BCB 410 Applied Bioinformatics
Fall 2009 - Course Webpage

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Terms:

Alpha Helix – Along with beta-strands, one of two primary forms of protein secondary structure.

Amino acid – A small organic molecule with a backbone (containing an amine group (N terminus) and an carboxyl group (C terminus)) and a sidechain.  There are 20 naturally occurring amino acids.  Sidechains vary between the amino acids (each with different chemical properties) but all amino acids (except proline) have a conserved, identical backbone.  The backbone carbon connected to the sidechain is known as the alpha carbon (Ca).  Amino acids may be grouped by chemical property.

Beta Strand – Along with alpha helices, one of two primary forms of protein secondary structure.  Beta strands can form beta sheets which can have parallel or anti-parallel strands.

Chirality – A chiral molecule is not superimposible with its mirror image (consider your hands).  Amino acids are chiral.

Codon – Three nucleotide word directing protein synthesis from a nucleotide template.  There are 64 nucleotides which code for the 20 amino acids (degeneracy), start, and stop.

Computational Structural Biology (aka Structural Bioinformatics, Structural Genomics) – Area of computational biology concerned with developing algorithms for the prediction, analysis, and modeling of molecular structure.

DNA / RNA – Deoxyribonucleic acid and Ribonucleic acid; the genetic blueprint for development and functioning of organisms.  Composed of a series of nucleotides (A,T,G,C in DNA; U replaces T in RNA).  In the context of this course, DNA contains genes which encode proteins.  DNA is transcribed into mRNA (messenger RNA) which is then translated by the ribosome into a linear chain of amino acids – a protein.

Domain – A compact region of protein structure.  Often capable of folding stably on its own.  Proteins may have one or more than one domain.

Empirical Force Field – The parameters and formulation of an equation to describe molecular forces and energy.  Empirical f    orce fields are derived from experiment.

Enzyme – A protein with catalytic function; that is, an enzyme catalyzes a chemical reaction (i.e., makes the reaction proceed more quickly towards equilibrium).

Homologue – Shared sequence of structure due to evolution from a common ancestor.

Hydrophilic – Water ‘loving’; Refers to molecules that generously interact with water.

Hydrophobic – Water ‘fearing’; Refers to molecules that do not interact well with water.

Inhibitor – A small molecule capable of binding to interfere with a target biomolecule’s normal functining.  Inhibitors are generally competitive inhibitors, competing with the natural substrate for a common biomolecular (typically prtoein) binding site.

Ligand – A small molecule, typically organic, able to bind a biomolecule to serve a purpose.  Some ligands function as substrates (starting materials for a reaction) or inhibitors.

Macromolecule – A large molecule, generally proteins or nucleic acids (DNA/RNA)

NMR (Nuclear Magnetic Resonance) Spectroscopy – An experimental method for determining protein structure.  Proteins must be labeled with NMR active atomic isotopes.  A series of experiments specify interatomic geometric constraints and an ensemble of structures maximally consistent with these constraints is generated.  The atoms involved in each geometric constraint are initially unknown; atoms must be assigned to each spectral peak in the NMR experiments; this is the assignment problem.

PDB – The Protein DataBank.  Also refers to files from the protein databank, i.e., pdb files.

Peptide – A small protein or linear sequence of amino acids.  Peptides have no strict length restrictions.

Pharmacophore – A molecular framework [or description] that carries the essential features responsible for a drug’s biological activity –Paul Erlich

Phi / Psi Angles – The two flexible (i.e., rotatable) backbone bonds in a protein.  Phi and Psi values cluster for different secondary structure types.

Products – The ending materials in a chemical reaction.

Protein – Large, organic molecules (macromolecules).  Composed of a linear chain of amino acids which (generally) folds into a unique compact three-dimensional structure.  A protein's sequence of amino acids (its 'primary structure') is specified by its encoding gene.  Sequences are generally listed in the N to C direction (from the N-terminus to the C-terminus).

Residue – Each amino acid position in a protein is called a residue.  Sometimes referred to by position (i.e., residue 38).

Rotamer – A discrete, static, sidechain conformation for an amino acid.  An amino acid will typically have a number of possible sidechain rotamers.  Rotamers are identified through molecular simulation or mined from structure databases.

Secondary Structure – Regularities in the structure of a run of amino acids within a protein.  Generally alpha helices, and beta strands.  Occasionally, turns and loops are considered as well.

Structural Biology – Area of molecular biology concerned with the study of molecular (generally macromolecular) structure.

Structural Motif – A common arrangement of multiple secondary structure elements or residues.

Substrate – The starting materials in a chemical reaction.

X-ray Crystallography – An experimental method for determining protein structure.  A protein crystal is grown and then used to diffract a beam of high-intensity x-rays.  The diffraction pattern is the magnitude of the Fourier transform of the crystal’s electron density.  The phases of this transform are not observed and must be approximated.  This is the phase problem.

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