Protein structure

Question 1

Describe where you would expect to find polar and nonpolar amino acids in a folded globular protein.

Answer 1

• proteins are compact, there is no empty space inside a protein (in a folded, globular protein)
• polar side. chains (usually contain groups made of “O” and “N” are charged, can form hydrogen bonds) are exposed on the surface of the protein
• non-polar side chain (mostly composed of carbon, thw aliphatics, aromatics_ are buried in the protein (disulfide bonds are also in the core)

Question 2

Describe were you would expect to find Gly and Pro in a folded protein.

Answer 2

• glycines always tend to occur in regions where the polypeptide is turning around, Gly has no side chains so is flexible
• Prolines also found in turns, Pro’s side-chain is fixed onto its backbone, has a restrictive geometry, can only be found in certain structures

Question 3

List the overall features of folded proteins.

Answer 3

1. proteins are compact: there tends to be no empty space inside proteins because of close packing of backbone & side chain atoms
2. water is generally excluded from the interior of proteins
3. nonpolar/hydrophobic side chains are usally located inside the protein
4. Polar/hydrophilic side chains are usually located on the outside of the protein

Question 4

Explain why protein folding is said to be cooperative.

Answer 4

• protein folding is co-operative (all-or-none)
• Transitions between two states occur (folded and unfolded)
• folded and unfolded states are in equilibrium
• protein folding is reversible
• generally, if any part of a protein is disrupted, interactions with the rest of the protein structure are disrupted and the remainder of the structure will be lost. Conditions that disrupt an part of the structure will lead to the whole protein unravelling.

Question 5

Explain how Christian Anfinsen’s experiments showed that under appropriate conditions protein folding is reversible.

Answer 5

1. native state, catalytically active
2. addition of urea and mercaptoethanol
3. unfolded state, inactive, disulphide cross-links reduced to yield Cys residues
4. removal of urea and mercaptoethanol
5. native, catalytically active state. Disulfide cross-links correctly re-formed.

Question 6

Describe the role of disulfide bonds in protein folding.

Answer 6

• oxidation in the presence of urea gave ‘mixed’ disulphides (scrambled), only a small fraction would have the pairing correct (105 different ways to arrange 8 cysteines), only the correct pairing can stabilise the native structure
• adding a trace of BME reduces scrambled disulphides and then the protein can refold correctly
• under appropriate conditions protein folding/refolding is reversible
• protein folding is reversible (all the ‘info’ is in the sequence)
• disulphide bonds don’t direct folding
• folding directs disulphide bond formation
• disulphide bonds increase the relative stability of the folded state over the unfolded state
  (lock on the correct folded state)

Question 7

Describe how cellular conditions are not ‘ideal’ for protein folding.

Question 8

Explain the role of protein folding chaperones in ‘protecting’ unfolded proteins from ‘misfolding’.

Question 9

List the forces drive protein folding and which chemical groups and amino acid type are involved in each interaction.

Question 10

Explain the thermodynamic basis of the hydrophobic interaction.

Question 11

List the different regions of a Ramachandran plot.

Question 12

Draw a labelled Ramachandran plot.

Question 13

Interpret structural information from a Ramachandran plot.

Question 14

Describe how hydrogen bonding helps make proteins compact. Identify different hydrogen bonding interactions in a protein

Question 15

List the structural properties of alpha-helices

Question 16

Explain why alpha-helices are often ‘amphipathic’.

Question 17

Draw a simplified helical wheel diagram.Read amino acid sequences to identify heptad repeat patterns

Question 18

Explain the difference between a beta-strand and a beta-sheet.

Question 19

List the structural properties of beta-sheets.

Question 20

Explain how a beta-sheet can have hydrophilic and hydrophobic face.

Question 21

Read amino acid sequences to identify alternating sequence patterns.

Question 22

Draw a diagrams illustrating hydrogen bonding in antiparallel and parallel beta-sheets.

Question 23

List the structural properties of reverse turns.

Question 24

Explain the difference between type-I and type-II turns.

Question 25

Read amino acid sequences to identify where turns are likely.

Question 26

Define regular and irregular structures.

Question 27

Identify regular and irregular structures from structural information.

Question 28

List the structural properties of proteins.

Question 29

Describe the three common supersecondary structures.

Question 30

Identify supersecondary structure in images of proteins.

Question 31

Explain the difference between primary, secondary, tertiary and quaternary protein structure.

Question 32

From images of proteins, identify secondary, tertiary and quaternary protein structures.

Question 33

Explain the difference between the terms domain fold and module.

Question 34

Define domain in terms of structure and evolution.

Question 35

Describe the genetic processes that create proteins with different functional properties using existing domain structures.

Question 36

Explain what is meant by the statement that protein sequences can be optimally aligned.

Question 37

Explain the link between sequence identity, ancestry, and structural similarity.

Question 38

Define homologue, orthologue and paralogue.

Question 39

what forces drive protein folding?

Answer 39

- electrostatic forces - van der waals interactions - h bonds - hydrophobic interactions - these interactions combine to stabilise the folded state making it favoured over the unfolded state - folded state has lower free energy - folded state is called the 'native' state - unfolded state is said to be 'denatured' - in solution, an unfolded polypeptide will spontaneously fold up