BIOCHEM MODULE 6 EXAM 6 2026 PROTEIN
STRUCTURE AND FUNCTION WORKBOOK
SOLVED QUESTIONS COMPILATION
◉ 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.
STRUCTURE AND FUNCTION WORKBOOK
SOLVED QUESTIONS COMPILATION
◉ 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.
