Session 2 ILOs - Protein structure

Question 1

Identify the structure and properties of a peptide bond

Answer 1

Structure: A peptide bond is formed by 2 amino acids being joined together - the link is between the carboxylic acid one amino acid and the amine of another amino acid (involves extraction of water). Peptide bonds are also planar (all lie in the same plane)

Properties: Peptide bonds are rigid and the C-N bond has partial double-and characteristics - means that the amide hydrogen and the carboxyl hydrogen are always on opposite sides of the peptide bond (R groups are also always on opposite sides) = always trans-confirmation
Also, bonds either side of the carbon can rotate, Psi (C-C) or Phi bonds (C-N) = what determines the 3D structure of protein molecules

Question 2

Describe the key features and properties of secondary structure, including why the properties of a peptide bond contribute to this

Answer 2

1. Alpha helix - hydrogen bonds between N-H and C=O stabilise the structure
2. Beta sheet - structure stabilised by hydrogen bonds between strands

The Phi & Psi bond rotation allows the protein to have these 2 secondary structures and also stabilises the structure

Question 3

Explain what is meant by tertiary (2 different types) and quaternary structure

Answer 3

Process of folding of the secondary structure to form tertiary/quaternary structures

Tertiary structure: Either globular proteins or fibrous proteins

Quaternary structure: more than one subunit coming together to form a quaternary structure

Question 4

Identify the types of bonds involved in maintaining the different levels of protein structure and appreciate what the consequences are of their disruption

Answer 4

1. Primary structure - only peptide bonds (type of covalent bonding)
2. Secondary structure - mainly hydrogen bonds between the sheets/molcules within the a-chain
3. Tertiary structure is determined by all electrostatic interactions (e.g. H-bond, Van der Waals) as well as disulfide bridges
4. Quaternary structure is determined by the subunits and the attractions between the different subunits

Question 5

Outline how proteins fold

Answer 5

The folding process is ordered, driven by the need to find the most stable confirmation. When it finds a conformation that works, it holds this confirmation as it makes it more stable, this then reduces the number of next available conformations

Question 6

Why is folding important for protein function?

Answer 6

Protein folding is very important because it determines the properties of the protein and its ability to carry out a specific function

Question 7

Why cam protein misfiling cause disease?

Answer 7

Misfolding can because disease as it changes the properties/function of a protein/enzyme etc.
EXAMPLE: amyloid fibres are misfolded and become insoluble (normally soluble) and can then go on to form plaques in Alzheimers disease

Question 8

Explain why some amino acid residues are charged

Answer 8

Depending on whether an amino acid group (either carboxyl group or amide group) is protonated or deprotonated
If both groups are protonated, then only the NH3+ group has a positive charge (COOH is neural)
If both groups are deprotonated, then the COO- group has a negative charge (NH2 is neutral)
Zwitterionic form is where both are charged (COO- & NH3+)