Terminology

-10 region (also called the Pribnow box) - A region in prokaryotic DNA sequences about 10 base pairs ahead of the transcriptional start sequence which contains the consensus sequence, TATAAT. Figure 26.11.
-35 Region - A region in prokaryotic DNA sequences about 35 base pairs ahead of the transcriptional start sequence which contains the consensus sequence, TTGACA. Figure 26.11.
Actinomycin D - A molecule that inhibits transcription by intercalating between adjacent GC base pairs in DNA. Figure 26.4.
Adenylate Cyclase - An enzyme that catalyzes synthesis of cAMP when glucose levels drop in E. coli.
-Amanitin -A toxin from Amanita mushrooms that inhibits eukaryotic RNA polymerase II at low concentrations and RNA polymerase III at high concentrations. Figure 26.4
Antisense RNA - An RNA molecule that is complementary to an mRNA; it can block translation of the mRNA by forming a duplex with it. Gene expression can be regulated by the production of antisense RNAs.
araC - A regulatory protein of the E. coli arabinose operon that activates transcription of the operon when it binds arabinose and represses transcription when no arabinose is bound. Figure 26.39
Attenuation - A transcriptional termination mechanism employed in prokaryotes in which synthesis of a nascent transcript is terminated before the RNA polymerase has reached the structural genes.
cAMP Receptor Protein (CRP) - An E. coli protein that interacts with cAMP and undergoes a conformational change that increases its affinity for several DNA sequences, including a site in the lac operon adjacent to the RNA polymerase binding site. Figure 26.19
cI - A repressor encoded by phage that along with cro, binds to each of the six operator sites of the virus with varying efficiencies. The protein can also act as a transcriptional activator, under certain conditions. Figure 26.23, Figure 26.27
Cis-Dominant - Mutations occurring in a genome that only affect gene expression in that one. An example is a mutation in a regulatory sequence of a promoter that affects transcription only of that promoter.
Closed Promoter Complex - A complex produced as a result of the initial interaction between RNA polymerase and promoter. Figure 26.6
Consensus Sequence - For a group of nucleotide or amino acid sequences that show similarity but are not identical (for example, the sequences for a family of related regulatory gene sequences), an artificial sequence that is compiled by choosing at each position the residue that is found there most often in the sequences under study.
Cordecypin - A transcriptional chain terminator, due to its lack of a 3' hydroxyl group.
Cro - A repressor protein encoded by phage that acts as both a repressor and as an antirepressor, antagonizing the action of cI in a very specific way. Figure 26.23, Figure 26.27
Downstream -A term used to indicate "in the 3' direction of".
Factor-Dependent Termination - A transcriptional termination mechanism in E. coli that employs a factor called (rho), which works by binding the RNA near the 3' end and unwinds the RNA strand from the DNA strand, causing release of the transcriptional complex. Figure 26.16.
Factor-Independent Termination - A transcriptional termination process that relies on base pairing of a GC-rich sequence near the 3' ends of many genes. Figure 26.15.
galR - The structural gene for the gal repressor that negatively regulates the gal operon of E. coli.
Guanosine 3',5'-tetraphosphate (ppGpp) - A molecule that accumulates during the bacterial stringent response.
Helix-Turn-Helix Motif - A protein structure found in the CRP-cAMP-DNA complex. It is a common structure in DNA-binding regulatory proteins.
Inducer - In the lac operon system, for example, a molecule, such as allolactose or IPTG, which binds to the repressor and inactivates it, thus removing a barrier to transcription. Figure 26.18
Intron Splicing - A posttranscriptional processing event of RNAs that occurs almost exclusively in eukaryotes.
Isopropyl Thiogalactoside (IPTG) - A synthetic inducer of the lactose operon.
Lac Repressor The 'i' gene product of the lac operon. It is a macromolecular repressor which, in the active form, binds to the operator, blocking transcription of the operator. Figure 26.18
Lactose Operon - An E. coli operon that consists of the three linked structural genes that encode enzymes of lactose utilization, plus adjacent regulatory sites. Figure 26.17
Messenger RNA (mRNA) - The form of RNA that is translated into protein by the ribosomes. Figure 26.2
NusA - A protein that may be involved in recognition of roew-dependent termination sites.
Open Promoter Complex - A complex produced as a result of a highly temperature-dependent unwinding of several base pairs of DNA by RNA polymerase during transcriptional initiation. Figure 26.6
Operator - A DNA site where a repressor protein binds to block the initiation of transcription from an adjacent promoter. Figure 26.2.
Operon - A set of contiguous prokaryotic structural genes that are transcribed as a unit, along with the adjacent regulatory elements that control their expression. Figure 26.2.
Operon Model - A model originally proposed by Jacob and Monod that was a unifying hypothesis of transcription in prokaryotic organisms. Figure 26.2
Polycistronic Messenger RNA - A messenger RNA molecule carrying coding sequences for more than one polypeptide sequence.
P RM - A 'maintenance' promoter from which cI gene is transcribed during maintenance of lysogeny.
Promoter - A DNA sequence recognized by RNA polymerase, resulting in the initiation of transcription.
Regulon - A group of unlinked (nonadjacent) genes that are all regulated by a common mechanism.
Repression - The turning off of the transcription of a gene or genes.
Repressor - A protein that inhibits the transcription of a gene by binding to an operator. Figure 26.2.
Ribonuclease III - An enzyme that cuts rRNAs in the stem loops during processing of the message made by the operon. It also performs posttranslational processing on some phage mRNAs. Figure 26.41
Ribosomal RNA (rRNA) - The form of RNA found in the ribosomes.
Rifampicin - An inhibitor of the prokaryotic RNA polymerase. Figure 26.4
RNA Polymerase - An enzyme that makes RNA using DNA as a template.
Stringent Response - A response to amino acid starvation in E. coli that inhibits synthesis of rRNA and tRNA.
T7 RNA Polymerase - A prokaryotic RNA polymerase composed on a single polypeptide subunit.
Trans-Dominant - Mutations that happen in one genome which can affect gene expression in others. An example is a mutation in the lac repressor gene which affects sequences to which the repressor binds.
Transcription - The process whereby RNA is made, using DNA as a template.
Transfer RNA (tRNA) - The form of RNA that provides translation between the three base codon sequence in the mRNA and amino acid corresponding to it.
trp Repressor - A 58-kilodalton protein encoded by the nonadjacent trpR gene that is activated by binding tryptophan. Bound to tryptophan, it can bind to the trp operator and block transcription.
Upstream - A term used to indicate "in the 5' direction of."