BIOCHEMISTRY C 785 READINESS CHECK 1B
EXAM PREP 2026 STUDY GUIDE QUESTIONS
AND ANSWERS
◉ FMOC Chemical Synthesis. Answer: 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). Answer: Changes soluble protein to
solid precipitate. Protein precipitates when the charges on the
protein match the charges in the solution.
◉ Size-Exclusion Chromatography. Answer: Separates sample based
on size with smaller molecules eluting later.
◉ Ion-Exchange Chromatography. Answer: 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. Answer: Beads are
coated with a carbon chain. Hydrophobic proteins stick better. Elute
with non-H-bonding solvent (acetonitrile).
,◉ Affinity Chromatography. Answer: Attach a ligand that binds a
protein to a bead. Elute with harsh chemicals or similar ligand.
◉ SDS-PAGE. Answer: Uses SDS. Gel is made from cross-linked
polyacrylamide. Separates based off of mass with smaller molecules
moving faster. Visualized with Coomassie blue.
◉ SDS. Answer: Sodium dodecyl sulfate. Unfolds proteins and gives
them uniform negative charge.
◉ Isoelectric Focusing. Answer: 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). Answer: 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). Answer: Reduces disulfide bonds.
◉ Iodoacetate. Answer: Adds carboxymethyl group on free -SH
groups. Blocks disulfide bonding.
,◉ Homologs. Answer: Shares 25% identity with another gene
◉ Orthologs. Answer: Similar genes in different organisms
◉ Paralogs. Answer: Similar "paired" genes in the same organism
◉ Ramachandran Plot. Answer: Shows favorable phi-psi angle
combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed
α-helices.
◉ Glycine Ramachandran Plot. Answer: Glycine can adopt more
angles. (H's for R-group).
◉ Proline Ramachandran Plot. Answer: Proline adopts fewer angles.
Amino group is incorporated into a ring.
◉ α-helices. Answer: 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 5.4A.
◉ Helix Dipole. Answer: Formed from added dipole moments of all
hydrogen bonds in an α-helix. N-terminus is δ+ and C-terminus is δ-.
, ◉ ß-sheet. Answer: Either parallel or anti-parallel. Often twisted to
increase strength.
◉ Anti-parallel ß-sheet. Answer: Alternating sheet directions (C & N-
termini don't line-up). Has straight H-bonds.
◉ Parallel ß-sheet. Answer: Same sheet directions (C & N-termini
line up). Has angled H-bonds.
◉ ß-turns. Answer: 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. Answer: Not highly structured. Not necessary highly
flexible, but can occasionally move. Very variable in sequence.
◉ Circular Dichroism. Answer: Uses UV light to measure 2°
structure. Can be used to measure destabilization.
◉ Disulfide-bonds. Answer: Bonds between two -SH groups that
form between 2° and 3° structure.
◉ ß-mercaptoethanol. Answer: Breaks disulfide bonds.
EXAM PREP 2026 STUDY GUIDE QUESTIONS
AND ANSWERS
◉ FMOC Chemical Synthesis. Answer: 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). Answer: Changes soluble protein to
solid precipitate. Protein precipitates when the charges on the
protein match the charges in the solution.
◉ Size-Exclusion Chromatography. Answer: Separates sample based
on size with smaller molecules eluting later.
◉ Ion-Exchange Chromatography. Answer: 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. Answer: Beads are
coated with a carbon chain. Hydrophobic proteins stick better. Elute
with non-H-bonding solvent (acetonitrile).
,◉ Affinity Chromatography. Answer: Attach a ligand that binds a
protein to a bead. Elute with harsh chemicals or similar ligand.
◉ SDS-PAGE. Answer: Uses SDS. Gel is made from cross-linked
polyacrylamide. Separates based off of mass with smaller molecules
moving faster. Visualized with Coomassie blue.
◉ SDS. Answer: Sodium dodecyl sulfate. Unfolds proteins and gives
them uniform negative charge.
◉ Isoelectric Focusing. Answer: 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). Answer: 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). Answer: Reduces disulfide bonds.
◉ Iodoacetate. Answer: Adds carboxymethyl group on free -SH
groups. Blocks disulfide bonding.
,◉ Homologs. Answer: Shares 25% identity with another gene
◉ Orthologs. Answer: Similar genes in different organisms
◉ Paralogs. Answer: Similar "paired" genes in the same organism
◉ Ramachandran Plot. Answer: Shows favorable phi-psi angle
combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed
α-helices.
◉ Glycine Ramachandran Plot. Answer: Glycine can adopt more
angles. (H's for R-group).
◉ Proline Ramachandran Plot. Answer: Proline adopts fewer angles.
Amino group is incorporated into a ring.
◉ α-helices. Answer: 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 5.4A.
◉ Helix Dipole. Answer: Formed from added dipole moments of all
hydrogen bonds in an α-helix. N-terminus is δ+ and C-terminus is δ-.
, ◉ ß-sheet. Answer: Either parallel or anti-parallel. Often twisted to
increase strength.
◉ Anti-parallel ß-sheet. Answer: Alternating sheet directions (C & N-
termini don't line-up). Has straight H-bonds.
◉ Parallel ß-sheet. Answer: Same sheet directions (C & N-termini
line up). Has angled H-bonds.
◉ ß-turns. Answer: 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. Answer: Not highly structured. Not necessary highly
flexible, but can occasionally move. Very variable in sequence.
◉ Circular Dichroism. Answer: Uses UV light to measure 2°
structure. Can be used to measure destabilization.
◉ Disulfide-bonds. Answer: Bonds between two -SH groups that
form between 2° and 3° structure.
◉ ß-mercaptoethanol. Answer: Breaks disulfide bonds.
