Alpha helix - peptide coil held together by H-bonds between carbonyl of residue and amine residue
R-groups point away from helical axis
Carbonyls point all in one direction while all amines point in one direction opposite of carbonyls
Amphipathic - one side polar the other non-polar
There must be chemical compatibility within residues stacked on each other
Alternating polarity can be seen every 2-3 amino acid residues’ R-groups in a-helicies
Betasheets are extended compared to alpha helicies
Backbone of beta sheets zig-zag at tetrahedral alpha carbon
Beta sheets are also amphipathic
Anti-parallel beta sheet - One sheet will go from N-C terminal, the next will go from C-N terminal, and then N-C repeating pattern. 7 Armstrong. More strong compared to parallel due to co-linear H-bonds and dipole.
Parallel Sheet - pattern exhibits equal spacing between parallel residue groups (not backbones) 6.5 Armstrong. Less strong sheet.
This is an antiparallel beta sheet.
It is common to see two parallel beta sheets sandwiched together due to net dipole across sheets
Exterior unsatisfied H-bond beta sheet atoms achieve H2O interactions if on surface, if buried they will interact with other parts of protein (tertiary structure)
Hairpin connection - where connection between beta sheets re-enters on the same side where it left. Can be farther than adjacent beta sheets
Crossover connections - connection re-enters on the opposite side of beta sheet it left. Can occur farther than adjacent beta-sheets
Type I Beta turn - proline based at lower left (2) position.
Type II Beta turn - glycine based at upper left (1) position.
Both stabalized by intra-chain H-bonds
RNA ligase - glues & condenses pieces of RNA together
Peptide bonds are ~40% doublebond character and are limited to ~1.33 Armstrong
Psi: The rotation of the carbonylcarbon to the alpha carbon: at 180 when fully extended, and 75% of conformational space is inaccessible
Phi: The rotation as described between the alpha carbon and the nitrogen: at 180 degrees when fully extended
Proline has a very limited range of phi angles (35-85 degrees) due to its cyclic imimo structure
-dH is favorable and creates bonds
H-bond acceptors are lone pairs, donors are H’s attached to e neg atoms
The pitch of an alpha helix is the distance per turn ~3.6 amino acid residues (~5.4 Armstrong)
A ribbon consists of 3-4 pitches (~12 residues): phi = -57 degrees; psi = -47 degrees
On a ribbon, all R-groups stick out to avoid interference with backbone
No prolines can be found in a-helix (except for terminus) as their amine does not have an H for H-bonding and therefore causes kink in structure
Beta sheet residues are ~3.5 armstrong apart, and have ~7 armstrong pitches
You can tell the difference between a-helix and beta-sheet by looking at primary structure
PNPNPNP… will be likely a beta sheet (polar vs. non-polar)