Lecture 5 - elements of protein structure Flashcards
what is the primary structure of a protein
the linear sequence of amino acids that make up the polypeptide
what the secondary structure of a protein
the three dimensional arrangement of a protein chain over a short stretch of adjacent amino acid residues (includes a-helices and b-sheets
what is the tertiary structure of a protein
the three dimensional structure of a complete protein chain
what is the quaternary structure of a protein
- only some have this
interchain packing and structure for a protein that contains multiple polypeptide chains (e.g haemoglobin)
what are Phi bond angles
between the N and alpha carbon
what are Psi bond angles
between the alpha carbon and the C
what are omega chain angles
between the C and N, usually or very close to 180 or 0 degs
why do Phi and Psi angles have restrictions in their values
because of steric hinderance
what is the shape of an a-helix
main chain spirals around the central axis like a staircase
what is the non covalent interaction (hydrogen bond) between in an a-helix
between the carbonyl of N and N-H of residue N+4
what is the role of hydrogen bonds in the alpha helix structure
to provide stability
What is the range of values for phi and psi?
0 +/- 180 degrees
Can phi bonds twist?
yes
Can psi bonds twist?
yes
Can omega bonds twist?
no
Where are the side chains in alpha helices?
They point outwards to help stabilise the alpha helix
Which amino acid residues break the alpha helix pattern?
Glycine and proline
What exists in the aloha helix?
A dipole, positive at the N terminus
What is the beta structure comprised of?
Peptide chains with a more extended structure than the alpha helix. Each is called a beta strand (not stable on own)
What occurs between adjacent beta strands?
hydrogen bonding
how many strands are there per beta sheet
2-10
what are the two types of hydrogen bonding interactions in a B sheet
anti parallel and parallel
describe the parallel structure
The two strands run in the same direction but the hydrogen bonds aren’t parallel
describe the anti parallel structure
The two strands run in the opposite direction and the hydrogen bonds are parallel
Where are the side chains in beta sheets?
above and below
What are turns needed for?
to form globular proteins
what are turns often like
Short, hairpin like, involving 3 or 4 residues
What amino acids are in high amounts in turns?
Gly (flexibility) and Pro (rigidity)
