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14

Th reason for this is that for the third base of the tRNA non-Watson-Crick pairing is allowed. This phenomenon is called "Wobble base pairing". See the figure (from here) for illustration (from here): If you have a look at the codon table for amino acids, than the variation in the code for one amino acid mostly happens on the third position (from here): ...


10

The RNA world hypothesis states that self-replicating RNA (that is, an autocatalytic RNA polymerase) was the first form or precursor of life. So, in that context, your question is basically asking how life originated. The obvious answer is that we don't know (currently anyways), but I'm going to take this opportunity to describe a few really neat experiments ...


10

I think given that you're just getting started with genetics, you can say that the codons are interchangeable. This is generally true, though not technically correct. Here are a few reasons for why this is the case, though there's probably more: Specific organisms use specific codons with different frequencies. This is usually related to the tRNA abundance ...


8

See this paper. They have studied RBP-protected sites in the entire human transcriptome by RNA-protein crosslinking followed by RNAse digestion and sequencing: PIPseq. Figure 1 of the paper shows distribution of protein protected sites in RNAs. They also correlate it with different regions of mRNA and its expression. They show number of protein protected ...


8

Nice question which leads to the fundamentals of DNA and RNA. DNA (Deoxyribonucleic acid) is the core of life in Earth, every known living organism is using DNA as their genetic backbone. DNA is so precious and vital to eukaryotes that its kept packaged in cell nucleus, its being copied but never removed because it never leaves the safety of nucleus. DNA ...


8

A pre-tRNA is transcribed from tRNA genes in DNA by RNA polymerase III. Processing occurs in the nucleus, where a 5' sequence is cleaved by RNase P, the 3's CCA motif is added, and ~10% of the nucleotides are substituted. The tRNA are transported out via the pore complexes. Aminoacyl-tRNA synthetase enzymes attach amino acids in the cytoplasm in a 2-step ...


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 ...


6

It's one for every phosphodiester bond formed. 11 nucleotides, but only 10 bonds needed to join them into an oligonucleotide: 1 2 3 4 5 6 7 8 9 10 11 N--N--N--N--N--N--N--N--N--N--N 1 2 3 4 5 6 7 8 9 10


6

There are some tools for predicting the binding: TargetScan (based on seed match [primary], extra pairing, sequence context 1 — nucleotide composition around the site etc [secondary]) miRanda (based on hybridization stability and seed match[primary] and sequence context [secondary]) PicTar (adds a layer of evolutionary conservation criteria) 1 Context ...


6

You have two possibilities: When you only need a quick check if your RNA is ok and you indeed only get one band, you can try a "quick and dirty" method. Heat the sample for 5 minutes at 65°C and then immediately cool it down in an icebath and keep it there until loading. By doing so, you melt up the secondary structure of the RNA and keep it in this state. ...


6

Top 10 long processed transcripts in humans (with multiple isoforms), from gencode 19 annotations: Transcript Length(bases) ------------------------ TTN-018 108861 <-- Titin TTN-019 103988 TTN-002 101206 KCNQ1OT1-001 91666 TTN-201 82413 TTN-202 82212 TTN-003 81838 MUC16-001 43732 ...


6

Addition to Jvrek's answer based on the comments. Most RNA degradation mechanisms catalysed by different RNAses (RNAse-A and RNAse-S, for example), involve the 2'-OH. Therefore the repertoire of RNAses is selective towards RNA and not DNA because of the 2'-OH.         ...


5

Short answer I can think of at least a dozen applications for which it would be useful to know the secondary structure of a given sequence of RNA off of the top of my head. In no particular order: Simulation/visualization of RNA Riboswitches MicroRNA RNA interference (RNAi) RNA-RNA interactions RNA-DNA interactions RNA-protein interactions Ribosomal ...


5

I think a good candidate is the human titin gene. The gene itself has 363 exons, depending on the isoform it has between 27.000 and 34.000 residues. This makes up a processed mRNA length of up to 100kb for the full length isoform. See either the Wikipedia article or the one linked below for more details: The complete gene sequence of titin, expression of ...


5

This question can't be answered with a simple yes/no, but I would say that the analogy of DNA being the "code" used by cells is a reasonable one, if taken with a number of other considerations. DNA function When Watson and Crick first described the structure of DNA (being a double-stranded sequence of the nucleotides Adenine, Cytosine, Guanine and ...


5

Start and stop codons are instructions for the ribosome to start and stop protein synthesis, respectively. The region between the start and stop codon (inclusive of them) is called ORF (open reading frame) or sometimes CDS (Coding sequence). Why does ribosome need explicit instructions for start and stop? Ribosome recognizes an RNA as a mRNA if it has ...


5

Not very common, and not found so far in nature, but they exist and are called deoxyribozymes. Additional information: Deoxyribozymes are the equivalent of ribozymes in the DNA world and can function as catalysts for different biochemical reactions, such as DNA cleavage. While DNAzymes (short name) were synthesized in a laboratory context (In-vitro) and ...


5

I think it is relatively unlikely that the RNA will degrade under this conditions. For the future, I would handle this differently: You can centrifuge the cells and snap freeze them in an appropriate buffer in liquid nitrogen and then store them at -80°C. I would not freeze the dry pellet, as these are often hard to re-dissolve after freezing. ...


4

Yes, that should be possible. And it is one of the ways antibodies work. It is already used as a treatment against rabies. There you get a dose of immunoglobulins directed against the rabies virus together with the vaccine. The immunoglobulins neutralize the virus. The same is possible when you vaccinate against the surface proteins which a virus uses to ...


4

Short answer: Yes, you can. Usually these are coupled systems for transcription and translation. For these you clone the gene of interest into a vector which contains a prokaryotic promoter which is then used to generate the mRNA in the tube. This mRNA is then translated in the second step into a protein. This works very well, but the protein is missing ...


4

Watson-Crick base pairing can be violated by wobble base pairing. The 5' of the anticodon has more freedom in binding, that is why, for many amino acids, the last part of the codon has more possible characters.


4

As far as I know this has never been thoroughly analyzed for RNA, but there is an excellent paper on the precipitation of DNA and the usual conditions in BRL Focus by Zeugin (see below for the paper). Since DNA and RNA are pretty much the same (except for one OH-Group) and the conditions used for precipitation are also similar, I think we can use this for a ...


4

According to my book Molecular Biology Principles of Genome Function by Craig et al, eukaryotic RNA degradation does not have an initiation, as in bacteria where pyrophoasphate hydrolase hydrolyses the 5'-triphosphate to 5'-monophosphate, and is therefore the initiatior. In eukaryotes the polyA-tail is shortened by a deadenylase enzyme complex which ...


4

Qiagen and Life Technologies call it RNA content, total RNA, or total cellular RNA.


3

Imagine you want to produce a widget. You have thousands of worker, but only one blueprint. Each worker needs the blueprint to build a widget (they're really forgetful and can't build from memory). So only one worker at a time can build your widgets. What you would do is to create copies of your blueprint and distribute them to your workers. That way ...


3

Yes, transcription of a polyA sequence will be unreliable: for a repetition of 15 times the same nucleotide, the rate of transcription errors will be huge. For example in E. coli, this paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC331007/ gives some order of magnitude of transcription errors caused by repeats of nucleotides. According to their data, for ...


3

A good answer is already provided by @canadianer, but as with many things in biology it is important to keep in mind what organism and/or cell type we are talking about. Because the nuances of the answer to a question about a seemingly universal process sometimes actually depend on whether we want to know about bacteria, or fungi, or mammalian stem cells, ...


3

Not all the RNA is to be translated into proteins. Actually most of it is for regulation and sometimes unknown use. There are non coding regions before the start codon and after the stop codon. Hence the need for both.


3

It is important to have start and stop codons so that the molecular machinery of the cell (ribosome etc.) "know" where the actual transcript starts and ends. This is especially important, since mature mRNA contains untranslated regions which are of regulatory importance. These regions occur on both sides of the coding sequence called 5' and 3'UTR ...



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