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Core Lectures > Determination of Protein Structure > Flashcards

Determination of Protein Structure Flashcards

1
Q

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

A

X-ray crystallography

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2
Q

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

A

Crystals

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3
Q

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

A

Over 90%

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4
Q

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

A

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

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5
Q

What have elucidating the structures of enzymes shown?

A

How biochemical processes are catalysed

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6
Q

What have elucidating the structures of virus particles shown?

A

How they assemble

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7
Q

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

A

How the proton gradient is used to make ATP

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8
Q

What can protein crystallography be used for?

A

Structure-based drug design, development and improvement

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9
Q

What happens when waves impinge on a body?

A

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

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10
Q

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

A

About the wavelength of radiation used

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11
Q

What do we want to resolve about molecules?

A

The distances between atoms

In Angstroms

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12
Q

What is 1 Angstrom equal to?

A

E-10 metres

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13
Q

When is the resolution limit reached?

A

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

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14
Q

What type of waves are needed to resolve atoms?

A

X-rays

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15
Q

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

A

Far too long

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16
Q

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

A

True

17
Q

What are X-rays scattered by?

A

Electrons and so heavier atoms with more electrons scatter more

18
Q

When were X-rays discovered and who by?

A

8th November 1895

Wilhelm Rontgen

19
Q

Do X-ray lenses exist?

A

No

20
Q

What is a crystal?

A

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

21
Q

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

A

E5 molecules in each dimension which is about E15 molecules

22
Q

What is the total scattering a sum of?

A

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

23
Q

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

A

The crystal lattice

24
Q

What does the fourier transform relate?

A

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

25
Q

Essentially, what does the fourier transform tell us?

A

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

26
Q

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

A

Phase information

27
Q

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

A

Molecular replacement
Multiple isomorphous replacement
Anomalous dispersion

28
Q

What can we calculate from diffraction data and phases?

A

Electron density to get an atomic model

29
Q

What can we calculate from an atomic model?

A

Electron density and from this diffraction data and phases

30
Q

What is the iterative process called?

A

Refinement and rebuilding

31
Q

What can the difference/omit map be used for?

A

Finding ligands

32
Q

What affects resolution?

A

The maximum scattering angle observed for the data

33
Q

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

A

Using a Ramachandran plot

34
Q

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

A

True

35
Q

How are protein crystals generated?

A

By removing the protein very slowly out of solution

36
Q

What factors affect protein solubility?

A

Concentrations of salt/precipitate
pH
Temperature

37
Q

Name a method for obtaining crytals

A

Vapour diffusion

38
Q

Crystals are easy to grow, true or fasle?

A

False, they need many different conditions testing and optimising

39
Q

What are the mechanics of X-ray data collection?

A

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

Core Lectures (13 decks)

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