Levels of Structure

Question 1

Primary Structure

Answer 1

Reflects gene sequence

Question 2

Which 2 parts of the primary structure dictates the end structure?

Answer 2

1. Reactivity of carbonyl O2 + amide nitrogen of peptide bond
2. Various reactivities of the R groups attached to a-carbon

Question 3

General types of secondary structure

Answer 3

1. Helices
2. Beta Sheets
3. Beta Turns

Question 4

What is the most common type of secondary structure?

Answer 4

Helices

Question 5

Structure of helices

Answer 5

1. Condensed so particular type + regular repeated
2. Every peptide bond involved in a helix is H-bonded except one on top and one on bottom
3. Al of R groups point outwards in helix
4. Can have amphipathic character

Question 6

Formation of helices

Answer 6

1. Generated by local H-bonds

2. Carbonyl oxygen atom (n) of each residue accepts an H bond from the amide nitrogen 4 residues down (n+4)

Question 7

Proline

Answer 7

Stops formation of helix

Question 8

Benefit of helix structure

Answer 8

1. Amphipathic character -> protein channels in membrane

2. No theoretical limit to length of helix

Question 9

Structure of beta sheets

Answer 9

1. No pattern to sheets
2. Run either parallel or antiparallel
3. Can have amphipathic character -> carrying more hydrophobic molecules

Question 10

Formation of beta sheets

Answer 10

H-bond between main chain amide hydrogen and carbonyl oxygen from backbone groups

Question 11

Difference between parallel and anti-parallel chains

Answer 11

1. Parallel always buried so aliphatic, hdryophobic amino acids
2. Anti-parallel generally more stable so can form barrel structures -> anti-parallel curves

Question 12

Formation of beta turns

Answer 12

H-bond on carbonyl oxygen of one residue (n) with amide N-H 3 amides down (n+3)

Question 13

Protein folding is dependent on

Answer 13

1. Primary structure
2. Driven by hydrocicity of amino acids
3. Flexibility of peptide bond plays a part

Question 14

Elements needed for protein folding

Answer 14

H-bonds between water + outer surface of protein holds shape

Question 15

Native state in protein folding =

Answer 15

Fully folded

Question 16

Why does protein folding occur?

Answer 16

1. Non-polar R groups disrupt H-bonded structure of water
2. Hydrophobic effect in side chains to minimise surface of hydrophobic chains
3. Polar + charged residues tend to be on surface making H-bond contact with water
4. Polar backbone amide groups make contact with secondary structural elements, main chain donors and acceptors

Question 17

Protein folding is a

Answer 17

Thermodynamic compromise -> denaturants compete for H-bonds

Question 18

Tertiary structure

Answer 18

1. R groups bonding together non-covalently form the main part of the tertiary structure
2. Bond lengths differ depedent on type of non-covalent bond
3. Can get trapped water -> weak interactions through the molecule form a hydration shell (sig force) which is stripped in denaturation

Question 19

Elements of tertiary structure

Answer 19

1. Compact shape, stabilised by weak interactions involving polar + non-polar groups
2. Beta turns + loops
3. Zinc-bound water -> catalysis
   4,. Flexibility stabilises metal ions

Question 20

Loops

Answer 20

1. Ligand binding
2. Surface of protein
3. Don’t contribute to solubility
4. Can tolerate mutation more readily
5. Flexible region active site

Question 21

Quaternary structure

Answer 21

Independently folded tertiary structures that are bound together

Question 22

Elements of Quaternary structure

Answer 22

1. Complimentarity -> sub-units more relative to each other e.g. binding of active site
2. Large range of oligometric possiblities

Question 23

Tertiary structure is stabilized by

Answer 23

1. Covalent bonds
2. Dative covalent bonds
3. Cofactor binding
4. Post-translational modification

Question 24

Oligomeric

Answer 24

Proteins composed of more than one polypeptide chain

Question 25

Monomers

Answer 25

Individual sub-units

Question 26

Oligomer containing 3 sub-units

Answer 26

Trimer

Question 27

Quaternary structures are held together by

Answer 27

Non-covalent forces allowing movement between sub-units and at interfaces between sub-units

Question 28

If two identical sub-units make up a dimer then

Answer 28

Homodimer

Question 29

The fit between sub-units depends on:

Answer 29

1. Shape
2. Proximity of opposite H-bond donors to acceptors
3. Non-polar groups are opposite other non-polar groups
4. Positive charges opposite negative charges
5. Number of weak interactions at surface determines tightness of binding between sub-units
6. Maximized if interfaces fit closely together

Question 30

Complementarity

Answer 30

1. Observed in all binding interactions whether at interfaces or at binding sites
2. Doesn’t rule out flexibility of protein