4. Proteins

Question 1

Rotation of bonds between amino acids

Answer 1

-Limited rotation around N-C=O as the electrons are shared across (resonance)
-bonds around α-carbon can rotate

Question 2

Types of diagrams showing protiens

Answer 2

-space-filling
-ball and stick
-backbone
-ribbon

Question 3

Collagen

Answer 3

Repeating unit of Gly-X-Y, and ringed stucture of proline and hydroxyproline put additional restraint on polypeptide chains

Question 4

3 possible non-polypeptide components in proteins

Answer 4

-heme group
-metal ions
-glycosylation (saccharides)

Question 5

When are proteins “native”?

Answer 5

-under physiological condition
-most stable structure
- biologically active structure.

Question 6

When are proteins denatured?

Answer 6

-Extreme temp breaks non-covalent bonds
-pH changes, ionization state of side-chains change; disrupts of electrostatic and H bonds
-Denaturation reagents e.g. ionic detergents (SDS), hydrogen bonding agents (urea), metal chelators (EDTA) [pull metal ions out to form bonds]
-Reducing agent (dithiothreitol) breaks disulphide bonds
-biologically inactive

Question 7

Structures lost after folding

Answer 7

1. Preproinsulin–> lose signal sequence= proinsulin
2. Di-sulfide bonds formed in the proinsulin
3. C-peptide bond is lost and leaves a mature insulin, holding the chains by the bonds

Question 8

Driving force of folded proteins

Answer 8

Unfolded proteins have:
-solvation of hydrophobic domains = neither entropy or enthalpy are favoured

Folded proteins have:
-stronger intermolecular forces as amino acids are in closer prximity = enthalpy favoured
-hydrophobic effect = entrophy favoured

Question 9

Levinthal paradox

Answer 9

-the large number of degree of freedom in the unfolded protein means the number of possible conformations is astronomical

Question 10

Conformational entropy in protein folding

Answer 10

-Unfolded protein=high entropy
-formation of 1st interaction = large loss in conformational entropy
-subsequent interactions occur and entropy decreases until no further loss of

Question 11

Chaperones

Answer 11

Bind to non-native proteins, assist in protein folding

Question 12

Prion

Answer 12

-a protein infective agent
-caused by mis-folding of a protein
-causes mis-folding of its natural counterpart which goes on to do the same; chain reaction