proteins 1

Question 1

proteins are macromolecules

Answer 1

• they are AA polymers
  -• They form from 1 or more polypeptide chain
  • Amino acids vary in their physiochemical properties

Question 2

proteins fold in 3D

Answer 2

• Function depends on 3D structure
• Conformation depends on the aa sequence
• Sequence is determined genetically

Question 3

primary structure

Answer 3

The primary sequence is simply the order in which amino acids have been linked together to make a peptide or protein
The direction is important:
- by convention protein sequences are written from the N-terminal end towards the C-terminus
- this is the same order in which they are synthesised

Question 4

secondary structure

Answer 4

• proteins fold up in three dimensions to maximise their stability (minimise free energy)
• folding starts while the polypeptide is being synthesised.
• repeated structures, termed secondary structure maximise the formation of stabilising interactions (hydrogen bonds)

Question 5

tertiary structure

Answer 5

Proteins fold into defined shapes, or structures. Secondary structure elements fold together into motifs and domains.
A specific sequence will tend to fold into a specific 3D structure – we usually talk about the structure of albumin. However, it is important to remember that:
- proteins can adopt multiple conformations (shapes), often related to their function (think “molecular machines”)
- even if they have a single main conformation, proteins are flexible, with the extent of movement related to temperature

Question 6

quaternary structure

Answer 6

number and arrangement of multiple polypeptides.
Functional proteins are often formed from more than one polypeptide
In other words, they are oligomeric complexes
The component proteins can be similar in structure and function

Question 7

motifs

Answer 7

Secondary structure elements can combine into larger units (“motifs”). These are secondary structure elements linked in specific combinations by loops .

Some motifs have specific roles (e.g. DNA binding), but most are found in a wide range of functionally unrelated proteins

Question 8

domains

Answer 8

Polypeptides greater than ~200 aa usually contain multiple 3° “domains”
These often serve as independent functional units

Question 9

many proteins are ‘modular’

Answer 9

Some motifs have specific roles (e.g. DNA binding), but most are found in a wide range of functionally unrelated proteins

domains act as ‘scaffolds’, loops offer functional variability

Question 10

protein complexes

Answer 10

• Most cellular proteins (>~100kDa) are oligomeric (>1 polypeptide chain). e.g. the average oligomerisation state in E. coli is four

• if an oligomer contains identical polypeptides, it is a homo-oligomer
• is an oligomer contains non-identical polypeptides, it is a hetero-oligomer
  • A protomer is the smallest distinct unit in a complex (e.g. haemoglobin is a dimer of  protomers

Question 11

spatial arrangement

Answer 11

Polypeptide subunits in oligomers associate with a specific geometry (quaternary, or 4° structure)
• In many cases subunits are symmetrically arranged
• They show rotational symmetry