ACS BIOCHEMISTRY EXAM
1. Henderson-Hasselbach Equation
Answer pH = pKa + log ([A-] / [HA])
2. 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.
3. Salting Out (Purification)
Answer Changes soluble protein to solid precipitate. Protein precipitates when the charges on the protein
match the charges in the solution.
4. Size-Exclusion Chromatography
Answer Separates sample based on size with smaller molecules eluting later.
5. Ion-Exchange Chromatography
Answer Separates sample based on charge. CM attracts +, DEAE attracts -. May have repulsion ettect on
like charges. Salt or acid used to remove stuck proteins.
,6. Hydrophobic/Reverse Phase Chromatography
Answer Beads are coated with a carbon chain. Hy- drophobic proteins stick better. Elute with non-H-
bonding solvent (acetonitrile).
7. Affinity Chromatography
Answer Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or similar ligand.
8. SDS-PAGE
Answer Uses SDS. Gel is made from cross-linked polyacrylamide. Separates based ott of mass with smaller
molecules moving faster. Visualized with Coomassie blue.
9. SDS
Answer Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative charge.
10. Isoelectric Focusing
Answer Variation of gel electrophoresis where protein charge matters. Involves electrodes and pH gradient.
Protein stops at their pI when neutral.
11. 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.
12. DTT (dithiothreitol)
Answer Reduces disulfide bonds.
13. Iodoacetate
Answer Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
14. Homologs
Answer Shares 25% identity with another gene
15. Orthologs
Answer Similar genes in ditterent organisms
16. Paralogs
Answer Similar "paired" genes in the same organism
17. Ramachandran Plot
Answer Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed
α-helices.
18. Glycine Ramachandran Plot
, Answer Glycine can adopt more angles. (H's for R-group).
19. Proline Ramachandran Plot
Answer Proline adopts fewer angles. Amino group is incorporated into a ring.
20. 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 5.4Å.
1. Henderson-Hasselbach Equation
Answer pH = pKa + log ([A-] / [HA])
2. 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.
3. Salting Out (Purification)
Answer Changes soluble protein to solid precipitate. Protein precipitates when the charges on the protein
match the charges in the solution.
4. Size-Exclusion Chromatography
Answer Separates sample based on size with smaller molecules eluting later.
5. Ion-Exchange Chromatography
Answer Separates sample based on charge. CM attracts +, DEAE attracts -. May have repulsion ettect on
like charges. Salt or acid used to remove stuck proteins.
,6. Hydrophobic/Reverse Phase Chromatography
Answer Beads are coated with a carbon chain. Hy- drophobic proteins stick better. Elute with non-H-
bonding solvent (acetonitrile).
7. Affinity Chromatography
Answer Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or similar ligand.
8. SDS-PAGE
Answer Uses SDS. Gel is made from cross-linked polyacrylamide. Separates based ott of mass with smaller
molecules moving faster. Visualized with Coomassie blue.
9. SDS
Answer Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative charge.
10. Isoelectric Focusing
Answer Variation of gel electrophoresis where protein charge matters. Involves electrodes and pH gradient.
Protein stops at their pI when neutral.
11. 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.
12. DTT (dithiothreitol)
Answer Reduces disulfide bonds.
13. Iodoacetate
Answer Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
14. Homologs
Answer Shares 25% identity with another gene
15. Orthologs
Answer Similar genes in ditterent organisms
16. Paralogs
Answer Similar "paired" genes in the same organism
17. Ramachandran Plot
Answer Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed
α-helices.
18. Glycine Ramachandran Plot
, Answer Glycine can adopt more angles. (H's for R-group).
19. Proline Ramachandran Plot
Answer Proline adopts fewer angles. Amino group is incorporated into a ring.
20. 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 5.4Å.
