MCB Lecture 6-7 Protein Structure Flashcards
Which groups must form hydrogen bonds?
Polar groups must form hydrogen bonds
Describe hydrogen bonding in proteins (h-bonds are between which atoms?)
Hydrogen bonding occurs between NH & C=O of two different residues
Compare hydrogen bond length and with that of VDW interactions
H-bonds are shorter and allow the protein to pack more closely together than VDW interactions would allow.
What are the three possibilities in terms of hydrogen bonding between different groups?
- Backbone - Backbone
- Backbone - Residue
- Residue - Residue
What is a feature of secondary structure of protein?
Regular dihedral angles of the residues
Why have secondary structure in proteins?
Secondary structure allows close packing of the peptide, and increased stability
What are the dihedral angles in Beta sheets?
Phi: -130
Psi: +130
Between which two residues can beta sheets form?
Any two within a peptide
i and j
Differentiate between beta sheets and beta strands
Individual beta strands make up a beta sheet
How do hydrophobic faces of the beta sheet arise?
Side chains point directly up and directly down alternatively.
By having an alternating sequence of hydrophobic and hydrophilic side chains, all the hydrophobic ones will be on one side of the sheet.
Differentiate between anti-parallel and parallel, as well as pure and mixed beta sheets
Anti parallel sheets: n termini are at different ends
Parallel: n termini are at the same end
Pure: sheet is made up of only parallel or anti parallel strands
Mixed: there are examples of parallel and anti parallel in the sheet
What is a beta-barrel?
A beta barrel is a structure that forms when the beta sheets curve round to form a barrel.
Hydrophobic side chain project into the cavity of the barrel
Hydrophilic side chains project out into the solvent
What are the dihedral angles in alpha helices?
Phi: -57
Pi: -47
What are beta-sheet twists? What are the two types?
When the plane of the sheet is contorted.
This is really common
The two types are left handed and right handed twists
Describe the handedness of alpha helices
Alpha helices are right handed.
Even when turned upside down, the handedness doesn’t change
Between which two residues do alpha helices form
NHi and C=O i-4
There are three residues between the two that form hydrogen bonds