Biochem Block 1

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Author:
honotay
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63724
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Biochem Block 1
Updated:
2011-02-02 19:55:47
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biochemistry block
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Medical biochemistry 1st block exam material.
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  1. Amphipathic molecules
    • molecules w/both polar and non-polar regions
    • form aggregates in water
  2. Alkyl
    ends in CH3
  3. Aryl
    • phenyl
    • benzene ring
  4. Carbonyl - ketone
    R- C=O -R
  5. Carbonyl - aldehyde
    C=O
  6. Carboxylate
    O=C-O-
  7. Hydroxyl (alcohol)
    -OH
  8. Enol
    C-OH =C
  9. Ether
    R- O -R
  10. Ester
    R- O-C=O -R
  11. Acetyl
    O=C-CH3
  12. Amino
    NH3+
  13. Amido
    O=C-NH2
  14. Imine
    R- C=NH -R
  15. Guanidium
    C=NH2+
  16. Imidazole
    sideways house, N's at the corners
  17. Sulfhydryl
    -SH
  18. Disulfide
    R-S-S-R
  19. Thioester
    R- O=C-S-R
  20. Phophoryl
    P=O, -O-, -OH
  21. Phophoanhydride
    R- O-, O-, O=P-O-P=O, O-, O -R
  22. pKa
    • pH @ which the acid and it's conjugate base are present in equal amt's
    • pKa @ 50% titration = pH
  23. Keq
    concentrations of all reactants and products at equilibrium
  24. Henderson-Hasselbach equation
    pH = pKa + log{[conjugate base]/[weak acid]}
  25. Amino acid general structure
  26. Amino Acid Values Table
  27. Glycine
    • GLY
    • -H
  28. Alanine
    • ALA
    • -CH3
  29. Valine
    • VAL
    • 2(-CH3)
  30. Leucine
    • LEU
    • longer chain - 2(-CH3)
  31. Methionine
    • MET
    • -S-CH3
  32. Isoleucine
    • ILE
    • -CH3
  33. Phenylalanine
    • PHE
    • -benzene ring
  34. Tyrosine
    • TYR
    • -benzene -OH
  35. Tryptophan
    • TRP
    • "sideways house" -N roof
    • -benzene
  36. UV light absorbtion of aromatic side chains
    • TRP + TYR = 280nm
    • PHE absorbs v. little UV light
  37. Serine
    • SER
    • -OH
  38. Threonine
    • THR
    • -OH
  39. Cysteine
    • CYS
    • -SH
    • important in disulfide bridge formation
  40. Proline
    • PRO
    • -CH2-CH2-CH2 "house"
    • alpha-helix breaker
  41. Asparagine
    • ASN
    • O=C-NH2
    • has N vs Aspartate which has no N
  42. Glutamine
    • GLN
    • O=C-NH2
    • has N vs Glutamate which has no N
  43. Disulfide bridges
    • 2 CYSTEINE's in air will lose H's and bond with each other reversibly
    • forming CYSTINE
  44. Lysine
    • LYS
    • -NH3+
  45. Arginine
    • ARG
    • NH2-C=NH2+
  46. Histadine
    • HIS
    • "sideways house" w/N's at corners of roof
  47. Aspartate
    • ASP
    • -COO-
  48. Glutamate
    • GLU
    • -COO-
  49. Zwitterion
    • "twin ion"
    • actual form, nonionic form doesn't exist in reality
  50. Isoelectric point
    • pI - the pH @ which no net electrical charge exists on a molecule
    • the average of 2 pKa's
    • if 3 pKa's then it is the avg of the 2 w/like charge
  51. Number of peptide bonds
    # of AA residues - 1
  52. Beta bend
    PRO-GLY
  53. Where do you find disulfide bonds?
    mainly in proteins that are secreted
  54. Myoglobin
    • ~75% alpha helices
    • hydrophobic core w/polar R groups facing out
    • heme iron gound in cleft
  55. Alzheimer disease
    • aggregation of beta-amloid plaques
    • alpha-secretase prevents this
    • but beta and gamma secretases cleave amyloid precursor protein forming plaques
  56. Prions
    • infectious proteins causing degenerative brain disorders
    • contagious across species
    • "mad cow disease" or Creutzfeld-Jacob in humans
  57. Prion mechanism of action
    • misfolded PrPSc converts normal PrPc
    • these polymerize into amyloid fibers
    • IRREVERSIBLE
  58. Cation exchange chromatography
    • negatively charged beads so - charged proteins move faster
    • opposite true for anion exchange
  59. Affinity chromatography
    • beads coated w/ligand
    • ex. immunoaffinity chromatograpy - ligand is an antibody and target protein is the antigen
  60. SDS-PAGE
    • sodium dodecyl sulfate - polyacrylamide gel electrophoresis
    • negative charge draws proteins of different sizes at different speeds through the gel
    • we learn if a particular protein is present and how much, and how big it is
    • MOST COMMON
  61. Mass spectroscopy
    • determining AA seq via fragmentation
    • MAINLY USED TODAY
    • proteases cleave @ specific sites
    • ***ex - trypsin cleaves @ LYS, ARG***
  62. How do you determine the sequence?
    • mass of each ion is known
    • loss of AA is from N terminus
    • therefore seq is 'read' from spectrum
    • ex.

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