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