Elements of Protein Structure Flashcards
Define primary protein structure
amino acid sequence of a protein
Define secondary protein structure
local 3D arrangement of a protein chain over a short stretch of an adjacent amino acid residues
Define tertiary protein structure
3D structure of a complete protein chain
Define quaternary protein structure
interchain packing and structure for a protein that contains multiple protein chains
what are key properties of the alpha helix?
- main chain spirals around the central axis like a spiral staircase; right-handed spiral
- H-bond is found between the carbonyl residue “n” and the N-H of residue “n+4”
- side chains point out from helix axis; help stabilise the helix
- stabilising H-bonds, 12-28kJ/mol
- some residues break the helix (eg. glycine and proline)
- helix dipoles exist (+ve at N terminus)
- 3.6 residues/turn; 5.4A rise/turn; d = 1.5A/residue
what are the key properties of the beta sheet?
- H-bonding occurs between adjacent strands (chains)
- Adjacent strands form a beta sheet with equal to or more than 2 strands
- Each strand may contain up to 15 residues
- typically 2-10 strands per sheet
- Average strand length ~6 amino acid residues
- Two types of rotation: parallel or antiparallel
- extended, pleated
- ‘sheet’ vs. ‘strand’
- sheets not planar, pleated with R-handed twist
- side chains point above and below the sheet
- any NP-P-NP-P stretches of residues will commonly form a beta strand
what are the key properties of turns?
- needed to form globular proteins
- often short, hairpin like and involve usually 3-4 residues
- high Gly and Pro content
- almost 30% of protein residues are turns
- H-bond across the turn is common
- type I and type II are common types of turns, and there are more than 16 types
what are the roles of side chains in proteins?
- varied chemical properties between amino acids
- perform the chemistry needed to carry out the protein’s biochemical reactions
Four different groups of amino acids based on side chains:
- Non polar
- Polar (uncharged)
- Polar (charged) acidic (-ve)
- Polar (charged) basic (+ve)
what are the two exceptions to the non-polar side chains group?
Proline: R-group bonds back to main side chain N, imino acid, rigid, almost in a group by itself
Glycine: R-double bond-H, non-chiral, flexible, almost in a group by itself
What is the definition of pKa?
The pKa value of an ionisable group on an amino acid or protein is the pH at which the group is 50% ionised
What are the amino acid post translational modifications?
- Phosphorylation (used to control enzyme activity - On/Off switch)
- Hydroxylation (needed to prevent connective tissue diseases and scurvy, often proline and lysine involved)
- Carboxylation (needed for blood clotting, often glutamate involved)
- Metal Binding
- Iodination
- Glycosylation
- Many others
Describe the properties of the peptide bond
- Planar (maxiises pi bonding overlap)
- Dipole
- Predominantly trans
- Rotational barrier of ~80kJ/mol
describe the flexible bonds that protein structures contain
- Main chain atoms in a protein are N, alpha C and C’
- Bond angles between N and alpha C are called phi
- Bond angles between alpha C and C’ are called psi
These angles take on values ranging from 0 to +/- 180 degrees - The chain angle between C’ and N is called omega and is usually very close to 0 or 180 degrees (the angle of rotation around the peptide bond/main chain angle is the omega angle)
This is one way that a proteins structure can be described
Describe the Phi-Psi limitations
Phi-Psi angles have limitations in their values due to steric hinderance
- Phi rotation can lead to O - O collision
- Psi rotation can lead to NH - NH collisions
Many limits are possible for these rotations
Describe the H-bonds between parallel and anti-parallel strands of a beta sheet
Parallel: H-bond lines are not straight up and down, they are on a slight angle
Antiparallel: H-bond lines are straight up and down (parallel)
