39

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 ...


15

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

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

They're both correct. The confusion stems from the book talking about the anticoding strand as well as the newly-formed coding RNA strand, whereas Khan Academy talks only about the coding strand. From the book: The anticoding strand is transcribed from 3' to 5'. Therefore the coding strand is produced from 5' to 3', meaning the very first nucleotide ...


9

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 ...


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

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

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 ...


7

@Thymine's answer is correct. I just thought I'd post a more graphic answer for clarity. <==(RNA Pol)3'------------------------- 5' 5' ------------------------------------------------------ 3' 3' ------------------------------------------------------ 5' The RNA Polymerase is synthesizing on the 3' to 5' strand, but nucleic acids are ...


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 ...


6

Disclaimer As I have pointed out in my comment, it is not clear whether the sources mentioned relate to eukaryotes or prokaryotes, assuming they are correct. I am a translation man, rather than a transcription man, and so am answering this from the 2002 edition of Berg et al. ‘Biochemistry’, as I happen to have a copy of my own (a freebie from when I was ...


6

The simple answer Under the assumption that each mRNA molecule is translated at least once, by necessity translation will happen more often than transcription. This is because the only way to get a protein is to translate an mRNA. In other words, as long as there are more protein molecules (translation products) than mRNA molecules in a cell, then the ...


6

No. I don’t think anybody would call the sigma factor of bacterial RNA polymerase — or indeed any other protein — a cofactor or a coenzyme, the subset of cofactors that are organic (the original poster is wrong in his declaration about cofactors, or at least one reputable text book disagrees with him). I could justify this statement by quoting a definition ...


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 ...


5

In my opinion they should mean the template strand, and they probably do. Perhaps if we had a link to the paper we could have examined the language more closely. Here is a paper which uses the term in that sense: Mugal, CF et al. (2008) Transcription-Induced Mutational Strand Bias and Its Effect on Substitution Rates in Human Genes. Molecular Biology and ...


5

This is the Curated database of mouse and human transcription factors. And this is the paper in which they describe how they curated the database. In summary, there are 3230 putative mouse TF, 1200 of which are described in scientific papers.


5

As the number of human TFs have been discussed by the previous answers, I'll limit myself to Anopheles gambiae. In the same issue of Science in which Holt et al. published a genome sequence for Anopheles gambiae (1), Zdobnov et al. published a comparison of the A. gambiae and Drosophila melanogaster genomes.(2) While the two species diverged about 250 ...


5

You mix up translation and transcription. Transcription creates mRNA from DNA template. Transcription also includes splicing, that is excision of introns so that mature mRNA contains only exons. In your example it goes like that: DNA (chromosome): ---A----B--...--Dstop---E--- premature mRNA: A----B---...---Dstop--E---polyA mature mRNA: AB..DstopE-polyA ...


5

Definitely not. There is a ton of variation from gene to gene, otherwise, as you say, regulation wouldn't work. That said, the word "promoter" sometimes gets used in different ways. Especially in eukaryotic systems, people will sometimes say "promoter" to mean the entire region upstream of the gene where transcription factors can bind (for yeast, typically ...


5

TATA box is a feature of organisms that have dsDNA as a genetic material. Like most dsDNA promoter elements, TATA box is basically a section of dsDNA. However a question like "On which DNA strand is TATA box present?" depends on what you define TATA-box as. If you go by this definition: In molecular biology, the TATA box (also called the Goldberg-...


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