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3

is the pseduoknot the alignment of these base pairs I'm not exactly sure what is meant by alignment, but if you mean base pairing from the flanking RNA to the loop of the hairpin you have depicted, then you would have an H-type pseudoknot. Since you are interested in predicting these structures, it's important to note that a nucleic acid sequence ...


5

The pKas of (neutral) guanine and thymine are 9-10 (ref). At high pH (>~10), those bases will be deprotonated and exist as negatively charged conjugate bases. As the deprotonated species, part of the G/C and A/T hydrogen bonding networks are eliminated. In the figure below, green dotted lines represent the hydrogen bonds that explain the observed base ...


2

As user137 said, the general base abstracts a proton from the 2'OH and subsequently the 2'O- renders a nucleophilic attack on the δ+ Phosphorous, leading to the hydrolysis of the phosphodiester bond. There can be slight variations in the mechanism and the intermediates; for details see this review. ...


1

I agree with March Ho in general: people are not rational about food. That said there are two fairly different kinds of GMO, with different implications on the fears to have about them. 1) GMO embedding genes from the same species These are not supposed to be any different from plants obtained using classical breeding techniques. The process in brief is ...


1

People are not always rational when it comes to what they eat, especially when the compounds that make up the food have long, arcane-sounding names. It is indeed possible to analyse the amino acid composition of a food substance. However, this has no bearing whatsoever on the safety of the food product. For example, the following are two truncated ...


-1

Since chemical reactions are governed by quantum physics, there is a whole lot of products that can come out of mixing together several multi-atom molecules. And all of those will have non-zero probability of occurrence. But this probability is extremely low at normal temperatures, so you don't see those products. Enzymes lower activation energy and so ...


0

Can it be a gene (that is piece of DNA, sequence) that encodes for certain receptor? In practical terms it will mean that cell uses that exact DNA code to produce named receptor. And if you create, say, yeast carrying plasmid with that sequence, that yeast will be able to produce that receptor molecule, even though wild-type yeast couldn't. So it is the ...


-1

Chris is right here, polymerases are generating sequences, the enzymes your asking about do a single type of reaction, so you would be assessing its activity not its fidelity. A good resource I've found for looking at qc data for enzymes like these are just the product inserts from the manufacturer. NEB for example generally seems to provide sufficient qc ...


2

But how do you get from double-strand breaks to editing genes in incredibly specific ways? You should read the wikipedia page on CRISPR-Cas system. The target specificity is provided by the tracrRNA. How do you specify which kind of repair mechanism is invoked? The repair can be done either by Non Homologous End Joining (NHEJ) or Homologous ...


3

Hallmarks of Cancer: The Next Generation is by far my favorite article at the moment explaining cancer in-depth. I'd recommend reading through it. The cells replicate themselves, without regard for normal cellular restriction, due to a number of mutations that accumulate: So our cancer cells are evading apoptosis. P53 might be knocked down, so cell cycle ...


2

So in a very broad definition, yes, chromatin encompasses DNA, RNA and protein. The primary function of chromatin is to provide a method to effectively package all the DNA in a cell. This packaging is dynamic, and it's constantly regulated in a cell type-specific manner. We can see the broad interactions of protein and DNA in this cartoon representation from ...


0

Proline is replaced by Glutamic acid. Pro16 indicated a position on the protein.


3

You are looking at a protein here, which is mutated in the higher host specificity, so glucose is not involved here. What is written here are the amino acids in the three-letter-code, the notation Pro→Glu means that Proline (Pro) is replaced by Glutamic acid (Glu). The notation Pro16 means the proline on amino acid position 16 in the protein. You often find ...


2

I had a similar problem. In my case, I realized that it is absolutely essential to wash the membrane in TBS without Tween (TBS, not TBST) before you use ECL. If you have any amount of soap (Tween) on your membrane it reacts in some way with ECL and each time you should be getting a different pattern of these stains. Washing the membrane in TBS and then ...


0

The T7 promoter is encoded for by the genome of T7 bacteriophage. The T7 RNA polymerase is specific for the T7 promoter, and so in the presence of the T7 promoter the T7 RNA Polymerase will transcribe everything going 5'-3'. If your T7 promoters are flanking your gene of interest, you can expect copies of your coding portions either way the insert goes in. ...


1

You will definitely get satellite colonies. Ampicillin breaks down after about a day, especially exposed to light. Kan, keeps pretty well at room temp, but that does you no good :)


1

Lets just go with the basic Hodgkin-Huxley equation: $$C_M \frac{\text{d}V}{\text{d}t}=-g_{Na}(V-E_{Na}) -g_K(V-E_K) -g_L(V-E_L)$$ At rest ${\large\frac{\text{d}V}{\text{d}t}}=0$ and therefore $V$ is dependent on the conductances ($g_X$) of different ions. Since $g_K \sim 30\times g_{Na}$, the resting potential is closer to $E_K$ (Nernst equilibrium ...


7

Housekeeping genes aren't clustered on a single chromosome. It is perhaps not that 'housekeeping' genes - broadly expressed genes - are 'above the laws of regulation'; rather that their regulation is merely more straight-forward than that of specialised genes. I can think of 2 factors that could be relevant: Abundance of methylation sites (CpG sites) ...


6

The problem with housekeeping genes is that they are often not stable and their expression depends on the cell types as well as the conditions. They can be stable under one condition, but are not under another. So this needs to be tested every time you have to choose a housekeeping gene - always use GAPDH or beta-Actin simply doesn't work or skews the ...


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CCCEEE etc. are the secondary structural elements. The C or E usually refers to whether the residue is coiled (C) or part of a strand (E). H would be used to denote a helix. However in this case the C refers to non-strand and non-helix regions i.e looping regions rather than a coiled region (although I think this is more of a point of semantics). e or - ...


4

As far as I know there are 5 receptors for far-red and red light which are the phytochroms(phyA-phyE) Its all about the ratio between red and far-red light. Each phytochrom has an inactive(PR) and an active(PFr) conformation. phyA is the only phytochrom which is activated by far-red light, so its active state is PR. (Only if the ratio between red and ...



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