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10

What should be the correct reason for bilayer arrangement? I'll answer your second question first, but there is an almost identical question on this site already: Why do cells have a bilayer? There is water on the extracellular and intracellular side of the membrane. What's actually happening at a molecular dynamics level is the self-association of the ...


7

Was it by chance? Yes, sometimes, Penicillin was discovered by chance (and good observation), see http://www.nobelprize.org/nobel_prizes/medicine/laureates/1945/fleming-bio.html. I know some where accidents, but how are the majority found, testing lots of chemicals on your target? Other important classes, like tetracyclines, were discovered by ...


3

Needleman-Wunsch does an end-to-end (global) alignment (BLAST uses Smith-Waterman). Needle from the EMBOSS toolkit performs Needleman-Wunsch alignment. It will report the highest scoring alignment. I am not sure which alignment it reports when there are two of them with equal scores (I don't think it is random). I just tried your case: replaced B with W as ...


3

I would add this as a comment to your question but do not have enough reputation. A simple look at Wikipedia (which is a very good source for general questions like these) would have provided you with an answer. I just did this to see how long it would take if I did not know the answer. It was about 20-30 seconds. Protein synthesis: Transcription In ...


3

It is common in biology to use a virus to deliver new genetic information to a cell. Such a virus is called a viral vector. Retroviruses can be used to enable the viral DNA to be incorporated into the cell's genome. Usually viral genes are removed, making the virus unable to replicate once the cell is infected 1. Using viral vectors in vivo to "correct" ...


3

Usually, toxicity is given in the units of mass of the substance per unit mass of body mass of the organism that will kill 50% of the organisms in a species if those organisms ingest the toxin at that dose (e.g. mg/kg, ng/kg). This measurement is called the median lethal dose, and is often abbreviated as LD50. In your table, they only provide the mass of ...


3

In a word: mutation. If you step back and think about it, multicellular organisms are really, really complex systems. Different cells have to do different kinds of things and interact with each other, they form organized tissues and organs and so on. That much is obvious. For all of this to work in concert, cells have to grow and divide (to replace dying ...


2

The lifetime of Calcium can be considered infinite in biological time scales, it is not a real biomolecule. The half-life time of other biomolecules like IP3, PIP2, receptors, hormones, etc. is species-dependent and within the species strongly depending on the cell and its metabolic state. Short answer: There is no overview for lifetimes of biomolecules. It ...


2

Your understanding of DNA is correct. DNA is a heteropolymer of monomers called nucleotides and each nucleotide is made up of a sugar (deoxyribose), phosphate and a "base" (A, T, G, C). As you already know, DNA is organized as a double helix with the Watson-Crick pairing rules. A chromosome contains a single DNA double helix. Many organisms have multiple ...


2

I don't think that computer modeling will be the way new antibiotics in the near future are discovered. Besides all the issues with modeling itself as mentioned above, it's also really easy to find something that kills bacteria (semi-relevant XKCD: https://xkcd.com/1217/), but you really need something that's also mostly harmless to human cells. So you'd ...


1

That is a very bad test case. The problem is that the sequences are too short and involve a long repetition. This means that the default gap penalties and the gap-length penalties are not applicable. They are designed to work with longer sequences, where the penalty of inserting a gap can be offset by an increase in matches. In any case you can get bad ...


1

Your guess is made without knowing protein substitution probabilities. Optimality of alignment in BLAST is a metrics of the scoring function. The scoring function depends on the word size (length of the seed that initiates an alignment), rewards and penalties for matches and mismatches - gap cost and substitution matrix. In general, BLAST uses BLOSSUM and ...


1

Your question is quite vague so I can only give you a vague answer saying what I would expect given only the information of your question. The vagueness mainly comes from the huge amount of functional sequences in the genome, particularly also in enzyme-coding genes, each being more or less conserved. You say I am surprised that there is no ...


1

There are several mechanisms by which the expression of a gene can be completely turned off. Certain network architectures can ensure foolproof repression (for e.g. by using multiple repressors parallely or additional epigenetic silencing mechanisms). Bistable switches can also ensure robustness of expression in a way that small fluctuations in the ...


1

You ask initially about the “sense” and “antisense” strands of DNA. These terms are explained in the Wikipedia reference entitled ‘Sense strand’. This states what you appear to be already aware of, that: “The sense strand is the strand of DNA that has the same sequence as the mRNA, which takes the antisense strand as its template during transcription…” ...


1

A retransformation should get you a pure plasmid. Transform the plasmid mix into empty E.coli (don't use too much DNA), plate on Kan / Amp depending on what you need. The probability that one cell took up both plasmids is extremely low, and you could check with colony PCR just to be sure. Otherwise: ask around, there must be (old) stocks of the single ...


1

You are correct in saying that Crick, in his Wobble Hypothesis, proposed that “the base on the third position of the codon and that on the anticodon need not be complementary”, but the “need not be” in your statement is a paraphrase of the “some” in Crick’s original statement: “It is suggested that while the standard base pairs may be used rather ...



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