Henderson-Hasselbach Equation - ✔✔ANSW✔✔..pH = pKa + log ([A-] / [HA])
FMOC Chemical Synthesis - ✔✔ANSW✔✔..Used in synthesis of a growing amino acid chain to a
polystyrene bead. FMOC is used as a protecting group on the N-terminus.
Salting Out (Purification) - ✔✔ANSW✔✔..Changes soluble protein to solid precipitate. Protein
precipitates when the charges on the protein match the charges in the solution.
Size-Exclusion Chromatography - ✔✔ANSW✔✔..Separates sample based on size with smaller
molecules eluting later.
Ion-Exchange Chromatography - ✔✔ANSW✔✔..Separates sample based on charge. CM attracts
+, DEAE attracts -. May have repulsion effect on like charges. Salt or acid used to remove stuck
proteins.
Hydrophobic/Reverse Phase Chromatography - ✔✔ANSW✔✔..Beads are coated with a carbon
chain. Hydrophobic proteins stick better. Elute with non-H-bonding solvent (acetonitrile).
Affinity Chromatography - ✔✔ANSW✔✔..Attach a ligand that binds a protein to a bead. Elute
with harsh chemicals or similar ligand.
SDS-PAGE - ✔✔ANSW✔✔..Uses SDS. Gel is made from cross-linked polyacrylamide. Separates
based off of mass with smaller molecules moving faster. Visualized with Coomassie blue.
SDS - ✔✔ANSW✔✔..Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative
charge.
Isoelectric Focusing - ✔✔ANSW✔✔..Variation of gel electrophoresis where protein charge
matters. Involves electrodes and pH gradient. Protein stops at their pI when neutral.
,FDNB (1-fluoro-2,3-dinitrobenzene) - ✔✔ANSW✔✔..FDNB reacts with the N-terminus of the
protein to produce a 2,4-dinitrophenol derivative that labels the first residue. Can repeat
hydrolysis to determine sequential amino acids.
DTT (dithiothreitol) - ✔✔ANSW✔✔..Reduces disulfide bonds.
Iodoacetate - ✔✔ANSW✔✔..Adds carboxymethyl group on free -SH groups. Blocks disulfide
bonding.
Homologs - ✔✔ANSW✔✔..Shares 25% identity with another gene
Orthologs - ✔✔ANSW✔✔..Similar genes in different organisms
Paralogs - ✔✔ANSW✔✔..Similar "paired" genes in the same organism
Ramachandran Plot - ✔✔ANSW✔✔..Shows favorable phi-psi angle combinations. 3 main
"wells" for α-helices, ß-sheets, and left-handed α-helices.
Glycine Ramachandran Plot - ✔✔ANSW✔✔..Glycine can adopt more angles. (H's for R-group).
Proline Ramachandran Plot - ✔✔ANSW✔✔..Proline adopts fewer angles. Amino group is
incorporated into a ring.
α-helices - ✔✔ANSW✔✔..Ala is common, Gly & Pro are not very common. Side-chain
interactions every 3 or 4 residues. Turns once every 3.6 residues. Distance between backbones
is 5.4Å.
, Helix Dipole - ✔✔ANSW✔✔..Formed from added dipole moments of all hydrogen bonds in an
α-helix. N-terminus is δ+ and C-terminus is δ-.
ß-sheet - ✔✔ANSW✔✔..Either parallel or anti-parallel. Often twisted to increase strength.
Anti-parallel ß-sheet - ✔✔ANSW✔✔..Alternating sheet directions (C & N-termini don't line-up).
Has straight H-bonds.
Parallel ß-sheet - ✔✔ANSW✔✔..Same sheet directions (C & N-termini line up). Has angled
Hbonds.
ß-turns - ✔✔ANSW✔✔..Tight u-turns with specific phi-psi angles. Must have gly at position 3.
Proline may also be at ß-turn because it can have a cis-omega angle.
Loops - ✔✔ANSW✔✔..Not highly structured. Not necessary highly flexible, but can occasionally
move. Very variable in sequence.
Circular Dichroism - ✔✔ANSW✔✔..Uses UV light to measure 2° structure. Can be used to
measure destabilization.
Disulfide-bonds - ✔✔ANSW✔✔..Bonds between two -SH groups that form between 2° and 3°
structure.
ß-mercaptoethanol - ✔✔ANSW✔✔..Breaks disulfide bonds.
α-keratin - ✔✔ANSW✔✔..formed from 2 α-helices twisted around each other. "Coiled coil".
Cross-linked by disulfide bonds.
FMOC Chemical Synthesis - ✔✔ANSW✔✔..Used in synthesis of a growing amino acid chain to a
polystyrene bead. FMOC is used as a protecting group on the N-terminus.
Salting Out (Purification) - ✔✔ANSW✔✔..Changes soluble protein to solid precipitate. Protein
precipitates when the charges on the protein match the charges in the solution.
Size-Exclusion Chromatography - ✔✔ANSW✔✔..Separates sample based on size with smaller
molecules eluting later.
Ion-Exchange Chromatography - ✔✔ANSW✔✔..Separates sample based on charge. CM attracts
+, DEAE attracts -. May have repulsion effect on like charges. Salt or acid used to remove stuck
proteins.
Hydrophobic/Reverse Phase Chromatography - ✔✔ANSW✔✔..Beads are coated with a carbon
chain. Hydrophobic proteins stick better. Elute with non-H-bonding solvent (acetonitrile).
Affinity Chromatography - ✔✔ANSW✔✔..Attach a ligand that binds a protein to a bead. Elute
with harsh chemicals or similar ligand.
SDS-PAGE - ✔✔ANSW✔✔..Uses SDS. Gel is made from cross-linked polyacrylamide. Separates
based off of mass with smaller molecules moving faster. Visualized with Coomassie blue.
SDS - ✔✔ANSW✔✔..Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative
charge.
Isoelectric Focusing - ✔✔ANSW✔✔..Variation of gel electrophoresis where protein charge
matters. Involves electrodes and pH gradient. Protein stops at their pI when neutral.
,FDNB (1-fluoro-2,3-dinitrobenzene) - ✔✔ANSW✔✔..FDNB reacts with the N-terminus of the
protein to produce a 2,4-dinitrophenol derivative that labels the first residue. Can repeat
hydrolysis to determine sequential amino acids.
DTT (dithiothreitol) - ✔✔ANSW✔✔..Reduces disulfide bonds.
Iodoacetate - ✔✔ANSW✔✔..Adds carboxymethyl group on free -SH groups. Blocks disulfide
bonding.
Homologs - ✔✔ANSW✔✔..Shares 25% identity with another gene
Orthologs - ✔✔ANSW✔✔..Similar genes in different organisms
Paralogs - ✔✔ANSW✔✔..Similar "paired" genes in the same organism
Ramachandran Plot - ✔✔ANSW✔✔..Shows favorable phi-psi angle combinations. 3 main
"wells" for α-helices, ß-sheets, and left-handed α-helices.
Glycine Ramachandran Plot - ✔✔ANSW✔✔..Glycine can adopt more angles. (H's for R-group).
Proline Ramachandran Plot - ✔✔ANSW✔✔..Proline adopts fewer angles. Amino group is
incorporated into a ring.
α-helices - ✔✔ANSW✔✔..Ala is common, Gly & Pro are not very common. Side-chain
interactions every 3 or 4 residues. Turns once every 3.6 residues. Distance between backbones
is 5.4Å.
, Helix Dipole - ✔✔ANSW✔✔..Formed from added dipole moments of all hydrogen bonds in an
α-helix. N-terminus is δ+ and C-terminus is δ-.
ß-sheet - ✔✔ANSW✔✔..Either parallel or anti-parallel. Often twisted to increase strength.
Anti-parallel ß-sheet - ✔✔ANSW✔✔..Alternating sheet directions (C & N-termini don't line-up).
Has straight H-bonds.
Parallel ß-sheet - ✔✔ANSW✔✔..Same sheet directions (C & N-termini line up). Has angled
Hbonds.
ß-turns - ✔✔ANSW✔✔..Tight u-turns with specific phi-psi angles. Must have gly at position 3.
Proline may also be at ß-turn because it can have a cis-omega angle.
Loops - ✔✔ANSW✔✔..Not highly structured. Not necessary highly flexible, but can occasionally
move. Very variable in sequence.
Circular Dichroism - ✔✔ANSW✔✔..Uses UV light to measure 2° structure. Can be used to
measure destabilization.
Disulfide-bonds - ✔✔ANSW✔✔..Bonds between two -SH groups that form between 2° and 3°
structure.
ß-mercaptoethanol - ✔✔ANSW✔✔..Breaks disulfide bonds.
α-keratin - ✔✔ANSW✔✔..formed from 2 α-helices twisted around each other. "Coiled coil".
Cross-linked by disulfide bonds.
