ACS BIOCHEMISTRY EXAM
Study online at https://quizlet.com/_18rdlu
1. Henderson-Has- pH = pKa + log ([A-] / [HA])
selbach Equation
2. FMOC Chemical Used in synthesis of a growing amino acid chain to a polystyrene bead. FMOC is
Synthesis used as a protecting group on the N-terminus.
3. Salting Out (Pu- Changes soluble protein to solid precipitate. Protein precipitates when the
rification) charges on the protein match the charges in the solution.
4. Size-Exclusion Separates sample based on size with smaller molecules eluting later.
Chromatography
5. Ion-Exchange Separates sample based on charge. CM attracts +, DEAE attracts -. May have
Chromatography repulsion effect on like charges. Salt or acid used to remove stuck proteins.
6. Hydrophobic/Re- Beads are coated with a carbon chain. Hydrophobic proteins stick better. Elute
verse Phase with non-H-bonding solvent (acetonitrile).
Chromatography
7. Affinity Chro- Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or similar
matography ligand.
8. SDS-PAGE Uses SDS. Gel is made from cross-linked polyacrylamide. Separates based off of
mass with smaller molecules moving faster. Visualized with Coomassie blue.
9. SDS Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative
charge.
10. Isoelectric Focus- Variation of gel electrophoresis where protein charge matters. Involves electrodes
ing and pH gradient. Protein stops at their pI when neutral.
11. FDNB FDNB reacts with the N-terminus of the protein to produce a 2,4-dinitrophenol
(1-fluoro-2,3-dini- derivative that labels the first residue. Can repeat hydrolysis to determine sequen-
trobenzene) tial amino acids.
, ACS BIOCHEMISTRY EXAM
Study online at https://quizlet.com/_18rdlu
12. DTT (dithiothre- Reduces disulfide bonds.
itol)
13. Iodoacetate Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
14. Homologs Shares 25% identity with another gene
15. Orthologs Similar genes in different organisms
16. Paralogs Similar "paired" genes in the same organism
17. Ramachandran Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices,
Plot ß-sheets, and left-handed α-helices.
18. Glycine Ra- Glycine can adopt more angles. (H's for R-group).
machandran Plot
19. Proline Ra- Proline adopts fewer angles. Amino group is incorporated into a ring.
machandran Plot
20. α-helices 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.
21. Helix Dipole Formed from added dipole moments of all hydrogen bonds in an α-helix. N-ter-
minus is δ+ and C-terminus is δ-.
22. ß-sheet Either parallel or anti-parallel. Often twisted to increase strength.
23. Alternating sheet directions (C & N-termini don't line-up). Has straight H-bonds.
, ACS BIOCHEMISTRY EXAM
Study online at https://quizlet.com/_18rdlu
Anti-parallel
ß-sheet
24. Parallel ß-sheet Same sheet directions (C & N-termini line up). Has angled H-bonds.
25. ß-turns 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.
26. Loops Not highly structured. Not necessary highly flexible, but can occasionally move.
Very variable in sequence.
27. Circular Dichro- Uses UV light to measure 2° structure. Can be used to measure destabilization.
ism
28. Disulfide-bonds Bonds between two -SH groups that form between 2° and 3° structure.
29. ß-mercap- Breaks disulfide bonds.
toethanol
30. α-keratin formed from 2 α-helices twisted around each other. "Coiled coil". Cross-linked by
disulfide bonds.
31. Collagen Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil". Contains gly core.
32. Myoglobin 4° Symmetric homodimer,
Structure
33. Hemoglobin 4° Tetramer. Dimer of dimers. α2ß2 tetramer.
Structure
34. Less distinct areas of α and ß folding.
Study online at https://quizlet.com/_18rdlu
1. Henderson-Has- pH = pKa + log ([A-] / [HA])
selbach Equation
2. FMOC Chemical Used in synthesis of a growing amino acid chain to a polystyrene bead. FMOC is
Synthesis used as a protecting group on the N-terminus.
3. Salting Out (Pu- Changes soluble protein to solid precipitate. Protein precipitates when the
rification) charges on the protein match the charges in the solution.
4. Size-Exclusion Separates sample based on size with smaller molecules eluting later.
Chromatography
5. Ion-Exchange Separates sample based on charge. CM attracts +, DEAE attracts -. May have
Chromatography repulsion effect on like charges. Salt or acid used to remove stuck proteins.
6. Hydrophobic/Re- Beads are coated with a carbon chain. Hydrophobic proteins stick better. Elute
verse Phase with non-H-bonding solvent (acetonitrile).
Chromatography
7. Affinity Chro- Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or similar
matography ligand.
8. SDS-PAGE Uses SDS. Gel is made from cross-linked polyacrylamide. Separates based off of
mass with smaller molecules moving faster. Visualized with Coomassie blue.
9. SDS Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative
charge.
10. Isoelectric Focus- Variation of gel electrophoresis where protein charge matters. Involves electrodes
ing and pH gradient. Protein stops at their pI when neutral.
11. FDNB FDNB reacts with the N-terminus of the protein to produce a 2,4-dinitrophenol
(1-fluoro-2,3-dini- derivative that labels the first residue. Can repeat hydrolysis to determine sequen-
trobenzene) tial amino acids.
, ACS BIOCHEMISTRY EXAM
Study online at https://quizlet.com/_18rdlu
12. DTT (dithiothre- Reduces disulfide bonds.
itol)
13. Iodoacetate Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
14. Homologs Shares 25% identity with another gene
15. Orthologs Similar genes in different organisms
16. Paralogs Similar "paired" genes in the same organism
17. Ramachandran Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices,
Plot ß-sheets, and left-handed α-helices.
18. Glycine Ra- Glycine can adopt more angles. (H's for R-group).
machandran Plot
19. Proline Ra- Proline adopts fewer angles. Amino group is incorporated into a ring.
machandran Plot
20. α-helices 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.
21. Helix Dipole Formed from added dipole moments of all hydrogen bonds in an α-helix. N-ter-
minus is δ+ and C-terminus is δ-.
22. ß-sheet Either parallel or anti-parallel. Often twisted to increase strength.
23. Alternating sheet directions (C & N-termini don't line-up). Has straight H-bonds.
, ACS BIOCHEMISTRY EXAM
Study online at https://quizlet.com/_18rdlu
Anti-parallel
ß-sheet
24. Parallel ß-sheet Same sheet directions (C & N-termini line up). Has angled H-bonds.
25. ß-turns 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.
26. Loops Not highly structured. Not necessary highly flexible, but can occasionally move.
Very variable in sequence.
27. Circular Dichro- Uses UV light to measure 2° structure. Can be used to measure destabilization.
ism
28. Disulfide-bonds Bonds between two -SH groups that form between 2° and 3° structure.
29. ß-mercap- Breaks disulfide bonds.
toethanol
30. α-keratin formed from 2 α-helices twisted around each other. "Coiled coil". Cross-linked by
disulfide bonds.
31. Collagen Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil". Contains gly core.
32. Myoglobin 4° Symmetric homodimer,
Structure
33. Hemoglobin 4° Tetramer. Dimer of dimers. α2ß2 tetramer.
Structure
34. Less distinct areas of α and ß folding.
