User:Proteins/MCB LONCAPA questions

The following LON-CAPA questions were written by me and are released into the public domain. They're intended for late undergraduate (junior/senior level) or first-year graduate students in biochemistry. This initial set focuses on protein science and enzymology.

Basic chemistry and molecular interactions

 * Definition of atomic number


 * Typical length of a covalent bond


 * Typical number of bonds made by atomic elements


 * Boiling points and molecular interactions

Amino acid structure

 * Identify the 1-letter codes for amino acids


 * Identify the 3-letter codes for amino acids


 * Identify the achiral amino acid


 * Identify the cyclic amino acid


 * Determine chirality of amino acid


 * Amino-acid side chains with a chiral carbon


 * Amino-acid side chains with an amide group


 * Amino-acid side chains with an aromatic ring


 * Amino acids branched at the Cβ atom


 * Amino-acid side chains with a guanidino group


 * Amino-acid side chains with a hydroxyl group


 * Amino-acid side chains with an imidazole group


 * Amino-acid side chains with an indole group


 * Amino acid most similar to cysteine


 * Amino acid most similar to glutamate


 * Amino acid most similar to serine


 * Amino acid most similar to tyrosine


 * Amino acid most similar to valine


 * IUPAC systematic names for the amino acids


 * Chemical formulae for the amino-acid side chains

Amino acid biophysics

 * Amino acids that absorb at 280 nm


 * Fluorescent amino acids


 * Free-radical amino acids


 * Amino acids that bind soft metals


 * Amino acids that bind hard metals


 * Hydrophobic amino acids


 * H-bonding properties of amino-acid side chains


 * pKa shifts due to H-bonding between aspartate and tyrosine side chains


 * Identify a molecular interaction between arginine and glutamate side chains


 * Identify a molecular interaction between arginine and tryptophan side chains


 * Identify a molecular interaction between two phenylalanine side chains

pH and buffers

 * Definition of pH


 * Inverse definition of pH


 * Deprotonated to protonated ratio

Titrations

 * Monoprotic titration


 * Diprotic titration


 * Polar but non-titrating amino acids


 * pKa values of amino acids


 * Identify an amino acid from its titration curve


 * Estimate pI of an amino acid


 * Estimate pI of a peptide from its primary sequence


 * Amino-acid composition from titration curve of peptide


 * Amino-acid composition from titration curve of cyclic peptide


 * Estimate pI of a peptide from its titration curve


 * Estimate pI of a cyclic peptide from its titration curve


 * Charge on a peptide at pH 1.0


 * Charge on a peptide at pH 5.0


 * Charge on a peptide at pH 7.4


 * Charge on a peptide at pH 9.0


 * Charge on a peptide at pH 11.5


 * Charge on a peptide at pH 14.0

Posttranslational modifications

 * Disulfide bonds


 * Acetylation sites on polypeptides


 * Carboxylation sites on polypeptides


 * Deamidation sites on polypeptides


 * Glycosylation sites on polypeptides


 * Glycosylphosphatidyl inositol (GPI) anchor location on polypeptides
 * Hydroxylation sites on polypeptides


 * Methylation sites on polypeptides


 * Myristoylation sites on polypeptides


 * Palmitoylation sites on polypeptides


 * Phosphorylation sites on polypeptides


 * Prenylation sites on polypeptides


 * Sulfation sites on polypeptides


 * SUMOylation sites on polypeptides


 * Ubiquitination sites on polypeptides

Dihedral angles and Ramachandran plots

 * Dihedral angles for cis and trans isomers


 * Estimating a generic dihedral angle


 * Definitions of protein dihedral angles


 * Match protein backbone dihedral angles φ and ψ to characteristic secondary structure


 * Amino acid typical of protein backbone dihedral angles (+120°, -120°)


 * Amino acid incapable of adopting protein backbone dihedral angles (-120°, +120°)


 * Identify the protein helix type from its backbone dihedral angles

Secondary structure

 * Amino acids that generally favor α-helical structure


 * Amino acids that generally favor β-sheet structure


 * Amino acids that generally favor irregular structure


 * Amino acids that disrupt α-helices and β-sheets


 * H-bond definitions of secondary structure


 * Relative orientation of adjacent peptide bonds in α-helices


 * Relative orientation of adjacent peptide bonds in β-strands


 * Sidechain direction in α-helices


 * Sidechain direction along a β-strand


 * Sidechain direction across a β-sheet

Peptide bonds and cis-trans isomerization

 * Peptide bond order


 * Peptide group properties


 * Dihedral angle for isomerization of peptide bond


 * Number of cis-trans isomeric states


 * Transition state for cis-trans isomerization


 * Factors affecting catalysis of peptidyl cis-trans isomerization

Tertiary structure and protein folding

 * Typical conformational stability of folded proteins


 * Typical structural domain size


 * Identifying foldases


 * Molten globule properties


 * Mechanisms of protein unfolding

Protein purification and analysis

 * SDS-PAGE gels


 * Two-dimensional SDS-PAGE gels


 * Principle of gel filtration


 * Principle of ion-exchange chromatography


 * Principle of isochromatic focusing chromatography


 * Principle of affinity chromatography


 * Principle of reverse-phase chromatography


 * Purification of (His)6-tagged proteins


 * Separation of protein digests


 * Gel-filtration elution dependence


 * Ion-exchange elution dependence

Ligand binding

 * Definition of allostery


 * Recognizing type of cooperativity from Hill plot

Enzyme basics

 * Definition of reaction transition state


 * Recognizing the first EC number of an enzyme


 * Enzyme properties essential for effective catalysis

Enzyme kinetics

 * Recognizing the Michaelis-Menten equation


 * Estimating enzymatic parameters from an Michaelis-Menten plot


 * Estimating enzymatic parameters from a Lineweaver-Burk plot


 * Estimating enzymatic parameters from an Eadie-Hofstee plot

Enzyme inhibition

 * Binding affinities of various enzyme inhibitors


 * Effects of various inhibitors on Km and Vmax


 * Recognizing the inhibition type from Michaelis-Menten plots


 * Recognizing the inhibition type from Lineweaver-Burk plots


 * Recognizing the inhibition type from Eadie-Hofstee plots