L5 & L6 - protein structure Flashcards
are naturally occurring AAs L or D?
L
how do you determine whether an AA is D or L?
CORN rule
H towards you
characteristics of amide bond
no rotation around C-N
C-N and close surrounding atoms lie in plane
electrons from C=O delocalise into the C-N
why is there no rotation around the C-N peptide bond
electrons from the C=O delocalise into the C-N making it a partial double bond
characteristics of a Carbons in a polypeptide
they are trans
a carbons of adjacent amino acids are on opposite sides of the peptide bond to avoid clashing
what atoms in a polypeptide helix H bonds
the O from the C=O bond and the H from the N-H
are most biological helices right or left handed and why?
right, because they are made from L AAs
what does a right handed helices mean?
they turn to the left whilst going up (imagine spiral stairs where your right hand is on the outside wall)
the ‘backbone’ is thee hand rail
are antiparallel or parallel B sheets more stable and why?
antiparallel, the O and H from the C=O and N-H groups line up better
what are the 3 main types of 2ndary structure
a helix
B pleated sheet
B turn / reverse turn
what is a B turn ( / reverse turn)
consists of 4 AAs where each rotates 180° to form a circle
what holds 2ndary structures together
H bonds
what is a polypeptides tertiary structure
combination of a helices B pleated sheets B turns and straight chain regions forming a 3D shape
what holds tertiary structure together
H bonds ionic R group interactions disulfide bridges (cysteine) VDW forces hydrophilic and hydrophobic interactions
define steric clash
angles of phi and psi that will cause a clash of the pp chain
what is the Ramachandran plot
a plot that shows the regions of phi and psi that are allowed
two different regions for a helix and B sheet
how many residues per turn of the a helix
3.6
what AA cannot be in an a helix??
proline
list possible super secondary structures
B barrel
a helix bundle
B sandwich
rossman fold
describe B barrel and why it forms
- B sheets have a slight twist (due to side chains and handedness of AA
- a B sheet with more than 8 strands can form a barrel
- this forms more H bonds making more stable
example of substance with B barrel
GFP
what is an alpha beta barrel
B barrel with a helices around outside
what is four helix bundle
4 helices wind round eachother
what is the rossman fold
super secondary structure
alternate B - a - B motifs
what is B sandwich
2 B sheets laying flat
what is quaternary structure
when a protein has more than one pp chain eg haemoglobin
give the 2 structural motifs used by proteins to span membrane
why are these the only 2 that can spam the membrane
helices
B barrel
any others would leave the Hphilic backbone exposed to the lipid bilayer
