Biochemistry - proteins

Biochemistry - proteins

1. Amino acids - types of side chains

   • Non polar:
     • Glycine, Alanine Valine Leucine Isoleucine Methionine Phenylalanine Tryptophan Proline
   • Polar:
     • Serine Threonine Cysteine Tyrosine Asparagine Glutamine
   • Electrically charged
     • Acidic (neagatively charged)
       • Aspartic acid Glutamic acid
     • Basic (positively charged)
       • Lysine Arginine Histidine
   • Glycine: small, not chiral, fits into small places - gives flexibility
   • Cysteine: Can form cross links (disulfide bridges)
   • Proline: kinky (because side chain is a ring) introduces kinks and rigidity. Cannot Hydrogen bond - either at the end of the chain or followed by Glycine.
   • Describing amino acids: charge (acidic/basic), polarity

2. Primary structure

   • Specific sequence of amino acids - contains all information for unique 3D shape Primary structure - peptide bonds
   • Delocalised peptide bond - no rotation about this. Rigid and planar: alpha carbons are usually always cis across d.b.
   • There is rotation about the alpha carbons attached to the C/N of the peptide bond (phi/psi bonds) - folding occurs by torsion

3. Secondary structure

   • Arrangement in space and hydrogen bonding of backbone alpha helices or beta sheets
   • Alpha helix
     • Right hand spiral Side chains 'poke' outwards  H-bond betw. 1-5, 2-6 etc.
     • Alpha keratin: long alpha helix with a globular head (monomer). Every 4th reside is hydrophobic. Alpha keratin forms a coiled coil structure (dimer) - with hydrophobic residues interacting with each other through Van der Waals forces
       • Protofilment - two rows of dimers head to tail. Protofibril: protofilaments stabilised by H-bonds and some disulphide bonds (and ionic bonds). Protofilaments are cylindrical
   • Beta sheet
     • Parallel beta sheet - 2 or more strands in the same direction ('diagonal' H-bonding) Antiparallet beta sheet - alternating direction of strands ('straight' H-bonding) Tend to be flexible - can twist/roll into a cylinder *membrane proteins
     • Fibroin (silk): Layered Beta sheet structure, repetitive sequence - Gly, Ala (/Ser)
     • Spider Silk: Mixture of 4stranded beta sheets, crystalline regions and amorphous regoins
       • Tensile strength and flexiblity - strong and stretchy Tough - ability to absorb energy and plastically deform 
     • Fibril formation ( more than 1 stable state for primary protein structure)
       • Native protein -> unfolded protein -> misfolded protein (2 stranded beta sheet) -> oligomers (association of double stranded beta sheets) -> (amorphous aggregates - can be destroyed by body)/ protofibrils -> fibrils (body can't degrade) - low energy, more are formed)
       • Prion (misfolded brain protein) infectious (bc low energy, causes others to unfold and refold the wrong way... virtually indestructable)

4. Tertiary structure

   • Specific 3D arrangement of all atoms Stabilised by: Van der Waals interactions, hydrogen bonds,  ion pairs (electrostatic interactions),  metal ion coordination,  disulfide bridges Can be denatured by: detergents, organic solvents, reducing agents, and changes in pH, temperature and pressure
   • Globular proteins
     • The tertiary structure of many proteins is globular Fold due to the 'hydrophobic effect' 
     • Myoglobin: 8 helices packed together Amphipathic Hydrophobic faces hidden

5. Quarternary Structure

   • Domain structure/oligomerisation Domain - 100-300 a.a.s
   • Lactoferrin (binds and transports iron - 2 Fe3+ ions. 691 residues, 4 domains. N1 Domain, N2 Domain - N lobe. C1 Domain, C2 Domain - C lobe. Binding site is in between the domains on either side. 3 negatively charged (to bind Fe3+s). (Tyrosine is deprotonated in Lactoferrin)
   • Hemoglobin: oligomeric (tetramer) - has co-operative binding
   • Antibodies: have both domain and oligomeric structure. Heavy chain (~500 aa): 4 domians, Light chain (~250 aa): 2 domians. Flexible hinges between domains. Each domain is made up of secondary beta sheets
     • 12 hypervariable regions - 3 in each variable domain - 2 variable domains on each side (1 from light chain, 1 from heavy chain)
     • Molecular recognition (of antigen) by: shape, size, charge, polarity

6. Influenza

   • RNA virus Natural reservoir: wild bird pop.s, can spread to chickens and pigs H1-H16 (3 adapted to affect humans) N1-N9 (not needed for infection)
   • Haemagglutinin (important for entry) - recognises host cell
   • Neuraminidase/sialidase (important for exit) Removes sialic acid to prevent budded viruses from sticking together
     • Neuraminidase inhibitor design: negatively charged cavity is a target for drugs (RELENZA, TAMIFLU - large, positively charged) Drug blocks active site, viruses stick together and can't affect other cells (NH3+ - positively charged but not big enough to fill hole)