Lecture 2 Flashcards
What levels of protein structure are there? What helps to create these different levels?
Primary:single letter code for protein
Secondary: 3D conformation of local amino groups
Tertiary: The 3D structure of the whole protein
Quarternary: The interacting pf multiple tertiary structures (multiple polypeptides interacting to form a single protein).
These different levels are created by rotation of the protein main chain and side chain bonds, there are four angles, given by the greek angles psi, chi, omega and phi.
What angle is fully extended and which is in the same plane?
fully extended = 180 degrees (180 and -180 are both fully extended, just in different directions), in the same plane is 0 degrees).
What bonds do each greek letter refer to?
phi: central carbon with nitrogen
psi: central carbon with terminal carbon
omega: nitrogen with terminal carbon
chi: central carbon with side chain and all bonds within that side chain, numbered from central carbon outwards.
What restricts the possible bond angles? What graph shows possible bond angles?
steric hindrance, phi = O-O, psi = NH-NH collisions. a Ramachandran plot catalogued these collisions, showing the possible bond angles.
What arrangement are chi angles normally in?
Staggered arrangement to minimize steric hindrance.
Where do X angles cluster?
Chi angles cluster in sterically free regions.
What are the two main secondary structures?
alpha helixes and beta strands.
What are the key properties of alpha helixes? Are they the only helix type? Give an example of another
3.6 resolutions per turn (5.4 angstroms)
Phi and Psi angles of roughly -50 degrees, psi is lower.
distance of 1.5 angstroms per residue
Side chains point out
Dipoles are present and some residues are common helix breakers (glycine and proline).
Stabilised by hydrogen bonds from the carbonyl carbon oxygen and nitrogens hydrogen.
There are other helix types, e.g polyprolinestabilised by steric hindrance.
What are the beta structures? What key properties do they have?
Beta strands and beta sheets. a sheet is made up of two or more beta strands (typically 2-10), created by hydrogen bonding of adjacent peptide chains (strands), each of these strands may have up to 15 amino acids (in the direction N-C) with an average length of 6, and the sheets may have strands arranged either parallel or antiparallel.
They are extended but pleates and the sheets are not planar, the side chains point above and below the sheet. An alternating pattern of non polar and polar amino acid sequence normally indicates a beta strand.
What is the difference between the hydrogen bonding between parallel and antiparallel beta strands?
parallel are more oblique to the strands as the hydrogen bonding regions don’t line up exactly, the antiparallel are more perpendicular.
What are the turn key properties and types? What is the difference between the types?
Sharp, hairpin like, typically involving 3 or 4 residues with a high glycine and proline content, can possibly be up to 30% of the protein’s residue content, hydrogen bonding across the turn is common and there are more than 16 types, but the main ones are type I and type II.
Type I has a straight down dip while type II is more straight (still has a slight dip).
What are the regions of the Ramachandran diagram?
slightly below middle left: alpha helix right handed
top left: parallel beta sheet in the bottom right of the top left area, anti parallel in the top left.
upper middle right: collagen
This assumes psi is on the left, increasing in value towards the top and that phi is on the bottom. increasing in value towards the right
