crystallography Flashcards
what is the storage form of DNA in chromatin
a long piece of DNA wrapped around a histone octamer
a beta 1 - 42
peptide that form fibres and is deposited in plaques in the brains of those with Alzheimers disease
- structure was determined via solid state NMR
optical microscope vs impossible xray microscope
optical microscope
lens recombine scattered visible light to reconstruct image
x rays shone onto a crystal
refracted beams
but can only measure intensity of waves = amplitude
phase info about relative time of arrival at the detector is lost
there cannot form an image
no lenses capable of focusing x ray
analytical procedures
comp calculations = phase info
then can construct electron sensitive maps
can put electron models = structure
cannot measure phases
can amplitude
phases contain bulk of structural info in image formation in X-ray crystallography
but all we can do is collect amplitudes
amplitude is hight of wave above mean
x rays
why do e use ansgstroms in crystallography
high frequency
energetic
good penetrating power
electromagnetic radiation w short wavelength
1A = 10 to the minus 8 cm
0.1nm
close to the distances between bonded atoms C-C = 1.5A
x ray diffraction
- must produce crystals of the protein or fibres = difficult - protein crystals made by repetition of a unique block many times into a strict lattice
unit cell hs to be repeated by translation in all dimensions
alll unit cells oriented in same way = 3d block
proteins highly solvated in the crystal
texture of cheesee crumble under manipulation
a static image is produced which is the average of all the molecules which we presume are all the same in the crystal to determine atomic positions
the phase problem associates with the way that we measure the diffraction data
any size protein
as small as sodium chloride and as big as 12 kDa
drug discover - can produce imaged of binding sites for ligands
bimolecular techniques to look at what?
DNA and replicate enzymes and catalysis virus organisation nucleosomes and DNA storage Ribosomes and protein synthesis Receptors and signalling Antibodies ion channels photo reaction centre chaperones transcription factors
b dna
hydrated form of DNA
calculate how much solvent is likely to be in a crystal
crystal solvent content
V = 1 / ( 1.23M / (V/Z) )
v = solvent content
M = molecular weight of protein V = vol of unit cell = x x y x z Z = no of protein molecules in unit cell
10% 90 %
early stage check check its sensible
how do the spots on diffraction patterns arise?
x rays interact w atoms scattered by cloud electrons waves shoot of in all directions most goes str8 through due to diffraction by electron cloud disperses rays over a significant anlgle scattered waves interfere w each other constructive and destructive
depending on symmetry of the atom
constructive interference
amplitude doube
phase is same
and destructive
annihilate each other - no signal
braggs law
n lambda = 2d sin theta
where theta = angle of incidence
d = distance
tells us when u get a diffraction spot occurring
stops considered existing as planes in a crystal
diffracted waves from planes of atoms one produce constructive interference when their path difference is an integral number of wavelengths
Ewald sphere
constructive interference only occurs as reciprocal lattice points pass through the sphere
after diffraction occurs
diffraction spots exist on an inverse lattice
edge a in real unit cell = length of reciprocal lattice = 1/a
Fourier transformations
enables dissection or construction of complex wave forms from simple constituents
the diffraction pattern of an object is its Fourier transform
enables domain inversions
from real space to diffraction space
=1/distance
time to frequency 1/time in NMA
optical diffraction patterns stimulate Fourier transforms
lattice sampling of the molecular transform
small spacings between molecules give wide spacings in the diffraction pattern
big spacings put spots close together
in the diffraction pattern
in a salt crystal - very spread not many of the
compete data set captured in shorter time
measuring intensity of acc spot bit easier