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Structural Biology > Protein Crystallography > Flashcards

Protein Crystallography Flashcards

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1
Q

Why is xray crystallography used

A

X ray has similar wavelength to atom
Mirrors in microscope can’t bend x rays as easily as light

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2
Q

What is the process of xray crystallography

A

Can model protein structure using electron density map

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3
Q

What is an atom

A
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4
Q

What is a molecule

A
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5
Q

What is a crystal

A

Crystals arranged in repeat units in 3D
Molecules within crystals
Nucleus small relative to electron clouds

X ray crystallography exploits interaction of x rays with electrons

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6
Q

How can you “ see” crystals molecular structure

A
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7
Q

What is an X ray
What is an EM wave

A

An EM wave is an oscillating electric (E) and magnetic (M) field
E and B oscillate at right angles to eachother and to direction of travel

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8
Q

What is diffraction and how can it be used to view crystals molecular structure

A
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9
Q

What is meant by oscillation *

A

involves repetitive motion that occurs at regular intervals

refers to any repetitive variation, typically in time, of some quantity around a central value or between two or more different states

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10
Q

What is the two slit experiment *

A
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11
Q

What is the volume + shape of a molecule defined as

A
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12
Q

What is an electric field

A
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13
Q

What happens when an electron is exposed to xrays

A
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14
Q

What is radians

A

radians are a unit of angular measurement commonly used to describe the angles involved in the diffraction pattern of X-rays as they scatter off a crystal lattice

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15
Q

What are sine waves

A

The sine wave starts at 0 when t=0, assuming no phase shift.
It oscillates between
+A and −A, producing a smooth, continuous curve.
It repeats after a period T, where T= 2 (pi)/ω

​

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16
Q

What is a cosine wave to

A

A cosine wave is another periodic wave, closely related to the sine wave, and is described by the equation (top of image )

Sine and cosine waves are identical but are out of phase by a quarter of a cycle

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17
Q

What is the phase angle of a wave

A

Phase (or phase angle): at a given position in space (x), the phase indicates the
position in the wave cycle (e.g. crest, trough or some intermediate part)

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18
Q

What are phase angles measured in

A
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19
Q

What are the properties of waves

A
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20
Q

Have can waves be added together (different types of interference )

A

For constructive interference:
Add the two amplitudes of the two waves to get new wave

Destructive interference:
Amplitude of new wave is zero when the two waves are added together

Intermediate interference:
Amplitude of new wave is less than the 2 amplitudes of the added waves added together

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21
Q

Which xrays are detected in x ray crystallography ( and why are two waves that were previously in sync before hitting 2 elections, no longer in sync)

A
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22
Q

What are the 2 ways to represent phase shift using vectors

A

Path difference vector
Scattering vector

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23
Q

How can phase shift be represented using vectors and how is path difference calculated

A
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24
Q

What is a scattering vector

A

Magnitude and direction of S contain information about l and the scattering angle (θ).
• At fixed l (typical in our experiments), |S| varies only with θ
• Key point: |S| is a convenient way of representing (encoding) the angle of scattering
• Note: S does not point in the direction of scattering (but we can use it to work out 2θ)

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25
Q

What is the general wave equation

A
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26
Q

What is the wave equation using complex numbers

A
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27
Q

What is the wave equation concerning phase shifts only

A
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28
Q

What is the wave equation when considering resultant wave

A
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29
Q

What is the equation when considering multiple electrons that all scatter waves at 2 radians

A
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30
Q

What is the equation for each scatterred wave in a molecule

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31
Q

What would angles of 2 radians result in

A
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32
Q

What would other angles result in

A
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33
Q

What percent of x rays are scattered by a crystal and why

A
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34
Q

How can an intensity reading be obtained for each diffracted ray

A
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35
Q

Why do you need to know the structures of proteins

A
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36
Q

How are x rays scattered by two electrons

A
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37
Q

How are x rats scattered by a single e-

A
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38
Q

What is the path difference and phase difference

A
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39
Q

What does the phase difference depend on

A
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40
Q

What is the equation for the resultant wave

A
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41
Q

How is scattering measured for more than two electrons

A
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42
Q

what is the structure factor

A
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43
Q

What is the function for electron density

A
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44
Q

What happens when an xray is applied to a molecule

A
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45
Q

What is the equation for each scattered wave from a molecule

A
46
Q

What is the equation for the structure factor for a multi electron system

A
47
Q

What is the equation for the structure factor for a protein

A
48
Q

What is the equation for the structure factor for a molecule

A
49
Q

What is the inverse Fourier transform

A
50
Q

What are the advantages of using crystals in x ray crystallography

A
51
Q

How are crystals organised

A
52
Q

What can scattering from a unit cell be considered as

A
53
Q

How does reflection from a mirror work

A
54
Q

How does reflection from a semi transparent layer of molecules work aka layers in crystals

A
55
Q

How do x rays go through crystals

A

Add all of the waves from all of the layers that have the same angle and are in phase ( so maximum amplitude signal )

56
Q

What is braggs law

A
57
Q

Why does destructive interference not obey braggs law

A
58
Q

Why does destructive interference not obey braggs law

A
59
Q

What do the dark spots on a x ray diffraction image mean

A
60
Q

Why are the signals more distinguishable when crystals are used compared to a single molecule for x ray crystallography

A
61
Q

Why is there first order diffraction for x ray crystallography*

A

First-Order Diffraction: For first-order diffraction,
n=1. This means that the path difference between X-rays scattered by adjacent planes of atoms must equal one wavelength. This leads to constructive interference and results in the first-order diffraction pattern observed.
Intensity and Structure Factor: The intensity of the diffracted X-rays is also influenced by the arrangement of atoms in the unit cell of the crystal, described by the structure factor. The first-order peaks are typically the most intense and informative for determining the crystal structure.

62
Q

How are all possible rotations recorded for x ray crystallography

A
63
Q

What is the first step for growing protein crystals

A
64
Q

Compare natural vs recombinant sources of proteins

A
65
Q

What are the pros and cons of using e. Coli in recombinant technology

A

Proteases used to cleave tag

66
Q

How can proteins be made more crystallisable

A
67
Q

What is the second step for growing crystsls

A
68
Q

Name the techniques used to grow crystals

A

Vapour diffusion- sitting drop
Microbridge
Hanging drop
Microdialysis
Microfluidics
Liquid cubic phase plate crystallisation

69
Q

Explain the sitting drop method of growing protein crystals

A
70
Q

Explain the microbridge method of growing protein crystals

A
71
Q

Explain the hanging drop method of growing protein crystals

A
72
Q

Explain the LCP plate method of growing protein crystals

A
73
Q

Explain the microfluidics method of growing protein crystals

A
74
Q

Explain the microdialysis method of growing protein crystals

A
75
Q

Explain the theory of crystallisation

A
76
Q

What possible results could you get from vapour diffusion

A

Crystal formation
Micro crystal formation
No crystals formed

77
Q

When would crystal formation occur

A

when a protein solution becomes supersaturated, meaning there is more protein in solution than can remain dissolved at equilibrium. This supersaturated state promotes the aggregation of protein molecules in an ordered, crystal-like arrangement

requires a stable temperature to maintain supersaturation without inducing too rapid aggregation, which could lead to precipitation rather than orderly crystal growth

78
Q

When would micro crystal formation occur

A
79
Q

When would no crystal formation occur

A
80
Q

How can crystal formation be optimised

A
81
Q

What are the properties of crystals

A
82
Q

How can a model for the protein structure be built

A
83
Q

Why is high resolution data important

A
84
Q

Why is knowledge about ideal stereochemistry important for building models on protein structure

A
85
Q

What are the different ways to refine a protein structure model

A

Positional refinement
Temperature factor (B factor) refinement
Adding bound water molecules

86
Q

What is positional refinement (in refinement of protein structure models)

A
87
Q

What is the B factor

A
88
Q

What is temperature factor (B factor) refinement (in refinement of protein structure models)

A
89
Q

Why is bound water molecules added to refine protein structure models

A
90
Q

How is refinement of protein structure models done

A
91
Q

What should each refinement macro cycle consider

A
92
Q

What percentage of the human genome codes for membrane proteins

A
93
Q

Why are membrane proteins important

A
94
Q

Give some examples of membrane protein related diseases

A
95
Q

How are membrane proteins removed from the membrane

A
96
Q

What are the different types of detergent

A
97
Q

What are the 3 ways to crystallise membrane proteins

A

Protein-detergent complex
Addition of lipid extract
Liquid cubic phase

98
Q

Explain the protein-detergent complex method of membrane protein crystallisation

A
99
Q

Explain the addition of lipid extract method of membrane protein crystallisation

A
100
Q

Explain the lipidic cubic phase method of membrane protein crystallisation

A
101
Q

What are three different ways of protein engineering (for unstable proteins )

A

Stabilisation by random mutagenesis
Scaffolds
Fusion proteins

102
Q

Explain the scaffolds method of protein engineering for unstable proteins

A

Eg can be done using antibodies or nanobodles

103
Q

How can antibodies be used to isolate protein of interest (an example of scaffolds)

A
104
Q

What are nano bodies

A
105
Q

How can fusion proteins be used in protein engineering for unstable proteins

A
106
Q

How is x ray diffraction of the protein crystals done

A
107
Q

How is data collected for membrane protein diffraction

A
108
Q

What is isotropic and anisotropic diffraction

A
109
Q

What is the new crystallography technique

A
110
Q

How can antibodies be used as scaffolds to increase the number of crystal contacts

A

Structural Biology (8 decks)

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