Secondary structure Flashcards
What is secondary structure?
The regular conformation and H bonding arrangement in a local part of the polypeptide peptide (close in sequence)
What are the 2 regular secondary structures?
Alpha helix and beta sheet
What are the 2 irregular secondary structures?
Beta turns and loops
What is the handedness of the turn in an alpha helix?
Right handed
What is the H bonding pattern in an alpha helix?
i to i+4 (C=O at position 1 to NH at position 5)
Which direction do the side chains project in an alpha helix?
Away from the core
How many amino acids per turn are there in an alpha helix?
3.6
How many angstroms per turn are there in an alpha helix?
5.4
What does a lower helical propensity number indicate?
It is more favourable for an amino acid to be in an alpha helix
What is the most favourable amino acid to be in an alpha helix?
Alanine
What are the least favourable amino acids to be in an alpha helix?
Proline and glycine
Why is it unfavourable for proline to be in an alpha helix?
The backbone NH can’t H bond because of the proline side chain, so the gets disrupted and destabilized
Why is it unfavourable for glycine to be in an alpha helix?
It has so much conformational flexibility that it is unfavourable to have it stuck in one conformation
Which side chains will interact in an alpha helix?
i, i+3 and i+4
What is the helix dipole?
The cumulative effect of all the peptide bond dipoles so the N terminus end of the helix is partially positive and the C terminus is partially negative
How does the helix dipole affect which amino acids make up the helix?
More favourable for positive amino acids to be near the C terminus and negative amino acids to be near the N terminus
What are the 2 types of beta sheets?
Parallel and antiparallel
What is a parallel beta sheet?
Adjacent strands run in the same direction
What is an antiparallel beta sheet?
Adjacent strands run in opposite strands
Where are the side chains in a beta sheet?
Above and below the backbone
Which side chains in a beta sheet will interact?
i and i+2
What sort of connecting structures will connect polypeptide chains parallel beta sheets?
An alpha helix
What sort of connecting structures will connect polypeptide chains antiparallel beta sheets?
Loops and turns
What is the handedness of the turn when a beta sheet is twisted into a beta barrel?
Right
Which amino acids are often found in beta turns?
Glycine and proline
Why is proline so good to have in a beta turn?
It can form a cis peptide bond that allows for a really tight turn (cis peptide bonds are still pretty rare)
Where in a protein are beta turns usually found?
On the outside, so the backbone can hydrogen bond with the water
Which enzyme catalyzes the formation of a cis peptide bond?
PPI (peptidyl prolyl cis-trans isomerase)
