ACS BIOCHEMISTRY EXAM | Questions &
Answers (Graded A+) |100% VERIFIED Latest
Update 2023
1). Henderson-hasselbach equation
Ans: pH = pKa + log ([A-] / [HA])
2). Fmoc chemical synthesis
Ans: 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)
Ans: Changes soluble protein to solid precipitate. Protein precipitates when the
charges on the protein match the charges in the solution.
4). Size-exclusion chromatography
Ans: Separates sample based on size with smaller molecules eluting later.
5). Ion-exchange chromatography
Ans: Separates sample based on charge. CM attracts +, DEAE attracts -. May have
repulsion effect on like charges. Salt or acid used to remove stuck proteins.
6). Hydrophobic/reverse phase chromatography
Ans: Beads are coated with a carbon chain. Hydrophobic proteins stick better. Elute
with non-H-bonding solvent (acetonitrile).
7). Affinity chromatography
Ans: Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or
similar ligand.
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, 8). Sds-page
Ans: 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
Ans: Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative
charge.
10). Isoelectric focusing
Ans: 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)
Ans: 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)
Ans: Reduces disulfide bonds.
13). Iodoacetate
Ans: Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
14). Homologs
Ans: Shares 25% identity with another gene
15). Orthologs
Ans: Similar genes in different organisms
16). Paralogs
Ans: Similar "paired" genes in the same organism
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, 17). Ramachandran plot
Ans: Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-
sheets, and left-handed α-helices.
18). Glycine ramachandran plot
Ans: Glycine can adopt more angles. (H's for R-group).
19). Proline ramachandran plot
Ans: Proline adopts fewer angles. Amino group is incorporated into a ring.
20). Α-helices
Ans: 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
Ans: Formed from added dipole moments of all hydrogen bonds in an α-helix. N-
terminus is δ+ and C-terminus is δ-.
22). Ss-sheet
Ans: Either parallel or anti-parallel. Often twisted to increase strength.
23). Anti-parallel ß-sheet
Ans: Alternating sheet directions (C & N-termini don't line-up). Has straight H-bonds.
24). Parallel ß-sheet
Ans: Same sheet directions (C & N-termini line up). Has angled H-bonds.
25). Ss-turns
Ans: 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.
PaperStoc.com Page 3 of 31
, 26). Loops
Ans: Not highly structured. Not necessary highly flexible, but can occasionally move.
Very variable in sequence.
27). Circular dichroism
Ans: Uses UV light to measure 2° structure. Can be used to measure destabilization.
28). Disulfide-bonds
Ans: Bonds between two -SH groups that form between 2° and 3° structure.
29). Ss-mercaptoethanol
Ans: Breaks disulfide bonds.
30). Α-keratin
Ans: formed from 2 α-helices twisted around each other. "Coiled coil". Cross-linked by
disulfide bonds.
31). Collagen
Ans: Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil". Contains gly core.
32). Myoglobin 4° structure
Ans: Symmetric homodimer,
33). Hemoglobin 4° structure
Ans: Tetramer. Dimer of dimers. α2ß2 tetramer.
34). Α/ß protein folding
Ans: Less distinct areas of α and ß folding.
35). Α+ß protein folding
PaperStoc.com Page 4 of 31
Answers (Graded A+) |100% VERIFIED Latest
Update 2023
1). Henderson-hasselbach equation
Ans: pH = pKa + log ([A-] / [HA])
2). Fmoc chemical synthesis
Ans: 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)
Ans: Changes soluble protein to solid precipitate. Protein precipitates when the
charges on the protein match the charges in the solution.
4). Size-exclusion chromatography
Ans: Separates sample based on size with smaller molecules eluting later.
5). Ion-exchange chromatography
Ans: Separates sample based on charge. CM attracts +, DEAE attracts -. May have
repulsion effect on like charges. Salt or acid used to remove stuck proteins.
6). Hydrophobic/reverse phase chromatography
Ans: Beads are coated with a carbon chain. Hydrophobic proteins stick better. Elute
with non-H-bonding solvent (acetonitrile).
7). Affinity chromatography
Ans: Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or
similar ligand.
PaperStoc.com Page 1 of 31
, 8). Sds-page
Ans: 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
Ans: Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative
charge.
10). Isoelectric focusing
Ans: 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)
Ans: 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)
Ans: Reduces disulfide bonds.
13). Iodoacetate
Ans: Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
14). Homologs
Ans: Shares 25% identity with another gene
15). Orthologs
Ans: Similar genes in different organisms
16). Paralogs
Ans: Similar "paired" genes in the same organism
PaperStoc.com Page 2 of 31
, 17). Ramachandran plot
Ans: Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-
sheets, and left-handed α-helices.
18). Glycine ramachandran plot
Ans: Glycine can adopt more angles. (H's for R-group).
19). Proline ramachandran plot
Ans: Proline adopts fewer angles. Amino group is incorporated into a ring.
20). Α-helices
Ans: 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
Ans: Formed from added dipole moments of all hydrogen bonds in an α-helix. N-
terminus is δ+ and C-terminus is δ-.
22). Ss-sheet
Ans: Either parallel or anti-parallel. Often twisted to increase strength.
23). Anti-parallel ß-sheet
Ans: Alternating sheet directions (C & N-termini don't line-up). Has straight H-bonds.
24). Parallel ß-sheet
Ans: Same sheet directions (C & N-termini line up). Has angled H-bonds.
25). Ss-turns
Ans: 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.
PaperStoc.com Page 3 of 31
, 26). Loops
Ans: Not highly structured. Not necessary highly flexible, but can occasionally move.
Very variable in sequence.
27). Circular dichroism
Ans: Uses UV light to measure 2° structure. Can be used to measure destabilization.
28). Disulfide-bonds
Ans: Bonds between two -SH groups that form between 2° and 3° structure.
29). Ss-mercaptoethanol
Ans: Breaks disulfide bonds.
30). Α-keratin
Ans: formed from 2 α-helices twisted around each other. "Coiled coil". Cross-linked by
disulfide bonds.
31). Collagen
Ans: Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil". Contains gly core.
32). Myoglobin 4° structure
Ans: Symmetric homodimer,
33). Hemoglobin 4° structure
Ans: Tetramer. Dimer of dimers. α2ß2 tetramer.
34). Α/ß protein folding
Ans: Less distinct areas of α and ß folding.
35). Α+ß protein folding
PaperStoc.com Page 4 of 31
