Protein structure dictates function

Question 1

What determines the shape of a protein?

Answer 1

The sequence of amino acids

Question 2

Name the levels of protein structure in order

Answer 2

Primary
Secondary
Tertiary
Quaternary
Supramolecular

Question 3

What is primary structure?

Answer 3

Amino acid sequence

Question 4

What is secondary structure?

Answer 4

Local folding

Question 5

What is tertiary structure?

Answer 5

Long range folding

Question 6

What is quaternary structure?

Answer 6

Multimeric organisation

Question 7

What is supramolecular structure?

Answer 7

Large-scale assemblies

Question 8

What is the Levinthal paradox?

Answer 8

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

Question 9

What restricts the possible shape of a protein?

Answer 9

The chemical properties of atoms and the peptide bond

Question 10

What constrains the folding of a protein?

Answer 10

Non-covalent interactions between amino acid side chains

Question 11

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

Answer 11

Alpha helix

Beta pleated sheet

Question 12

Describe the bonds in an alpha helix

Answer 12

Intra-strand interactions of the amino acid backbone

Hydrogen bonds

Question 13

Describe the bonds in a beta pleated sheet

Answer 13

Inter-strand interactions of amino acid side chains

Hydrogen bonds

Question 14

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

Answer 14

0.54nm

Question 15

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

Answer 15

0.7nm

Question 16

What is important about the orientation of beta pleated sheets?

Answer 16

They run counter parallel to one another

Question 17

Which bond stabilises structures?

Answer 17

Hydrogen bonding

Question 18

What is a hydrogen bond?

Answer 18

The electrostatic attraction between polar molecules

Question 19

Which atoms can form hydrogen bonds?

Answer 19

Nitrogen
Oxygen
Fluorine

Question 20

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

Answer 20

0.3nm

Question 21

Which non-covalent interactions are present in proteins?

Answer 21

Ionic bonds
Hydrogen bonds
Van der Waals
Hydrophobic associations

Question 22

Which amino acids form ionic bonds?

Answer 22

Amino acids with carboxylic acid side chains

Amino acids with amine side chains

Question 23

What is important in the formation of ionic bonds?

Answer 23

pH

Question 24

Give a basic explanation of van der Waals interactions

Answer 24

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

Question 25

Van der Waals are only significant...

Answer 25

...when combined

Question 26

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

Answer 26

...other non-covalent interactions | Because side chains are brought close enough together to interact

Question 27

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

Answer 27

A contact site for other proteins | Once the subunits come together the hydrophobic region is away from the water

Question 28

Which amino acid forms disulphide bridges?

Answer 28

Cysteine

Question 29

Disulphide bridges are present in what structural level?

Answer 29

Quaternary

Question 30

What do weak non-covalent interactions determine?

Answer 30

Geometry Specificity Kinetics

Question 31

What is entropy?

Answer 31

Disorder | Everything is increasing towards a state of disorder

Question 32

What is deltaG?

Answer 32

A measure of the change of free energy

Question 33

What does a negative or positive value of deltaG mean?

Answer 33

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

Question 34

What is deltaG in the context of protein folding?

Answer 34

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

Question 35

DeltaG is defined by

Answer 35

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

Question 36

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

Answer 36

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

Question 37

When a protein folds, energy is ______

Answer 37

Released

Question 38

What is the deltaH value for protein folding?

Answer 38

Negative

Question 39

What is the deltaG value for protein folding?

Answer 39

Negative | Favourable