niche L 13 and 14

what is the pattern of scattering in X ray diffraction dependent on

symmetry

which type of protein structure determination method allows you to do electron microscopy in a cell

cryoelectron microscopy

• thinly slices the cell so electrons can flow through

what does the variation of local structure that doesnt break the covalent bond structure correspond to

changes in conformatioin

what is the “sheet region” for phi and psi angles, what else is in this range

-60 < phi < -180

30 < psi < 180

collagen

where is the helix region found in phi and psi angles, and what type of helices is this

-30 < phi < -180

-30 < psi < -90

alpha, 310, and pi helices

all right handed

what is the left handed alpha helices phi and psi region

30 < phi < 60

30 < psi < 90

what are the H bonds bonding to between amino acids in alpha helices and in what direction is the H pointing? which one is further down to the C terminus

amide CO (i) and amide NH (i+4)

H is pointing up towards CO and N terminus

the amide NH group is further down

are there voids in the alpha helix (holes)

no, optimum packing

what do the terminal 3 residues on an alpha helix do since they cannot form a hydrogen bond with another amino acid on the helix

either capped with H bonds provided by side chains within the helix or by water

what type of shape does the B sheet bave

pleated shape

• kind of goes up and down like a hill

what are the two types of dominant reverse turns and how are they distinguished

type 1 and 2

distinguished via orientation of peptide bond between residue 2 and 3

why is glycine used in residue 3 for type 2 and why is proline often used as residue 2

glycine → steric issues

proline → stability

what are most commonly connected by reverse turns, what about loops or helices

reverse turns → antiparallel

loops or helices → parallel

what type of structures form motifs

secondary

are motifs associated with a specific function or no

many are

can proteins have multipel sheet motifs

yes, ribonuclease has 3 BBB and 1 BB

what are the amino acid characteristics for a keratin, b keratin, and collagen

a keratin → rich in cysteine

B keratin → Gly -X - Gly 0 X where X is alanine or serine

collagen → G - X - Y where X is proline and Y is oftern hydroxyproline

where is B keratin typically found in

silk fibers and in reptilian hair, claws, horns, and beaks

what does the B sheets of B keratin stack to form

microcrystalline arrays

what is a popular variation to the affinity chromatogrpahy

one takes advantage of the ability to express a gene that codes for the protein with the tail of His6

what do you elute the target protein in affinity chromatography with

high concentration of imidazole