BIOCHEMISTRY CONCEPTS AND
CONNECTIONS 2026 QUESTION
COLLECTION DNA RNA AND GENE
EXPRESSION MODULE SOLVED ITEMS AND
RESPONSE KEY
◉ 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. 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.
◉ ß-mercaptoethanol. Answer: Breaks disulfide bonds.
◉ α-keratin. Answer: formed from 2 α-helices twisted around each
other. "Coiled coil". Cross-linked by disulfide bonds.
, ◉ Collagen. Answer: Repeating sequence of Gly-X-Pro. 3 stranded
"coiled coil". Contains gly core.
◉ Myoglobin 4° Structure. Answer: Symmetric homodimer,
◉ Hemoglobin 4° Structure. Answer: Tetramer. Dimer of dimers.
α2ß2 tetramer.
◉ α/ß Protein Folding. Answer: Less distinct areas of α and ß
folding.
◉ α+ß Protein Folding. Answer: Two distinct areas of α and ß
folding.
◉ Mechanism of Denaturants. Answer: Highly soluble, H-binding
molecules. Stabilize protein backbone in water. Allows denatured
state to be stabilized.
◉ Temperature Denaturation of Protein. Answer: Midpoint of
reaction is Tm.
◉ Cooperative Protein Folding. Answer: Folding transition is sharp.
More reversible.
CONNECTIONS 2026 QUESTION
COLLECTION DNA RNA AND GENE
EXPRESSION MODULE SOLVED ITEMS AND
RESPONSE KEY
◉ 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. 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.
◉ ß-mercaptoethanol. Answer: Breaks disulfide bonds.
◉ α-keratin. Answer: formed from 2 α-helices twisted around each
other. "Coiled coil". Cross-linked by disulfide bonds.
, ◉ Collagen. Answer: Repeating sequence of Gly-X-Pro. 3 stranded
"coiled coil". Contains gly core.
◉ Myoglobin 4° Structure. Answer: Symmetric homodimer,
◉ Hemoglobin 4° Structure. Answer: Tetramer. Dimer of dimers.
α2ß2 tetramer.
◉ α/ß Protein Folding. Answer: Less distinct areas of α and ß
folding.
◉ α+ß Protein Folding. Answer: Two distinct areas of α and ß
folding.
◉ Mechanism of Denaturants. Answer: Highly soluble, H-binding
molecules. Stabilize protein backbone in water. Allows denatured
state to be stabilized.
◉ Temperature Denaturation of Protein. Answer: Midpoint of
reaction is Tm.
◉ Cooperative Protein Folding. Answer: Folding transition is sharp.
More reversible.
