Protein Structure
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What is a native protein
A protein in its folded and functional state
What are the forces in a protein that give it its 3D shape
-ionic bonds -hydrogen bonds -hydrophobic interactions -London forces -disulphide bonds
Why do hydrophobic molecules clump together in water
Hydrophobic molecules immobilise the surrounding water in an ice like shell called clathrate. The reduced entropy is less thermodynamically stable, so molecules clump together to reduce their surface area and the amount of clathrate formed
Explain how proteins fold with reference to the Gibs energy equation
-as the protein folds it becomes more ordered, lowering the entropy (unfavourable) -the amount of weak forces and interactions between the protein R-groups are maximised resulting in a lower change in H (favourable) -the entropy of the surrounding water increases as the hydrophobic groups move inwards and less clathrate is formed (favourable) In total, the change in free energy (G) is slightly negative, so a protein will always fold in cellular conditions
What is a chaperone protein
A protein that assists with the folding of other proteins
What is a prion
A misfolded protein that has the ability to misfold other proteins. This often leads to a loss of biological functions as the enzymes can not perform their functions.
Is a Ramachandran plot
A plot that shows all the energetically stable configurations for psi and sphi inside a protein. It is the same for all proteins
Why aren’t all configurations for psi and sphi energetically stable
Steric crowding of the oxygen atom and R groups in a peptide chain prevent the configuration from being stable
What is the structure of an alpha helix
Right handed helix Helix is stabilised by hydrogen bonds between the n and n+4 amino acids Hydrogen bonds run parallel to the helix axis
Which amino acids are helix breakers
-proline and glycine are unable to form alpha helixes -long strings of charged amino acids usually are unable to form helixes due to charge repulsion -long chains of bulky amino acids destabilise the helix due to steric hinderance
What is the structure of an antiparallel beta sheet
Chains of amino acids run side by side in opposite directions Stabilised by hydrogen bonds between the chains The hydrogen bonds line up well with each other so are stronger than in parallel beta sheets
What is the structure of a parallel beta sheet
Chains of amino acids run side by side in the same direction Hydrogen bonds do not line up as well so are weaker The ends of each chain contain a beta turn which brings the protein back on itself