Lehninger Principles of Biochemistry: Chapter 3 Key Terms

amino acids

α-Amino-substituted carboxylic acids, the building blocks of proteins.

residue

A single unit in a polymer; for example, an amino acid in a polypeptide chain. The term reflects the fact that sugars, nucleotides, and amino acids lose a few atoms (generally the elements of water) when incorporated in their respective polymers.

R group

(1) Formally, an abbreviation denoting any alkyl group. (2) Occasionally, used in a more general sense to denote virtually any organic substituent (e.g., the R groups of amino acids).

chiral center

An atom with substituents arranged so that the molecule is not superposable on its mirror image.

enantiomers

Stereoisomers that are nonsuperposable mirror images of each other.

absolute configuration

The configuration of four different substituent groups around an asymmetric carbon atom, in relation to ᴅ- and ʟ-glyceraldehyde.

ᴅ, ʟ system

Make sure that the molecule is drawn as the Fischer projection in which the carboxylic acid group is on top and the side chain on bottom. If the amine group is on the right of the carbon chain, assign the label ᴅ to the compound; if it is on the left of the carbon chain, assign the label ʟ.

polarity

(1) In chemistry, the nonuniform distribution of electrons in a molecule; polar molecules are usually soluble in water. (2) In molecular biology, the distinction between the 5' and 3' ends of nucleic acids.

absorbance, A

A measure of the capacity of a substance to absorb light of a specified wavelength. It is equal to the logarithm of the reciprocal of the transmittance.

zwitterion

A dipolar ion with spatially separated positive and negative charges.

isoelectric pH (isoelectric point, pI)

The pH at which a solute has no net electric charge and thus does not move in an electric field.

peptide

Two or more amino acids covalently joined by peptide bonds.

protein

A macromolecule composed of one or more polypeptide chains, each with a characteristic sequence of amino acids linked by peptide bonds.

peptide bond

A substituted amide linkage between the α-amino group of one amino acid and the α-carboxyl group of another, with elimination of the elements of water.

oligopeptide

A short polymer of amino acids joined by peptide bonds.

polypeptide

A long chain of amino acids linked by peptide bonds; the molecular weight is generally less than 10,000.

oligomeric protein

A multisubunit protein having two or more polypeptide chains.

protomer

A general term describing any repeated unit of one or more stably associated protein subunits in a larger protein structure. In a protomer with multiple subunits, the subunits may be identical or different.

conjugated protein

A protein containing one or more prosthetic groups.

prosthetic group

A metal ion or organic compound (other than an amino acid) covalently bound to a protein and essential to its activity.

crude extract

Usually of cells when they are suspended in buffer and broken up and nothing is removed.

fraction

A portion of a biological sample that has been subjected to a procedure designed to separate macromolecules based on a property such as solubility, net charge, molecular weight, or function.

fractionation

The process of separating the proteins or other components of a complex molecular mixture into fractions based on differences in properties such as solubility, net charge, molecular weight, or function.

dialysis

Removal of small molecules from a solution of a macromolecule by their diffusion through a semipermeable membrane into a suitably buffered solution.

column chromatography

A chromatography method used to isolate a single chemical compound from a mixture.

ion-exchange chromatography

A process for separating complex mixtures of ionic compounds by many repeated partitionings between a flowing (mobile) phase and a stationary phase consisting of a polymeric resin that contains fixed charged groups.

size-exclusion chromatography

A procedure for separation of molecules by size, based on the capacity of porous polymers to exclude solutes above a certain size; also called gel filtration.

affinity chromatography

A method of separating biochemical mixture based on a highly specific interaction between antigen and antibody, enzyme and substrate, receptor and ligand, or protein and nucleic acid.

high-performance liquid chromatography (HPLC)

Chromatographic procedure, often conducted at relatively high pressures using automated equipment, which permits refined and highly reproducible profiles.

electrophoresis

Movement of charged solutes in response to an electrical field; often used to separate mixtures of ions, proteins, or nucleic acids.

sodium dodecyl sulfate (SDS)

A synthetic organic compound with the formula CH₃(CH₂)₁₁SO₄ Na. It is an anionic surfactant used in many cleaning and hygiene products.

isoelectric focusing

An electrophoretic method for separating macromolecules on the basis of isoelectric pH.

specific activity

The number of micromoles (μmol) of a substrate transformed by an enzyme preparation per minute per milligram of protein at 25 ℃, with a specified concentration and light path.

primary structure

A description of the covalent backbone of a polymer (macromolecule), including the sequence of monomeric subunits and any interchain and intrachain covalent bonds.

secondary structure

The local spatial arrangement of the main-chain atoms in a segment of a polymer (polypeptide or polynucleotide) chain.

tertiary structure

The three-dimensional conformation of a polymer in its native, folded state.

quaternary structure

The three-dimensional structure of a multisubunit protein, particularly the manner in which the subunits fit together.

Edman degradation

A method of sequencing amino acids in a peptide.

In this method, the amino-terminal residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues.

proteases

Enzymes that catalyze the hydrolytic cleavage of peptide bonds in proteins.

MALDI MS

An ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation.

ESI MS

A technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules because it overcomes the propensity of these molecules to fragment when ionized.

consensus sequence

A DNA or amino acid sequence consisting of the residues that most commonly occur at each position in a set of similar sequences.

bioinformatics

The computerized analysis of biological data, using methods derived from statistics, linguistics, mathematics, chemistry, biochemistry, and physics. The data are often nucleic acid or protein sequences or structural data, but can also include other experimental data, patient statistics, and materials in the scientific literature. Bioinformatics research focuses on methods for data storage, retrieval, and analysis.

horizontal gene transfer

The movement of genetic material between unicellular and/or multicellular organisms other than by the transmission of DNA from parent to offspring.

homologous proteins

Proteins having similar sequences and functions in different species; for example, the hemoglobins.

homologs

Genes or proteins that possess a clear sequence and functional relationship to each other.

paralogs

Genes or proteins present in the same species that possess a clear sequence and functional relationship to each other.

orthologs

Genes or proteins from different species that possess a clear sequence and functional relationship to each other.

signature sequence

Contiguous patterns of amino acids 10-50 residues long that are associated with a particular structure or function in proteins.