Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Y2S2 - Adv. Molecular Biology > MolBio2 - 45 > Flashcards

MolBio2 - 45 Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
1
Q

Define K-off[AB]

A

Rate of dissociation of AB into A+B

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Define K-on[A+B]

A

Rate of association of A+B into AB

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Define protein interaction equilibrium

A

Association rate = dissociation rate; K-on = K-off

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Define the protein interaction equilibrium constant

A

K-on / K-off

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

List 5 major methods of protein binding detection

A

ELISA, PAGE, Western Blot, Far Western Blot, Surface Plasmon Resonance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What does ELISA stand for?

A

Enzyme-linked immunosobrent agent

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What does PAGE stand for?

A

Poly-acrylamide gel electrophoresis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is surface plasmon resonance also known as?

A

Biacore

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Draw how Biacore works

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Describe how surface plasmon resonance works.

A

Bait molecule added to gold film by flexible tether, and inserted. Solution of prey molecules passes by, binding to some bait molecules. Binding causes measurable alterations in the plasmon resonance field.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is plasmon resonance?

A

Magnetic field close to the gold strip, setup by incident light

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What are the 2 key disadvantages to surface plasmon resonance?

A

Tether can block binding site, gold can affect the bait protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

List 4 methods of protein structure detection

A

Circular dichroism spectroscopy, x-ray crystallography, NMR, EM

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is circular dichoism?

A

Profile of the differences in absoprtion of left and right-handed polarised light

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What does CD stand for?

A

Circular Dichroism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What spectral region of CD reveals protein secondary structure?

A

Far-UV - 190-250nm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What three types of protein secondary structure are there?

A

Beta-pleated sheet, alpha-helix and random coil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What does CD spectroscopy tell us about proteins?

A

% proportion of each kind of secondary structure, but no information on arrangement

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What spectral region of CD reveals protein teriary structure?

A

Near-UV - 250-350nm

20
Q

What particular signals are shown on teriary structure CD spectroscopy?

A

Aromatic amino acids and disulfide bonds

21
Q

Why are aromatic acids and disulfide bonds particularly sensitive to CD spectroscopy?

A

Their absorbance is affected by the local environment and can be observed dynamically

22
Q

What pre-requisites are there to x-ray crystallography?

A

Proteins need to be highly pure and in crystal form

23
Q

Describe the mechnism of x-ray crystallography

A

High energy and focussed beam mof x-rays fired through protein crystal. Most pass straight through, some deflected giving diffraction pattern

24
Q

How is the strucure of a protein determined from an x-ray crystallograph?

A

Structure traced back from diffraction pattern

25
Q

What is the resolution of an x-ray crystallograph dependent on?

A

How high energy the x-ray is and how fine the detector is

26
Q

What molecules are used in NMR?

A

H1, C13, N15

27
Q

How does NMR work?

A

NMR active nuclei resonate at specific frequencies in magnetic fields. Dependent on local environment, different protons resonate at different frequencies - chemical shift

28
Q

What is chemical shift?

A

Difference in proton resonation in NMR dependent on local environment

29
Q

How are proteins generated for NMR?

A

Recombinantly in bacteria with only C13/N15 available, so they are NMR-active

30
Q

Describe NMR structure results

A

Iterative process, so several possible structures are represented as an ensemble for analysis

31
Q

How are specimens preserved in EM?

A

Negative stain or vitreous ice (cryo-EM)

32
Q

What kinds of structure are best for EM?

A

More symmetrical and ordered leads to easier averaging process

33
Q

What are the slowest protein structure analysis methods?

A

Crystallography - growing crystals; NMR - analysis

34
Q

What are the quickest protein structure analysis methods?

A

Solution biochemistry or CD

35
Q

What are the most expensive protein structure analysis methods?

A

Crystallography and NMR

36
Q

What is the cheapest protein structure analysis method?

A

Solution biochemistry

37
Q

What protein structure analysis method has the highest resolution?

A

Crystallography

38
Q

What protein structure analysis method has the lowest resolution?

A

Solution biochemistry/CD - affinities/secondary structure only

39
Q

What protein structure analysis methods have no limit on protein size?

A

Solution biochemistry, CD, crystallography

40
Q

What is the limit on NMR protein sample sizes?

A

50kDa

41
Q

What protein structure analysis methods require only small samples?

A

Solution biochem, CD, EM (to some extent)

42
Q

What protein structure analysis methods require large sample sizes?

A

Crystallography, NMR

43
Q

What are the possible problems with crystallography?

A

Can have crystallisation artefacts and dynamics analysis is limited

44
Q

What are the disadvantages of NMR?

A

Need very high concentrations of sample AND isotopic labels, size limitation

45
Q

What is a key limitation in EM analysis of proteins?

A

No dynamics

Y2S2 - Adv. Molecular Biology (14 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions