Protein Structure and Function

Question 1

What are the 4 structures that a protein can take? Explain each.

Answer 1

Primary - sequence of amino acids in peptide chain
Secondary - Folding/coiling of the peptide chain
Tertiary - Peptide chains fold upon themselves
Quaternary - folded peptide chains join together

Question 2

Name some forces that stabilise the protein structure

Answer 2

Covalent (disulphide bridges)

Non - covalent (hydrogen, electrostatic interactions, Van der Waals, Hydrophobic effect)

Question 3

What are the main features of the hydrogen bond?

Answer 3

Strong dipole - dipole force between an electronegative atom and a hydrogen atom bonded to F, O, Cl.

Question 4

Give details of the alpha helix structure

Answer 4

• They are formed by hydrogen bonds in the same polypeptide chain
• H bonds form between carbonyl group in the peptide bond and N-H of the amine group every 4th peptide
• Right handed helix
• 3.6 amino acids residues per turn
• Rigid cylinder shape

Question 5

Give details of the beta pleated sheet structure

Answer 5

• Linear peptide chains
• H-bonding between peptide chains hold the strands together
• Side chains in each strand lie above and below the plane of the sheet
• 0.7nm
• Can be a parallel beta sheet of a antiparallel beta sheet . Antiparallel is most common in globular proteins

Question 6

What percentage of haemoglobin is an alpha helix?

Answer 6

60%

Question 7

What is a supersecondary structure?

Answer 7

Combinations of alpha and beta sheets form domains in the protein.

Question 8

At physiological pH, what amino acids have ionised carboxyl groups? COO-
What amino acids have ionised amino groups? NH3+

Answer 8

carboxyl - aspartic acid and glutamic acid

amino - lysine and arginine

Question 9

Give some information on Van der Waals. What do they exclude? What are they dependant on?

Answer 9

The sum of the attractive or repulsive forces between molecules. They exclude those due to covalent bonds, hydrogen bonds and electrostatic interaction. They are transient.

Question 10

What are hydrophobic regions of amino acids unable to do? What occurs due to this?

Answer 10

Hydrophobic regions are unable to form hydrogen bonds. This means these regions fold in a way that minimises the contact with the aqueous environment.

Question 11

How do membrane proteins have their hydrophilic/phobic groups arranged?

Answer 11

Hydrophilic R groups on the inside and hydrophobic groups on outside. Opposite way around to expected.

Question 12

What are the 3 types of post - translational modifications that can occur to a protein?

Answer 12

1 = glycosylation which is the addition of a sugar. The sugar can either join to an oxygen or a nitrogen.
2= phosphorylation which is addition of a phosphate group. This is needed for cell signalling and to change enzyme activity.
3= methylation/acetylation of NH2 groups in side chains of lysine and arginine.

Question 13

Collagen -
What modified amino acids does it contain?
Where does the glycine amino acid appear? Why is is good for collagen to have this amino acid?
Give details on the structure of the protein e.g. number of chains, type of helix

Answer 13

Hydroxyproline and hydroxlysyine.

Glycine appears every third amino acid. Good for collagen as it only have a H as the R group so allows for close packing.

Collagen has 3 chains with each chain having 3 amino acids per turn. Each chain is a left - handed helix and three chains wrap to form a right - handed super helix.

Question 14

Give an example of a protein with functional domains and what the domains are

Answer 14

Pyruvate kinase has functional domains.

These are alpha and beta barrel catalytic domains and regulatory domains.

Question 15

What type of collagen is 90% of the total collagen? What does this type form in the body?

Answer 15

Type 1

Forms skin, bone, tendon, dentine.

Question 16

MCQ
The a helix and b sheet are found in many different proteins because they are formed by …
A. hydrogen bonding between atoms of the polypeptide backbone.
B. hydrogen bonding between the amino acid side chains most commonly found in proteins.
C. hydrophobic interactions between the many nonpolar amino acids.
D. ionic interactions between charged amino acid side chains.
E. non covalent interactions between amino acid side chains and the polypeptide backbone.

Answer 16

A

Question 17

MCQ
The α helix structure found in proteins
A. forms a triple superhelix in the structure of collagen.
B. has 10 amino acid residues per 360°turn.
C. has a diameter of 2 nm.
D. is a right handed helix with a diameter of 0.54 nm.
E. is a right handed helix with a pitch of 0.54 nm

Answer 17

E