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169 Cards in this Set
- Front
- Back
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A (aminoacyl) site
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The tRNA -binding site on the ribosome to which each incoming charged tRNA is initially bound
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Amino terminus
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The end group of a polypeptide chain at which the amino acid bears a free amino group (-NH2)
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Aminoacyl-tRNA synthetase
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The enzyme that attaches the correct amino acid to a tRNA molecule.
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Aminoacylated tRNA
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A tRNA covalently attached to its amino acid; charged tRNA
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Anticodon
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The 3 bases in a tRNA molecule that are complementary to the 3-base codon in mRNA
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Cap
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A complex structure at the 5' termini of most eukaryotic mRNA molecules, having a 5'-5' linkage instead of the usual 3'-5' linkage.
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Carboxyl terminus
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The end of a polypeptide chain at which the amino acid has a free carboxyl group (-COOH).
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Chaperone
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A protein that assists in the 3-D folding of another protein.
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Charged tRNA
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A tRNA molecule to which an amino acid is linked; aminoacylated tRNA.
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Coding sequence
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A region of DNA strand with the same sequence as is found in the coding region of a messenger RNA, except that T is present instead of U.
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codon
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A sequence of 3 adjacent nucleotides in an mRNA, specifying either an amino acid group or a stop signal in protein synthesis.
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consensus sequence
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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.
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coupled processes
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Processes that are biochemically or functionally connected such that the occurrence of the earlier process initiates or regulates the later process.
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elongation
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Addition of amino acids to a growing polypeptide chain or of nucleotides to a growing nucleic acid chain.
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E (exit) site
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The tRNA-binding site on the ribosome that binds each uncharged tRNA just prior to its release.
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exon
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The sequences in the DNA that are retained in the mRNA after the introns have been removed from the primary transcript.
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exon-shuffle model
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The theory that new genes can evolve by the assembly of separate exons from pre-existing genes, each coding for a discrete functional domain in the new protein.
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folding domain
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A short region of a polypeptide chain within which interactions btwn amino acids result in a 3-D conformation that is attained relatively independently of the folding of the rest of the molecule.
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frameshift mutation
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A mutational event caused by the insertion/deletion of one or more nucleotide pairs in a gene, resulting in a shift in the reading frame of all codons following the mutation site.
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gene expression
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The multistep process by which a gene is regulated and its product synthesized.
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initiation
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The beginning of protein synthesis.
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intervening sequence
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See intron
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intron
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A noncoding DNA sequence in a gene that is transcribed but then excised from the primary transcript in forming a mature mRNA molecule; found primarily in eukaryotic cells
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lariat structure
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Structure of an intron immediately after excision in which the 5' end loops back and forms a 5'-2' linkage with another nucleotide.
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messenger RNA (mRNA)
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An RNA molecule transcribed from DNA sequence and translated into the amino acid sequence of a polypeptide. In euk, the primary transcript undergoes elaborate processing to become the mRNA.
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nonsense mutation
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A mutation that changes a codon specifying and amino acid into a stop codon, resulting in premature polypeptide chain termination; also called chain-termination mutation.
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open reading frame (ORF)
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In the coding strand of DNA or in a mRNA, a region containing a series of codons uninterrupted by stop codons and therefore capable of coding for a polypeptide chain; abbreviated ORF.
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P (peptidyl) site
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The tRNA binding site on the ribosome to which the tRNA bearing the nascent polypeptide becomes bound immediately after formation of the peptide bond.
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peptide bond
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A covalent bond btwn the amino group (-NH2) of one amino acid and the carboxyl group (-COOH) of another.
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peptidyl transferase
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The enzymatic activity of ribosomes responsible for forming a peptide bond.
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poly-A tail
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The sequence of adenines added to the 3' end of many euk mRNA molecules in processing.
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polycistronic mRNA
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An mRNA molecule from which 2 or more polypeptides are translated; found primarily in prokaryotes.
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polypeptide chain
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A polymer of amino acids linked together by peptide bonds.
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polysome
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A complex of 2 or more ribosomes associated with an mRNA molecule and actively engaged in polypeptide synthesis; a polyribosome.
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primary transcript
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An RNA copy of a gene; in euk, the transcript must be processed to form a translatable mRNA molecule.
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promoter
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A DNA sequence at which RNA polymerase binds and initiates transcription.
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protein subunit
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Any of the polypeptide chains in a protein molecule made up of multiple polypeptide chains.
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reading frame
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The phase in which successive triplets of nucleotides in mRNA form codons; depending on the reading frame, a particular nucleotide in mRNA could be in the 1st, 2nd, 3rd position of a codon. The reading frame actually used is defined by the AUG codon that is selected for chain initiation.
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release factor
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A protein that functions in translation in the release of a completed polypeptide chain from the ribosome.
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ribosome
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The cellular organelle on which the codons of mRNA are translated into amino acids in protein synthesis; Ribosomes consist of 2 subunits, e/ composed of RNA and proteins. In prok, the subunits are 30S and 50S particles; in euk, they are 40S and 60S particles.
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ribosome-binding site
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The base sequence in a prok mRNA molecule to which a ribosome can bind to initiate protein synthesis; also called the Shine-Dalgarno sequence.
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RNA polymerase
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An enzyme that makes RNA by copying the base sequence of a DNA strand.
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RNA polymerase holoenzyme
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A large protein complex in euk nuclei consisting of Pol II in combination with at least 9 other subunits; Pol II itself includes 12 subunits.
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RNA processing
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The conversion of the primary transcript into an mRNA, rRNA, or tRNA molecule; includes splicing, cleavage, modification of termini, and (in tRNA) modification of internal bases.
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RNA splicing
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Excision of introns and joining of exons.
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sigma factor
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The subunit of RNA polymerase needed for promoter recognition.
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snRNP
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Abbreviation for "small nuclear ribonucleoprotein particle"
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spliceosome
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An RNA-protein particle in the nucleus in which introns are removed from RNA transcripts
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TATA box
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The base sequence 5'-TATA-3' in the DNA of a promoter.
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template strand
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A nucleic acid strand whose base sequence is copied in a polymerization reaction to produce either a complementary DNA or RNA strand.
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transcription
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The process by which the information contained in a template strand of DNA is copied into ss RNA molecule of the complementary base sequence.
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transfer RNA (tRNA)
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A small RNA molecule that translates a codon into an amino acid in protein synthesis; it has a 3-base sequence, called the anticodon, complementary to a specific codon in mRNA, and a site to which a specific amino acid is bound.
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translation
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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.
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wobble
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The acceptable pairing of several possible bases in an anticodon with the base present in the 3rd position of a codon.
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aporepressor
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A protein converted into a repressor by binding with a specific molecule.
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attenuation
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See attenuator
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attenuator
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A regulatory base sequence near the beginning of an mRNA molecule at which transcription can be terminated; when an attenuator is present, it precedes the coding sequences.
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autoregulation
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Regulation of the gene expression by the product of the gene itself.
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β-galactosidase
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An enzyme that cleaves the lactose into its glucose and galactose constituents; produced by a gene in the lac operon.
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coordinate regulation
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Control of synthesis of several proteins by a single regulatory element; in prok, the proteins are usually translated from a single mRNA molecule.
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co-repressor
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A small molecule that binds with an aporepressor to create a functional repressor molecule
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enhancer
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A base sequence in euk and euk viruses that increases the rate of transcription of nearby genes; the defining characteristics are that it need not be adjacent to the transcribed gene and that the enhancing activity is independent of orientation with respect to the gene.
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epigenetic
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Inherited changes in gene expression resulting from altered chromatin structure or DNA modification (usually methylation) rather than changes in DNA sequence.
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inducer
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A small molecule that inactivates a repressor, usually by binding to it and thereby altering the ability of the repressor to bind to an operator.
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inducible transcription
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A gene that is expressed, or an enzyme that is synthesized, only in the presence of an inducer molecule.
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lactose permease
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An enzyme responsible for transport of lactose from the environment into bacteria.
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leader polypeptide
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A short polypeptide encoded in the leader sequence of some operons coding for enzymes in amino acid biosynthesis; translation of the leader polypeptide participates in regulation of the operon through attenuation.
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microRNA (miRNA)
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Small ds RNA molecules that repress translation of mRNAs containing complementary sequences.
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negative regulation
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Regulation of gene expression in which mRNA is not synthesized until a repressor is removed from the DNA of a gene.
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operator
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A regulatory region in DNA that interacts with a specific repressor protein in controlling the transcription of adjacent structural genes.
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operon
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A collection of adjacent structural genes regulated by an operator and a repressor.
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operon model
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A model depicting the coordinate regulation of a set of closely linked genes, such as those for lactose utilization in E. coli; many genes for metabolic pathways in bacteria are organized into operons.
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positive regulation
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Mechanisms of gene regulation in which an element must be bound to DNA in an active form to allow transcription. Positive regulation contrasts with negative regulation, in which a regulatory element must be removed from DNA.
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promoter
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A DNA sequence at which RNA polymerase binds and initiates transcription.
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regulatory RNA
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An RNA molecule that plays a role in gene regulation, such as small RNAs that regulate translation.
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repressible transcription
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A mode of regulation in which the default state of transcription is "on" unless a protein (the repressor) binds to the DNA and turns it "off"
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repressor
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A protein that binds specifically to a regulatory sequence adjacent to a gene and blocks transcription of the gene.
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RNA interference (RNAi)
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The ability of small fragments of ds RNA to silence genes whose transcripts contain homologous sequences.
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silencer
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A nucleotide sequence that binds with certain proteins whose presence prevents or modulates gene expression.
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small interfering RNA (siRNA)
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Small cleavage products of ds RNA used to target RNAs containing complementary sequences for destruction or for inhibition of their function.
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TATA-box-binding protein (TBP)
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A protein that binds to the TATA motif in the promoter region of a gene.
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transcriptional activator protein
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Positive control element that stimulates transcription by binding with particular sites in DNA.
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UTR (untranslated region)
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The untranslated region of mRNA; the 5' UTR is upstream of the protein-coding region and the 3' UTR is downstream.
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anaphase-promoting complex (APC/C)
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A ubiquitin-protein ligase that targets proteins whose destruction enables a cell to transition from metaphase to anaphase
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apoptosis
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Genetically programmed cell death, especially in embryonic development.
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cancer
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Any of a large number of diseases characterized by the uncontrolled proliferation of cells.
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cell cycle arrest
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A blockage in the progression of the cell cycle.
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cell division cycle (cdc)
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The growth cycle of a cell; in euk, it is subdivided into G1, S, G2, M.
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mutant
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Any heritable biological entity that differs from wildtype, such as mutant DNA molecule, mutant allele, mutant gene, mutant chromosome, mutant cell, mutant organism, or mutant heritable phenotype; also, a cell or organism in which a mutant allele is expressed.
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cell senescence
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A normal process in which mammalian cells in culture cease dividing after about 50 doublings.
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centriole
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In animal cells, one of a pair of particulate structures composed of an array of microtubules around which the spindle is organized.
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centrosome
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A localized region of clear cytoplasm found near the nucleus of nondividing cells, which in dividing cells duplicates to form the centers around which the spindle is organized.
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centrosome duplication checkpoint
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A mechanism that arrests the cell cycle while the centrosome remains undivided.
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checkpoint
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Any mechanism that arrests the cell cycle until one or more essential processes are completed.
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contact inhibition
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A phenomenon in normal mammalian cells in culture whereby cells cease to grow and divide when they are in close physical proximity.
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cyclin
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Any of a number of proteins that help regulate the cell cycle and whose abundance rises and falls rhythmically, during the cell cycle.
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cyclin–CDK complex
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Protein complex formed by the interaction btwn a cyclin and a cyclin-dependent protein kinase (CDK).
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cyclin-dependent protein kinase (CDK)
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Any of a number of proteins that are activated by combining with a cyclin and that regulate the cell cycle by phosphorylation of other proteins.
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DNA damage checkpoint
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A mechanism that arrests the cell cycle while damaged DNA remains unrepaired.
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G protein
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One of a family of signaling proteins that is activated by binding to a molecule of guanosine triphosphate (GTP).
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G1 restriction point (start)
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The "start" point at which cells are arrested in the G1 phase until they become committed to division.
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G1/S transition
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Transition btwn the first "growth" phase of the cell cycle to DNA synthesis
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G2/M transition
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Transition btwn the second "growth" phase of the cell cycle to mitosis.
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loss of heterozygosity
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Loss of presence of the WT allele, or a loss of its function, in heterozygous cell, enabling the phenotype of a recessive mutant allele to be expressed; mechanisms for loss of heterozygosity include chromosome loss, gene conversion, and mutation.
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oncogene
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A gain of function mutation in a cellular gene, called a proto-oncogene, whose normal function is to promote cell proliferation or inhibit apoptosis; oncogenes are often associated with tumor suppressor genes.
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p53 transcription factor
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An important protein that helps regulate a mammalian cell's response to stress, especially to DNA damage.
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programmed cell death
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Cell death that happens as part of the normal development process..see also apoptosis
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proto-oncogene
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A euk gene that functions to promote cellular proliferation or inhibit apoptosis, in which gain of function mutations (oncogenes) are associated with tumor progression.
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retinoblastoma (RB) protein
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Any of a family of small proteins found in animal cells that functions to hold cells at the G1/S restriction point ("start") by binding to and sequestering a transcription factor that initiates the cell cycle.
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spindle assembly checkpoint
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A mechanism that arrests the cell division cycle until the spindle is properly deployed.
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tumor-suppressor gene
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A gene that normally controls cell proliferation or that activates the apoptotic pathway, in which loss-of-function mutations are associated with cancer progression.
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adaptation
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Any characteristic of an organism that improves its chance of survival and reproduction in its environment; the evolutionary process by which a species undergoes progressive modification favoring its survival and reproduction in a given environment.
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allele frequency
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The relative proportion of all alleles of a gene that are of designated type.
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consanguineous mating
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A mating between relatives.
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equilibrium
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In population genetics, a situation in which the allele frequencies remain constant from one generation to the next.
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evolution
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Cumulative change in the genetic characteristics of a species through time, resulting in greater adaptation.
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fixed allele
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An allele whose allele frequency equals 1.0
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forward mutation
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A change from a WT allele to a mutant allele.
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gene pool
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The totality of genetic information in a population of organisms.
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genotype frequency
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The proportion of members of a population that are of a prescribed genotype.
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Hardy–Weinberg principle
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The genotype frequencies expected with random mating.
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heterozygote superiority
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The condition in which the heterozygous genotype has greater fitness than either of the homozygotes.
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migration
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Movement of organisms among subpopulations ; also, the movement of molecules in electrophoresis.
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mutation
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A heritable alteration of a gene in a chromosome; also, the process by which such alteration happens. Used incorrectly, but with increasing frequency, as a synonym for mutant.
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natural selection
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The process of evolutionary adaptation in which the genotypes genetically best suited to survive and reproduce in a particular environment give rise to a disproportionate share of the offspring and so gradually increase the overall ability of the populations to survive and reproduce in that environment.
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orthologous genes
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Genes that are present in 2 or more related species that descend from a single gene present in a common ancestor of the species.
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overdominance
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A condition in which the fitness of a heterozygote is greater than the fitness of both homozygotes.
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paralogous genes
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Two or more genes that derive from a common ancestral gene through one or more gene duplications followed by sequence divergence.
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pseudogene
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A DNA sequence that is not functional because of one or more mutations but that has a functional counterpart in the same organism; pseudogenes are regarded as mutated forms of ancient gene duplications.
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random genetic drift
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Fluctuation in allele frequency from generation to generation resulting from restricted population size.
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random mating
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System of mating in which mating pairs are formed independently of genotype or phenotype.
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relative fitness
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The fitness of a genotype expressed as a proportion of the fitness of another genotype.
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reverse mutation
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A mutation that undoes the effect of a preceding mutation.
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selection coefficient
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The amount by which relative fitness is reduced or increased.
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selection–mutation balance
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Equilibrium determined by the opposing effects of mutation tending to increase the frequency of a deleterious allele and selection tending to decrease its frequency.
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selectively neutral mutation
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A mutation that has no (or negligible) effects on fitness.
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subpopulation
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Any of the breeding groups within a larger population btwn which migration is restricted.
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viability
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The probability of survival to reproductive age.
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bacterial artificial chromosome (BAC)
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A recombinant DNA plasmid in which a large fragment of DNA has been ligated into a suitable vector , making possible its replication and segregation in bacterial cells.
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bioinformatics
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The use of computers in the interpretation and management of biological data.
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blunt end
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Ends of the DNA molecule in which terminal bases are paired; the term usually refers to termini formed by restriction enzyme that does not produce ss ends.
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cloned DNA
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A DNA sequence incorporated into a vector molecule capable of replicating in the same or different organisms.
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complementary DNA (cDNA)
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A DNA molecule made by copying RNA with reverse transcriptase ; usually abbreviated cDNA.
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DNA ligase
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An enzyme that catalyzes formation of a covalent bond btwn adjacent 5'-P and 3'-OH termini in a broken polynucleotide strand of ds DNA
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DNA microarray
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Tiny dots of e/ of a large number of DNA fragments or oligonucleotides immobilized on a solid surface about the size of a postage stamp; typically used for hybridizing DNA or RNA samples to identify genotypes, copy number polymorphisms, or gene-expression levels.
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electroporation
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Introduction of DNA fragments into a cell by means of an electric field.
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embryonic stem cell
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Cells in the blastocyst that give rise to the body of the embryo.
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expressed sequence tag (EST)
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Nucleotide sequences of cDNA molecules that have been reverse-transcribed from messenger RNAs.
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functional genomics
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Use of DNA microarrays and other methods to study the coordinated expression of many genes simultaneously.
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genomics
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Study of the DNA sequence, organization, function and evolution of genomes.
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Human Genome Project
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A worldwide project to map genetically and sequence the human genome and those of selected model organisms.
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knockout mutation
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Any mutation that completely eliminates the function of the gene; synonyms include null mutation, loss-of-function mutation, and amorphic mutation.
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gene library
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A large collection of cloning vectors containing a complete (or nearly complete) set of fragments of the genome of an organism.
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map-based cloning
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A strategy of gene cloning based on the position of a gene in the genetic map; also called positional cloning.
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multiple cloning site
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see polylinker
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partial digestion
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Condition in which a restriction enzyme cleaves some, but not all, of the restriction sites present in a DNA molecule.
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physical map
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A diagram showing the relative positions of physical landmarks in aDNA molecule; common landmarks include the positions of restriction sites and particular DNA sequences.
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plasmid
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An extrachromosomal genetic element that replicates independently of the host chromosome; it may exist in one or many copies per cell and may segregate in cell division to daughter cells in either a controlled or random fashion. Some plasmids, such as the F factor, may become integrated into the host chromosome.
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polylinker
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A short DNA sequence that is present in a vector and that contains a number of unique restriction sites suitable for gene cloning.
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proteomics
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Study of the complement of proteins present in a cell or organism in order to identify their localization, functions, and interactions.
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recombinant DNA
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A DNA molecule produced by joining 2 or more DNA fragments that are not normally in physical proximity and that are often from different organisms.
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reporter gene
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A gene whose expression can readily be monitored.
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retrovirus
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A class of RNA animal viruses that cause the synthesis of DNA complementary to their RNA genomes on infection.
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reverse genetics
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Procedure in which mutations are deliberately produced in cloned genes and introduced back into cell or the germ line of an organism.
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reverse transcriptase
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An enzyme that makes complementary DNA from ss RNA template.
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reverse transcriptase PCR (RT-PCR)
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Amplification of duplex DNA molecule originally produced by reverse transcriptase using an RNA template.
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site-directed mutagenesis
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Method of engineering mutations at specific nucleotide sites or in specific regions of DNA.
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sticky ends
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A ss end of a DNA fragment produced by certain restriction enzymes capable of reannealing with a complementary sequence of another strand.
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transgenic organism
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Refers to animals or plants in which novel DNA has been incorporated into the germ line.
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