question 12

What is a beta pleated sheet?

Answer 12

When the chain of amino acids zig zags and folds over themselves

Question 13

What are fibrous proteins?

Answer 13

Long parallel polypeptide chains with occasional cross linkages that form into fibres

Question 14

What is an example of a fibrous proteins?

Answer 14

Collagen is one of the most abundant fibrous proteins in the body, it has 3 polypeptide chains, each up to 1000 amino acids long, arranged in a triple helix held together by lots of hydrogen bonds

Question 15

Why are fibrous proteins insoluble and globular proteins are soluble?

Answer 15

• In a globular protein, the amino acid chain can twist in a way that polar groups lie at the protein’s surface making it hydrophilic

Question 16

What are globular proteins?

Answer 16

• They are compact and spherical
• Hydrophobic R groups on the inside, hydrophilic on the outside, making them soluble
• Have tertiary or quaternary structures

Question 17

What is an example of a globular protein?

Answer 17

Haemoglobin, 2 alpha subunits and 2 beta subunits, with 4 haem prosthetic groups

Question 18

How are ionic bonds formed in proteins?

Answer 18

Formed between positively and negatively charged R groups

Question 19

How are disulfide bonds/covalent bonds formed in proteins?

Answer 19

Forms between sulphur molecules in sulphur containing R groups (cysteine)

Question 20

How are hydrogen bonds formed in proteins?

Answer 20

The negatively charged oxygen from the carboxyl group attracts to the positively charged hydrogen from the amino group

Question 21

What causes VDWFs between proteins?

Answer 21

Non-polar attraction

Question 22

Explain the effect of changing enzyme concentration on the initial rate of reaction.

Answer 22

• Reduce Ea
• More enzyme-substrate complexes
• More active sites occupied
• Eventually substrate becomes limiting factor

Question 23

Describe an experiment that could be carried out to investigate the effect of enzyme concentration on the initial rate of reaction.

Answer 23

• Range of concentrations of enzymes/catalase (independent variable)
• A substrate concentration/hydrogen peroxide (control variable)
• Measure the volume of O2 produced (dependent variable) and plot on graph
• Repeat

Question 24

The primary structure of lysozyme is a specific sequence of 129 amino acids. Two of the amino acids that make up the active site are in positions 35 and 52 in the primary structure.
i) Suggest how these two amino acids could be brought closer together to form
part of the active site of this enzyme.

Answer 24

• Formation of secondary structure
• Bonding of R groups
• Ionic bonds formed

Question 25

Haemophilia is a disease that affects blood clotting. People with haemophilia are sometimes
given a protein called factor VIII. Factor VIII is an enzyme that is involved in the process of blood
clotting.
i) Explain how a change in the primary structure of factor VIII could cause difficulties with blood
clotting.

Answer 25

• Results in a different sequence of amino acids
• Affects the folding of the secondary structure
• Changes shape of active site
• Reducing production of fibrin (or another specific aspect of the blood clotting cascade)