3D, primary and secondary Flashcards
what kind of double bond do peptide bonds feature and why
partial double bond due to resonance
describe the length of the C=O bond in a peptide bond
longer than usual
describe the length of the C-N bond in a peptide bond
shorter than usual
what configuration are most peptide bonds in in proteins
trans
which bonds can rotate in an polypeptide
the ones attached to alpha carbons only, phi and psi
which atoms define torsion
central 2 and the 2 on either side
draw trans 180 newman conformations for phi and psi
see slide 13
why is L-proline restricted in rotation? which bond is this around?
phi bond restricted because cyclic side chain
what kind of bonds are found in regular secondary structure?
repeating phi and psi angles for sequential amino acids
what kind of H-bonding patterns do stable forms of secondary structures feature?
repeating
what are 3 examples of regular secondary structure
alpha helix, beta sheets, collagen helixes
what kind of bonds are found in irregular secondary structures
non repeating phi and psi angles
what are 3 types of irregular secondary structure
beta turns, coils, loops
what kind of twist is in the alpha helix
right handed
where are the H-bonds in an alpha helix
c=o of i and NH of i+4
where do the sidechains project in an alpha helix
away from core
what is the bond angle for phi and psi in an alpha helix
(-57,-47)
how many residues per turn of alpha helix
3.6
which R-groups from the primary sequence interact favourable in alpha helix
3-4 residues apart
what are atoms in the alpha helix backbone stabilized by
van der waals and H-bonding
which terminus in the alpha helix is negatively charged
C-terminus
which terminus in the alpha helix is positively charged
N-terminus
which direction is the C=O bonds pointing towards in an alpha helix
C-terminus
what is found at each end of the alpha helix
4 unpaired amino acids not involved in H-bonds
which amino acids are usually found ar the N-terminus of an alpha helix?
what about the C-terminus
glu and asp
lys and arg
which end of an amino acid would interact with phosphates or nucleotides
the N terminus
what are the 3 kind of beta sheets
parallel antiparallel mixed
what is phi and psi for parallel beta sheets
what is phi and psi for antiparallel beta sheets
(-120, +120)
(-140, +140)
what are beta sheets formed by
H-bonds between strands
what are the 2 types of situations involving strands for beta sheets
separated within primary structure or coming from different peptides
compare the repeat period for parallel vs antiparallel beta sheets
shorter for parallel
T or F: the hydrogen bonding pattern for antiparallel vs parallel beta sheets is the same
false
T or F: individuals strands in a beta-sheet always follow each other in the primary sequence
false
are beta sheets planar
no they are not planar
what can beta sheets twist into
saddle shapes or barrels
where are the H-bonds between in beta turns
C=O of residue 1 to NH of residue 4
what is the degree change in the direction of the polypeptide in a beta turn
180 degrees
how are the types of beta turns characterized
combinations of phi and psi angles
which amino acids are often found in beta turns
proline and glycine
what is always the third residue in a type II beta-turn?
why is this?
what is the name/ designation for this third residue?
glycine
geometry (80,0)
i+2
which amino acids have the highest propensity for alpha helix formation
ala glu and met
