BIOCHEMISTRY LAB 1 TO 9 REPORTS
PORTAGE LEARNING WITH PROCEDURES
EXPLANATION AND FINAL RESULTS
LATEST UPDATE 2024 ACTUAL
EXAMINATION PAPER 2026 QUESTIONS
WITH ANSWERS GRADED A+
⩥ 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 5.4Å.
, ⩥ 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.
PORTAGE LEARNING WITH PROCEDURES
EXPLANATION AND FINAL RESULTS
LATEST UPDATE 2024 ACTUAL
EXAMINATION PAPER 2026 QUESTIONS
WITH ANSWERS GRADED A+
⩥ 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 5.4Å.
, ⩥ 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.
