aminoacyl tRNA synthetase               The enzyme that attaches the correct amino acid to an rRNA molecule.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    amino terminus                          The end of a polypeptide chain at which the amino acid bears a free amino group (--NH2).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                anticodon                               The three bases in an rRNA molecule that are complementary to the three-base codon in mRNA.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             AUG                                     The usual initiation codon for polypeptide synthesis as well as the internal codon for methionine. In prokaryotes it codes for formyl-methionine when used as a START codon                                                                                                                                                                                                                                                                                                                                                                                                                                             cap                                     A complex structure containing the G base at the 5' termini of most eukaryotic mRNA molecules, having a  5'-5' linkage instead of the usual 3'-5' linkage.                                                                                                                                                                                                                                                                                                                                                                                                                                                              carboxyl terminus                       The end of a polypeptide chain at which the amino acid has a free carboxyl group (--COOH).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              chain elongation                        The process of addition of successive amino acids to the growing end of a polypeptide chain.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            chain initiation                        Process by which polypeptide synthesis is begun.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        chain termination                       Process of ending polypeptide synthesis and releasing the polypeptide from the ribosome; a chain-termination mutation creates a new stop codon, resulting in premature termination of synthesis of the polypeptide chain.                                                                                                                                                                                                                                                                                                                                                                                               charged rRNA                            A tRNA molecule to which an amino acid is linked; acylated tRNA.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        codon                                   A sequence of three adjacent nucleotides in an mRNA molecule specifying either an amino acid or a stop signal in protein synthesis.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     colinearity                             The linear correspondence between the order of amino acids in a polypeptide chain and the corresponding sequence of nucleotides in the DNA molecule.                                                                                                                                                                                                                                                                                                                                                                                                                                                                    consensus sequence                      A generalized base sequence derived from closely related sequences found in many locations in a genome or in many organisms; each position in the consensus sequence consists of the base found in the majority of sequences at that position.                                                                                                                                                                                                                                                                                                                                                                          coupled transcription-translation       In prokaryotes, the translation of an mRNA molecule before its transcription is completed.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              cryptic splice site                     A potential splice site not normally used in RNA processing unless a normal splice site is blocked or mutated.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          exon                                    The sequences in a gene that are retained in the messenger RNA after the introns are removed from the primary transcript.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               exon shuffle                            Theory in which new genes can evolve by the assembly of separate exons from preexisting genes, each coding for a discrete functional domain in the new protein.                                                                                                                                                                                                                                                                                                                                                                                                                                                         folding domain                          Part of a polypeptide chain within which interactions between amino acids result in a characteristic three-dimensional conformation.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    frameshift mutation                     A mutational event caused by the insertion or deletion of one or more nucleotide pairs in a gene, resulting in a shift in the reading frame of all codons following the mutational site.                                                                                                                                                                                                                                                                                                                                                                                                                                gene expression                         The multistep process by which a gene is regulated and its product synthesized.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         gene product                            A term used for the polypeptide chain translated from an mRNA molecule transcribed from a gene; if the RNA is not translated (for example, ribosomal RNA), the RNA molecule is the gene product.                                                                                                                                                                                                                                                                                                                                                                                                                        genetic code                            The set of 64 triplets of bases (codons) corresponding to each amino acid and to signals for initiation and termination of polypeptide synthesis.                                                                                                                                                                                                                                                                                                                                                                                                                                                                       inosine (I)                             One of a number of unusual bases found in transfer RNA.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 intervening sequence                    See intron.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             intron                                  A transcribed noncoding DNA sequence in a gene that is excised from the primary transcript in forming a mature mRNA molecule; found primarily in eukaryotic cells.  See also exon.                                                                                                                                                                                                                                                                                                                                                                                                                                      lariat structure                        Structure of an intron immediately after excision in which the 5' end loops back and forms a 5'-2' linkage with another nucleotide.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     leader                                  The untranslated region of an mRNA molecule from the 5' end to the beginning of the coding sequence, sometimes containing regulatory sequences; in prokaryotic mRNA, it contains the ribosomal binding site.                                                                                                                                                                                                                                                                                                                                                                                                            mRNA = messenger RNA                    An RNA molecule transcribed from a DNA sequence that is translated into the amino acid sequence of a polypeptide.  In eukaryotes, the primary transcript undergoes elaborate processing to become the mRNA.                                                                                                                                                                                                                                                                                                                                                                                                             peptide bond                            A covalent bond between the amino group (--NH2) of one amino acid and the carboxyl (--COOH) group of another.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           poly-A tail                             The sequence of adenines added to the 3' end of many eukaryotic mRNA molecules in processing.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           polypeptide chain                       A polymer of amino acids linked together by peptide bonds.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              polysome                                A complex of two or more ribosomes associated with an mRNA molecule and actively engaged in polypeptide synthesis; a polyribosome.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      primary transcript                      An RNA copy of a gene as produced directly following transcription;  in eukaryotes, the transcript must be processed to form a translatable mRNA molecule.                                                                                                                                                                                                                                                                                                                                                                                                                                                              promoter                                A DNA sequence at which RNA polymerase binds and initiates transcription.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               protein subunit                         Any of the polypeptide chains present in a protein.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     reading frame                           The phase in which successive triplets of nucleotides in mRNA form codons; depending on the reading frame, a particular nucleotide in an mRNA could be in the first, second, or third position of a codon.  The reading frame actually used is defined by the AUG codon that is selected for chain initiation.                                                                                                                                                                                                                                                                                                          redundancy                              The feature of the genetic code in which more than one codon corresponds to the same amino acid ; also called degeneracy.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ribosome                                The cellular organelle on which the codons of mRNA are translated into amino acids in protein synthesis.  Ribosomes consist of two subunits, each composed of RNA and proteins: in prokaryotes, the subunits are 30S and 50S particles; in eukaryotes, they are 40S and 60S particles.                                                                                                                                                                                                                                                                                                                                  ribosome-binding site                   The base sequence in a prokaryotic mRNA molecule to which 16S rRNA in a ribosome can bind to initiate protein synthesis; also called the Shine-Dalgarno sequence.                                                                                                                                                                                                                                                                                                                                                                                                                                                       ribozyme                                An RNA molecule able to catalyze one or more biochemical reactions ie to behave like a typical protein enzyme                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           rRNA = ribosomal RNA                    3 or 4 species of RNA that are important structural parts of ribosomes along with many different proteins. The most abundant form of RNA.                                                                                                                                                                                                                                                                                                                                                                                                                                                                               RNA polymerase                          An enzyme that makes RNA by copying the base sequence of a DNA strand.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  RNA processing                          The conversion of a primary transcript into an mRNA, rRNA, or tRNA molecule; includes splicing, cleavage, modification of termini, and (in tRNA) modification of internal bases.                                                                                                                                                                                                                                                                                                                                                                                                                                        RNA splicing                            Excision of introns and joining of exons.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               splice acceptor                         The 5' end of an exon.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  splice donor                            The 3' end of an exon.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  spliceosome                             An RNA-protein particle in the nucleus in which introns are removed from RNA transcripts.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               start codon                             An mRNA codon, usually AUG, at which polypeptide synthesis begins.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      stop codon                              One of three mRNA codons -- UAG, UAA, and UGA -- at which polypeptide synthesis stops.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  TATA box                                The base sequence 5'-TATA-3' in the DNA of a promoter to which RNA polymerase binds.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    template strand                         A nucleic acid strand whose base sequence is copied in a polymerization reaction.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       trailer                                 The untranslated region of an mRNA molecule from the end of the coding sequence to the 3' end of the molecule.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          transcription                           The process by which the information contained in the coding strand of DNA is copied into a single-stranded RNA molecule of complementary base sequence.                                                                                                                                                                                                                                                                                                                                                                                                                                                                transcription complex                   An aggregate of RNA polymerase (consisting of its own subunits) along with other polypeptide subunits that enables transcription.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       tRNA = transfer RNA                     A small RNA molecule that translates a codon into an amino acid during protein synthesis; it has a three-base sequence, called the anticodon, complementary to a specific codon in mRNA, and a site to which a specific amino acid is bound (using a specific aminoacyl tRNA synthetase)                                                                                                                                                                                                                                                                                                                                translation                             The process by which the amino acid sequence of a polypeptide is synthesized on a ribosome according to the nucleotide sequence of an mRNA molecule.                                                                                                                                                                                                                                                                                                                                                                                                                                                                    triplet code                            A code in which each codon consists of three bases.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     uncharged tRNA                          A tRNA molecule lacking an amino acid.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  wobble                                  The acceptable pairing of several possible bases in an anticodon with the base present in the third position of a codon - the range of acceptable possibilities goes beyond normal A to U and C to G pairing to include the unusual modified bases found in the tRNA anticodon eg inosine.