text:
Why does the affinity of haemoglobin for oxygen decrease at high altitudes?
My class 12 NCERT book says, Pg 226

The body compensates low oxygen availability by increasing red blood cell production, decreasing the binding affinity of haemoglobin and by increasing breathing rate.

Why should the haemoglobin binding capacity decrease at high altitude?
I think it should increase for better oxygen transfer and uptake from air. The concentrtion of oxygen in the atmosphere decreases with height. Hence, if the haemoglobin binding increases, we will be able to draw more oxygen from the air and transport it to the cells.

Haemoglobin's job is to transport oxygen and not store it. Therefore it should also be able to release oxygen effectively. When the differences in partial pressure of oxygen between the tissues and blood are low then oxygen will not be transported to the tissues from blood, leading to hypoxia.
2,3 Bisphosphoglycerate (2,3-BPG) stabilizes the T- (taut; oxygen unbound) form of haemoglobin thereby reducing its affinity to bind to oxygen. 2,3-BPG is found to be elevated in people living at high altitudes. The production of 2,3-BPG is controlled by a negative feedback (Mulquiney et al., 1999; also see wikipedia) so that it does not overdo its job.
David's answer explains the dynamics in details and addresses the non-linear (sigmoidal) nature of Hb-Oxygen binding which is a critical point for understanding how the effect of 2,3-BPG is actually favourable.
However, haemoglobin content also increases so that higher amounts of oxygen can be captured. This is a fine balance and as you may notice (even if you do not read it to great depth) in the linked paper, there are many mechanisms that are working towards this.

The answer to this question is yes, a decrease in oxygen affinity will decrease the oxygen taken up by the haemoglobin (Hb), but it is an appropriate response because it will have a greater effect in increasing the release of oxygen to the tissues.
This is not intrinsically obvious. It happens because of the (sigmoid) shape of the oxygen binding curve, and can only really be appreciated if you examine the curves for the normal situation and that in which there is increased 2,3 Bisphosphoglycerate (2,3-BPG) producing the change in oxygen affinity. I have devised a figure to demonstrate this, although it is not based on actual data, so should only be regarded as illustratative.

At sea level the lungs pick up oxygen at 1 (say 100% saturation of
Hb) and when the oxygen pressure drops to 40 mm Hg in the tissues (2)
the Hb will be 55% saturated. Hence in this example they have
released 45% of a full complement of oxygen.
If we look at the same curve for high altitude, in this example the oxygen pressure at the lungs (1') will be such that the Hb is only 80% saturated. Thus at 40 mm Hg in the tissues (2) when Hb is only 55% saturated it will only have released and made available 25% of a full complement of oxygen.
Now consider the effect of high altitude acclimatization with increased 2,3-BPG production changing the equilibrium and the oxygen binding curve (red). At the lungs (3) the Hb will be less charged with oxygen — only 70% saturation — but at 40mm Hg in the tissues (4) it will be much less saturated than on the black curve — 30%. Thus it will have made available 40% of a full complement of oxygen.

This is not a perfect solution, which is why over a longer term there is increased production of red blood cells to provide more haemoglobin to compensate for the smaller amount of oxygen it can bind.

+1 for the graph and pointing out the effect of non-linearity in the dynamics. That is a critical point that I missed.

beautiful answer


text:
What, if any, is the difference between covalently closed circular DNA and plasmids?
Are cccDNA (covalently closed circular DNA) and plasmids the same thing? What about DNA topoisomers?

Please add some indication that you've performed prior research to try to answer your own question. This is a requirement on Bio.SE. Unfortunately, if you do not, your question will remain closed and possibly deleted.

The short answer to this question is no, they are not the same thing.
The long answer, however, is in some cases they can be interchangeable. I would like to make the comparison with the coin-just like you can flip it on one side or the other in some(actually, far from always)cases a cccDNA can become a plasmid and the vice versa. cccDNA isn't an entity on its own right-it isn't a component of the cell like a plasmid can be. It is a phase of the replication cycle of some viruses. It can be found in the group I and VII viruses according to the Baltimore classification. This means viruses containing DNA in their virion(the virion is what you would normally consider to be the virus, it is what you see on all those electron microscope pictures on the Internet and is what exists out of the cell as the virus). Some of the members of those groups of viruses have genomes which once inside the cell can replicate using cccDNA, Here is an example of a virus using its circular DNA to replicate:

It uses this form of its genome, because it makes its replication easier since once the enzyme starts to replicate it can do several circles without stoping. It is a replication strategy viruses use, while a plasmid is a mobile genetic element. It means it always needs a cell by definition. Now, it is true plasmids can become viruses and viruses plasmids if genes coding for the proteins needed to construct their virions are present but from a purely definitial point of view they are different things. In reality however it is possible for a plasmid to acquire the genes it needs to become a virus and for a virus to lose them and become a plasmid. Actually this is process often used in recombinant DNA technology to transfer genes from one bacterium to another by viruses because often these plasmids can get included in the cellular genome and include in it the genes they carry. See 3 This is the big difference between a circular viral genome replicating in the cell and a plasmid. Yes, they can look similar in shape but they are not the same as function.
Topoisomers are different forms of DNA which are the same in sequence but differ in their special structure. DNA can have different forms depending on the particular way it folds in space. These different shapes are what is called topoisomers.

Woah, thanks for the detailed answer, I appreciate your help.

As a descriptive term, we can take covalently closed, circular DNA (cccDNA) at face value: any DNA that is circular, with the ends joined by covalent bonds, can be described as cccDNA. Thus, plasmids are a type of cccDNA, but not all cccDNA are plasmids. Textbooks and lecturers describe plasmids as cccDNA for the purposes of DNA topology. This usage also appears in literature. cccDNA can also refer to circularized viral DNA, which is another type of episome. Note that the linked to papers are merely examples of how the term is used, not authoritative definitions.

What about DNA topoisomers then?

@JewelJohnson I don't follow you completely with that question. cccDNA can have topoisomers, but so can topologically constrained linear DNA.

I'm sorry, I thought DNA topoisomers are a different class. My bad.

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Why aren't 'exons' named 'introns'?
Why are introns called 'introns' when they are the actual ones who are getting spliced out from the pre-mRNA. Shouldn't exons be named introns as they are the ones that are 'in' and are not 'exiting'? On what criteria were they named like this?

It confuses me too. Shrug.

It’s not actually true that introns always stay inside the nucleus. There is a lot of research discussing the role of extranuclear introns playing a role in translation regulation.

I'm amazed how many votes this has got. Shows that there is a general confusion among those new to the topic. If I were still teaching this, I'd make an extra effort to clarify the origin of the expression. I withdraw my close vote.

@David It was in the "Hot Questions" list, which makes it visible to everyone across Stack Exchange.

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 corresponded to a polypeptide chain, now must be replaced by that of a transcription unit containing regions which will be lost from the mature messenger - which I suggest we call introns (for intragenic regions) - alternating with regions which will be expressed - exons. The gene is a mosaic: expressed sequences held in a matrix of silent DNA, an intronic matrix.

Yeah I got the link of the article from Nature.com . Thanks

Well, as this question seems to be about helping the X- or M- generations get to grips with baby boomer terminology, let me explain how I remember what introns are.
Before Gilbert coined the term (as @xusr explains) original reports of the research that established the mosaic nature of eukaryotic genes refered to

in-tervening sequences.

For example, there was a paper from Phil Leder’s lab in 1978 entitled

Intervening sequence of DNA identified in the structural portion of amouse β-globin gene

So intron was really related to intervening in its origin, and knowning this it is easy to remember which is which — introns and exons.

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text:
The effect of pH on catalase
Why does catalase still produce oxygen when mixed with 1 mL of 0.1M NaOH (pH 13), but not when mixed with 1 mL of 0.1M HCl (pH 1)? Catalase's ideal from what ive researched is 7. In other words, since both are on opposite side of the pH scale and equally distant from catalase's ideal, why does the acid mixture stop working, but the base still function, even if a little slower? Why did the catalase denature after the acid, but not the base? Thanks for any help, I'm pretty curious

The pH profile of an enzyme is not necessarily symmetrical. As random examples, see Figure 7 here, or Figure 5b here. Or if you have access, a pH profile for Magnaporthe grisea catalase can be seen in Figure 7 of http://dx.doi.org/10.1042/BJ20081478
The reasons for this go back to why enzymes are pH dependent in the first place. One of the major reasons for a pH dependence is that key catalytic residues become  (de)protonated as the pH changes. But different residues have different effects and different pKas, so you need to look at the sum of all their effects.
Example:
Imagine that a key catalytic residue must be in a deprotonated form, and has a pKas of 4.0. At any pH above about 5.0, it's all in the deprotonated form, so that residue should work. Any pH below about 3.0 and the enzyme is completely dead.
But an enzyme might have more than one residue that's pH sensitive. So now imagine that there's another residue which in the protonated form helps the reaction, but isn't as critical to catalysis such that the deprotonated still has residual activity. For the sake of argument let's say this residue has a pKa of 9.0.
Now imagine a third pH sensitive residue with a pKa of 6.5, but it's even more removed from the active site and has an even lower effect on catalysis (for example, it's a remote electrostatic effect based on the polarization of the transition state).
What would the pH profile for this enzyme look like? Here's an example:

"Activity" is the estimated total activity, and Residue 1/2/3 are the fractions of "active" form of each residue. - Diagram was made using the Henderson–Hasselbalch equation to determine the fraction of "active" states of each individual residue, and then assuming that the inactive forms are 0%, 80%, and 33% the activity of the fully active form for the pKa 4.0, 6.5, and 9.0 residues, respectively.
Note that the maximal activity occurs at about pH 5.7, but the activity drops off asymmetrically - the enzyme is much more sensitive to low pH than high pH.
A similar thing happens with natural enzymes, except that they may have many more residues which have minor contributions. They also may have $\ce{H+}$ and $\ce{OH-}$ playing a role as reactants (thus affecting the intrinsic reaction rate), and pH may play other effects, such a denaturing the enzyme. That's what leads to the complex pH profiles: multiple small effects all adding together.


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Is there an Exit site (E-site) on the eukaryotic ribosome?
One of my professors mentioned something about the e-site (the exit site for the t-RNA) on a eukaryotic ribosome.  There was a student in the class who objected, saying that there is no e-site on eukaryotic ribosomes; it only exists on prokaryotic ribosomes.  I've tried to find some reliable source to figure out who's right, but to date the only thing I've found is an obscure sentence in a wikipedia article, which doesn't look all that official.
Is there indeed an e-site on the eukaryotic ribosome?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331703/#s4title

http://case.edu/med/coller/Coller%20C3MB%20Lecture%201.pdf

@theforestecologist — citing a peer-reviewed publication is acceptable evidence because the references therein can be followed up. Citing somebody's lecture notes is not.

Both are acceptable. Just like citing Wikipedia is acceptable here. However, I agree that a peer-reviewed publication is often an optimal resource.

Why not do the research yourself? Download a free copy of pymol and start looking at ribosomes from the pdb database... You might want to compare bacterial and eukaryotic ribosome structures. Try identifying the A,P and E sites. It will be a nice little project and you will learn a lot doing it

@theforestecologist — Depends what you mean by acceptable. WIkipedia may not necessarily be correct, but its virtue is that it is correctable. Someone's lecture notes are surely no more likely to be correct than the professor of the question.

@David I mean that all those source types are allowed to be used on biology stack exchange without closure or deletion,and their use need not be challenged every time they're used here. If you find something to be wrong in a cited source, please point it out to the poster (or downvote the post accordingly) and include (and by all means suggest the use of) more reputable sources to support your challenge. If you have additional comments or opinions about the use of such sources, please write a [Meta] post about it. Thanks

Prelude: Thinking about protein synthesis
I remember the time when there were only two sites on the ribosome, and when it became clear there were more, I resented the need to make my lecture notes and my contribution to a venerable text book more complicated. So I am neither a devotee nor an expert on the exit site, but if asked to guess who was right (even if, or especially if, the student was supported by Campbell’s Biology as @CSharp informs us) I would put my money on the ‘professor’. Why? Because protein synthesis and the ribosome are so ancient that although there have been changes in eukaryotic proteins synthesis, something so fundamental as the sites for the fundamental process would not change.
Answer
Yes, Virginia, the eukaryotic ribosome does have an exit site.
The evidence
Although editions of the venerable text book no longer appear and my research no longer impinges on protein biosynthesis, I still collect papers on the subject with my bibliographic software. The latest relevant publication I have is by Khatter et al. from Nature in 2015, entitled Structure of the Human 80S Ribosome.
As not all list members have access to Nature, as a subscriber I have taken the liberty to reproduce a a section from the abstract (my emphasis) and a pertinent illustration:

Here we report the near-atomic structure of the human ribosome derived
  from high-resolution single-particle cryo-electron microscopy and
  atomic model building. The structure has an average resolution of 3.6A
  ̊, reaching 2.9A ̊ resolution in the most stable regions. It provides
  unprecedented insights into ribosomal RNA entities and amino acid side
  chains, notably of the transfer RNA binding sites and specific
  molecular interactions with the exit site tRNA.

The cryo-EM map and atomic coordinates have been deposited in the EMDB and Protein Data Bank under accession codes EMD-2938 and 4ug0, respectively.
I admit I haven’t researched and rehearsed the evidence, but I think that would be another question.

Here is an open access source for structural information regarding the eukaryotic ribosome, figure 3 in particular seems to contain the answer to the question being asked. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331703/

No. According to page 369 of the 9th edition of Biochemistry by Campbell:
"The structure of the eukaryotic ribosome is different in that there is no E site, only the A and P sites."

Welcome to SE Biology, Unfortunately Campell is a general biology text book, not a more specialist biochemistry or molecular biology text, which is where you are likely to find a better coverage of ribosomes. I do not have a copy of Campbell but I see from Amazon that it is now in its 11th edition, so perhaps this mistake (see my own answer) has been corrected now.

Down voted due to low information content in the answer. You refer to a book which state the structure is different, but you do not go into much depth of how they are different. Also, how old is the book...

@CSharp Welcome to biology stack exchange! We appreciate your well-cited answer. I just wanted to ensure you that the downvotes you are getting on your answer appear to be due to the accuracy of your source and not the quality of your answer. Even downvoted answers like this are sometimes useful as they clarify a common misconception or point out inaccurate, commonly-used sources. Please don't be discouraged, and I invite you to check out our [tour] and welcome you to continue posting here. Thanks!

Further to the remark from @theforestecologist, although I think your answer incorrect I did not downvote you because you provided support for your conclusion. You were just unlucky to hit a mistake in a text book. One wonders whether that same mistake provoked the original controversy.

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How does plant life obey the constraint that the change in Gibbs free energy in a reaction must be negative?
My understanding is that if a reaction takes place, either entropy of the system must rise, or energy must be released from the system as heat, or both. (Citation: paraphrasing from The Vital Question, by Nick Lane). But plant life seems to both decrease entropy, and absorb (not release) energy from its surroundings, by way of photosynthesis. How is this adhering to the constraint that the change in Gibbs free energy in a reaction must be negative?

You are not looking at a closed system (energywise). Which would be necessary to be able to make such observations.

Your title was nonsense as it stood (as was your last sentence). It mentioned free energy, rather than free energy change, and did not indicate what it referred to. I have altered it in accordance with your actual question, but please take more care in future. Titles are used for indexing and are important.

Possible duplicate (or at least quite related) to question on entropy and evolution

"My understanding is that if a reaction takes place, either entropy of the system must rise, or energy must be released from the system as heat, or both."... No, that is if a reaction takes place spontaneously. You can  perform work on the system to move it against the energy gradient. That's what the second law of thermodynamics says. In photosythesis, the energy of the light is indirectly used to perform that work.


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How can one identify an organism from its dissymmetry ratio?
If I am given the dissymmetry ratio of an organism ((A+T)/(G+C) is a constant), how can I identify the source of the DNA and classify the organism?

What information have you found so far on your own?

@kmm uhh absolutely nothing scratches head

The point is that we need to better understand you motivation for trying to do this. What do you know, what do you need to know, etc. Take a look at the  tour to see how the site works: http://biology.stackexchange.com/tour Without more information, your question will likely be closed as either too broad or without sufficient information.

You cannot. That information is too little for identification.

It depends what lineage (bacteria, virus, eukaryotes) you are interested in and what level of accuracy you are hoping to reach.
We know the (A+T)/(G+C) ratio for a handful of eukaryotes only. So if you were thinking about eukaryotes, there is no need to look much further. You cannot match a (A+T)/(G+C) ratio to a species because we don't know the (A+T)/(G+C) for the vast majority of species.

You could compare the (A+T)/(G+C) to those of higher orders; see "applications in systematics" on https://en.wikipedia.org/wiki/GC-content
( While the (A+T)/(G+C) ratio doesn't provide enough resolution to identify the species, OP didn't ask for identification of species.)


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How to generate protein graphics for illustrating articles?
The structure of insulin shown below appears in a Wikipedia entry.
What software was (or can be) used to create pictures of this type?

Have you tried to Google protein 3D visualization?

Please give a reference to this particular example. You are surely aware that Wikipedia's contributors (not users) are completely independent and thus use whatever software they choose to create molecular images. This is hardly a question about biology, and, as @Remi.b  said, you can find out about different molecular graphics software. You might also wish to look at the PDB site, which used two alternatives in their displays. But none are simple push-button programs, but require you to learn proprietory scripting commands.

I really appreciate your comments

there are plenty. Try autodock for a start

All comments are great, there are numerous software programs that allow you to make such images.

Gathering information about the insulin structure
By simply clicking on the image in wikipedia it will provide you with  valuable information:

Created by Isaac Yonemoto created with en:pymol, en:inkscape, and
  en:gimp from NMR structure 1ai0 in the en:pdb. Ref: Chang, X.,
  Jorgensen, A.M., Bardrum, P., Led, J.J.

So the creators used pymol, inkscape and gimp, but let's dig a bit deeper. Unfortunately Isaac Yonemoto, the editor of this wiki, did not provide a direct link to the original publication (see wiki file history). However by searching the author names in combination with insulin we quickly find the article: Solution structures of the R6 human insulin hexamer. In the first paragraph we see:

The atomic coordinates of the 20 refined hexamer structures and the
  NMR-derived restraints have been deposited in the Brookhaven Data Bank
  (PDB ID codes 1AIY and 1AI0 for the symmetric and the nonsymmetric
  hexamer, respectively)

You can find the structure that was depicted in this wiki article by searching the PDB id.

Creation vs visualization
You can interpret 'create' in your question in two ways here:

Creating this whole structure from nothing
Visualizing a structure someone else determined

If you refer to the former you should look at the article corresponding to this structure. Note that this is quite detailed and requires  knowledge of several concepts, such as molecular dynamics and NMR spectroscopy. If you refer to the latter than you should take a look at the programs mentioned earlier such as pymol, inkscape and gimp

Not generalizable
This boils down to what @David already said in his comment:

You are surely aware that Wikipedia's contributors (not users) are
  completely independent and thus use whatever software they choose to
  create molecular images.

Just to add, the author of that specific image did cite the PDB ID which allows you to find the structure, paper, etc in RCSB.

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text:
Why are proteins always made in N to C direction?
Why are proteins always synthesized from the N-terminus to the C-terminus? Can there be any “reverse” peptide-bond formation to synthesize proteins in the C-terminal to the N-terminal direction?

Are you talking about natural processes only, or also about chemical ones? Because chemistry really doesn't care (in either case actually) and can do both directions. Nature just stuck with the direction that was easier 'to implement'.

@nicolai I think the OP wants to know about natural processes (lest this question would be better for chemistry.SE). I tried to make the concept as clear as possible in my answer, yet it basically comes down to what you say ;)

Actually 3′→5′ synthesis is possible … synthetically: http://www.news-medical.net/news/20120830/DNA-synthesis-in-the-3e28099-and-5e28099-direction-possible-using-new-template-directed-method.aspx

I have edited your question to remove the irrelevant and incorrect preliminary statements.

Nice question! As you already know, DNA is always shown in 5'$\rightarrow$3' direction because it is always synthesized in this direction (amino acids are joined by CO-NH peptide bond). So, a polypeptide looks like this (source):

In fact, if you just look at the polypeptide in the reverse direction, you could view it in C terminus to N terminus direction. But we don't do so because that is not the conventional direction of the polypeptide's biosynthesis.
Tracing the Roots: To know why there is no "reverse" peptide bond (NH-CO), we first need to know how peptide bonds are formed in polypeptides. Polypeptides are formed in ribosome, and the process of formation of peptide bond occurs in the peptidyl transferase complex of ribosome. Since ribosome is a ribozyme, this reaction is also catalyzed by the catalytic sites of RNA (i.e. 2'-OH) instead of proteins. See the image below for the mechanism (from Marina V. Rodina):

As visible from the diagram, nitrogen (in -NH2) from acceptor tRNA (A site) attacks the ester linkage at the peptidyl tRNA (P site). Carboxylic carbon cannot attack the nitrogen (for "reverse" bond formation) because it is already in ester linkage. One might ask then "if the nitrogen was joined to tRNA at P-site, the carboxylic carbon could have attacked on amino acid at A-site. Why is amino acid not joined to tRNA by the amine nitrogen?" To know why it is so, lets go a step further and see how tRNAs are charged i.e. how aminoacyl tRNA synthetase works. Aminoacyl tRNA synthetase charges tRNA in a two-step reaction. For displaying mechanism, I will take the example of histidyl-tRNA synthetase (diagrams from Proteopedia):

amino acid + ATP → aminoacyl-AMP + PPi
→
aminoacyl-AMP + tRNA → aminoacyl-tRNA + AMP

As is clearly visible now, whether amine nitrogen or carboxylic carbon will attach to phosphate of ATP is decided in the first step. See the image again:

You might ask that since nitrogen (in -NH2) also has a lone pair of electrons, it could also make a nucleophilic attack on the phosphate group, similar to the oxygen (in -COOH). Why doesn't this happen then? This cannot be accounted for by saying that the amine nitrogen is far away from the reaction site (look at the diagram again, and pay attention to how close the carboxylic carbon and amine nitrogen are. If we could move the amino acid even a little bit, this reaction could easily occur). Well, here's the twist: the optimum pH of this reaction lies near pH 6 i.e. in the acidic pH range (Lui et al, 1978). Now, as we know, under acidic pH, -NH2 exists in the protonated form i.e. -NH3+. In this condition, nitrogen lacks lone pair and thus cannot attack phosphate on ATP. Thus, it is not possible to attach amino acid to AMP via -NH2 group and, thus, form a "reverse" peptide bond. I hope this depth of the answer would be enough to satisfy your curiosity :)

Two comments. 1. You are explaining the directionality in terms of the way the activation of the amino acid occurs today. As long as you make that clear, that is fine. However the question of why it evolved that way is not answered. 2. Your arguments about ionization of amino groups at low pH do not hold water. The pH optimum of the charging reaction is irrelevant. What is relevant is the pH under which the reaction occurs, which is the cellular pH of, say 7.4–7.6. And if the amino group lacks a lone pair there, how does it manage to make a peptide bond, as per the first diagram?

@david 1. It evolved this way because evolving in the other direction was not possible (again, due to pH, I don't know if you understood what I wanted to convey through the pH factor) 2. I don't think you read Lui et al, the reaction does occur at a rather acidic pH (to make it faster). I don't know about peptidyl transfer reaction, most probably it occurs at cellular pH (about pH 7.5 or because the reaction occurs in almost isolated condition. Also, these are all suggested mechanisms, nobody has seen how the reaction actually occurs.

All the stages of protein synthesis occur at the same pH in a cell. If a particular reaction requires an ionization state of a group in the substrate different from that in aqueous solution (e.g. an unionized amino group in the peptidyl synthetase reaction) that is provided by the enzyme environment. In evolutionary terms, when one assumes there was a non-enzyme catalysed reaction first, you still have a problem. And one unexplained assumption of your answer is that activation of amino acids for attachement to tRNA has to be via ATP (not acetyCoA or something else).

@david the truth is that we don't yet know the true reaction mechanism, I used histidyl-tRNA synthetase as an example. The main point is that the $\alpha$-amino nitrogen is in the protonated form; if the cell can't provide this proton, the enzyme must. I did not explain acetyl-coA or other residues since the major (and I think only) substrate for aminoacyl-tRNA synthetase is ATP (I don't know if you have studied about aminoacyl-tRNA synthetase, or maybe there are some other enzymes about which I don't know).

This is just in addition to the other answers; some somewhat relevant thoughts I had.
Interestingly, even non-ribosomal peptide synthesis seems to proceed N to C terminal. Given the modular nature of such enzymes, synthesis in the reverse direction doesn't seem to be outside the realm of possibility, though I haven't found any known examples.
This might be a stretch as a counterexample, but if you consider the biosynthesis of the tripeptide glutathione, a γ-peptide bond is first formed between cysteine and glutamate, after which glycine is attached to the carboxyl group (ie C-terminus) of cysteine with an α-peptide bond.


text:
Is the variance of a trait related to its rate of evolution?
Posed with a question that has me stuck:

Is increased variance of a phenotypic trait in a population associated with slower evolution of that trait?

I have to either 'disagree or agree' and argue my point. And I disagree. For this question, I think that if the variance of phenotypic trait has a genetic basis (additive genetic variance =/= 0) then increased additive genetic variance should speed up it's evolution. The greater the additive genetic variance, the greater the response to selection in the next generation. So increased additive genetic variance should increase the rate of evolution of that trait.
However, at the same time, if there is variation in a phenotypic trait but it does not have a genetic basis (narrow sense heritability is zero) and the basis for variation is due to an environmental, dominance, or interactive effect, then increased variation would have no effect in the rate of evolution. Or so I think. I'm not too sure how the rate of evolution would be affected in the case of a non-genetic basis of variation.

The question can be understood in different ways
Causality
I think the question is a bit unclear in using the term associated in terms of what is being causal. Is the interest to understand how do processes that affect speed of evolution also affect phenotypic variance or is the question `how does a change in phenotypic variance affect the speed of evolution.
What is meant by speed of evolution
Speed of evolution has no strict definition. Or rather it has two standard definitions and it can be measured in Haldanes or in Darwins (which are units).
Quite often by "speed of evolution" authors mean "response to selection over medium to long term" as for example in the wiki article for rate of evolution.
Below I am answering to two different questions.
How does processes that affect "speed of evolution" at neutral sequences also affect phenotypic variance
At neutral sequences, the rate at which mutations fixes is equal to the mutation rate (see this answer for explanation). And all else being equal (typically without changing the mutational effect), high mutation rate leads to high phenotypic variance.
How does a sudden change in the phenotypic variance affect the response to selection in regard to this trait?
I think you pretty much said it all. I will just rephrase what you just said with a few simple equations.
Breeder's equation and heritability
The response $R$ to selection $S$ is given by
$$R=S h_N^2$$
, where $h_N^2$ is the heritability in the narrow sense. This above equation is known as the breeder's equation and is a fundamental result from quantitative genetics. The heritability in the narrow sense is defined as
$$h_N^2 = \frac{V_A}{V_P}$$
, where $V_A$ is the additive genetic variance and $V_P$ is the phenotypic variance.
Partitioning phenotypic variance
So it feels like increasing $V_P$ would decrease $h_N^2$ and therefore the response to selection $R$, but that would be very naive as $V_P$ is not independent of $V_A$. It is quite standard to decompose the phenotypic variance into genetic ($V_G$) and environment variances ($V_E$) $\left(V_P = V_G + V_E\right)$. Of course in reality, we should take into account variance due to other factors such as epistasis or developmental noise for example and all of their covariances. The genetic variance can further be decomposed into additive genetic variance $V_A$ and dominance genetic variance $V_D$ $\left(V_G = V_A + V_D\right)$.
Interdependence between $V_P$ and $V_A$
$V_P$ is a function of $V_A$. So as currently stated, it is impossible to answer the question by a simple yes or no. The shortest correct answer would probably be "The response to selection will decrease if the increased variance is not (not mainly) related to increase in additive genetic variance".
To be perfectly accurate, let $\Delta_P$ be the increase phenotypic variance and $\Delta_A$ be the increased genetic additive variance such that $\Delta_P > \Delta_A$. All else being equal the increase in $V_P$ will cause faster response to selection if and only if $\frac{Va+\Delta_A}{V_P+\Delta_P} > \frac{Va}{V_P}$. Isolating the term of interest $\Delta_P$, we got
$$\Delta_P < \frac{\Delta_A V_P}{V_A} = \frac{\Delta_A}{h_N^2} $$
In other words, all else being equal, an increase of phenotypic variance of $\Delta_P$ above the original variance $V_P$ increases the response to selection if and only if this increase is lower than the increase in additive genetic variance $\Delta_A$ multiplied by the inverse of the original heritability (heritability before a change in phenotypic variance occured)."

I think the question is supposed to be
" How does a sudden change in the phenotypic variance affect the response to selection in regard to this trait? "

Perfect, this is on this part of the post that I spent most time! Do you feel like it answers your question?

Depends on how you phrase the question, ie, on how you write the breeder's equation.
The breeder's equation can be written in two ways:
$R=h^2 \cdot S$
or
$R=V_A \cdot \beta$
where $R$ is response to selection, $h^2$ is narrow sense heritability, $S$ is selection differential, $V_A$ is additive genetic variance, and $\beta$ is selection gradient.$^*$
Total phenotypic variance is pretty much a denominator which gets shunted between the right-hand quantities of the two versions, since $h^2=\frac{V_A}{V_P}$ and $\beta = \frac{S}{V_P}$. Rewriting the two versions, they become
$R=\frac{V_A}{V_P} \cdot S$
and
$R= V_A \cdot \frac{S}{V_P}$
So to answer your question: for a fixed selection gradient $\beta$, only the additive genetic variance $V_A$ matters. But for a fixed selection differential $S$, it is the ratio $\frac{V_A}{V_P}$ (narrow sense heritability) which matters.

$^*$The selection differential is the covariance between relative fitness and the trait value: $S=cov(w,z)$. The selection gradient is the regression coefficient between relative fitness and trait value: $\beta=\frac{cov(w,z)}{cov(z,z)}$. Note that the denominator $cov(z,z)$ is just the covariance of trait value with itself, ie, the variance of trait value: hence, $\beta = \frac{S}{V_P}$.
The selection differential is often described as the difference between the overall first generation's mean phenotype, and the selected parents' mean phenotype; this is true for viability selection, where parents either simply do or don't reproduce, with no other differences in fecundity.
For multivariate evolution of correlated traits, the selection gradient is actually the partial regression coefficient of relative fitness and trait value: partial because it isolates the 'direct effect' due to selection on the trait (as opposed to the residual 'indirect effect' due to selection on other, correlated traits). The multivariate breeder's equation is $\vec{R}=\mathbf{G}\cdot\vec{\beta}$, where: $\vec{R}$ is a vector of responses to selection (each element being the response of one trait); $\vec{\beta}$ is a vector of selection gradients on those traits; and $\mathbf{G}$ is the additive genetic variance-covariance matrix (each element being the additive genetic covariance of one trait with another; the elements on the diagonal give the additive genetic covariance of the traits with themselves, ie, their additive genetic variances).

Variance of a phenotype/genotype with respect to the rate of mutagenesis is an indicator of selection pressure. High variance would denote lower selection and vice versa. Note that this has to be normalized to the mutation rate; if you have high mutation rate then you would get high variance even in the presence of a moderate selection pressure.
With protein coding genes, the rate of selection is measured by comparing the number of non-synonymous mutation with the number of synonymous mutations (a gross indicator of general mutation rate). Se Ka/Ks ratio.
For more information you can have a look at this review by Gingerich (2009).


text:
Are there any non-pathogenic gram-positive bacteria in human gut?
I wish to know if there are any non-pathogenic (not even opportunistic pathogen) gram-positive bacteria in the human gut? Is there any reference that shows there exists a non-pathogenic gram-positive bacterium in the human gut?
I searched the internet but was unable to find anything conclusive.

A recent Nature article, entitled A new genomic blueprint of the human gut microbiota, contains the following Figure:

[Fig. 3 Phylogeny of reference and uncultured human gut bacterial genomes]
I don’t know much about bacteria, but, according to their entries in Wikipedia, Actinobacteria, and most Firmicutes are gram-positive and, as these appear to be present in abundance in the human gut of healthy individuals, one assumes that they are not pathogenic to humans.

Link to wiki: https://en.m.wikipedia.org/wiki/Gut_flora
Found this under Composition -> Intestines:
The small intestine contains a trace amount of microorganisms due to the proximity and influence of the stomach. Gram-positive cocci and rod-shaped bacteria are the predominant microorganisms found in the small intestine.


text:
What does the term "recruitment of T-cell" mean?
With respect to the article, what does the term "recruitment of T-cell" mean? Who recruits T- cell? Does recruiting T-cell mean the T-cells get a sense of directionality to get activated by the APC's?

Read into MHC-class molecules, and how they're processed. You have Wiki for that, but if you're interested in the evolutionary mechanisms that are very importantly in play in our modern times, check out this Biostars tutorial: https://www.biostars.org/p/5817/#95075 for some nice explanations and software examples, @CMosychuk (also relevant)

If I'm interpreting it properly, it's the adaptive response that's recruiting the T cell, evidenced by the last line in their abstract:
"Therefore, the contribution of a T cell clone to the immune response is mostly determined by the time of its entry into the immune repertoire, i.e., the time of first cell division after antigen encounter."
It's strange because when i think of recruiting a T cell it's always to the tissue or site of infection or what have you.


text:
Why is an initiator tRNA required, distinct from the methionine tRNA used in elongation?
I'm confused by why there is a need for different tRNA-methionine complexes for translational initiation and elongation.
This paper mentions that

It is important that each type of methionyl tRNA be restricted to its separate function, as competition for tRNA by the initiation and elongation machinery could lead to serious problems for the cell

I don't understand what these problems may be.

Interaction with tRNA-binding factors is why separate tRNAMet species are employed

A specific tRNAMet is required for initiation as the initiating
  met-tRNA must interact with a specific tRNA-binding initiation factor
  (IF2) in order for it to bind to the P-site on the small ribosomal subunit.
  The elongator tRNAs share common structural features that enable them to
  interact with an elongation factor (EF1), which is needed for binding
  to the A-site of the whole ribosome. If the elongator met-tRNAMet were
  able to interact with the initiation factor, so would all the other
  aminoacyl-tRNAs. It is this competition for the initiation factor (and
  the small ribosomal subunit) that a separate initiator tRNAMet avoids.

This answer applies to all modes of prokaryotic and eukaryotic initiation, regardless of the manner in which the ‘correct’ initiation codon is recognized, as the interactions mentioned (shown in the cartoon below for those unfamiliar with this) are universal and ancient.

[E-TBF and I-TBF are my own non-standard abbreviations for Elongation tRNA-binding factor and Initiation tRNA-binding factor, respectively. The several arrows following the formation of the ternary complex are to indicate that several steps (which for initiation may differ between kingdoms — and between mRNAs in a single genome) occur before the final specific interaction of the tRNA anticodon with the appropriate mRNA codon on the appropriate ribosomal species.]
The cartoon representation of the factors and complex are taken from a diagram by Awchen and illustrates the interaction of the bacterial elongation factor (the original name, EF-Tu is used) and aminoacyl-tRNA. The structure of the initiation factor and its interaction with the tRNA is different (as is the conformation of the tRNA). Although not important for this answer, they are shown below in a comparison diagram from Schmitt et al., which unfortunately does not show the same orientation for the tRNA.

Why separate tRNAs, rather than a single multifunctional tRNAMet?
The answer given above describes how — in contemporary biological systems — the existence of two tRNAs for methionine prevents competition from elongator tRNAs for the initiation factor, IF-2, and hence competition for the small ribosomal subunit in its ‘initiation state’. However it is reasonable to ask why a separate initiator tRNAMet was necessary for such discrimination — surely IF-2 could have been specific for a single tRNAMet by recognising the same features that a single met-tRNA synthetase does. (The argument that then there would have been competition for EF-1 seems weak.) This is a distinct question, about which one can only speculate. My observations regarding it follow.
This argument presupposes that in the development of a single AUG initiation codon from what one assumes was a non-specific initiation system, all that was required in the tRNA was an appropriate anticodon — the sequence context and accessory proteins (initiation factors) being responsible for selecting the initiating AUG and triggering the initiation process. However this is evidently not the case in contemporary biological systems.
The initiator tRNAMet is structurally distinct from the elongator tRNAs. There is a striking reflection of this in the fact that although eukaryotic initiator tRNAMet is not formylated and no transformylase exists in eukaryotic cells, this species — but not the elongator species — can be formylated in vitro by the E. coli transformylase (see, for example, review by Kolitz and Lorsch). Clearly, specific structural features of initiator tRNAMet have been conserved over a long period of time, despite the evolution of different methods of selecting the ‘correct’ initiation codon (Shine and Dalgarno, Kozak scanning, ribosome landing pad).
Because of these latter differences in contemporary initiation it is impossible to know what the ‘original’ system was and why there was a need for structural differences in the initiator tRNA. However one answer is suggested by the fact that in contemporary eukaryotic initiation by the predominant Kozak scanning method the initiator tRNA binds to the small ribosomal subunit in the absence of the AUG codon. One suspects recognition of the P-site on a single subunit was as important as  codon–anticodon recognition.
Given the requirement for major structural changes in tRNAMet for initiation, the development of multi-functionality in single species would seem considerably more difficult than the creation of new species by gene duplication and subsequent mutation. Creation of new tRNAs by gene duplication is a relatively common process, and in this case would have left the original elongator tRNAMet untouched while the duplicate (still containing the recognition features for the met-tRNA synthetase) was free to evolve features which changed its ribosome- and factor-recognition properties.

I have added this answer because although one answer has been accepted, it does not address what I regard as the key point — the interaction of tRNAs and proteins synthesis factors. I will add more references to some of the protein synthesis background later, if requested.

(This comment is in two parts to get around the character limit.) Does this answer address the key point? Clearly there ARE different tRNAs for initiation and elongation so it would be surprising if the translation system had not evolved to exploit these differences. But why does it have to be this way at all?

Part 2. If there were only a single species of met-tRNA it doesn't seem to me to be much of a tall order to imagine that initiation factors would be able to discriminate between met-tRNA and other tRNAs.  After all, this level of discrimination between uncharged tRNAs is what aminoacyl tRNA synthetases do. Meanwhile the elongation pathway wouldn't need to discriminate. So what was the driving force behind the partitioning of met-tRNA into two separate pools?

@AlanBoyd — The answer addresses the question in a factual manner. It makes it clear that the key point is to prevent elongator tRNAs competing for the P site on the small subunit during initiation and that that is done at the stage of interaction with the initiation factor responsible for binding the initiation tRNA. You raise a different question — why did this mechanism for preventing competition arise, rather than a single met-tRNA binding both EF-1 and IF-2. That is argument and speculation, which I decided not to include unless there was interest. I'll extend my answer over the week end.

@AlanBoyd — It's not the weekend yet, but I have now extended my answer to deal with the points you raise. I was going to discuss the evolution of the initiation codon and protein synthesis factors, but that would make the answer far too long — perhaps a separate question. However I would like to make the answer to this question as useful as possible, so if you have any other points that you would like me to clarify do say so.

I didn't mean to imply that the use of a single tRNA "would be more advantageous to the cell", and I can't see that in my comment. My purpose was to ask, like the OP, "why there is a need for different tRNA-methionine complexes for translational initiation and elongation". You say: because that makes it easier to separate those processes. Yes, but I still don't see the driving force behind that separation. If you think it likely that initiator tRNA arose before the protein factors then all sorts of possibilities arise for an initiator tRNA having 'special powers' in relation to the P site.

@AlanBoyd — OK. Are we agreed on: 1. At some stage a single initiation codon (strictly aa) arose, 2. There would be an advantage in not having all the other aatRNAs competing for initiation, 3. Two possible ways this might have evolved were (i) a change in the structure and function of tRNA-met (ii) gene duplication and change of function of a second tRNA. ? If we are agreed, then you seem to be suggesting that alternative (ii) required some special "driving force" which (i) did not. I say the driving force was 2, and that alternative (ii) was at least as likely as (i) and argue in its favour.

@AlanBoyd — On reflection, perhaps your concern is something on the  lines of "Why wasn't it enough to have IF-2 recognise the same features that met-tRNA synthetase does on the single met-tRNA when initiation plumped for AUG (in a particular context)? One could argue that there would be competition for EF-1, but I don't find that very convincing. What is clear is that the initiating tRNA developed structural changes that one presumes must have reflected other requirements for interaction on the ribosome than codon–anticodon interaction. I can revise my additional section to deal with this.

Yes, agreed, the more functional requirements you posit for the initiator tRNA then the stronger the case for having to evolve a separate tRNA species. I was groping towards a case based upon the kinetic limitations of two different processes feeding from a single pool of met-tRNA, but I haven't even convinced myself.

@AlanBoyd — Done that now. Cut down the previous arguments to a single para and focussed on what would appear to be the main concern. Also depersonalized it.

+1 from me. According to Fig 2 in https://doi.org/10.1017/S0033583505004026 initiator tRNA binds the 30S subunit before mRNA in all three kingdoms.

@AlanBoyd — Thanks. Makes sense. When I was following the protein synthesis literature seriously (20 years or more ago) I used to feel that that would be a unifying feature, but the data then didn't seem clear. This has made me think about the evolution of proteins synthesis. For example, were there ribosomes without subunits originally, and subunits emerged when the RNA transcript got cleaved and this allowed specific initiation? I'm sure there must be literature discussing this sort of thing, but I tend to be rooted more in the present.

I think the key to understanding this is to appreciate how different the initiation process is from the rest of translation.
The 30S ribosomal subunit recognises start codons via an interaction with the Shine-Dalgarno sequence that lies upstream in the mRNA. The remaining steps of initiation involve recruiting fMet-tRNA and, critically, placing it into the P site of the ribosome. In contrast, during elongation, aminoacyl tRNAs enter at the A site before their amino acid cargo is joined to the growing polypeptide which is held in the P site as a peptidyl tRNA. So you can see that the initiation process is special because of the need to prime the whole translation process by placing the first 'peptidyl' tRNA (actually N-formylmethionyl tRNA) into the P site.
There are two tRNAs for methionine, tRNAfMet and tRNAMet, and only the former is a substrate for the enzyme methionyl-tRNA formyltransferase. This effectively partitions the supply of methionine into two separate pools, one for use in initiation and one for use in elongation. In fact you could argue that initiation involves a different amino acid (N-formylmethionine) which is also coded by AUG.
Since an N-formylmethionine is essential for initiation, the simplest alternative would be to have a situation where a single species of methionyl-tRNA was a substrate for the transformylase. This would mean that N-formylmethionine would have to be allowed into the A site, and all those formyl groups would have to be subsequently removed from the internal methionines.
Update in response to comment from the OP
Having re-read the original question, I can see that I jumped the gun and actually answered a different question. The real question is much deeper.
Firstly, although the details differ, both bacteria and eukaryotes feed methionine through separate pathways for initiation and elongation.  Bacteria are discussed above; eukaryotes channel methionine through two different pools of tRNA, tRNAiMet and tRNAMet. Clearly this channelling is a universal feature of translation systems.
Next, let's look at tRNAMet abundances in E. coli. Since all protein-coding genes have a single start codon and, on average, a few internal methionine codons, we might anticipate that there would be more tRNAMet than tRNAfMet. But this isn't the case: according to Dong et al 1996 tRNAfMet is present at around 3x the level of the elongation species.
This suggests to me that there is something inherent to initiation that requires a higher level of the corresponding methionyl tRNA. Now you might say that this discrepancy is rather small but bear in mind that one of the properties of Met-tRNAfMet is that is easily rejected by elongation factors (reference). This is important because any charged tRNA can enter the A site before being compared to the current codon. By being easily recognised as 'wrong' for elongation, Met-tRNAfMet is, to some extent, excluded from the elongation process.
So far I have presented facts -  what follows are my own ideas.
If a single Met-tRNA species was used both for elongation and for initiation it would have to optimised for entry into the elongation process, spending time interacting with ribosomal  A sites. In order to maintain the level of free Met-tRNA required to drive initiation I conclude that much higher levels of this single Met-tRNA would therefore be needed. This in turn would increase the transient entry of this species into all A sites, and it would essentially act as an inhibitor of elongation.

thank you, but I still don't understand. The recruitment of the initiator tRNA into the P site is dependent on IF2. In fact the formyl group is not necessary – in eukaryotes, Met is not formylated, and the process is driven by the closely homologous eIF2. So what problems would there be if IF2 recognized "standard" Met-tRNA?

@AlexMayorov I've extended my answer.

Thank you! Your idea is very interesting and makes a lot of sense!

@AlexMayorov and thanks to you for a great question!

The same paper states the following just before the part you have quoted:

The cell acquires an additional degree of control by having a separate tRNA for initiation, and thus regulates the levels of
  initiator and elongator methionyl tRNAs separately.

It is just another factor that controls translation. If there is no initiator tRNA, the ribosome cannot start synthesizing a certain protein. Imagine the cell needs to synthesize e.g. 100 copies of a protein. If initiation and elongation tRNA were the same, it would be much harder to determine how many methionyl tRNAs would be required to synthesize 100 copies, especially since the cell cannot tell how many methionins are required for a certain protein. Instead, if initiator tRNA is separate, 100 initator tRNAs will lead to 100 synthesized proteins (provided the other initiation factors are present, obviously).

Thanks! But isn't the cell face the same problem with other elongation tRNA, e.g. with glutamoyl tRNAs the cell doesn't know how many to synthesize and the synthesis is just based on the average demand? So how is this different? Couldn't the cell just synthesize a bit more Met tRNAs?


text:
Interpretation of table on analysis of genetic diversity between groups
I am very confused about how to interpret Table 8.3 in Smith's Evolutionary Genetics.
Is the GST in the table the same as the G,ST (with the comma), which is defined (pg. 156; Box 8.3) as "the probability that two genes drawn at random from the same deme are identical"?  If so, is it not the same as Hs, the probability that two homologous genes from the same deme are identical?  If it is the same, why do they differ?
And why would Hr be larger than Hs?  That is, why would a gene be more likely to be identical with a gene from a different deme than the same deme?  Doesn't this suggest negative assortment?
Thank you very much to anyone who can help!
This is the table:

Welcome to Biology.SE. Can you please just display the figure directly on the post (screenshot the image from the pdf and add the image using the icon dedicated to adding images). Users don't want to click on a link, load a pdf, screen through 362 pages trying to find Table 8.3!

The title is really not informative. You could ask "What is the difference between Hs and Gst". Also, can you please use the > symbol for quotation and indicated where (what page, what column, what paragraph) the quote comes from.

GST or GST' (I've never seen G,ST) is not "the probability that two genes drawn at random from the same deme are identical". This definition matches $H_s$ (as you figured out). $GST = \frac{H_t - H_s}{H_t}$. I have never seen $H_r$. Hopefully, there is a definition of $H_r$ in the text. It could be defined as $H_r = H_t - H_s$ given what you seem to say but please make sure to quote the book on that definition.

I apologize to you.  After zooming in on the text, I found that what I thought was the definition for Hr was actually the definition for Ht.  I did a text search:  that was the only mention of "Hr" in the book.  So, I do not know the definition for Hr.  So by that definition of GST, if GST is positive, does it mean assortment is negative?  Which of these measures would represent "relatedness" in Hamilton's rule?  (Or would there be a combination necessary?)  Thank you!

The link given appears to be to an illegal copy of a book.  I have deleted it and vote to close.

I'm voting to close this question as off-topic because cites pirated text.

The text was cited by an article I am reading.  I am trying to complete a paper (not for school).  I do not currently live near a university library and therefore cannot get it via interlibrary loan.  The cost of the text is prohibitive, since I am only interested in one page of it.  I believe voting to close would be unnecessarily severe.

I would appreciate an answer to my questions.  That would be a productive way of responding.

If it makes a difference, I do not expect to be paid in any way for said paper.

Is Hs equivalent to Hamilton's relatedness?  Thank you.

No $H_S$ is not equivalent to $r$ (relatedness). $r$ comes from the field of quantitative genetics for which you need to consider a phenotype, while $H_S$ comes from classical population genetics and is independent of the phenotype. You can find book recommendation here for a good intro to population genetics.

Remi, I thank you very much and I am very sorry.  I didn't realize I had a response.  I guess we don't receive an email notification.  After asking this question, it occurred to me that Hs would be equivalent to relatedness if one omits intergroup effects?  I have a couple of intro to population genetics texts (the Gillespie text and the Hartl text), but Hs is not in the index of either of them.  Does it go by another term?  I do not understand the distinction you made between considering a phenotype and independent of phenotype.  Can relatedness be calculated from a combination of Hs and GST?

For context, Schonmann, VIcente & Caticha, 2013 says the following, "For these games, the condition for altruism to proliferate is Hamilton’s classical rule...Therefore, in this setting, altruism can only spread when either relatedness is large, or the cost/benefit ratio is low. And since relatedness is often low [28] (Table 8.3), [30], [31] (Tables 6.4 and 6.5), [32], [33](Table 4.9), exceptionally low cost/benefit ratios are required, as observed for instance in [34]."   The measures listed in the citations are:  hr, hs, gst, and fst.  How can relatedness be determined from these measures?


text:
ATP stoichiometry of the Na+/K+ pump
The Na+/K+ ATPase pump exports 3 Na+ for every 2 Ka+ imported. This process is ATP dependent, but I have not been able to find how many ATPs are required in each translocation. What is the stoichiometric ATP cost of this reaction?

Sodium/potassium-exchanging ATPase (EC 3.6.3.9):

An enzyme from the plasma membrane of animal cells that catalyzes the efflux of three Na(+) and influx of two K(+) per ATP hydrolyzed.

You can read about the mechanism on Wikipedia:

The pump, after binding ATP, binds 3 intracellular Na+
  ions.
ATP is hydrolyzed, leading to phosphorylation of the pump at a highly conserved aspartate residue and subsequent release of ADP.
A conformational change in the pump exposes the Na+
  ions to the outside. The phosphorylated form of the pump has a low affinity for Na+ ions, so they are released.
The pump binds 2 extracellular K+ ions. This causes the dephosphorylation of the pump, reverting it to its previous conformational state, transporting the K+
  ions into the cell.
The unphosphorylated form of the pump has a higher affinity for Na+
  ions than K+
  ions, so the two bound K+
  ions are released. ATP binds, and the process starts again.

So the stoichiometry is 3 Na+ exported, 2 K+ imported, 1 ATP hydrolyzed. Thanks.


text:
RMSD during conformational transition in proteins
When I was investigating the differences between protein structures obtained by X-ray crystallography and NMR spectroscopy, I found the paper [1] compairing structures of several proteins resolved both with X-ray and NMR. The average root-mean-square deviation (RMSD) between NMR and Xray structures is 1.4Å (max. 3.6Å), and the average RMSD between different NMR structures for same protein is 0.4Å (max. 1.3Å). I've checked some proteins studied in this paper, and they are mostly within 100–200 residues long.
However, there are plenty of papers (e.g. [2], [3], dealing with similarly sized proteins) that base their statements about conformational transitions on structures with RMSD difference 1–2Å.
I wonder what is considered reliable RMSD between two structures to draw any solid conlusions about conformational transitions (e.g. upon ligand binding) as opposed to simple thermal fluctuations or perturbance caused by the method to obtain structure?
Of course, the best way (at least in my opinion) to distinguish actual conformational transition from thermal fluctuations is to measure its lifetime, but it is often not an option.

 Andrec M, Snyder DA, Zhou Z, Young J, Montelione GT, Levy RM. 2007. A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins 69: 449–65.
 Grant BJ, Gorfe AA, McCammon JA. 2009. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Computational Biology 5(3): e1000325.
 Kumaraswami M, Newberry KJ, Brennan RG. 2010. Conformational plasticity of the coiled-coil domain of BmrR is required for bmr operator binding: the structure of unliganded BmrR. Journal of Molecular Biology 398: 264–75.


text:
Difference between Peptone, Peptide and Proteose
In my school textbook, it is given that Pepsin converts proteins to peptones, proteose and peptides.
What is the difference between the three products? On googling the terms, the definition was similar.
Peptone: a soluble protein formed in the early stage of protein breakdown during digestion.
Proteose: A proteose is any of various water-soluble compounds that are produced during digestion by the hydrolytic breakdown of proteins short of the amino acid stage.
Peptide: a compound consisting of two or more amino acids linked in a chain, the carboxyl group of each acid being joined to the amino group of the next by a bond of the type -OC-NH-.
Peptide has a different definition, but it can be applied to the other two too as all are degraded proteins but not amino acids.

This, from Collins dictionary, claims peptones come from proteoses. But i am not sure if there is a definitive line between a peptone and a proteose.

And, a peptide, is just a molecule containing a peptide bond: amino group bound to carboxyl group, as you stated. Therefore peptones and proteoses, and I guess maybe even proteins can all be considered peptides.

Personally, I hate biological semantics.  I once had a professor tell me that it's better to understand a chemical process than be able to define mundane boundaries between said processes. This same professor taught genetics, but admitted to not knowing the dictionary-defined stages of the cell cycle.

Burn your school textbook! That's the only way it will provide any illumination. Nobody talks about peptones or uses the term proteose.

Quick Answer

Peptide refers to at least two amino acids joined by amide bonds.
Proteoses are products of acid proteolysis which precipitate with saturating ammonium sulfate.
Peptones are products of acid proteolysis which do not precipitate with saturating ammonium sulfate.
While peptide is a term of significant relevance today, proteose and peptone are anachronistic.

Long, Confusing and Out-Dated Details
The terms peptone and proteose were first used in the late 19th century, which makes finding substantive definitions, well, difficult. I refer you to the following paper (yes, 1891...). It is not the first to discuss proteoses, but I can't find any earlier ones and the explanation is quite clear (emphasis added).
Chittenden RH, Hartwell JA. 1891. The Relative Formation of Proteoses and Peptones in Gastric Digestion. J Physiol 12:12-22.

In the digestion of proteid matter by pepsin-hydrochloric acid there are three well-defined products or classes of products, viz. acid-albumin or syntonin, albumoses or proteoses, and peptones. We look upon the first as the initial product of gastric digestion and identify it by its well known precipitation by neutralization. In the filtrate, the [proteoses] can be detected... best by saturation with ammonium sulphate, while the true peptones... are found in the filtrate from the latter precipitate... True peptones are bodies not precipitated by saturation with ammonium sulphate, and are the final products of pepsin digestion.

NB: proteid = protein
So, according to this paper (and apparently "all physiologists" at the time, see below), there are three main products resulting from pepsin-acid digestion of protein:

syntonin - the initial product, precipitates upon neutralization (likely due to acid denaturation)
proteose - the main product after continued digestion, characterized by precipitation with saturating ammonium sulfate

Study of the individual proteoses formed in the gastric digestion of albumin, fibrin, globulin, myosin, casein and other proteids has seemingly already shown that these so-called preliminary bodies are the main products of the digestive action of pepsin

peptone - the final product of digestion, does not precipitate with saturating ammonium sulfate

All physiologists are presumably agreed that peptone is the final product of gastric digestion

They further emphasize that peptone is a product of continued proteose digestion:

Since the discovery of the [proteoses] and of their characteristics, frequent study of digestive mixtures has given convincing proof that in an ordinary gastric digestion of any common proteid only a comparatively small amount of peptone is formed; peptonization in the true sense of the word results only from the long-continued action of pepsin-acid, and even then complete peptonization rarely if ever occurs. The... proteoses are to be considered as the primary products of gastric digestion, while peptones are the end products of proteolytic action, the latter being formed by the gradual hydration of the primary products...

It would seem that peptone differs from proteose only in the length of its constituent peptides, with peptone containing shorter peptides due to continued proteose digestion. However, a more recent paper (with more recent meaning 1924) challenged this view and claimed that both proteose and peptone consist of small peptides which differ in amino acid composition rather than length. In their view, different composition rather than length explains their differential solubility in saturating ammonium sulfate.
Rudd GV. 1924. Proteoses, Peptones, and Polypeptides. Aust J Exp Biol Med Sci 1:187-190.

...each fraction must consist of a mixture of comparatively simple peptides, which differ among themselves in the amino-acid units of which they are constituted. The fact that some, at least, of these peptides are precipitated by ammonium sulphate shows that they belong to the group of proteoses, which therefore are partially, if not entirely, made up of simple peptides.
It is possible that the terms, "proteose," "peptone," and "polypeptide,*' will all have to be considered to apply to substances of the nature of peptides... each built up of a small number of amino-acid units and differing from each other, not so much in the number of amino-acids in the molecule, but rather in the variety of these acids. The differences in solubility in various solutions shown by these compounds are thus to be attributed to differences in their chemical constitution, rather than in their molecular complexity. If this be so, these substances would be considered, not as successive stages in hydrolysis, but as products of one completed stage, differing in their solubility's.

They also quote another paper with supporting evidence:

Fischer produced tripeptides and tetrapeptides of known composition and structure, which were precipitated when their aqueous solutions were saturated with ammonium sulphate. If these peptides were found in the solution obtained by the hydrolysis of a protein with pepsin they would be classed as proteoses.

I wasn't able to find any subsequent research. Nevertheless, such definitions from this period are based on macroscopic physical, rather than molecular, properties of the substance. This old terminology is not particularly informative in modern biology, and it would seem that they remain in use only as historic anachronisms. Today, both peptone and proteose are terms used almost exclusively when describing microbiological culture media (which dates from the period) or when making general reference to digestion products. In fact, they are often used in conjunction (ie proteose-peptone) which suggests they are now synonymous.

Let me first give the definitions of the three terms before differentiating them.
Peptide: Peptides are biologically occurring short chains of amino acid monomers linked by peptide (amide) bonds1.
Peptone: Peptones are derived from animal milk or meat digested by proteolysis. In addition to containing small peptides, the resulting material includes fats, metals, salts, vitamins and many other biological compounds2.
Proteose: any of a group of compounds formed during proteolysis that are less complex than metaproteins but more so than peptones3.
Now, peptides are the most basic components. Like proteins, they too are polymers of amino acids, the difference being that they are just shorter than the original protein which the protease acted upon.
Peptones can be considered as derivatives of peptides i.e. they also contain some other substances like fats, salts, vitamins, etc. in addition to peptide.
At last, there does not seem to be a clear definition of proteose. The only definition (that I found informative) was from Collins, according to which proteose is also derived from proteins, which are quite more conplex than peptones. Meaning, in the order of decreasing complexity:

Proteose > Peptone > Peptide

Yet, the final verdict would be that there is no clear cut difference between the three terms4. I hope this helps a bit (if not much).
References:

Peptides - Wikipedia
Payne JW (1976). "Peptides and micro-organisms". Advances in Microbial Physiology. Advances in Microbial Physiology. 13: 55–113. doi:10.1016/S0065-2911(08)60038-7. ISBN 9780120277131. PMID 775944.
Proteose - Collin's Dictionary
Proteoses, Peptones and Polypeptides, by G. Vincent Rudd


text:
(Why) can't blood sugar spikes be countered by consuming fiber generally?
Excessive sugar consumption is a widely-acknowledged problem in the modern Western diet.
One of the specific problems often stated is that the quick consumption of highly sugar-laden foods leads to spikes in blood sugar, the corresponding burden placed on the pancreas to produce a sufficient amount of insulin, etc.
But these same warnings on the ills of sugar always give a pass to fruit, and the justification is usually that the fiber in fruit slows down the processing of the sugar in the blood, thereby avoiding the spikes in blood sugar levels.
This is just one example of an article articulating what I've summarized above about blood sugar spikes, fruit, and fiber, but the same has been described in an innumerable number of articles: https://www.johnson.k-state.edu/health-food-safety/agents-articles/should-you-avoid-sugars-in-fruit-and-milk-for-weight-loss.html
In my mind, this then raises the question: can the blood sugar spikes caused by all sugar consumption be avoided by consuming a compensatory amount of fiber?
E.g. can a person mitigate the blood sugar spikes from eating an ice cream or cheesecake by eating Metamucil, or some other such fiber supplement?
An obvious response might be: if it was that simple, everyone would do it, which implies that the short answer is "no" -- but if so, I'd like to learn why it isn't that simple: if blood sugar spikes from sugar in fruit is mitigated by its inherent fiber, why can't blood sugar spikes from added-sugar in human-made food be mitigated by consuming some "compensatory" amount of fiber?

One reason that sugary food producers are not supplementing their products with fiber might be that slowing the uptake of sugar may decrease its addictive potential. I certainly notice cane sugar rich products are much more addictive to me than fruit juice concentrate or honey sweetened products.  Or sugar rich fruit itself.

Yes, adding fiber to diet can reduce the "spikes" in blood sugar. Just a couple references I found quickly, I have not reviewed them closely so I'm not sure of their quality and there may be better examples, just want to demonstrate that these things are commonly studied:
Cassidy, Y. M., McSorley, E. M., & Allsopp, P. J. (2018). Effect of soluble dietary fibre on postprandial blood glucose response and its potential as a functional food ingredient. Journal of Functional Foods, 46, 423-439.
Pastors, J. G., Blaisdell, P. W., Balm, T. K., Asplin, C. M., & Pohl, S. L. (1991). Psyllium fiber reduces rise in postprandial glucose and insulin concentrations in patients with non-insulin-dependent diabetes. The American journal of clinical nutrition, 53(6), 1431-1435.
Sharma, R. D. (1986). Effect of fenugreek seeds and leaves on blood glucose and serum insulin responses in human subjects. Nutrition Research, 6(12), 1353-1364.
Torsdottir, I., Alpsten, M., Holm, G., Sandberg, A. S., & Tölli, J. (1991). A small dose of soluble alginate-fiber affects postprandial glycemia and gastric emptying in humans with diabetes. The Journal of nutrition, 121(6), 795-799.
However, the proposed mechanisms are mostly based on impacts on the digestive system and how quickly sugars are taken up. This mechanism has an obvious ceiling in that slowing digestion indefinitely is not going to be a good feeling. So, while you could certainly extract the fiber of an apple and pair it with some apple-equivalent amount of sugar, you're going to get a result comparable (though quite a bit less convenient) to just eating an apple, but there's no algebraic "canceling" of sugar and fiber, just a modest delay in uptake. While adding fiber may always reduce blood glucose peaks compared to no fiber, that doesn't mean you can add more and more fiber to compensate for any amount of sugar.

Prof. Dr. Robert Lustig says that both soluble and insoluble fibers are needed to avoid sugar spikes. Excerpts:

The fiber in real food is of two kinds: soluble, which is globular (e.g. beta-glucan, pectin, inulin, etc.); and insoluble, which is stringy (e.g. psyllium, cellulose, chitin, etc.). You need both, as they do different jobs. The insoluble fiber forms a latticework (like a fishing net) in the duodenum, and the soluble fiber plugs the holes in that latticework.
Psyllium is an insoluble fiber. Alone It could form the latticework, but not plug the holes.

One can further assume that the mixing of the sugar into the soluble and insoluble fibers has to take place before consumption in a way that makes the sugar stick to the fiber. This is apparently not done immediately.

agreed the the fiber cannot slow the absorption of sugar much unless the sugar is mixed into the fiber before digestion.


text:
Are there any natural cases of direct translation of DNA to protein?
I'm aware direct translation of DNA to protein (without the need for RNA) has been observed in test-tubes using e-coli. (Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC219759/)
I wanted to know whether there have been any natural cases for this that have been observed. And suppose there aren't, would it be theoretically possible in a cellular environment?

Please provide a reference for your assertion. But in any case the answer is NO. Why do you think the complex system that exists developed?

I have edited the post to provide a reference.

OK. You should consider whether the technology used in that work over 50 years ago was able to demonstrate and compare it with your assertion.

I'm aware that RNA is of course an essential role in molecular biology for almost all complex systems as far as I know. Its importance to biology is unquestionable. However, the reason I asked this question in the first place was from reading Crick's Central Dogma of Biology article (https://cs.brynmawr.edu/Courses/cs380/fall2012/CrickCentralDogma1970.pdf). In it, while he ruled any transfers from Protein to nucleic acids impossible, he argues that while there is no evidence for direct DNA to protein translation nor is it impossible either.

But that was 60 years ago. It’s of historical interest — no more. Do you realize how little was known at the time?

I seem to remember that paper coming up here in a previous question. Is there some person or source still churning it up? You might try to check. Otherwise I may respond with a history lesson sometime in the next few days.

https://www.sciencedirect.com/science/article/pii/S0006291X09009127?via%3Dihub  It cannot just be historical interest alone; this 2009 paper shows researchers attempted (though also failed) direct DNA to protein translation. Still, the abstract does mention "the question still remains whether or not DNA could be directly translated into protein".  So it cannot be of historical interest alone if a study in 2009 attempted this.  Surely it's still an open question? Although I suppose the evidence renders it very unlikely.

@neuro Why does it matter to you? What thing are you trying to get at by studying this? Even that 2009 paper is essentially throwing it away. It's an open question only because you cannot prove a negative scientifically. It's a possible, but low-probability poorly-supported alternative to an RNA-world hypothesis.

@BryanKrause  I was just curious. Central dogma of biology interests me. But yes, the overall consensus seems to be that in vivo dna to protein direct translation is highly unlikely, if not impossible.

Ah thanks for this @David . This post unintentionally seems to be a duplicate of that previous post. But your answer  on that post was what I was looking for anyhow. Thanks again.

No problem. Your post was expressed in different terms and had a different focus, but most of the problems around it are discussed there and in another post mentioned in a comment. Regarding The Central Dogma, I have an answer to a question on that, referencing the original 1956 formulation. 1956 — Transfer RNA wasn't discovered until 1965! What Crick was doing was emphasizing that you couldn't get back to NA from protein, but not ruling out other possibilities which might be possible in principle.


text:
Effect of paracetamol or any antipyretic tablets
We all consume a paracetamol or any antipyretic tablet when we have cold or flu. And these tablets just reduce the body temperature. So my question is, when we have an infection and due to that infection we get fever, so unknowingly if we consume antipyretic tablets it will reduce the body temperature, so that means during that condition reduction of body temperature is harmful for our body as the infectious agent can make copies of it, as the body temperature is decreasing.

http://biology.stackexchange.com/questions/7627/how-does-paracetamol-interfere-with-immune-system?rq=1   also, http://biology.stackexchange.com/questions/7541/if-fever-is-a-natural-immune-defense-why-do-people-take-drugs-to-lower-it?noredirect=1&lq=1

This is a controversial topic. I co-authored a paper that drew on this research to make conclusions about population-level effects. The only situations I can recall where antipyretics have been shown to be clinically beneficial is in severe cases where inflammation itself is causing neurological damage (e.g., acute brain injuries); results for e.g. infectious diseases are ambiguous. In our paper, we summarized previous research on the costs and benefits of fever suppression as follows (our summary may be slightly biased in the direction of "fever suppression is bad" ...)

Previous investigations of the effects of fever suppression have focused on the clinical benefits and costs to the individual [8,9]. The adaptive value of fever [10–13] is well known to immunologists; for example, Janeway's Immunobiology [14, p. 110] notes that ‘At higher temperatures, bacterial and viral replication is less efficient, whereas the adaptive immune response operates more efficiently’. Others argue that the adaptive value of fever arises instead from activation and coordination of the immune response [12]. By contrast, a common view in the medical community, as expressed for example in Harrison's Principles of Internal Medicine, is that the ‘treatment of fever and its symptoms does no harm and does not slow the resolution of common viral and bacterial infections’ [15, p. 107] ...

References from this section:

Mackowiak PA. 2000 Physiological rationale for suppression of fever. Clin. Infect. Dis. 31, S185–S189. (doi:10.1086/317511)
Eyers S, Weatherall M, Shirtcliffe P, Perrin K, Beasley R. 2010 The effect on mortality of antipyretics in the treatment of influenza infection: systematic review and meta-analyis. J. R. Soc. Med. 103, 403–411. (doi:10.1258/jrsm.2010.090441)
Kluger MJ. 1991 The adaptive value of fever. In Fever: basic mechanisms and management (ed. Mackowiak PA), pp. 105–124. New York, NY: Raven Press Ltd.
Hasday JD, Fairchild KD, Shanholtz C. 2000 The role of fever in the infected host. Microbes Infect. 2, 1891–1904. (doi:10.1016/S1286-4579(00)01337-X)
Blatteis CM. 2003 Fever: pathological or physiological, injurious or beneficial? J. Thermal Biol. 28, 1–13. (doi:10.1016/S0306-4565(02)00034-7)
Simon HB. 2003 Hyperthermia, fever, and fever of undetermined origin. In Infectious diseases: the clinician‘s guide to diagnosis, treatment, and prevention. (ed. Dale DC). New York, NY: WebMD Professional Publishing.
Murphy KM. 2011 Janeway‘s immunobiology, 8th edn. New York, NY: Garland Science.
Dinarello CA, Porat R. 2008 In Harrison's principles of internal medicine (eds Fauci AS, Kasper DL, Longo DL, Braunwald E, Hauser SL, Jameson JL, Loscalzo J), 17th edn, p. 2958. New York, NY: McGraw-Hill.

Both @ashafix and @benbolker have given a pretty nice answer, I just wanted to add some more points to it. First of all, it wouldn't be correct to say that these tablets just reduce the body temperature as in that case, intaking antipyretics would be the same as drinking a glass of cold water in fever which, generally, shows the same effect as you mention in the question.
Paracetamol does reduce body's temperature. Though its exact mechanism is unknown, a theory from here[1] suggests that:

The COX family of enzymes are responsible for the metabolism of arachidonic acid to prostaglandin H2, an unstable molecule that is, in turn, converted to numerous other pro-inflammatory compounds. Classical anti-inflammatories such as the NSAIDs block this step. Only when appropriately oxidised is the COX enzyme highly active. Paracetamol reduces the oxidised form of the COX enzyme, preventing it from forming pro-inflammatory chemicals. This leads to a reduced amount of prostaglandin E2 in the CNS, thus lowering the hypothalamic set-point in the thermoregulatory centre.

But, it also does other jobs like this[1]:

An article in Nature Communications from researchers in London, UK and Lund, Sweden in November 2011 has found a hint to the analgesic mechanism of paracetamol, being that the metabolites of paracetamol e.g. NAPQI, act on TRPA1-receptors in the spinal cord to suppress the signal transduction from the superficial layers of the dorsal horn, to alleviate pain.
This conclusion has been contested in a new hypothesis paper on how paracetamol might act. The author concedes that NAPQI is the active metabolite but that this reactive compound should react not only with the thiol in TRPA1 but also with any other suitably available nucleophile that it happens to encounter. It is suggested that thiol groups in cysteine proteases, e.g. the proteases that take part in the processing of procytokines, such as those generating IL-1β and IL-6, might be the targets giving rise to overall analgesic effects.

Coming back to your main point i.e. when paracetamol reduces the body temperature (which it does), how is it helpful for the body to fight infections. Refer to this answer[2]:

So when your body begins to fight an infection you get a fever (which can make the environment uncomfortably hot/cold) and the tissues around your joints swell (which makes movement and relaxation uncomfortable). NSAIDs like Ibuprofen reduce those symptoms, making the duration of the infection more bearable. They do not reduce the length of the infection by any measure (and might increase it, though the research is not particularly conclusive), but can make the day go by better if you've used up all your sick days or have a child to take care of.
Basically, people take NSAIDs to reduce fevers for the same reason most take any over-the-counter pain medications. To make life a little easier in the meantime.

A direct answer is given here[3]:

While quality research has been lacking, there's some evidence that shows reducing a fever actually hinders recovery from infections, the cause of most fevers in the community, Young says...Also, if you take paracetamol to lower a fever, it may make you feel better because it also acts as a painkiller. (Whether lowering a fever in itself makes you feel better isn't clear.)...But when you're critically ill, some evidence suggests treating a fever might make it less likely you'll survive.

References:
1.https://en.wikipedia.org/wiki/Paracetamol
2.If fever is a natural immune defense, why do people take drugs to lower it?
3.http://www.abc.net.au/health/talkinghealth/factbuster/stories/2012/07/31/3557498.htm

According to this study paracetamol/acetaminophen does not have any effect on the influenza virus.

Regular paracetamol had no effect on viral shedding, temperature or clinical symptoms in patients with PCR‐confirmed influenza. There
  remains an insufficient evidence base for paracetamol use in influenza
  infection.

Your statement "And these tablets just reduce the body temperature." might be an oversimplification. The mechanism of action of paracetamol is still a mystery but it is an analgesic which explains its use during viral infections.


text:
How does the brain immediately know when one's thirst has been quenched?
The question struck me the other day when I drank a glass of water. I understand that there are at least two conditions under which the brain signals thirst: extracellular thirst, when there's not enough fluid in the blood, and intracellular thirst, when the cells need more water to lower the concentration of osmolites.
However, it takes time for water to enter the bloodstream after it has been ingested, and it spends at least a little while in the stomach.
Why does the sensation of thirst disappear despite the water having not yet made it into my bloodstream?

There are two different aspects to or drivers of thirst, osmolality and hypovolemia, with plasma osmolality elevation being the more potent stimulus of thirst.
As stated by @arboviral (and supported by his link), not a lot is known about the mechanisms of immediate thirst satiety. Much more is known about the mechanisms causing thirst, and the mechanisms of return to normal serum osmolality over 120-180 minutes after rehydration than those immediately satisfying it.
Most of the research on this is old (pre-2000). In one often-cited very small study 1, swallowing and esophageal reflexes (or as the authors termed it, “oropharyngeal metering”) had a significant effect on relief of thirst, that is,

the act of swallowing helps to regulate the volume of fluid ingested by providing an integrated signal proportional to the cumulative ingested volume.2

Study participants were all mildly dehydrated. One (control) group was allowed to drink ad lib. Another was allowed to drink ad lib but as they did so, the fluid was simultaneous extracted from the stomach by a nasogastric (ng) tube already in place. Interestingly, the difference in the amount of fluid ingested between these two groups (N.B. ad lib) was only 15% (the latter group drank a bit more.) The third group was given fluid by ng tube only.
The very act of swallowing fluid boluses induced satiety. However, plasma arginine vasopressin levels (involved in the regulation of fluid intake) dropped rapidly during the first 5 minutes of drinking in both ad lib groups, but not in those given fluids via ng tube, so it is not only mechanical receptors that are involved in quenching of thirst.
This confirmed an older study which demonstrated the importance of the rapid drop in plasma vasopressin in hydration before major changes in plasma osmolality occurred.3
Given the lack of extensive research and the relative immediacy of thirst suppression, The most likely explanation is a combination of sensory modalities and reflexes (mucosal wetness, temperature of rehydration fluid, mechanicoreceptors in the oropharynx, esophagus, etc.), and some rapid hormonal changes - e.g. in AVP - are responsible for limiting the amount we drink when thirsty.
1 Regulation of fluid intake in dehydrated humans: Role of oropharyngeal stimulation
2 Influence of age on thirst and fluid intake
3 Acute suppression of plasma vasopressin and thirst after drinking in hypernatremic humans

Satiety is divided into pre-absorption and post-absorption - the mechanism you're asking about is preabsorption satiety, which as you point out occurs long before the water can be absorbed into the bloodstream and appears to be remarkably accurate. The receptors and underlying mechanisms of pre-absorption satiety are not fully known but are thought likely to include moistening of the mucosa of the mouth and stretch receptors of the stomach and intestine.
I'll try to fill this out later but there's a longer description with diagrams on p309 of Schmidt & Thews (2013) "Human Physiology" (published by Springer).

Interesting. I considered the possibility of stretch receptors in the stomach, but I don't see how they could distinguish between water and food, since eating doesn't make you any less thirsty. And it seems to me, from a layman's perspective, that moistening of the mucosa could signal that some fluid has passed recently, but not the amount or the composition of the fluid.

I'd say the answer is easy.

Since the whole body is one body all you need is the change of of water saturation in a part of you to determine / extrapolate how much water has been ingested.
We all came from the water and are mostly made out of water. So it's not like water is a foreign substance and we needs special receptors in order to determine water content.
We are water. And the system has evolved over time to be built in. I.e. the ones with a broken system have died of dehydration and anybody else survived.
Of course you might be looking for one singular mechanism that says stop, that's enough. But it's a mixture of body temperature, what you have eaten, how much energy you have, etc. (water requires energy in order to be heated to your body temperature)
That reminds me that apparently in hot regions you are supposed to drink tea or warm water because that allows you to drink more / be better hydrated. Based on that I'd guess it's just a temperature gradient? I.e. the water cools you down, and when it becomes too cold in your insides, you stop until you are hot enough again.

It would be most helpful if you could provide links for these assertions.

I could post a link to my own answer. Would that help?


text:
Is there evidence for higher human genetic diversity prior to the alleged Toba Catastrophe genetic bottleneck?
I've been reading on the Toba Catastrophe theory and that it supposedly caused a genetic bottleneck in humans some 70k years ago, which raised a question that I couldn't find an answer to by searching the internet.
According to wikipedia:

It is supported by genetic evidence suggesting that today's humans are
  descended from a very small population of between 1,000 and 10,000
  breeding pairs that existed about 70,000 years ago

My question is regarding this evidence.
Is it a case of simply observing expansion of genetic diversity form a projected point of low genetic diversity and pinning it on the event that is most likely to have caused it?
Or is there genetic evidence, obtained from sequencing DNA from humans from say 80k and 60k years ago that proves genetic diversity 80k years ago was indeed higher and abruptly dropped due to that exact catastrophic event?
The former seems kinda possible, because as severe as the eruption might have been, most of the people back then were in Africa, which is on the other side of the planet, and the estimated global impact doesn't seem to be anywhere nearly as severe as to cause the extinction of a substantial amount of the human population.
I think the human, as a more intelligent omnivore, should be somewhat more resilient to such catastrophes than any large herbivore or apex predator. Yet there is no information on such species being largely affected by that event, although there are a few species that appear have been affected.
Furthermore, there appears to be evidence that human populations were not completely extinct even in areas as close as southern India.
Last but not least:

genetic analysis of Alu sequences across the entire human genome has
  shown that the effective human population size was less than 26,000 at
  1.2 million years ago; possible explanations for the low population size of human ancestors may include repeated population bottlenecks or
  periodic replacement events from competing Homo subspecies

and

A study by Chad Yost and colleagues of cores from Lake Malawi dating
  to the period of the Toba supereruption showed no evidence of a
  volcanic winter, and they argue that there was no effect on African
  humans.[51] In the view of John Hawks, the study confirms evidence
  from a variety of studies that the eruption did not have a major
  climatic effect or any effect on human numbers

Which further goes to add substance to my suspicion that the Toba event, as unlikely as it may be as a cause, was simply picked as the most convenient / least unlikely candidate.

So, in short:
Is it known for an evidence supported fact that this particular eruption caused an abrupt drop in genetic diversity and a genetic bottleneck, and if so, reference to said evidence will be appreciated, or is it merely the most plausible candidate to explain an observable genetic diversity expansion from a projected fairly recent initial condition of low genetic diversity?
Or to put it even shorter, is there evidence that humans were more genetically diverse prior to said event?

Tried to improve the title question to relate more closely to what you are asking in the body of your question - feel free to edit if I haven't got it right.

I think some of the information you edited in to your question might distract a bit from your original question...I thought you were looking for earlier evidence of genetic diversity but it looks like your new edits are more about the validity of the Toba catastrophe hypothesis...nothing wrong with that part except it makes your question more broad than is typically ideal for a stack exchange format.

I decided to include that stuff as it all hints at the lack of any evidence. Especially the part with the even longer trailing poor genetic diversity spreading across all "homos" :)

New research suggests that The so-called Toba bottleneck didn't happen.