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42

This question makes a number of incorrect assumptions and I don't have time to correct them. The short answer is that the virus has mutated probably hundreds of times since it entered humans in late 2019. The lower figure on the NextStrain.org ncov page, "Diversity", shows the known mutations that have been identified so far. As I look at it now, there are ...


33

There is still a lot to be learned about the roles introns play in biological processes, but there are a couple of things that have been pretty well established. Introns enable alternative splicing, which enables a single gene to encode multiple proteins that perform different functions under different conditions. For example, a signal the cell receives ...


17

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): ...


17

It does fold on to itself. There are secondary structures in RNA and some of these secondary structures also have regulatory functions (for example, riboswitches). Some of these structures can also inhibit translation (by different mechanisms such as the masking of the ribosome binding site or analogous eukaryotic sequences, or stalling of ribosome etc). ...


16

Thymine has a greater resistance to photochemical mutation, making the genetic message more stable. This offers a rough explanation of why thymine is more protected then uracil. However, the real question is: Why does thymine replace uracil in DNA? The important thing to notice is that while uracil exists as both uridine (U) and deoxy-uridine (dU), ...


15

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 ...


12

DNA polymerases need a primer oligonucleotide (RNA or DNA) - their substrates are an existing 3'-OH group and a dNTP. The primase however is a typical RNA polymerase, capable of initiating polynucleotide synthesis de novo by positioning a complementary ribonucleoside 5'-triphosphate opposite its complementary DNA base. The primase makes an RNA primer that ...


12

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 ...


12

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 ...


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

One of the primary reasons to use poly(A) selection is to eliminate the massive amount of ribosomal RNA (rRNA) present in the samples. The alternative is to use ribosomal RNA depletion kits / techniques to remove as much rRNA as possible before sequencing. Without rRNA depletion a large proportion (~60-80%) of the reads would map to rRNAs. poly(A) ...


11

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 ...


11

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 Thymine)...


10

From my understanding sense and anti sense is contextual. If you are looking at a gene from 5'->3'(which is convention) that strand is the sense strand and the complement to the gene is the anti sense strand. However further along the DNA there could be a gene on the 'original' anti sense strand, if you are discussing this new gene, there is a new context ...


10

Regardless of the question† of which came first*, RNA or DNA, it is possible to rationalize the absence of thymine in RNA by a cost–benefit analysis. There is a cost to using thymine, so there must be sufficient benefits to make this worth while. Cost of using thymine rather than uracil The most obvious cost of using thymine is the energy requirement for ...


9

You should check out Howald C, et al[1]. This is one of the many recent papers tied to the ENCODE data. They've used RT-PCR to amplify exon-exon junctions and then sequenced the results. Supplemental table 2 shows 3076 validated exon-exon junctions in putative processed transcripts which, in the main body of the paper may be sub-classified as: Non-coding,...


9

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 ...


9

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 ...


9

Yes there are reports of RNA directly inhibiting transcription. RNA induced transcriptional silencing (RITS) is a well known pathway in Schizosaccharomyces pombe (fission yeast). Initial heterochromatinization is dependent on the RNA (as a DNA identfication module) that guides other functional proteins to the target (Also see Djupedal et al., 2009). piRNA ...


8

The helix shape of DNA molecule is a consequence of its secondary structure. This refers to the bases contained in the molecule which pair, thus determining tertiary structure [1]. Basepairing also occurs in RNA, so it can form a double helix. In fact, RNA is composed of short helices packed together [2]. Base pairs maintain DNA's helical structure no ...


8

RNA (single or double stranded) actually can and does form a helix in the absence of certain complex 3D structures. The RNA helix is typically A-form, as opposed to B-form for typical DNA. The A-form helix is right-handed like the B-form but is more compact (2.6 Å rise versus 3.4 Å) and wider (26 Å diameter vs 20 Å). The differing helices arise from the 2'-...


8

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.                  ...


8

Though this is a basic question (a few google searches will provide all answers) and you have asked a lot of questions, I shall answer them one-by-one. Why is RNA single stranded (and not double stranded like DNA)? dsRNA is less stable than dsDNA. See this: http://en.wikipedia.org/wiki/RNA#Structure. An important structural feature of RNA that ...


7

DNA-RNA triplex formation is well-documented. It was originally analysed in simple model polynucleotides where the DNA has a polypurine strand and the RNA has a polypyrimidine, e.g. rCCCCCC dGGGGGGGGGGGGGG dCCCCCCCCCCCCCC rUUUUUU dAAAAAAAAAAAAA dTTTTTTTTTTTTT but it is now known to occur in more complex sequences. One of the best studied examples is in ...


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

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 ...


7

This is a badly-worded phrase that means nothing in the context of the paragraph in which it occurs. There is no way the reader could be expected to understand it from this awful book on its own. Normally I would not think it the role of this site to remedy deficiencies in text books. However, as this involves some interesting questions I will try to read ...


7

Aminoacyl-tRNA sythetases are highly specific to their corresponding amino acid. First, the activation site, where the amino acid binds, constitutes a complex network of intermolecular interactions. For example, threonine, catalyzed by threonyl-tRNA synthetase, is very similar to valine and serine. Valine has a methyl group instead of the hydroxy group of ...


6

In simple terms: Function of the RNA primer: DNA polymerases need a double-stranded DNA region to which they can attach in order to begin copying the rest of the DNA strand. In order to provide this double-stranded attachment site, RNA primers are added by primase, an RNA polymerase which does not require such an attachment site itself. When DNA ...


6

Evolution - Douglas J. Futuyma, Chapter 19, p. 461 Michael Lynch and John Conery (2003) have pointed out that a variety of genomic features that appear to have little fitness advantage for organisms-introns, transposable elements, large tracts of noncoding DNA-may be more prevalent in species with small effective population sizes. They have ...


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