Protein Folding And Function

Question 1

Describe the primary structure of a protein

Answer 1

Linear sequence of amino acids linked COVALENTLY by peptide bonds

Question 2

What 2 conformations can exist in the secondary structure of a protein?

Answer 2

• α - helix

- β - pleated sheet

Question 3

Describe the properties of an α-helix

Answer 3

• RIGHT HANDED
• 3.6 AA per 360 turn
• ~1.5nm between each AA
• 0.54nm pitch/wavelength
• R groups arranged on outside
• H bonds form between C=O on one amino acid and N-H group on another 4 AA away

Question 4

Explain how an α-helix structure can be altered

Answer 4

• Structure depends on nature of AA residues
• Small hydrophobic AA support helix formation e.g Ala, Leu
  HELIX BREAKERS:
• PROLINE - no rotation around N-Ca bond
• GLYCINE - tiny R group supports other conformations

Question 5

Describe the properties of a β-pleated sheet

Answer 5

• Fully extended conformation
• R groups alternate on opposite sides of chain
• 0.35nm between adjacent AA

Question 6

Describe how a β-pleated sheet can be arranged

Answer 6

• ANTIPARALLEL -> chains run in opposite directions with multiple vertical H bonds between C=O and N-H
• PARALLEL -> chains run in same direction with multiple H bonds at an angle
• MIXED -> chains run antiparallel and parallel in sheet

Question 7

State 4 interactions that occur in the tertiary folding of a protein

Answer 7

• H bonding
• Ionic bonding
• Disulphide bridges
• Hydrophobic interactions

Question 8

Describe the nature of a GLOBULAR protein

Answer 8

• COMPACT
• Several types of secondary structure
• Role is for catalysis and regulation (ENZYMES)

Question 9

Describe the features of a FIBROUS protein

Answer 9

• LONG STRANDS/SHEETS
• Single type of secondary structure
• Role is for structure and support (COLLAGEN)

Question 10

What is a MOTIF? Give an example

Answer 10

• Folding pattern that contains 1 or more element of secondary structure (e.g. contains both α-helix and β-sheets)
• β-barrel

Question 11

How does the folding of a membrane protein differ from that of a water soluble protein?

Answer 11

• Water soluble proteins have hydrophobic regions on inside and hydrophilic regions on outside
• Membrane proteins are ‘inside out’ as membranes are hydrophobic (hydrophobic on outside and hydrophilic on inside)

Question 12

Explain the formation of disulphide bonds and how they can be broken

Answer 12

• COVALENT
• Form between S molecules on Cys residues
• Can be broken with reducing agents e.g. β-mercaptoethanol

Question 13

Explain how pH and temperature can affect protein structure

Answer 13

• Can cause DENATURATION
• pH can alter ionisation states of amino acids
• Heat can increase KE of molecules so increased vibrations which can break forces within protein e.g H bonds

Question 14

Explain how the mis-folding of proteins can lead to AMYLOIDOSIS

Answer 14

• Mutation causes change in amino acid sequence
• Mis-folding of protein occurs as nature of AA residues changes (α-helix–>β-sheet)
• Previously soluble proteins may become insoluble
• Deposition of amyloid fibres which can cause disease

Question 15

What determines the folding of a protein?

Answer 15

• Sequence of amino acids
• Nature of amino acid residues (R groups)
• Angles in the protein backbone

Question 16

Name 3 diseases of the brain associated with amyloidoses

Answer 16

• Alzheimer’s disease
• Huntingdon’s disease
• Parkinson’s disease

Question 17

Briefly explain how folding of proteins occurs

Answer 17

• Not a random process
• Localised folding by interaction of AA residues
• May be assisted by CHAPERONES to prevent misfolding