ACS BIOCHEMISTRY EXAM (ANSWERED) COMPLETE
VERIFIED SOLUTION 100%
Henderson-Hasselbach Equation
pH = pKa + log ([A-] / [HA])
FMOC Chemical Synthesis
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)
Changes soluble protein to solid precipitate. Protein precipitates when the charges on
the protein match the charges in the solution.
Size-Exclusion Chromatography
Separates sample based on size with smaller molecules eluting later.
Ion-Exchange Chromatography
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
Beads are coated with a carbon chain. Hydrophobic proteins stick better. Elute with
non-H-bonding solvent (acetonitrile).
Affinity Chromatography
Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or similar
ligand.
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.
SDS
Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative charge.
Isoelectric Focusing
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)
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)
Reduces disulfide bonds.
Iodoacetate
Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
Homologs
Shares 25% identity with another gene
Orthologs
Similar genes in different organisms
Paralogs
Similar "paired" genes in the same organism
Ramachandran Plot
Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-sheets, and
left-handed α-helices.
,Glycine Ramachandran Plot
Glycine can adopt more angles. (H's for R-group).
Proline Ramachandran Plot
Proline adopts fewer angles. Amino group is incorporated into a ring.
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.
Helix Dipole
Formed from added dipole moments of all hydrogen bonds in an α-helix. N-terminus is
δ+ and C-terminus is δ-.
ß-sheet
Either parallel or anti-parallel. Often twisted to increase strength.
Anti-parallel ß-sheet
Alternating sheet directions (C & N-termini don't line-up). Has straight H-bonds.
Parallel ß-sheet
Same sheet directions (C & N-termini line up). Has angled H-bonds.
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.
Loops
Not highly structured. Not necessary highly flexible, but can occasionally move. Very
variable in sequence.
Circular Dichroism
Uses UV light to measure 2° structure. Can be used to measure destabilization.
Disulfide-bonds
Bonds between two -SH groups that form between 2° and 3° structure.
ß-mercaptoethanol
Breaks disulfide bonds.
α-keratin
formed from 2 α-helices twisted around each other. "Coiled coil". Cross-linked by
disulfide bonds.
Collagen
Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil". Contains gly core.
Myoglobin 4° Structure
Symmetric homodimer,
Hemoglobin 4° Structure
Tetramer. Dimer of dimers. α2ß2 tetramer.
α/ß Protein Folding
Less distinct areas of α and ß folding.
α+ß Protein Folding
Two distinct areas of α and ß folding.
Mechanism of Denaturants
Highly soluble, H-binding molecules. Stabilize protein backbone in water. Allows
denatured state to be stabilized.
Temperature Denaturation of Protein
Midpoint of reaction is Tm.
, Cooperative Protein Folding
Folding transition is sharp. More reversible.
Folding Funnel
Shows 3D version of 2D energy states. Lowest energy is stable protein. Rough funnel is
less cooperative.
Protein-Protein Interfaces
"Core" and "fringe" of the interfaces. Core is more hydrophobic and is on the inside
when interfaced. Fringe is more hydrophilic.
π-π Ring Stacking
Weird interaction where aromatic rings stack on each other in positive interaction.
σ-hole
Methyl group has area of diminished electron density in center; attracts electronegative
groups
Fe Binding of O2
Fe2+ binds to O2 reversible. Fe3+ has an additional + charge and binds to O2
irreversibly. Fe3+ rusts in O2 rich environments.
Ka for Binding
Ka = [PL] / [P][L]
ϴ-value in Binding
ϴ = (bound / total)x100%
ϴ = [L] / ([L] + 1/Ka)
Kd for binding
Kd = [L] when 50% bound to protein.
Kd = 1/Ka
High-Spin Fe
Electrons are "spread out" and result in larger atom.
Low-Spin Fe
Electrons are less "spread out" and are compacted by electron rich porphyrin ring.
T-State
Heme is in high-spin state. H2O is bound to heme.
R-State
Heme is in low-spin state. O2 is bound to heme.
O2 Binding Event
O2 binds to T-state and changes the heme to R-state. Causes a 0.4Å movement of the
iron.
Hemoglobin Binding Curve
4 subunits present in hemoglobin that can be either T or R -state. Cooperative binding
leads to a sigmoidal curve.
Binding Cooperativity
When one subunit of hemoglobin changes from T to R-state the other sites are more
likely to change to R-state as well. Leads to sigmoidal graph.
Homotropic Regulation of Binding
Where a regulatory molecule is also the enzyme's substrate.
Heterotropic Regulation of Binding
Where an allosteric regulator is present that is not the enzyme's substrate.
Hill Plot
VERIFIED SOLUTION 100%
Henderson-Hasselbach Equation
pH = pKa + log ([A-] / [HA])
FMOC Chemical Synthesis
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)
Changes soluble protein to solid precipitate. Protein precipitates when the charges on
the protein match the charges in the solution.
Size-Exclusion Chromatography
Separates sample based on size with smaller molecules eluting later.
Ion-Exchange Chromatography
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
Beads are coated with a carbon chain. Hydrophobic proteins stick better. Elute with
non-H-bonding solvent (acetonitrile).
Affinity Chromatography
Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or similar
ligand.
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.
SDS
Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative charge.
Isoelectric Focusing
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)
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)
Reduces disulfide bonds.
Iodoacetate
Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
Homologs
Shares 25% identity with another gene
Orthologs
Similar genes in different organisms
Paralogs
Similar "paired" genes in the same organism
Ramachandran Plot
Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-sheets, and
left-handed α-helices.
,Glycine Ramachandran Plot
Glycine can adopt more angles. (H's for R-group).
Proline Ramachandran Plot
Proline adopts fewer angles. Amino group is incorporated into a ring.
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.
Helix Dipole
Formed from added dipole moments of all hydrogen bonds in an α-helix. N-terminus is
δ+ and C-terminus is δ-.
ß-sheet
Either parallel or anti-parallel. Often twisted to increase strength.
Anti-parallel ß-sheet
Alternating sheet directions (C & N-termini don't line-up). Has straight H-bonds.
Parallel ß-sheet
Same sheet directions (C & N-termini line up). Has angled H-bonds.
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.
Loops
Not highly structured. Not necessary highly flexible, but can occasionally move. Very
variable in sequence.
Circular Dichroism
Uses UV light to measure 2° structure. Can be used to measure destabilization.
Disulfide-bonds
Bonds between two -SH groups that form between 2° and 3° structure.
ß-mercaptoethanol
Breaks disulfide bonds.
α-keratin
formed from 2 α-helices twisted around each other. "Coiled coil". Cross-linked by
disulfide bonds.
Collagen
Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil". Contains gly core.
Myoglobin 4° Structure
Symmetric homodimer,
Hemoglobin 4° Structure
Tetramer. Dimer of dimers. α2ß2 tetramer.
α/ß Protein Folding
Less distinct areas of α and ß folding.
α+ß Protein Folding
Two distinct areas of α and ß folding.
Mechanism of Denaturants
Highly soluble, H-binding molecules. Stabilize protein backbone in water. Allows
denatured state to be stabilized.
Temperature Denaturation of Protein
Midpoint of reaction is Tm.
, Cooperative Protein Folding
Folding transition is sharp. More reversible.
Folding Funnel
Shows 3D version of 2D energy states. Lowest energy is stable protein. Rough funnel is
less cooperative.
Protein-Protein Interfaces
"Core" and "fringe" of the interfaces. Core is more hydrophobic and is on the inside
when interfaced. Fringe is more hydrophilic.
π-π Ring Stacking
Weird interaction where aromatic rings stack on each other in positive interaction.
σ-hole
Methyl group has area of diminished electron density in center; attracts electronegative
groups
Fe Binding of O2
Fe2+ binds to O2 reversible. Fe3+ has an additional + charge and binds to O2
irreversibly. Fe3+ rusts in O2 rich environments.
Ka for Binding
Ka = [PL] / [P][L]
ϴ-value in Binding
ϴ = (bound / total)x100%
ϴ = [L] / ([L] + 1/Ka)
Kd for binding
Kd = [L] when 50% bound to protein.
Kd = 1/Ka
High-Spin Fe
Electrons are "spread out" and result in larger atom.
Low-Spin Fe
Electrons are less "spread out" and are compacted by electron rich porphyrin ring.
T-State
Heme is in high-spin state. H2O is bound to heme.
R-State
Heme is in low-spin state. O2 is bound to heme.
O2 Binding Event
O2 binds to T-state and changes the heme to R-state. Causes a 0.4Å movement of the
iron.
Hemoglobin Binding Curve
4 subunits present in hemoglobin that can be either T or R -state. Cooperative binding
leads to a sigmoidal curve.
Binding Cooperativity
When one subunit of hemoglobin changes from T to R-state the other sites are more
likely to change to R-state as well. Leads to sigmoidal graph.
Homotropic Regulation of Binding
Where a regulatory molecule is also the enzyme's substrate.
Heterotropic Regulation of Binding
Where an allosteric regulator is present that is not the enzyme's substrate.
Hill Plot
