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Cellular Biology and Biochemistry > Protein structure dictates function > Flashcards

Protein structure dictates function Flashcards

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1
Q

What determines the shape of a protein?

A

The sequence of amino acids

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2
Q

Name the levels of protein structure in order

A 
Primary
Secondary
Tertiary
Quaternary
Supramolecular
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3
Q

What is primary structure?

A

Amino acid sequence

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4
Q

What is secondary structure?

A

Local folding

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5
Q

What is tertiary structure?

A

Long range folding

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6
Q

What is quaternary structure?

A

Multimeric organisation

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7
Q

What is supramolecular structure?

A

Large-scale assemblies

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8
Q

What is the Levinthal paradox?

A

Assuming each amino acid can be in 3 conformational states
A protein of 101 amino acids has 3^100 possible conformations
Clearly structure is not down to chance

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9
Q

What restricts the possible shape of a protein?

A

The chemical properties of atoms and the peptide bond

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10
Q

What constrains the folding of a protein?

A

Non-covalent interactions between amino acid side chains

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11
Q

Which two regular folding patterns are seen at the secondary level?

A

Alpha helix

Beta pleated sheet

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12
Q

Describe the bonds in an alpha helix

A

Intra-strand interactions of the amino acid backbone

Hydrogen bonds

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13
Q

Describe the bonds in a beta pleated sheet

A

Inter-strand interactions of amino acid side chains

Hydrogen bonds

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14
Q

What is the length it takes for one turn of an alpha helix?

A

0.54nm

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15
Q

What is the length it takes for one pleat of a beta pleated sheet?

A

0.7nm

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16
Q

What is important about the orientation of beta pleated sheets?

A

They run counter parallel to one another

17
Q

Which bond stabilises structures?

A

Hydrogen bonding

18
Q

What is a hydrogen bond?

A

The electrostatic attraction between polar molecules

19
Q

Which atoms can form hydrogen bonds?

A

Nitrogen
Oxygen
Fluorine

20
Q

How close together must two atoms be for a hydrogen bond to form?

A

0.3nm

21
Q

Which non-covalent interactions are present in proteins?

A

Ionic bonds
Hydrogen bonds
Van der Waals
Hydrophobic associations

22
Q

Which amino acids form ionic bonds?

A

Amino acids with carboxylic acid side chains

Amino acids with amine side chains

23
Q

What is important in the formation of ionic bonds?

A

pH

24
Q

Give a basic explanation of van der Waals interactions

A

Electron cloud is constantly fluctuating
Small areas of charge created in an atom
Attraction or repulsion occurs

25
Q

Van der Waals are only significant…

A

…when combined

26
Q

When clustering of hydrophobic side chains occurs, it leads to…

A

…other non-covalent interactions

Because side chains are brought close enough together to interact

27
Q

If there is a hydrophobic region on the exterior of a folded protein, what might be its function?

A

A contact site for other proteins

Once the subunits come together the hydrophobic region is away from the water

28
Q

Which amino acid forms disulphide bridges?

A

Cysteine

29
Q

Disulphide bridges are present in what structural level?

A

Quaternary

30
Q

What do weak non-covalent interactions determine?

A

Geometry
Specificity
Kinetics

31
Q

What is entropy?

A

Disorder

Everything is increasing towards a state of disorder

32
Q

What is deltaG?

A

A measure of the change of free energy

33
Q

What does a negative or positive value of deltaG mean?

A

Negative: releases energy, favourable
Positive: requires energy, not favourable

34
Q

What is deltaG in the context of protein folding?

A

The energy released or require when a protein folds into its native conformation

35
Q

DeltaG is defined by

A

DeltaG = deltaH - TdeltaS
where deltaH = enthalpy
deltaS = entropy

36
Q

What happens to the entropy of water as a protein folds?

A

When unfolded, water forms hydration spheres around hydrophobic side chains
Entropy is decreased
When protein folds, the water molecules are released
Entropy is high

37
Q

When a protein folds, energy is ______

A

Released

38
Q

What is the deltaH value for protein folding?

A

Negative

39
Q

What is the deltaG value for protein folding?

A

Negative

Favourable

Cellular Biology and Biochemistry (22 decks)

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