Determination of Protein Structure Flashcards Preview

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Flashcards in Determination of Protein Structure Deck (39):
1

What is the primary technique for determining 3D structures, ranging from salt to whole virus particles?

X-ray crystallography

2

What form does the sample need to be in for X-ray crystallography?

Crystals

3

What proportion of structures in the PDB archive has X-ray diffraction techniques solved?

Over 90%

4

Give examples of the achievements of crystallography in the last 50 years

The structure of DNA has shown how genetic information is stored, replicated and used
Cro repressor-operator complex shows how proteins can interact with DNA and control the regulation of gene expression

5

What have elucidating the structures of enzymes shown?

How biochemical processes are catalysed

6

What have elucidating the structures of virus particles shown?

How they assemble

7

What have elucidating the structures of proton-translocating ATPase shown?

How the proton gradient is used to make ATP

8

What can protein crystallography be used for?

Structure-based drug design, development and improvement

9

What happens when waves impinge on a body?

They are scattered and converted into an image by means of a lens

10

Using waves for large objects works fine but what are they limited to?

About the wavelength of radiation used

11

What do we want to resolve about molecules?

The distances between atoms
In Angstroms

12

What is 1 Angstrom equal to?

E-10 metres

13

When is the resolution limit reached?

When two point-like objects can not be imaged as two distinct images

14

What type of waves are needed to resolve atoms?

X-rays

15

Is visible light far too long or short to resolve atoms?

Far too long

16

X-rays interact with matter weakly, true or false?

True

17

What are X-rays scattered by?

Electrons and so heavier atoms with more electrons scatter more

18

When were X-rays discovered and who by?

8th November 1895
Wilhelm Rontgen

19

Do X-ray lenses exist?

No

20

What is a crystal?

A repeating ordered array (LATTICE) of molecules in 3D in which the molecules are identically oriented

21

How many molecules will a typical protein crystal of 0.3mm in each direction have in each dimension?

E5 molecules in each dimension which is about E15 molecules

22

What is the total scattering a sum of?

The individual scatterers, or one thousand million million times stronger than the individual molecule

23

Scattering from a crystal is concentrated in discrete directions determined by what?

The crystal lattice

24

What does the fourier transform relate?

Te sum of all the reflections to the electron density at all points in the crystal repeating unit

25

Essentially, what does the fourier transform tell us?

What mixture of sine-waves is required to make up any function

26

What information about a wave is needed for the fourier transform?

Phase information

27

What techniques can you use to get phase information of a wave?

Molecular replacement
Multiple isomorphous replacement
Anomalous dispersion

28

What can we calculate from diffraction data and phases?

Electron density to get an atomic model

29

What can we calculate from an atomic model?

Electron density and from this diffraction data and phases

30

What is the iterative process called?

Refinement and rebuilding

31

What can the difference/omit map be used for?

Finding ligands

32

What affects resolution?

The maximum scattering angle observed for the data

33

What is the primary way that stereochemistry of a model can be assessed?

Using a Ramachandran plot

34

Protein crystals need to be obtained gently, true or false?

True

35

How are protein crystals generated?

By removing the protein very slowly out of solution

36

What factors affect protein solubility?

Concentrations of salt/precipitate
pH
Temperature

37

Name a method for obtaining crytals

Vapour diffusion

38

Crystals are easy to grow, true or fasle?

False, they need many different conditions testing and optimising

39

What are the mechanics of X-ray data collection?

The crystal is oscillated about a small angle and the resultant diffraction recorded