ACS BIOCHEMISTRY EXAM|200+ QUESTIONS AND
ANSWERS
What is the Henderson-Hasselbalch Equation?
-pH = pKa + log ([A-] / [HA])
What is the purpose of FMOC in chemical synthesis?
FMOC is used as a protecting group on the N-terminus in synthesizing a growing amino acid
chain to a polystyrene bead.
What is the principle of Salting Out (Purification)?
Salting out changes soluble protein to a solid precipitate when the charges on the protein match
the charges in the solution.
How does Size-Exclusion Chromatography work?
It separates samples based on size, with smaller molecules eluting later.
What are the characteristics of Ion-Exchange Chromatography?
Ion-exchange chromatography separates samples based on charge; CM attracts positively
charged proteins, while DEAE attracts negatively charged proteins. There may be a repulsion
effect on like charges, and salt or acid is used to remove stuck proteins.
Describe Hydrophobic/Reverse Phase Chromatography.
In this method, beads are coated with a carbon chain, allowing hydrophobic proteins to stick
better. Elution is performed with a non-H-bonding solvent, such as acetonitrile.
What is Affinity Chromatography?
Affinity chromatography involves attaching a ligand that binds a protein to a bead and eluting
with harsh chemicals or a similar ligand.
What is SDS-PAGE and how does it work?
SDS-PAGE uses SDS in a gel made from cross-linked polyacrylamide to separate proteins based
on mass, with smaller molecules moving faster. The proteins are visualized with Coomassie blue.
What is SDS?
Sodium dodecyl sulfate (SDS) is a detergent that unfolds proteins and provides them with a
uniform negative charge.
What is Isoelectric Focusing?
Isoelectric focusing is a variation of gel electrophoresis where protein charge matters, involving
electrodes and a pH gradient, causing proteins to stop at their isoelectric point (pI) when neutral.
, What is the function of FDNB (1-fluoro-2,3-dinitrobenzene)?
FDNB reacts with the N-terminus of proteins to produce a 2,4-dinitrophenol derivative that
labels the first residue, which can be hydrolyzed to determine sequential amino acids.
What is the role of DTT (dithiothreitol)?
DTT reduces disulfide bonds.
What is the purpose of iodoacetate in protein chemistry?
Iodoacetate adds a carboxymethyl group to free -SH groups, blocking disulfide bonding.
Define Homologs in the context of genes.
Homologs share 25% identity with another gene.
What are Orthologs?
Orthologs are similar genes found in different organisms.
Describe Paralogs.
Paralogs are similar "paired" genes within the same organism.
What does a Ramachandran Plot depict?
A Ramachandran Plot shows favorable phi-psi angle combinations, with main "wells" for alpha
helices, beta sheets, and left-handed alpha helices.
How does glycine influence the Ramachandran Plot?
Glycine can adopt more angles due to its small R-group (hydrogen).
What are the characteristics of α-helices?
Alanine is a common component, while glycine and proline are less common. There are side-
chain interactions every 3 or 4 residues, and it turns once every 3.6 residues with a distance of
5.4 Å between backbones.
What is the Helix Dipole?
The helix dipole is formed from the added dipole moments of all hydrogen bonds in an α-helix,
with the N-terminus being 6+ and the C-terminus being 6-.
Describe the characteristics of β-sheets.
β-sheets can be either parallel or anti-parallel and are often twisted to increase structural strength.
What distinguishes Anti-parallel β-sheets from Parallel β-sheets?
In anti-parallel β-sheets, the C and N-termini alternate (do not line up) with straight hydrogen
bonds, while in parallel β-sheets, the C and N-termini align, leading to angled hydrogen bonds.
ANSWERS
What is the Henderson-Hasselbalch Equation?
-pH = pKa + log ([A-] / [HA])
What is the purpose of FMOC in chemical synthesis?
FMOC is used as a protecting group on the N-terminus in synthesizing a growing amino acid
chain to a polystyrene bead.
What is the principle of Salting Out (Purification)?
Salting out changes soluble protein to a solid precipitate when the charges on the protein match
the charges in the solution.
How does Size-Exclusion Chromatography work?
It separates samples based on size, with smaller molecules eluting later.
What are the characteristics of Ion-Exchange Chromatography?
Ion-exchange chromatography separates samples based on charge; CM attracts positively
charged proteins, while DEAE attracts negatively charged proteins. There may be a repulsion
effect on like charges, and salt or acid is used to remove stuck proteins.
Describe Hydrophobic/Reverse Phase Chromatography.
In this method, beads are coated with a carbon chain, allowing hydrophobic proteins to stick
better. Elution is performed with a non-H-bonding solvent, such as acetonitrile.
What is Affinity Chromatography?
Affinity chromatography involves attaching a ligand that binds a protein to a bead and eluting
with harsh chemicals or a similar ligand.
What is SDS-PAGE and how does it work?
SDS-PAGE uses SDS in a gel made from cross-linked polyacrylamide to separate proteins based
on mass, with smaller molecules moving faster. The proteins are visualized with Coomassie blue.
What is SDS?
Sodium dodecyl sulfate (SDS) is a detergent that unfolds proteins and provides them with a
uniform negative charge.
What is Isoelectric Focusing?
Isoelectric focusing is a variation of gel electrophoresis where protein charge matters, involving
electrodes and a pH gradient, causing proteins to stop at their isoelectric point (pI) when neutral.
, What is the function of FDNB (1-fluoro-2,3-dinitrobenzene)?
FDNB reacts with the N-terminus of proteins to produce a 2,4-dinitrophenol derivative that
labels the first residue, which can be hydrolyzed to determine sequential amino acids.
What is the role of DTT (dithiothreitol)?
DTT reduces disulfide bonds.
What is the purpose of iodoacetate in protein chemistry?
Iodoacetate adds a carboxymethyl group to free -SH groups, blocking disulfide bonding.
Define Homologs in the context of genes.
Homologs share 25% identity with another gene.
What are Orthologs?
Orthologs are similar genes found in different organisms.
Describe Paralogs.
Paralogs are similar "paired" genes within the same organism.
What does a Ramachandran Plot depict?
A Ramachandran Plot shows favorable phi-psi angle combinations, with main "wells" for alpha
helices, beta sheets, and left-handed alpha helices.
How does glycine influence the Ramachandran Plot?
Glycine can adopt more angles due to its small R-group (hydrogen).
What are the characteristics of α-helices?
Alanine is a common component, while glycine and proline are less common. There are side-
chain interactions every 3 or 4 residues, and it turns once every 3.6 residues with a distance of
5.4 Å between backbones.
What is the Helix Dipole?
The helix dipole is formed from the added dipole moments of all hydrogen bonds in an α-helix,
with the N-terminus being 6+ and the C-terminus being 6-.
Describe the characteristics of β-sheets.
β-sheets can be either parallel or anti-parallel and are often twisted to increase structural strength.
What distinguishes Anti-parallel β-sheets from Parallel β-sheets?
In anti-parallel β-sheets, the C and N-termini alternate (do not line up) with straight hydrogen
bonds, while in parallel β-sheets, the C and N-termini align, leading to angled hydrogen bonds.
