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Transcription
Terms from Transcription unit of 04-350 at NW
| Term | Definition |
|---|---|
| complete media | growth media that contains all the necessary biomolecules required for growth pre assembled. |
| minimal media | growth media that only contains the chemical precursors required to assemble the biomolecules needed for growth. only organisms that are capable of carrying out the full range of biochemical reactions can grow on this media |
| prototroph | an organism capable of growing on minimal media. it has the ability to catalyze a wide range of biochemical reactions |
| auxotroph | a mutant that has lost a key biochemical activity due to a mutation. unable to grow on minimal media as a result |
| genetic screen | the process of identifying mutant individuals. involves exposing wild type individuals to a mutagen and then looking for altered phenotypes |
| mutagen | a substance capable of causing a mutation. examples include x rays, gamma rays, uv light, and various chemicals |
| supplement | material added to growth media |
| biochemical pathway | a series of related biochemical reactions. For example X is converted to Y which is converted to Z. Each reaction is catalyzed by an enzyme. |
| transcriptional unit | another name for a gene. a sequence of DNA that will go through transcription to produce an RNA molecule |
| mRNA | messenger RNA. A type of RNA that serves as a short term information molecule. The sequence of bases will dictate the order of amino acids in a protein when translation occurs. Very unstable. |
| rRNA | ribosomal RNA. A type of RNA. When it folds into hair pins and stem loops due to internal base pairing it forms the bulk of the machinery (ribosome) responsible for synthesizing proteins |
| tRNA | transfer RNA. A type of RNA. When it folds into clover leaf structure due to internal base pairing, a loop will form at the bottom (anticodon). Responsible for carrying amino acids to the ribosome and reading the code in the mRNA |
| snRNA | small nuclear RNA. Found in eukaryotes. A key component of snRNP (snurps) that are responsible for cutting out introns and pasting together exons of eukaryotic mRNA |
| RNA polymerase | a general term for the enzyme responsible for synthesizing molecules of RNA |
| core RNA polmerase | term used when talking about prokaryotic RNA polymerase. It is able to synthesize RNA but has low affinity and indiscriminate initiation which means it doesn't work very well. composed of multiple polypeptide subunits. |
| RNA polymerase holoenzyme | forms when sigma factor combines with core RNA polymerase. used to initiate transcription because it has high affinity and is discriminate in initiation site. |
| sigma factor | protein found in prokaryotes that combines with the core RNA polymerase to make it more efficient. When part of the polymerase holoenzyme, it interacts with the -35 consensus sequence of a prokaryotic promoter |
| promoter | sequence at the beginning of a gene (transcriptional unit) that signals where RNA polymerase is supposed to bind and initiation of transcription should occur. Upstream of the transcriptional start site. |
| -35 box | common consensus sequence found ~ 35 nucleotides upstream of the transcriptional start site. site where sigma factor will directly interact with the DNA by attaching to the major groove. |
| -10 box | common consensus sequence found ~ 10 nucleotides upstream of the transcriptional start site. Largely composed of A and T bp which makes strand separation relatively easy |
| consensus sequence | a commonly observed sequence (average) found at a specific location in a gene to serve a particular purpose. the sequence does not need to always be a perfect match but the closer it is to the consensus, the more likely it is to serve its proper function |
| transcriptional start site | TSS, +1, the first nucleotide copied from the DNA template into the RNA strand being synthesized during transcription. Not the start codon |
| active site | the location in an enzyme where substrate will interact and the actual chemical reaction takes place |
| NTP | nucleoside triphosphate, the substrate that RNA polymerase uses to synthesize new strands of RNA |
| template strand | strand of DNA that is directly copied into the RNA during transcription. should be complementary and antiparallel to the RNA being made |
| nontemplate strand | the strand of DNA that is not being directly copied into the RNA during transcription. should be identical to the RNA with the exception of substitution of U for T |
| transcriptional bubble | forms when template and nontemplate strands separate from each other during initiation and the formation of a open complex |
| open complex | term used to describe RNA polymerase that has been fully activated by phosphorylation and causing a transcriptional bubble to form |
| closed complex | term used to describe RNA polymerase that has not been fully activated and therefore no transcriptional bubble has formed. |
| RNA coding | the sequence of the gene that will actually be copied into the RNA during transcription |
| terminator | the sequence at the end of a gene that marks where transcription is supposed to end. |
| inverted repeat | used in the terminator of all prokaryotic genes. in the DNA the sequence on the template left to right is identical to the non template right to left. causes the formation of a stem loop structure in the RNA transcript which pauses transcription. |
| rho | protein involved in rho dependent termination of transcription in prokaryotes. Helicase activity separates RNA from DNA template and stem loop within RNA |
| rho independent termination | termination of transcription in prokaryotes that occurs spontaneously after formation of stem loop within RNA strand |
| affinity | the probability that two molecules will remain bound together. applies to situations where an enzyme may bind to a template or substrate but break apart before a reaction occurs. |
| initiation | the beginning stages of either transcription or translation. usually involves the binding and assembly of the machinery necessary to carry out a molecular process |
| elongation | the stage of transcription or translation where the RNA or polypeptide is getting longer as synthesis occurs |
| termination | the stage of transcription or translation where the process is coming to an end |
| exit pore | the opening in the RNA polymerase that allows the growing RNA chain to emerge as new nucleotides are added to the 3' end |
| core promoter | basal element, sequence of DNA in a eukaryotic gene that serves as the assembly point of the transcriptional apparatus |
| TATA box | a consensus sequence that may be found in a eukaryotic core promoter |
| IRE | a consensus sequence that may be found in a eukaryotic core promoter |
| TFIIDRE | transcription factor two D recognition element, a common consensus sequence that may be found in a eukaryotic core promoter. |
| RNA polymerase II | the form of RNA polymerase in eukaryotes responsible for synthesizing mRNA |
| RNA polymerase I | the form of RNA polymerase in eukaryotes responsible for synthesizing large RNA, especially rRNA |
| RNA polymerase III | the form of RNA polymerase in eukaryotes responsible for synthesizing small RNA including some rRNA but especially tRNA |
| general transcription factors | a general group of proteins that bind to the core promoter in eukaryotes, their binding increases the affinity of RNA polymerase to the promoter, serve the same purpose as sigma factor |
| regulatory promoter | part of a eukaryotic promoter where regulatory transcription factors bind to stimulate transcription |
| CAAT box | a possible consensus sequence found in the regulatory promoter |
| OCT box | a possible consensus sequence found in the regulatory promoter of eukaryotes |
| activator | a type of regulatory transcription factor that stimulates transcription when it binds to a DNA sequence |
| repressor | a type of regulatory transcription factor that interferes with transcription |
| enhancer | a sequence of DNA found far upstream or downstream of the core promoter that serves as a binding site for activator proteins |
| basal transcriptional apparatus | a combination of general transcription factors, RNA polymerase, and mediator proteins that bind to the core promoter but do not necessarily begin transcription |
| coactivator | a protein that attaches to another protein causing stimulation of transcription |
| mediator | a complex of many proteins that serve as a bridge, allowing activators to stimulate the RNA polymerase |
| pre mRNA | primary mRNA, the form of mRNA before processing occurs |
| mature mRNA | the form of mRNA after processing has been completed |
| processing | a series of events that alter the composition of a mRNA. Includes capping, splicing, cleavage, tailing and editing |
| capping | occurs during elongation of eukaryotic transcription. involves the addition of a conserved guanosine to the 5' end of the mRNA as soon as it emerges from the exit pore of the RNA polymerase. also involves addition of methyl groups to the cap |
| splicing | alteration of the mRNA that removes intron sequences and joins exons together due to the action of snurps |
| exon | sequence of nucleic acid found in DNA, copied into primary mRNA, and retained in mature mRNA. includes all the sequences that will make up the open reading frame coding for the protein |
| intron | sequence of nucleic acid found in DNA, copied into primary mRNA, but discarded during spicing so it is not part of the mature mRNA. |
| snurp | snRNP, small nuclear ribonuclear protein. combination of snRNA and protein. responsible for identifying splice sites at the boundary of exons/introns |
| 5' splice site | consensus sequence found at the junction of the end of an exon and the beginning of intron |
| 3' splice site | consensus sequence found at the junction of the end of an intron and the beginning of an exon |
| branch point | conserved A within an intron, site where the 5' end of the intron will attach to form the lariat structure during splicing |
| alternative splicing | selective use of 5' and 3' splice sites allows splicing to occur in multiple ways, changing the sequence of the mature mRNA |
| cleavage | cutting the primary mRNA away from an actively transcribing RNA polymerase towards the end of the transcriptional unit |
| cleavage signal | consensus sequence that indicates approximately where cleavage will occur, AAUAAA in the primary mRNA |
| cleavage factors | proteins responsible for recognizing cleavage signal and cutting the mRNA away |
| tailing | process of adding a long string of As to the 3' end of the mRNA after cleavage, forming the poly A tail, also known as polyadenylation |
| editing | making directed chemical modifications to specific bases within the RNA |
| alternative cleavage | selective use of one cleavage signal or another that alters the sequence of the mature mRNA |
Created by:
jthorns
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