Terminology

amino acid - An organic acid containing an amino group on the carbon immediately adjacent to the carboxyl group (Figure 5.3). The building blocks of proteins.

Aminoacyl-tRNA - tRNA molecules carry amino acids to the ribosomes to be incorporated into polypeptide chains in translation. tRNAs linked to amino acids are called aminoacyl-tRNAs (Figure 5.19).

Aminoacyl-tRNA synthetases - Enzymes that catalyze the covalent linkage of amino acids to specific tRNAs are called aminoacyl-tRNA synthetases (Figure 5.19).

Anticodon loop - A loop at one end of a tRNA molecule that is complementary to the codon of a mRNA. Since amino acids are put onto tRNAs (to form an aminoacyl-tRNA) according to the sequence of the anticodon loop, pairing of the aminoacyl-tRNA's anticodon and the mRNA's codon provides a mechanism for a specific amino acid to be incorporated into a growing polypeptide chain in translation (Figure 5.20).

Asymmetric center - (center of chirality) - With respect to organic compounds, a carbon atom that has four different substituents attached to it; such a group cannot be superimposed on its own mirror image and therefore can occur in two enantiomers (Figure 5.5).

Chiral - With respect to a molecule or other object, the property of being nonsuperimposable on its mirror image. An atom that makes a molecule chiral, such as a carbon with four different substituents, is called a chiral atom or center of chirality (Figure 5.5).

Cystine - The amino acid cysteine frequently forms disulfide bonds with other cysteines. The resulting disulfide form of cysteine is called cystine (see here).

Dipeptide - A dipeptide is a molecule containing two amino acids joined by a peptide bond (Figure 5.8).

Disulfide bond - A direct covalent bond between two sulfur atoms is called a disulfide bond. The amino acid cysteine frequently forms disulfide bonds with other cysteines. The resulting disulfide form of cysteine is called cystine (Figure 5.15).

Enantiomers - (also called optical isomers) - Stereoisomers that are nonsuperimposable mirror images of each other. The term optical isomers comes from the fact that the enantiomers of a compound rotate polarized light in opposite directions (Figure 5.5).

Enzymes - Proteins that catalyze chemical reactions are called enzymes.

Genetic code - The code by which the nucleotide sequence of a DNA or RNA molecule specifies the amino acid sequence of a polypeptide. It consists of three-nucleotide codons that either specify a particular amino acid or tell the ribosome to stop translating and release the polypeptide. With a few minor exceptions, all living things use the same code (Figure 5.16).

Leader Sequence - For a protein, a short N-terminal hydrophobic sequence that causes the protein to be translocated into or through a cellular membrane (Figure 5.21).

Oligopeptide - An oligonucleotide is a chain of several amino acids linked by peptide bonds.

Optical Isomers - See enantiomers

Peptide - Molecules containing peptide bonds are referred to generically as peptides.

Peptide bond - The bond that links successive amino acids in a peptide; it consists of an amide bond between the -carboxyl group of one amino acid and the -amino group of the next (Figure 5.21).

Polyampholytes - Molecules which contain multiple acidic and basic groups.

Polypeptide - A polypeptide is a chain of many amino acids linked by peptide bonds.

Primary structure of a protein - Refers simply to the sequence of amino acids in a protein.

Proteases - (also called proteolytic enzymes) - Enzymes that cleave peptide bonds in a polypeptide. Many show specificity for a particular amino acid sequence.

Proteins - Proteins can be thought of as mature polypeptide chains. Like a polypeptide, proteins are a chain of amino acids joined by peptide bonds, but proteins differ from polypeptides in being folded into the proper 3D configuration and/or modified. Proteins may consist of one or more polypeptide chains (Figure 5.20).

Stereoisomers - Molecules containing a center of asymmetry can exist in different 3D isomeric forms. Stereoisomers refers to the different forms (Figure 5.5).

Tetrapeptide - A tetrapeptide is a chain of four amino acids linked by peptide bonds (Figure 5.9).

Translation - The synthesis of a polypeptide under the direction of an mRNA, so that the nucleotide sequence of the mRNA is "translated" into the amino acid sequence of the protein (Figure 5.20).

Zwitterion - A molecule with equal numbers of positive and negative charges - thus the net charge is zero (Figure 5.2).