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2011-12-07 16:18:24
ross semester mini biochem

biochem for mini 1
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  1. aliphatic amino acids
    • pro, gly, ala, val, leu, ile
    • proline, glycine, alanine, valine, leucine, isoleucine
    • PGAVIL "pros like PGAville, no water hazards"
  2. aromatic amino acids
    • phe, tyr, trp
    • phenylalanine, tyrosine, tryptophan

    tpt smells "trailer park trash smells"
  3. suflur containing amino acids
    • met, cys
    • methionine, cysteine
    • mc sulfur "one of my favorite rappers, mc sulfur"
  4. acidic amino acids
    • asp, glu
    • aspartate, glutamate
    • acid forms: aspartic acid, glutamic acid
  5. basic amino acids
    • his, lys, arg
    • histidine, lysine, arginine
    • "his lies are basic"
  6. polar uncharged amino acids
    • ser, thr, asn, gln
    • serine, threonine, asparagine, glutamine
    • "a relaxed polar stag"
  7. amino acids that recieve energy through phosphorylation
    • ser, thr, tyr
    • serine, threonine, tyrosine
    • "SETHs Tys are energetic"
  8. state of most amino acids under basic conditions
    -1, COOH group ionized to COO-
  9. state of most amino acids under acidic conditions
    +1, NH2 group ionized to NH3+
  10. simplest amino acid
    • gly
    • glycine
  11. these make alpha keratin H2O insoluble and resistant to stretching
    • disulfide bonds between cys residues (which are covalent linkages and require a reducing agent to break)
    • cysteine
  12. these amino acids destabalize the alpha helix
    gly and pro

    ser,asp,asn- interfering H bonds

    ile, val- steric effect
  13. these are to important constituents to collagen
    gly- must be every 3rd residue and allows the very tight winding of the 3 alpha helix strand

    hyp (hydroxyproline)- allows for extensive hydrogen bonding between the chains

    note: can also contain modified AA; hydroxylysine
  14. interior tertiary interaction
    hydrophobic interaction between ampiphilic and aromatic AA
  15. exterior tertiary interactions
    ionic interactions between 2 charged side chains, one acidic one basic
  16. these aid protein folding, but do not determine native structure
  17. these amino acids can be O-glycosylated
    ser and thr
  18. this amino acid can be N-glycosylated
  19. this aa is only found on peptides that have cis peptide linkages
  20. normal blood values for pH, [HCO3-] and [CO2]
    • pH= 7.35-7.45
    • ]HCO3]= 24 mM
    • [CO2]= 1.2mM= 40 mmHg
  21. aldose
    C=O located on C1
  22. ketose
    C=O located on C2
  23. biologically relevent sugars
    • D- sugars (OH on right)
    • determined by the chiral carbon farthest from the carbonyl C.
  24. simplest sugars
    aldose: D-glycerldehyde, all other sugars can be synthesized from this molecule

    ketone: dihydroxyacetone
  25. van't Hoffs rule
    • # of steroisomers= 2^n
    • n= # assymetric carbons
  26. epimers
    • differ in configuration about a single chiral carbon
    • a type of stereomer
  27. hemiacetal
    aldehyde + R-OH = hemiacetal HO-C-O-R (where C is the anomeric C)

    sugars with hemiacetal groups can act as reducing sugars. free OH on the anomeric carbon is essential
  28. hemiketal
    ketone + R-OH = hemiketal
  29. anomeric C
    • the new chiral center formed from the carbonyl C in cyclization of a sugar
    • -it has the free OH group that can participate in redox reactions
  30. mutarotation
    change in optical rotation as an equilibrium mixture of anomers ocurs
  31. glycosidic bond
    • bond between anomeric C of CHO and some other group or molecule
    • O= O-glycosidic
    • N= N-glycosidic
  32. reducing sugar
    • -must have free OH on anomeric C(H2OC-O)
    • - ketose sugars, glucose, fructose
    • -sucrose is NOT a reducing sugar
  33. amylose
    > 1000 glucopyranose molecules linked by alpha(1-4) glycosidic linkages

    alpha(1-4) linkages are flexible allowing coiling
  34. amylopectin
    similar to amylose, but has alpha(1-6) branches every 24-30 glucose molecules

    mjor constituent in starch
  35. glycogen
    very similar to amylopectin but with branches every 8-12 glucose units
  36. cellulose
    • has beta-glycosidic bonds, humans lack the enzymes to break this linkage, therefor cannot metabolize cellulose
    • the beta bonds greatly increase the stability of the chains
  37. phosphate esters
    OH groups can be easily phosphoylated, not just on anomeric C
  38. Fatty acids
    • HC chain with COOH at one end
    • always an even number of C
  39. this aa is found in large numbers on Hb and is able to buffer blood
  40. this aa can be both hydrophobic and hydrophilic
    • tyr
    • tyrosine, because of its ring
  41. these aa can be hydroxylated
    pro- hydroxyproline

    lys- hydroxylysine
  42. these aa can have phosphorylated hydroxy groups
    ser, thr
  43. alpha helix stabalization (3)
    • INTRAmolecular H bonding, straight
    • -has poles due to H bonds(+N...OH-)

    side groups pointing out

    gly and proline DESTABALIZE
  44. beta- pleated sheet
    • INTERmolecular H bonding
    • perpendicular H bonding
    • antiparrallel arrangement is more stable
  45. this enzyme catalizes this reaction
    pro --> hyp
    prolyl hydroxylase

    vit c is a cofactor
  46. domains
    • segments within a peptides tertiary structure that can have biological function
    • ie, active site of an enzyme, allosteric site
  47. where does disulfide bonding occur
  48. equatorial linkage
    - rigid beta-beta linkage
  49. axial linkage
    - flexible alpha-alpha linkage
  50. constitutional isomer
    • same formula, different name
    • -2-methylpentane v 3-methylpentane
  51. sterioisomers
    • - same formula, same name except prefix
    • - cis v trans
  52. chiral
    - rotated molecule cannot be superimposed on its mirror image
  53. enantiomers
    • - identical properties
    • - only way to differentiate is how they bend polarized light (L= CCW, D=CW)
  54. epimers
    • two optical isomers that differ i configuration arounf one chiral carbon
    • -type of diastereomer
  55. aspartame
    • -hydrolyzed to methanol which is the oxidized into formaldehyde, which is toxic to the optic nerve
    • -short dipeptide AA- Asp-Phe-OMe
  56. polypeptide chain disrupters
    • -pro- no H for bonding
    • -gly- too much rotation
    • - ser,asp,asn- interfering H bonds
    • - ile, val- steric effect
  57. fibrous proteins
    • alpha keratin in mammals
    • -fibrous, insoluble, strength based on number of disulfide bonds(via cys)

    • collagen
    • - most abundant protein in humans