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 C^β 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

• pK_a 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 K_m and V_max

• Recognizing the inhibition type from Michaelis-Menten plots

• Recognizing the inhibition type from Lineweaver-Burk plots

• Recognizing the inhibition type from Eadie-Hofstee plots