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Cell and Molecular Biology > Protein Structure > Flashcards

Protein Structure Flashcards

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1
Q

The misfolding of what protein causes Alzheimers?

A

Amyloid B-peptide or Tau in the ER

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2
Q

The misfolding of which protein causes Parkinsons?

A

a-synuclein in the cytosol

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3
Q

The misfolding of which protein causes Cancer?

A

p53 in the cytosol

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4
Q

How many different amino acids are there?

A

20

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5
Q

What are the two major protein structures?

A

Alpha helix

Beta sheet

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6
Q

How can the alpha helix be represented?

A

Backbone
Sticks
Ribbons
Space filling

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7
Q

Where was the alpha helix first seen?

A

In the protein alpha keratin

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8
Q

Where do hydrogen bonds form in an alpha helix?

A

Between every forth peptide bond

So on C=O is linked to a N-H

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9
Q

How often do alpha helixes have a complementary turn?

A

Every 3.6 amino acids

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10
Q

Where are alpha helixes abundant in the cell?

A

Cell membranes ie in transport proteins or receptors

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11
Q

Which amino acids do not favour helix forming?

A

Proline and Glycine

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12
Q

Beta Sheets can run in what two directions?

A

Parallel or anti-parallel

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13
Q

Which amino acids are usually found in the middle of the B sheets and why?

A

Aromatic residiues - Tyr, Phe, Trp, Val and Ile

They are hydrophobic

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14
Q

What is always at the start of a protein?

A

The N terminus - NH2

COOH is always at the end

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15
Q

What are the four subunits of Src tyrosine kinase?

A

SH3 domain
SH4 domain
Small kinase domain
Large kinase domain

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16
Q

In general, more complex organisms’ proteins have more what?

A

They have additional domains

17
Q

What are the 3 types of non covalent weak bonds that can hold proteins together?

A

Hydrogen bonds
Electrostatic attraction
Van der Waals Attractions

18
Q

Where do disulphide bonds form?

A

Inbetween two adjacent cysteine residues

19
Q

Where do polar side chains tend to form in a folded protein?

A

On the outside of the folded protein so they can interact with water

20
Q

The core of a folded protein can be known as what?

A

Hydrophobic

21
Q

How can primary sequence be determined?

A

Inferred from DNA sequence
Determined directly by amino acid sequencing using Edman degredation (chemical degredation)
Mass Spectrometry (physical degredation)

22
Q

What chemical does edman degredation use?

A

Phenylisothyocyanate (PITC)

23
Q

Adding PITC to an amino acid chain forms what?

A

Phenylthiocarbamoyl derivative with the N terminus

24
Q

What is formed when the N terminus is cleaved?

A

Cyclic compound of phenylthiohydantoin forms
PTH amino acid
This does not change the amino acid

25
Q

Why is Edman degredation useful?

A

The protein is not damaged

26
Q

How is Edman degredation carried out?

A

In cycles ie each cycle for each amino acid

27
Q

What are the techniques to obtain real protein structure?

A

Circular dichroism
Xray crystallography
NMR
Electron Microscopy

28
Q

Circular Dichroism is used for what?

A

Estimating the secondary structure

29
Q

How does CD work?

A

CD if the differential absorption of circulatory polarised light of pure protein structure
CD spec in the spectral region (190 - 250nm) reveals secondary structure
Different structure give different characteristic shapes of the CD spectrum
It gives a percentage for each secondary structure but no information on the arrangement

30
Q

How can CD tell us about the stability of the protein?

A

The less stable it is faster it will lose its CD characteristics upon heating

31
Q

How can CD tell us if the protein can reform after being heated?

A

After cooling the CD should show the original structure

32
Q

What is calmodulin?

A

A small calcium binding protein which activates protein kinases and other proteins

33
Q

What is NMR useful for?

A

Understanding the dynamics of protein structures

ie how proteins change upon binding

34
Q

How does xray crytsallography work?

A

Proteins are first crystallised
High energy beam of Xrays is fired through the crystal
Some are deflected giving rise to diffraction patterns

35
Q

How much can set up of crystallography cost?

A

In house = £200,000

High resolution, synchrotonous based crystallography = £300,000,000

36
Q

Why is transmission electron microscopy useful?

A

Looking at large protein structures

Looking at actin filaments

37
Q

What does EM use?

A

A negative stain eg heavy metal for shading

38
Q

What is cryo-electron microscopy?

A

Uses liquid nitrogen to freeze the specimen
No shading is used just differences in electron density
The more ordered and symetrical the structure, the easier the averaging process
eg viruses have radial symetry

Cell and Molecular Biology (17 decks)

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