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Charles Deber

Biochemistry Exam review Lectures 4 to 6 Protein Backbone angles  the angel at each backbone bond determines the actual 3D progress of the protein chain  Helices and sheets have characteristic backbone angle every AA takes on  Phi (ball with stick) is the angel around the N-C alpha  Psi (the fork) is the angel around the C alpha – C=O  W (omega) is the angel around the C-N bond (peptide bond) Ramachandran plot of backbone angles  only shows AA that are in Bsheet or Ahelix- not unstructured regions  can do this because the phi psi angles in Bsheet or Ahelix are usually the same in each AA  does not give location of Ahelix or Bsheet just tells you how many amino acids have the Phi Psi angles that are characteristic of the secondary structure  Ala seems to be evenly distributed in Bsheet and Ahelix  Arg seems to prefer Ahelix  There is a mirror image in Gly because it is not chiral and can fit in a lot of reigions  For most residues 25% of space is populated but in Gly there is 75% of space occupied (tight packing)  Proline can only have one Phi angel and two Psi angles because of the ring bond The Peptide Bond  the peptide bond is planar and trans – always trans the Calpha’s are diagonal from each other and the O- and H are always diagonal to each other  The omega bond (C-N) is always fixed because the peptide bond is a resonance which gives it a partial double bond Fibrous proteins -proteins that go on and on and on. They are like string and do not have a distinct form. Fibrous protein: Silk  Silk has repeating unit: Gly-Ser-Gly-Ala-Gly-Ala which is formed in a B-sheet  Inter chain- H-bonds are formed while side chains are above and below the plane of the H-bond network  45% glycine and 30% ala, which are small residues which allow tight packing  Strong fibers that are resistant to tension because of covalent bonds  Does not stretch when you pull with the covalent bonded plane but it can stretch if you pull with the h-bonds (perpendicular to the covalent bonded plane) Fibrous protein: Keratins  Keratins are wool, hair etc  Fairly even distribution of helix forming residues  Low sulfur keratins are soft= skin callus  High sulfur keratins are hard- horns claws hooves  Keratins are a complex macromolecule. 3 alpha helixes are twisted into a protofibril. 9-11 proto fibrils are packed together into a micro fibril  Wool can be stretched to twice its length- in the stretched sate, intra helix H bonds may be broken and inter-strand H-bonds may form: Ahelix and Bsheet transition  Sulfur content- the disulfide crosslinks- constitute the main restoring force Fiberous protein: Collagen  about 1/3 of our protein is collagen  inert material resistant to stretching  used for connective tissue, skin, tendons  composition: 33% Gly, 22% (pro + Hypro)- typically gly at every third residue with a pro in between  fundamental unit: triple Helix  Not alpha- Helix but polyproline helix  Hydroxyproline- OH attached in the ring is used to form H-bonds crosslinks between collagen strands. Proline normally cannot form H-bonds because the the N already has 3 bonds because of the ring structure (does not form Intramolecular bonds)  Three left handed single chain helices wrap around one another with a right-handed twist  Each strand is a polyproline helix with a repeat distance of 3 residues per turn (less packed then the Ahelix)  Occurrence of Gly residues at every third position is the single factor which allows the three stands of collagen m
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