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BI1014: Biological Chemistry > Protein Structure and Purification > Flashcards

Protein Structure and Purification Flashcards

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1
Q

What configuration are amino acids in protein?

A

L-configuration

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2
Q

What is the side chain for glycine?

A

H

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3
Q

What is the side chain for alanine?

A

CH3

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4
Q

What is the side chain for serine?

A

CH2OH

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5
Q

What is the side chain for cysteine?

A

CH2SH

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6
Q

How are peptide bonds formed?

A

Via a condensation reaction.

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7
Q

What is the basic structure of an amino acid?

A

CHNH3RCOO

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8
Q

Why is the C-N bond non-rotational?

A

Due to electron delocalisation, there is resonance.

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9
Q

What is an amino acid residue?

A

The bit of the amino acid left behind after it joins a polpeptide chain.

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10
Q

What are the two forms of secondary protein structure?

A

Alpha helices and beta sheets.

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11
Q

What are some of the properties of alpha helices?

A

Right handed helix.
3.6 residues per turn.
Single helix.
H-bonds link across spirals to stabilise the helix.
Carbonyl of 1 links to amino 5.
n to n+4 linkage.
Side-chains/R groups project at 100 degrees.

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12
Q

Which amino acid is a helix destabiliser?

A

Tyrosine (Y).

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13
Q

Which amino acid is a helix breaker?

A

Proline (P).

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14
Q

Why is proline a helix breaker?

A

(alpha)C-N bond cannot rotate meaning it has an exceptionally rigid structure and the R-group folds back on itself.

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15
Q

What are the two forms of beta sheets?

A

Parallel and anti-parallel.

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16
Q

How do beta sheets interact above and below?

A

They interdigitate - like fingers interlinking.

17
Q

Which form of beta sheets are stronger?

A

Anti-parallel beta sheets are stronger as the H-bonds are more linear.

18
Q

How does tertiary structure differ from secondary structure?

A

Tertiary structure involves side-chain interactions.

19
Q

Define hydrophobic collapse.

A

The idea that a protein would collapse rapidly around its hydrophobic side-chains and then rearrange from restricted conformational space occupied by the intermediate.

20
Q

Why is hydrophobic collapse favoured?

A

Hydrophobic collapse leads to greater disorder; positive entropy change.

21
Q

What are disulphide bonds?

A

Covalent bonds between two cysteine side-chains formed by oxidation.

22
Q

What is the Henderson-Hasselbach Equation?

A

pH = pKa + log(base/acid)

23
Q

What is a domain?

A

A globular unit formed from part of a polypeptide.

24
Q

What is a protein domain?

A

A conserved part of a given protein sequence that can evolve, function and exist independently.

25
Q

What is quarternary structure?

A

The assembly of more than one polypeptide chain.

26
Q

What are some examples of quarternary structure?

A

Haemoglobin and collagen.

27
Q

What is HIV proteinase?

A

A homodimer (two identical polpeptide chains) that helps produce the proteins for the virus, acting as a pair of scissors in a model kit.

28
Q

What is SDS-PAGE?

A

Sodium Dodecyl Sulphate - PolyAcrylamide Gel Electrophoresis. It is a type of protein purification using marker proteins of known molecular masses to estimate the molecular masses of other proteins.

29
Q

How does separation by solubility work?

A

Solubility of proteins differ because their surfaces differ.

30
Q

What is isoelectric focusing?

A

Utilises a protein’s isoelectric point (the pH where a molecule has no net charge). Uses an immobilised pH gradient and an electric field. The proteins move towards the + or - end depending on their net charge. When they reach an area where their net charge is zero they stop moving.

31
Q

What is size exclusion chromatography?

A

Involves lots of tiny beads cross-linked with polydextran. Beads catch the smallest proteins as they can be ‘pocketed’. Larger proteins get ‘pocketed’ less often.

BI1014: Biological Chemistry (7 decks)

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