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Amphipathic molecules
- molecules w/both polar and non-polar regions
- form aggregates in water
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Carbonyl - ketone
R- C=O -R
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Imidazole
sideways house, N's at the corners
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Phophoanhydride
R- O-, O-, O=P-O-P=O, O-, O -R
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pKa
- pH @ which the acid and it's conjugate base are present in equal amt's
- pKa @ 50% titration = pH
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Keq
concentrations of all reactants and products at equilibrium
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Henderson-Hasselbach equation
pH = pKa + log{[conjugate base]/[weak acid]}
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Amino acid general structure
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Leucine
- LEU
- longer chain - 2(-CH3)
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Tryptophan
- TRP
- "sideways house" -N roof
- -benzene
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UV light absorbtion of aromatic side chains
- TRP + TYR = 280nm
- PHE absorbs v. little UV light
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Cysteine
- CYS
- -SH
- important in disulfide bridge formation
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Proline
- PRO
- -CH2-CH2-CH2 "house"
- alpha-helix breaker
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Asparagine
- ASN
- O=C-NH2
- has N vs Aspartate which has no N
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Glutamine
- GLN
- O=C-NH2
- has N vs Glutamate which has no N
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Disulfide bridges
- 2 CYSTEINE's in air will lose H's and bond with each other reversibly
- forming CYSTINE
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Histadine
- HIS
- "sideways house" w/N's at corners of roof
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Zwitterion
- "twin ion"
- actual form, nonionic form doesn't exist in reality
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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
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Number of peptide bonds
# of AA residues - 1
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Where do you find disulfide bonds?
mainly in proteins that are secreted
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Myoglobin
- ~75% alpha helices
- hydrophobic core w/polar R groups facing out
- heme iron gound in cleft
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Alzheimer disease
- aggregation of beta-amloid plaques
- alpha-secretase prevents this
- but beta and gamma secretases cleave amyloid precursor protein forming plaques
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Prions
- infectious proteins causing degenerative brain disorders
- contagious across species
- "mad cow disease" or Creutzfeld-Jacob in humans
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Prion mechanism of action
- misfolded PrPSc converts normal PrPc
- these polymerize into amyloid fibers
- IRREVERSIBLE
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Cation exchange chromatography
- negatively charged beads so - charged proteins move faster
- opposite true for anion exchange
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Affinity chromatography
- beads coated w/ligand
- ex. immunoaffinity chromatograpy - ligand is an antibody and target protein is the antigen
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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
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Mass spectroscopy
- determining AA seq via fragmentation
- MAINLY USED TODAY
- proteases cleave @ specific sites
- ***ex - trypsin cleaves @ LYS, ARG***
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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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