Term
|
Definition
| In bacterial DNA, a cluster of continuous genes transcribed from one promoter that gives rise to an mRNA containing coding sequences for multiple proteins. |
|
|
Term
|
Definition
| Many bacterial mRNAs encode for several proteins that function together in a biological process. These mRNAs are polycistronic. |
|
|
Term
|
Definition
| Refers to the number of plasmid or other DNA molecules in a cell. |
|
|
Term
|
Definition
An enzyme that copies one strand of DNA (the template strand)to make the complementary RNA strand using ribonucleoside triphosphates as substrates.
The core enzyme - binds to loose sites with high affinity. It participates in promoter recognition and interacts with activators and repressors. It is contained within the holoenzyme.
The holoenzyme - binds loose sites with low affinity, but binds promoters with high affinity. The holoenzyme, or complete enzyme, can be separated into two components, the core enzyme and the sigma factor. Only the holoenzyme can bind DNA at the promoter and initiate transcription. |
|
|
Term
|
Definition
| DNA sequence that determines the site of transcription initiation for a RNA polymerase. |
|
|
Term
|
Definition
| DNA sequence at the end of a transcription unit that causes RNA Polymerase to stop transcription. |
|
|
Term
|
Definition
| Region of sequenced DNA that is not interrupted by stop codons in one of the triplet reading frames. An ORF of 100 codons or more has a high chance of encoding a protein. |
|
|
Term
-35 region
-10 region
Spacer b/w -35 and -10 regions
Purine at +1 |
|
Definition
| Bacterial promoters share these four conserved elements. RNA polymerase and transcription factors bind at the -35 and -10 regions. The two regions are separated by a spacer region between them. And an A or G is found at the +1 position, which is the transcription start site. |
|
|
Term
|
Definition
| Gene that can be attached to a regulatory sequence of another gene of interest to indicate whether the gene has been taken up by or expressed in the cell of an organism. |
|
|
Term
|
Definition
| A region where the ds-DNA is separated while RNA polymerase is actively transcribing RNA. A short region of RNA-DNA duplex is formed between the newly synthesized RNA and the template DNA in this region. |
|
|
Term
|
Definition
E. coli has six different possible sigma factors. Sigma factors are concerned with promoter recognition and make sure that the RNA polymerase binds to DNA in a stable manner at the promoter.
Sigma-70 interacts directly with both the -35 and -10 regions.
TTGACAT--16/18 spacer--TATAAT |
|
|
Term
|
Definition
| The core enzyme has a general affinity for DNA. Any sequence of DNA that is bound by the core polymerase in this general binding reaction is described as a loose binding site. |
|
|
Term
|
Definition
| 1st part of transcription initiation, when RNA polymerase binds to the promoter sequence in duplex DNA |
|
|
Term
|
Definition
| 2nd part of transcription initiation, when RNA Polymerase melts duplex DNA near the transcription start site, forming a transcription bubble. |
|
|
Term
|
Definition
3rd part of transcription initiation, when
RNA polymerase catalyzes phosphodiester linkage of two initial rNTPs. |
|
|
Term
|
Definition
| Occurs at max rate of 1 bp/sec, and the sigma factor dissociates from the RNA polymerase, leaving the core polymerase behind for elongation. |
|
|
Term
|
Definition
| Elongation is catalyzed by the core enzyme and has a max. rate of 40 bp/sec. (Elongation pauses in the absence of the correct nucleotide) |
|
|
Term
|
Definition
| During transcription elongation, it adds negative supercoils in advance of RNA polymerase. |
|
|
Term
|
Definition
| During transcription elongation, it removes excess supercoils behind RNA polymerase. |
|
|
Term
|
Definition
| The DNaseI footprint of the core enzyme is approx. 40 bp. |
|
|
Term
|
Definition
| Rho-protein is a sequence-dependent RNA binding protein - it binds a C-rich element in the growing mRNA. Rho is an RNA helicase that pursues RNA polymerase along the nascent (growing) transcript - this movement is ATP dependent. Normally, RNA poly. is too fast for rho, but if a secondary structure forms, the RNA polymerase pauses and Rho collides with the RNA polymerase resulting in termination (core enzyme released) and mRNA release. |
|
|
Term
| Rho-independent termination |
|
Definition
| An Rho-independent terminator sequence will have a GC-rich inverted repeat on along with a row of Thymines. The transcribed mRNA will have a row of uracils. The GC sequence will for a stable hairpin structure followed by the row of uracils. The formation of the hairpin weakens the mRNA-DNA heteroduplex, which allows the elongation complex and mRNA to dissociate. |
|
|
Term
|
Definition
| Active for transcription all the time; often "houskeeping genes". They are mostly unregulated, allowing for continual transcription. |
|
|
Term
|
Definition
| Activator is a DNA-binding protein that regulates one or more genes by increasing the rate of transcription. The activator may increase transcription by supporting RNA polymerase binding to the promoter, or by supporting promoter clearage by RNA polymerase. Also, it may operate through a coactivator. |
|
|
Term
|
Definition
| A protein that binds to an operator of a gene, and prevents RNA pol. from binding, thereby inhibiting its transcription. Can also inhibit promoter clearage of the RNA Pol. The binding affinity of repressors for the operator may be affected by other molecules. Inducers bind to repressors and decrease their binding to the operator, while co repressors increase the binding. |
|
|
Term
|
Definition
| These operons can be turned on and off. They are not always necessary for life, so they are turned off. |
|
|
Term
|
Definition
| A physiological inducer that binds the lac repressor protein. |
|
|
Term
|
Definition
| An inducer molecule binds to the repressor and changes its conformation so that it is unable to bind to the operator. This allows for expression of the operon. |
|
|
Term
|
Definition
| When the holoenzyme (RNA poly.) is bound to the promoters and ready to transcribe. |
|
|
Term
| LacI protein aka lac repressor |
|
Definition
| Homotetramer - 4 identical subunits. It makes sequence-dependent and sequence-independent reactions with DNA (operator). The 'head' portion of the lac repressor is a helix-turn-helix and binds DNA. The 'hinge' portion is stiff (oxymoron). |
|
|
Term
|
Definition
| Two copies of a gene or operon were inserted into a cell and used to study regulatory proteins. |
|
|
Term
|
Definition
| Coordinate control of more than one operon by a single activator or repressor. Catabolite Repression and the lexA repressor are both regulons. |
|
|
Term
|
Definition
| The AraC protein is both an activator and a repressor. It is a dimer that recognizes two "half binding sites". In the absence of arabinose, araC protein adopts a confirmation favoring selection of two distant half sites, which blocks transcription. However, binding of arabinose to araC protein results in a major confirmational change that favors selection of two adjacent half-sites, and transcription of araBAD occurs. |
|
|
Term
|
Definition
| LexA, a regulon, represses many genes involved in repairing DNA damage. (recA protein interacts with the lexA repressor when there is DNA damage, and causes it to self-destruct, which derepresses many genes. |
|
|
Term
|
Definition
| These promoters are activated or undergo expression only in the presence of a particular molecule. |
|
|
Term
|
Definition
TrpR repressor binds to the operator preventing RNA polymerase from binding to the promoter when trp is abundant. TrpR repressor is a classical homordimeric helix-turn-helix protein.
When trp is scarce, trpR repressor is released from the operator allowing RNA polymerase to access the promoter. |
|
|
Term
|
Definition
| Translation of a specific leader peptide tests for the concentration of a specific amino acid or set of amino acids in the cell. If the concentration is high transcription is terminated in the attenuator, if low continued leading to the production of enzymes for amino acid synthesis and hence more amino acid |
|
|
Term
|
Definition
| Enhancers are position and orientation independent DNA elements that are binding sites for transcriptional activators. |
|
|
Term
|
Definition
| Both are protein kinases, which modifies other proteins by adding phosphate groups to them (phosphorylation). |
|
|
Term
|
Definition
| RNA primers (less than 15 nucleotides long) are added to the leading and lagging strand. DNA Pol III then adds nucleotides to the 3' end of the primers to replicate DNA. RNA primers must be added to the lagging strand many times because they are needed each time an Okazaki fragment is created, however, the leading strand only requires the primers to be added at the oriC. |
|
|
Term
|
Definition
| The Pol III holoenzyme consists of the Pol III core, a B clamp, and a clamp loader. It is the primary enzyme complex involved in prokaryotic DNA replication. This complex has high processivity, meaning it adds many nucleotides per binding event. In addition, it has 3'-->5' exonuclease proofreading activity, which allows it to correct replication errors. |
|
|
Term
|
Definition
| DnaB is a helicase. In bacteria, DnaB opens the replication fork during DNA replication. Initially, when DnaB binds to DnaA (a replication initiation factor), it is associated with DnaC, a negative regulator, whose sole purpose is to deliver DnaB. After DnaC, dissociates, DnaB binds dnaG, or primase. |
|
|
Term
| B-clamp and B-clamp loader |
|
Definition
The B-clamp serves as a processivity-promoting factor in DNA replication. the clamp protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand.
The B-clamp loader requires ATP hydrolysis to "close" the clamp around the DNA. |
|
|
Term
|
Definition
| Involved in base excision repair; they remove the damaged nitrogenous base while leaving the sugar-phosphate backbone intact, creating an apurinic/apyrimidinic site, commonly referred to as an AP site. (Apurinic/Apyrimidinic site has neither a purine nor a pyrimidine) |
|
|
Term
|
Definition
| A specific sequence of nucleotides on the lagging strands of E. coli, and that strongly encourage recombination and crossing over to occur at that site. The Chi sequences are not uniformly distributed. |
|
|
Term
|
Definition
| A mobile junction between four strands of DNA.Because these junctions are between homologous sequences they can slide up and down the DNA. In bacteria, this sliding (or branch migration) is facilitated by the RuvABC complex or RecG protein, molecular motors that use the energy of ATP hydrolysis to push the junction around. The junction must then be resolved, split up, to restore 2 linear duplexes. This can be done to either restore the parental configuration or to establish a crossed over configuration. |
|
|
