Protein structure and analysis

Question 1

Name 3 misfolding diseases

Answer 1

Alzheimers- amyloid beta peptdie
Parkinsons- alpha synuclein
Cancer- p53

Question 2

What bonds form in alpha helices?

Answer 2

Hydrogen bonding between N-H group in the backbone to a C=O group on an amino acid 4 residues earlier

Question 3

What bonds form in beta sheets?

Answer 3

Backbone H bonds

Question 4

Examples of interactions between protein strands

Answer 4

Hydrogen bonds
Ionic/ electrostatic
Weak van der walls
Disulphide bonds

Question 5

How can you obtain the primary structure?

Answer 5

Edman degradation

Mass spectrometry

Question 6

How can you obtain the secondary structure?

Answer 6

Circular dichroism
X-ray crystallography
NMR
Electron microscopy

Question 7

What are the two types of ultracentrifugation?

Answer 7

1. Velocity sedimentation- stabilising shallow sucrose gradient
2. Equilibrium sedimentation- steep sucrose gradient

Question 8

What are the 3 types of chromatography?

Answer 8

1. Gel filtration- size of molecules
2. Affinity- enzymes binding to substrates
3. Ion-exchange- -vly charged molecules bind to +vly charged beads

Question 9

What does SDS do to proteins?

Answer 9

1. Denature them

2. Give them a negative charge in proportion to their size

Question 10

What are the steps in 2 dimensional gel electrophoresis?

Answer 10

1. Isoelectric focussing- separates proteins based on their isoelectric point
2. SDS PAGE- separates based on size

Question 11

What does mass spectrometry do?

Answer 11

Ionize peptides and calculate their abundance- mass to charge ratio

Question 12

Which amino acids can be phosphorylated?

Answer 12

Serine
Threonine
Tyrosine

Question 13

Examples of post translational modifications of amino acids

Answer 13

1. Hydroxylation
2. Methylation
3. Acetylation
4. Lipids (palmitoylation)