40

I'll keep this short and simple. The direction of transcription (which determines which strand is used as the template) is controlled by the promoter, which is a region of specific DNA motifs at the 5' end of a gene. RNA polymerase binds to the promoter, which orients it on the correct strand and in the correct direction, after which it can proceed to ...


20

The terms intron and exon were coined by Walter Gilbert in a renowned 'News and Views' article, Why Genes in Pieces, published in the journal Nature in 1978. Introns are the intragenic regions and exons are the regions which are expressed. This is the relevant passage in full: The notion of the cistron, the genetic unit of function that one thought ...


18

I'd like to know what is the reference for amoebic learning. I cannot comment directly on this, but there is some evidence for "adaptive anticipation" in both prokaryotes and single-celled Eukaryotes which do not have a nervous system. In the case of E. coli, it has been shown that the bacteria can anticipate the environment it is about to enter. E. coli ...


16

To add to canadianer's answer, in fact genes can be found on both strands of the DNA in most eukaryotic cells, in the sense that the sense and anti-sense strands are not always the same strand. The direction is therefore completely determined by the promoter. Furthermore, there are bidirectional promoters.


13

Here I will assume we are talking about eukaryotic sequence specific transcription factors (ssTFs) and try to answer your first and part of the second question. There is in any case not definitive answer yet. An estimate of ssTFs genes in humans is given in the 2009 Nature Reviews Genetics paper by Vaquerizas, JM et al, A census of human transcription ...


12

The NF-κB family of transcription factors is very modular, with different combinations having different effects. The active (nuclear, DNA-bound) TF is a dimer, composed variously of RelA/p65, RelB, c-rel, NFKB1/p50, and/or NFKB2/p52 subunits. For example, the "canonical" p65/p50 dimer is activated in response to stimulants like TNF-α (tumor necrosis factor ...


12

Nice question! But sadly, it comes under the category of questions about which we don't know everything yet. We don't yet know how RNA Polymerase differentiates between uracil and thymine while adding nucleotides to growing mRNA chain (at least, I was unable to find research papers online), most probably because it has proved difficult to know the exact ...


11

Methylation is increasingly seen as a consequence of gene activity rather than a regulatory mechanism. There are cases where methylation is controlled because of gene regulatory control, especially at the famous H19/Igf2 locus[1]. Here is a generally good recent review[2], note they mention that DNA methylation does not cause transcriptional silencing, and ...


10

I don't believe anything should change in the majority of DNA->RNA transcription. DNA methylation typically occurs on the non-watson crick side of Cytosine so it shouldn't affect the base-pairing. However, there are a few hypothetical situations that would result in alterations of the transcribed RNA. The sponatneous deamination of the 4' amine would ...


9

The techniques used to do this are ChIP-seq and ChIP-chip. Basically, you let the pathogen bind to the (highly replicated) DNA cut up the DNA into little random pieces by sonication enrich (“pull down”) the pathogen-bound DNA fragments by using a known antibody which binds to the pathogen sequence the thus enriched DNA map the sequenced fragments back to ...


9

The answer given by Sadegh gives a general correct broad view. But one part of the puzzle is missing, which is molecular recognition. Molecules bind to each other via physical/chemical interaction like forming hydrogen bonds, electrostatic interactions and other mechanisms. The sum of all interaction defines the strength of the binding. If molecules have ...


8

In addition to the excellent response up top (by Poshpaws), one can also imagine how these systems work by looking at recent synthetic examples of single-celled organism memory. It is possible to design various bistable switches using protein pathways, RNAi, or other means that will latch a particular state. In that way, an organism could effectively "...


8

There are two mechanisms of transcriptional termination in prokaryotes. The one shown here is "rho-dependent" because it involves rho, a DNA-RNA helicase that loads on and unwinds the RNA from the DNA, terminating the elongation by the polymerase. Check out [1] which shows a model for how rho multimers move through the RNA. The other mechanism involves ...


8

The answer to this question depends upon the definition of the word 'promoter'. In the simplest possible model of prokaryotic transcription the promoter is the site where RNA polymerase binds to the DNA before initiating RNA synthesis. In this process the σ factor recognises the core promoter elements directing the polymerase to bind to the DNA to ...


8

Take a look at this schematic of a mature mRNA. [source] The coding region (ie the part that is translated) is between the start and stop codons, but the 5' and 3' untranslated regions (UTRs) are also transcribed by RNA polymerase; these are part of the first and last exons, respectively. The transcription start site is labelled right in front of the 5' ...


7

Still if you change your question as (If histidine is abundant, HisP's job is to stop the histidine pathway as a "repressor." If HisP binds less tightly to promotors, the pathway should not produce as much histidine.) Then it should be under another assumption that what is the effect of HisP binding promoter of enzyme's gene. Is it suppressing the ...


7

That really depends on your system. At least for yeast the difference influences the strength of the activation ("Analysis of Transcriptional Activation at a Distance in Saccharomyces cerevisiae"). For bacteria such long distance regulations have recently been identified. Before that it was thought that this does happen only in eukaryotes. See the paper: "...


7

No, this will not happen. mRNAs are inspected in the nucleus before they are exported into the cytoplasm (at least in eukaryotes), where transcription and translation don't happen at the same place. This ensures that no mRNAs without stop codons or premature stop codons are exported. This phenomenon is called "mRNA surveillance". mRNAs that do not pass this ...


7

Transcription occurs in a special structure known as transcription bubble. Inside the bubble are present the mRNA, template DNA being transcribed and the RNA Polymerase. Upstream of bubble is the DNA already transcribed and downstream is the DNA to be transcribed. There is not enough space in cell to have completely unfolded DNA for transcription, so ...


7

It's both simple and complex. The simple answer is Brownian motion. All the particles in the cell do have mobility which is related to their mass. A small particle like a soluble enzyme undergoes random walks through the cytoplasm or nucleoplasm. Thus by having a grand number of a certain molecule you can be sure that at some point it interacts with the ...


6

Yes. For an example, see this list of targets of NF-kB (a transcription factor). Many other transcription factors are included there. As for a TF that does nothing except activate another, single TF? I don't know that those exist - TFs tend to modulate multiple genes.


6

From the Methods section: Human TfR in plasmid cDNA was a gift from Tim McGraw (Weill-Cornell Medical College, New York, NY). Human TfR cDNA was subcloned in frame with EGFP in the Clontech pEGFP-N1 vector at the XhoI and BamHI restriction sites. This TfR-GFP fusion protein does not have the endogenous TfR promoter. So it is not likely to be ...


6

Genetic code and codons are always used with reference to RNA. When talking about DNA, the the sense strand of a gene is considered its sequence. The anti-sense strand though is the template for mRNA synthesis, does not represent the gene. DNA-codon table has simply U replaced by T. Apart from a wikipedia article, I don't find the term being popularly (not ...


6

Multiple RNA Polymerase transcription complexes engaged on the lacZ gene at the same time, staggered along the gene.


6

Most (almost all, AFAIK) mRNAs and lncRNAs start with exons for the reasons already mentioned by David. In a typical splicing event, the nucleotide that is 5' to the splice donor site (lets call it pre-donor) and the one that is 3' to the acceptor site (lets call it post acceptor) are joined together and the intronic sequence between them is removed. If ...


6

The breakdown and reassembly of proteins is a ubiquitous process within cells, and yes this is expensive but transport is expensive, too, and recycling has the added benefit of dealing with proteins that become misfolded or otherwise damaged as well as allowing for transcription and translation to regulate overall protein levels. The Toyoma & Hetzer 2013 ...


5

A quick search on T7 cysteines gave some clues: Bacteriophage T7-induced DNA polymerase is composed of a 1: 1 complex of phage-induced gene 5 protein and Escherichia coli thioredoxin. Preparation of active subunits in the absence of sulfhydryl reagents indicates the reduced form of thioredoxin is sufficient for formation of the active ...


5

As you pointed out, the repressor gene lacI is transcribed as a one mRNA, and three structural genes: lacZ, lacY and lacA are transcribed into a single polycistronic mRNA. The two mRNAs are translated independently of one another. The polycisronic mRNA is not broken into pieces. Rather, it is translated by ribosomes (at least three, explanation below), ...


5

A large number of prokaryotes do indeed have nucleosome-like structures. The most well studied is H-NS in E. coli, Salmonella and some other deltaproteobacteria. H-NS like molecules have also been found in mycoplasma (Lsr2). One of its roles is to bind AT-rich DNA and silence transcription. The binding is usually to suppress the expression of foreign DNA ...


5

From the wikipedia article on TFs: In molecular biology and genetics, a transcription factor (sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to messenger RNA. The nature of the gene affected is irrelevant, a protein ...


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