Protein Structure

Question 1

What are some of the function of proteins in the body?

Answer 1

Function as;
Catalysts (enzymes)
Ion transporters(NA/K ion pump)
O2 transporters(haemoglobin)
Motion coordination(Actin/myosin filaments
Immune protection(antibodies)

Question 2

What do amino acids exist as in a neutral solution?

Answer 2

Zwitterions

Question 3

Explain why carbons in amino acids are called alpha/beta etc.

Answer 3

The alpha carbon refers to the first carbon atom that attaches to a functional group the second carbon atom is called the beta carbon

Question 4

What does the presence on an OH group on an amino acid side chain allow for?

Answer 4

Increases hydrophilic character as it forms hydrogen bonds with water. Also increases reactiveness compared to other amino acids

Question 5

Describe the reaction of a disulphide bond formation between two cysteine residues.

Answer 5

Two -SH molecules on different molecules react to form a disulphide bond (-S-S-) between the molecules and producing 2e- and 2H+

Question 6

Define the term pKa.

Answer 6

An acid dissociation constant, Ka, (also known as acidity constant, or acid-ionization constant) is a quantitative measure of the strength of an acid in solution

Question 7

Describe the general reaction for peptide bond formation. What type of reaction is it?What is special about the equilibrium?

Answer 7

Condensation reaction. Equilibrium lies on hydrolysis side as formation of peptide bond requires input of free energy. Hydrolysis is thermodynamically downhill

Question 8

Describe the general reaction for peptide bond formation. What type of reaction is it?What is special about the equilibrium?

Answer 8

Condensation reaction. Equilibrium lies on hydrolysis side as formation of peptide bond requires input of free energy. Hydrolysis is thermodynamically downhill

Question 9

What is special about peptide bonds in terms of bond strength and rotation?

Answer 9

Peptide bonds are rigid and planar
Peptide bonds have a considerable double bond character – this prevents rotation about the double bond
They are also between the length expected of C=N and a C-N bond, so they are similar to a double bond
The rigidity of peptide bonds allows proteins to have a well defined 3D structure
All other bonds are single bonds (between amino and alpha carbon + between carboxyl and alpha carbon)
- This allows for free rotation of atoms in the side chains
- If the side chains are big/bulky rotation will not occur (steric effects) two atoms cannot occupy the same space
- Rotation allows for proteins to fold in many ways

Question 10

Explain the terms Phi and Psi.

Answer 10

Nitrogen from amine and alpha carbon is Phi rotation (φ) -80

Carbon from carbonyl) and alpha carbon is psi (ψ) +85

Question 11

What is the tertiary structure of proteins?

Answer 11

3D structure that is devoid of symmetry

Question 12

What is the quaternary structure of proteins?

Answer 12

Proteins contain more than one polypeptide chain
Each polypeptide chain in such a protein is called a subunit
Polypeptide chains can assemble into multisubunit structures

Question 13

Give some examples of quaternary structured proteins?

Answer 13

Haemoglobin

Myoglobin

Question 14

What are beta pleated sheets?

Answer 14

A common motif of regular secondary structure in proteins that consist of beta strands (also β-strand)

Question 15

What are antiparallel beta sheets and what are parallel beta sheets?

Answer 15

Antiparallel;
Side chains (in green) are alternatively above and below the strand
Hydrogen bonds between NH and CO groups connect each amino acid with a single amino acid on an adjacent strand, stabilising the structure
Strands move in opposite directions
1:1 ratio

Parallel;
Side chains are alternatively above/ below the strand
Hydrogen bonds connect each amino acid on one strand to 2 different amino acids on another strand
1:2 ratio

Question 16

What is the tertiary structure of proteins?

Answer 16

3D structure that is devoid of symmetry