text:
Why is the hexose monophosphate shunt called a direct oxidative pathway?
Why is the hexose monophosphate shunt (pentose phosphate pathway) called a direct oxidative pathway( Ref. Biochemistry by Satyanarayana , 4th edition, pg.no: 244) , even though oxygen molecule is not used for oxidation? It uses NADP for its oxidation. So if utilisation of NADP is direct oxidation then what will be indirect oxidation?
How can I differentiate direct and indirect oxidation? Is the use of Electron transport chain considered as secondary oxidation?

You should avoid using abbreviations in titles and always repeat the question and define any abbreviations in the text. HMP is not a standard abbreviation anyway, as most biochemistry texts refer to the pentose phosphate pathway. I have corrected this and the use of direct when you meant indirect in the penultimate sentence. Finally, please provide a reference to the use of the term "direct oxidative pathway". It's not one I have heard of and, though it's not my field, I used to lecture on the subject.

@David please view question again , I have added the reference.

OK. Satyanarayana is not a text I am familiar with, but as my comment to @AnubhavGoel indicates, the term seems to have been current in the 1950s, but has fallen out of use in US texts. I think it would require some effort to track down. All I can suggest (and as I don't know if it is correct I am doing that as a comment rather than in an answer) is that complete oxidation of one glucose molecule is achieved in the pathway, whereas glycolysis produces pyruvate, which requires further metabolism for complete oxidation (PDH and TCA cycle), and this seemed important at the time (if no longer).

I had a try at tracking it down and have now posted an answer.

This answer is based on a 2002 autobiographical account of the work of Bernard L. Horecker entitled The Pentose Phosphate Pathway. Here he refers to “direct oxidative pathway” but does not unambiguously explain this, so I shall summarize my interpretation and then provide evidence in terms of quotations.
Summary of my interpretion of Horecker’s account
When what I shall initially refer to as the hexose monophosphate shunt (HMS) was being elucidated in the late 1930s and the 1940s it was thought that its main purpose was the same as that was envisaged for aerobic glycolysis — to oxidize glucose to provide energy — and was merely an alternative way of doing this. The term ‘direct oxidative pathway’ was used to distinguish it from the glycolytic pathway (then refered to as the Embden–Meyerhof–Parnas pathway), presumably because six cycles of the oxidative phase e could completely oxidize one molecule of glucose 6-phosphate to carbon dioxide, whereas glycolysis only oxidized it to pyruvate. Presumably this was regarded as ‘indirect oxidation’ because complete oxidation required the further metabolism of pyruvate using the tricarboxylic acid cycle.
The term ‘direct oxidative pathway’ fell out of use as it was realized that the main functions of the pathway were to provide pentoses for nucleic acid synthesis and NADPH for synthesis of fatty acids, steroids, and reduction of oxidized glutathione. It was for this reason also that the name most commonly used for the pathway changed to the pentose phosphate pathway, transfering the emphasis to one of the products.
Quotations from Horecker

…Haas arrived from Warburg’s laboratory in 1939. Haas asked me to join
  him in the search for an enzyme that would catalyze the reduction of
  cytochrome c by reduced TPN (now NADP). This reaction was thought to
  be the missing link in the electron transport chain from substrate to
  oxygen and marked the beginning of my interest in what was then
  thought to function as a direct oxidative pathway for the metabolism
  of carbohydrate but is now known as the pentose phosphate pathway…
…These observations gave rise to the hypothesis that the oxidative
  pathway was really a cyclic mechanism for the direct oxidation of
  carbohydrate. With each turn of the cycle one molecule of carbon
  dioxide would be produced, and the pentose phosphates formed would be
  metabolized back to hexose phosphates to start another cycle. Six
  turns of the cycle would result in the complete oxidation of one
  molecule of glucose…
…The function(s) of the new
  pathway, however, turned out to be quite different from the pathway
  for the direct oxidation of carbohydrate that we had expected. It
  provides two mechanisms for the production of ribose 5-phosphate. One
  is the “oxidative branch” of the pathway, which also generates 2 eq of
  TPNH (NADPH). Ribose 5-phosphate can also be formed directly from
  hexose and triose phosphates by the non-oxidative rearrangements
  catalyzed by transketolase and transaldolase. Where large quantities
  of NADPH are required, as in the synthesis of fatty acids or sterols,
  the excess pentose phosphates produced would be recycled back to
  hexose monophosphates.

[My emphasis]
Google Books ngrams of term usage

Addition of $O_2$ or removal of H means oxidation.
In this process H is removed from sugar, added to NADP as well
C is oxidised to $CO_2$.
Hence , it is oxidation reaction.
HMP pathway is used to produce NADPH. The process directly oxidise glucose to $CO_2$ and $H_2O$. It does not require TCA cycle or ETC. Hence is called direct oxidative pathway.
Glycolysis on other hand does not produce any $CO_2$ and $H_2O$.Hence, is indirect, as it needs TCA and ETC for complete oxidation.
Source: Biochemistry
U. Satyanarayan
Edition: 2013
Pg: 244 and 245(written in brackets on Pg 245)

This sounds nonsense. How can the fact that ATP is generated make a pathway indirect? The papers I find in which this term are used date from  the 1950s. Please cite a reference supporting this explanation. If it is true it certainly explains why it is no longer used (e.g. Berg et al.section on pentose phosphate pathway.)

@Anubhav Goel could you please cite a reference  for further information?

@David Removed nonsense. Added relevant source as backup.

@JM97 Maan gya bhai ko?  I use Vasudevan. But, teri hi book me dhoond diya.


text:
Why gout attacks mostly big toe?

A gout attack typically causes pain, swelling, redness, and warmth (inflammation) in a single joint, most often the big toe.

What makes big toe more susceptible for gout?
Also I was said that it mostly occurs in right big toe, if this is correct then what could be the reason for its right sidedness?

Source : http://www.webmd.com/arthritis/gouty-big-toe

That link doesn't say anything about the right side being more often affected.

it was told in my class by the lecturer.

Then I think you should drop the part about the right toe. Without a peer reviewed source, I don't think it's relevant.

Edited the title. the part about right toe is now subordinate.

The question has been explored in great depth in the cited paper. Have a look.
Roddy E. Revisiting the pathogenesis of podagra: why does gout target the foot?. Journal of foot and ankle research. 2011 May 13;4(1):13.
Summary:

Nucleation factors: The site of Gout depends on where the Monosodium Urate (MSU) crystals are likely to form. This process of nucleation depends on a variety of factors. One is temperature, its solubility decreases with temperature and hence the fingers and the toes are more likely sites of MSU precipitation. Further, trauma and pH also affect the nucleation. Repeatedly stubbing a toe makes the first metatarsophalangeal joint (MTPJ) specifically vulnerable.
Cartilage damage and Osteoarthritis(OA).OA sites are correlated with those of higher MSU deposition and cartilage damage (for reasons and evidence, refer to the cited paper). Hence, factors which make MTPJ more susceptible to OA can increase the predilection for MSU deposition. These include "increased concentrations of chondroitin sulfate, degradation of protein-polysaccharide complexes, and epitaxial MSU crystal nucleation and growth on cartilage fragments"

The right sided predilection might be because most people are right-handed, and they might be more likely to injure or stub their right toe.

Is it true that it also attacks mostly right side?

See the edit @JM97

could you answer this: https://biology.stackexchange.com/questions/58779/why-are-sutural-bones-more-common-in-lambdoid-suture  ?

@JM97 I went through the question. I couldn't find a satisfactory resolution of the query, only peripheral hints and such. Will post, in case no one does.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
How could this molecule affect the body? (Lysergic acid derivative)

First of all, could you please help me name this molecule? I think the name of it is something like this: N,N-pentamethylene lysergic acid. Secondly, my main question is what could be the pharmacology / mechanism of action (eg the target receptors, etc.) of this molecule? I couldn't find any info on DrugBank, so I'm all ears to your ideas. Please help me on this; it is quite a burning question.
P.S.: If there are any mistakes in my English, please excuse me.

That is lysergic acid piperidide, an analog of lysergic acid diethylamide (LSD). According to Wikipedia, it is an agonist of the 5-HT2A receptor, but is much less potent than LSD.

@ostal123 You're welcome. Please consider accepting the answer if it has, in fact, answered your question.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Competition in DNA hybridization to RNA
After we separate the two DNA strands, what makes one of the two strands combine with the labelled mRNA strand instead of the old complementary strand?

You usually add your labelled probe in a large excess to avoid this.

Like chris said it is only a question of Ratio, some will recombine with their complementary strand, but a lot more with the mRNA.

Then why don't you guys write an answer? Comments are NOT for answers. It says so when you open the comment box.

@David Because I had no time to write up a proper answer. One line is not an answer.

Yup, same here. I really dislike not having references in the biology SE. I guess for this type of question it is ok.

In this type of experiment the concentration of the mRNA will be greater than the concentration of the starting DNA.
When the DNA strands separate, the DNA and mRNA will be in competition for the complementary strand. Using really high concentrations of mRNA compared to the DNA will give it advantage to recombine with a higher frequency and give a higher ratio of the DNA-mRNA combination.
It is all a question of ratio.


text:
How does taking drugs speed up the development of drug resistant or viruses?
First, here is what I know:
Some infectious illnesses, such as HIV or Hepatitis B, can be treated with the help of some drugs. The problem is that the virus sometimes undergoes mutations which grant resistance to the drug.
First question : Is it so far right?
Secondly, what is not totally clear is why taking drug does speed up the development of the drug-resistant version of the virus. In my point of view, the drug resistant virus will develop anyway with or without taking drugs. I don't see what taking drugs changes. Is it like an intra-competition between the different mutated versions of the virus and in this case, taking drug will eliminate all the mutated versions that are not drug-resistant and, this way, favour the development of the drug-resistant versions?

Welcome to Bio.SE! your both assertions are quite correct. yes, mutations are random and it is the drug itself which favours evolution of drug-resistant strains by killing non-resistant ones.

Ok, thanks! If I understand well, there is a competition between all the forms, versions of the virus? If yes, why cannot they develop together? Is that because they need the same resources to develop?

I am no expert in evolution, so I can't give you very precise answers. The point is that without the drug, both resistant and nonresistant strains can live happily without competition (what would they compete for?) but when drug comes in, it kills nonresistant ones, leaving resistant ones able to dominate.

My central question is : why does taking drugs favour the development of drug-resistant strains? If there was no competition between strains, taking drugs would have no effect on the development of drug-resistant strains, and it's not the case. So, this is why I suggest a kind of competition between strains. Do you understand my reasoning?

I get your point. Someone more familiar with the topic (like @Remi.b) can explain this better to you.

No, they mutate at a similar rate; taking the drug does not affect mutation rate, but the idea of drugs is to inhibit the virus somehow. This happens in nature all the time (an organism develops - through a mutation - a product which can inhibit growth of a competitor. Taking the drug provides a selective advantage for the drug resistant 'organism' (or virus) to proliferate, as @another'Homosapien' has already stated.

In fact, I didn't talk about the mutation rate but about the growth rate of amutated drug-resistant strain which is higher when taking the drug, because of the elimination of a part of its "competitors". Is it right?

Actually, I believe I answered the exact question you asked, even on rereading it.


text:
How to edit/insert new gene after cutting with CRISPR/cas9
I'm a student started who has started learning about CRISPR/Cas9. As I understand it, CRISPR/Cas9 is an enzyme that is used to cut a gene at a specific sequence.  I would like to know how scientist do the next step to insert/edit a genome.
For example, say I have an original sequence ...AAATTT... Is it possible for me to insert a new sequence into the middle so it becomes like this: ...AAAGCGCGCTTT... ? Or is it possible for me to edit a single nucleotide of the sequence like this : ...AACTTT... ?
How is a new sequence inserted at the cut region? Is there any enzyme required to make them join each other?  How is it ensured that the sequence is not inserted or joined at the wrong position ?

https://youtu.be/2pp17E4E-O8?t=1m50s

@Dale thank you for this video, i looked at the video but don't clearly understand, does it mean that the cut make a sticky end instead of blunt end and we need to design a sticky oligo so they can join each other?  And as i see on the video, no enzyme is required for joining them together. Can you explain more a bit?

@Dale As i known, to join 2 sticky end dna together, it seems that we need to use an enzyme called 'dna ligase', isn't it ?

Cas9 is used to create a double-stranded break (DSB) in genomic DNA. The cell can then use homology directed repair (HDR) to repair the break. The cell can also use non-homologous end joining (NHEJ) to repair DSBs, but this isn't useful for inserting specific sequences. In HDR, a sequence homologous to either side of the break site is used as a template so that the break can repaired error free. Naturally, the homologous template could be a homologous chromosome or replicated copy of the broken chromosome.
However, consider a situation where you introduce DNA into the cell with regions of homology to the break site and whatever other sequence(s) you wish to insert/delete/change. In this case, the break can be repaired using this exogenous DNA as a template and your changes will then be incorporated into the genome.
There are other methods of introducing site-specific DSBs to the genome, such as TALENs. The big advantage of CRISPR/Cas9 is that site recognition is performed by RNA rather than protein (it is much easier to synthesize small RNAs than to engineer large proteins).

While this answers covers all of the OP's points, it might be worth to point out a few more specifics. (i.e. which proteins are needed for HDR or the probability of successful target integration)

@Nicolai More detail is always good but, given the lack of interest in this question and answer, I'm not sure it's warranted. I encourage you to post your own answer or edit this one if you have more information to add.

There are multiple Cas9 proteins so much of the information is specific to a particular protein for the specifics.
Inserting genes in the point cleaved by CRISPR is definitely possible--of course this requires other proteins. Cells often contain those proteins, so complementary sequences on the ends of the insertion sequence is technically all that should be needed for insertion inside cells. There are many details to all this, but that is not what your question is asking about.
A single point mutation has recently been edited: however it was not inside a cell:
https://www.statnews.com/2016/04/20/clever-crispr-advance-unveiled/


text:
How detailed a construction of the family tree of known human fossils do we have?
For the sake of this question, by "human" I mean Hominina. The best I could find is this, which isn't very detailed. Of the dozens of paleospecies we'd seek to link up, do we have a more detailed tree attempt? Of course, it would be provisional and approximate, and the details would be somewhat debated; but I'm trying to gauge how fuzzy it is with our current knowledge.


text:
What is the mechanism of monofunctional glycosylases?
I am learning about the base excision repair mechanism. I understand generally how glycosylases work, but I am trying to understand this with much more detail. I found a paper where they write:

Monofunctional glycosylases catalyze the single-step displacement of damaged base via attack of an activated water molecule on c1' of the substrate.

I am not sure what an activated water molecule is and how, for example, an aspartate residue is making a water molecule 'activated'. Furthermore, how is this activated water molecule hydrolyzing the N-glycosyl bond to remove the damaged base. Thank you for any help.

The article referred to in the question is Fromme et al. (2004). I was able to find several proposed mechanisms for the monofunctional uracil-DNA glycosylase but I'll discuss two that seem most relevant in the context of your question.

The first I'll mention was outline by Parikh et al. (2000) who studied recombinant human mitochondrial uracil-DNA glycosylase. They report a mechanism where the glycosidic bond cleavage is not induced by a nucleophilic attack by water but rather by valence electron rearrangement, induced by conformational changes of the substrate by the enzyme, leading to a resonance stabilized oxocarbenium intermediate. This figure shows an electron pushing representation as well as the various stabilizing effects produced by orbital overlaps which favours cleavage of the C-N bond:

Original caption: Structure-based reaction mechanism that resolves the apparent orthogonal paradox for electron transpositions by altering the substrate stereochemistry. (A) A simplified valence-bond representation of the glycosylic bond dissociation hides the paradox that the three electron pairs to be transposed are involved in orthogonal orbitals. (B) In the normal anti-conformation of deoxyuridine, the σ*-orbital involved in the anomeric effect and the π-orbital of the C2⩵O bond are orthogonal to one another, thus preventing orbital overlap. (C) Severe distortions of the deoxyribose and the glycosylic bond in the strained conformation of deoxyuridine enforced by the UDG active center align the pairs of atomic orbitals participating in each electron transposition, thereby electronically coupling the anomeric and σ-πArom effects to promote bond cleavage.

They also go on to say (emphasis added):

A water is tightly positioned 3.54 Å below the deoxyribose C1′ by four hydrogen bonds (Fig. 3B) but is likely a poor nucleophile. Instead, the UDG–DNA substrate structure suggests this water is well positioned to become the 1′-α-OH after dissociation of the incipient deoxyribose oxocarbenium ion from the uracil ring.

Here is Fig. 3B from the article, where the water molecule is the red sphere at the bottom of the image coordinated by four hydrogen bonds:

The next mechanism involves a nucleophilic attach by an activated water molecule and was outlined by Drohat et al. (1999) studying Escherichia coli uracil-DNA glycosylase. Here is the first step of the mechanism:

From the Wikipedia article on uracil-DNA glycosylase (accessed 15 Jul 2014)

Drohat et al. (1999) describe this:

UDG apparently follows a [...] mechanism by deprotonating the incoming water nucleophile using the completely conserved residue Asp64 as the general base. Site-directed mutagenesis studies of the human enzyme support the structural evidence that His187 and Asp64 act as a general acid and base, respectively, because conversion of these groups to leucine and asparagine resulted in 300- and 2500-fold losses in activity (11). However, structural and mutagenesis data alone cannot establish the catalytic roles and ionization states of active site groups; thus other complementary approaches must be utilized to establish a chemical mechanism.

To answer your question, the water molecule is considered activated because it is a better nucleophile due to proton abstraction by the aspartate residue side chain. Thus the electrons used in in the original O-H bond in water (which are polarized towards the electronegative oxygen) are free to attack the partial positive 1' carbon of the deoxyribose. Although it is a concerted mechanism, you could perhaps think of the nucleophile being the hydroxide anion, which is much stronger than water.

So which mechanism is correct you might ask. Well, I don't know, but I refer you to a paragraph from Parikh et al. (2000):

Despite the importance of UDG and the many proposed mechanisms for its catalysis of glycosylic bond cleavage, the structural chemistry underlying efficient catalysis by UDG has remained elusive. Two groups, including our own, have proposed a traditional acid-base catalysis carried out by a cationic His-268 and an absolutely conserved Asp-145 (13, 26). Two proposals (27, 28) invoke only general base catalysis via the same catalytic aspartate and a neutral histidine. Another proposal (29), based on a computationally simulated uncleaved-substrate complex, predicts that Asp-145 is fully solvated in the substrate complex so that it cannot act as a general-base catalyst. These proposed mechanisms are inconsistent with each other and with the uncleaved-substrate crystal structure presented here. Moreover, they are problematic in that they rely entirely on functional group chemistry and thus do not adequately explain UDG's efficiency or the activity of mutants that alter evidently key functional groups (13, 27). UDG mutations that remove apparently key active site functional groups are actually faster enzymes than several wild-type DNA glycosylases (30). Thus, without knowledge of a substrate complex structure, the characterization of UDG mechanism is severely hindered. Here, we present the structures of UDG bound to both uncleaved-substrate analog at 1.8-Å resolution and cleaved-product DNA oligonucleotides at 2.0-Å resolution. These high-resolution cocrystal structures suggest how UDG applies part of the DNA-binding energy to glycosylic bond cleavage by conformationally altering its deoxyuridine substrate to take advantage of stereoelectronic and strain effects in what is then an apparently dissociative process.

References:
Drohat AC, Jagadeesh J, Ferguson E, Stivers JT. 1999. Role of electrophilic and general base catalysis in the mechanism of Escherichia coli uracil DNA glycosylase. Biochemistry-US. 38(37):11866-11875.
Fromme JC, Banerjee A, Verdine GL. 2004. DNA glycosylase recognition and catalysis. Curr Opin Struct Biol. 14(1):43-49.
Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA. 2000. Uracil-DNA glycosylase–DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. P Natl Acad Sci USA. 97(10):5083-5088.

To answer your question in brief: an "activated water molecule" is one which is partially deprotonated (in this case... in other cases, partially protonated or metallated). Here, the bond between the water oxygen and one of the hydrogen atoms is partially broken, having been elongated (HO-----H). This is accomplished by a protein residue, which is often a carboxylate-containing residue, such as Asp or Glu in glycosylases. The negatively-charged carboxylate residue acts like a base (called a "general base"), removing the proton from water, thus leaving behind hydroxide ion (OH-). Now, why do all of this? Because water is a poor nucleophile and hydroxide a strong nucleophile. Here, the nucleophile is intended to attack the deoxyribose at C1' after the glycosylase has cleaved the sugar/base - or "N-glycosidic" - bond. This "quenches" the carbocation that forms after losing the base (the "oxocarbenium ion")... because having a strong electrophile hanging around the vicinity of DNA would be bad! Hope that helps!

You should add some references to your answer (Wikipedia articles are sufficient for basic claims) to (i) ensure that what you are saying is scientifically valid (ii) allow others to read up/deeper on the problem.


text:
Why isn't acetyl-coA an entry point for gluconeogenesis?
The process of gluconeogenesis starts from various possible precursors - plausible entry points like, Pyruvate, OAA, Fumarate, Propionate (as succinate) and alpha-KG. It is important to note that, acetyl-coA is not an entry point for Gluconeogenesis.
Entry points shown as blue circles.

The most common reason cited for this is the irreversibility of the enzyme, pyruvate dehydrogenase. Since it is irreversible, Acetyl coA can't get back to pyruvate to go on forming glucose.
But, Acetyl CoA naturally enters the Krebs cycle, so why can't it go ahead and form glucose via gluconeogenesis using one of the Krebs intermediates?
I have had this doubt for very long and tried to come up with an explanation to satisfy myself but I still don't know if it is valid.
So here it goes. All the entry points to gluconeogenesis (mentioned before) are an addition to the Krebs cycle. They get on the boat, sail along, get off at oxaloacetate and leave. They don't bother the boat in any other way. Even Pyruvate, forms oxaloacetate via pyruvate carboxylase and then gets on the boat for gluconeogenesis.
On the other hand, Acetyl coA would be a part of the Krebs cycle itself. It is not adding anything to it (2 carbons that are added are lost as CO2). So an Acetyl CoA added, can't leave as OAA. It would be analogous not sailing on the boat but eating it down itself. Slowly, it would lead to a decay and loss of the intermediates Krebs cycle and it would come to a standstill (?)
Is this explanation right? Are there any other ways to explain why irreversibility of PDH results in this?
Although acetyl-coA can enter gluconeogenesis via pathways like glyoxylate cycle (not in humans) and pathways to make pyruvate from acetone (not economical) to form glucose, the question is why it can not do so directly via the Krebs cycle.
Image: Harper's Biochemistry, 29th Edition.

There is also this paper that shows alternative pathways in silico that could be used to convert FAs to glucose, but at a high energetic cost to the human host. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002116

Does this answer your question? Can the human body create glucose out of fat?

The problem is that acetyl-CoA enters the TCA cycle by condensing with oxaloacetate in the citrate synthase reaction. Therefore, you need 1 oxaloacetate for each acetyl-CoA added. Now, if the citrate formed goes on to oxaloacetate which is then removed for gluconeogenesis, there is no oxalocatete left for the next citrate synthase reaction. The reactions do not balance. Therefore, an anaplerotic substrate like glutamine or asparate is needed to replenish the lost oxaloacetate.

Maybe it's also useful to note that organisms that have the glyoxylate shunt can bypass the decarboxylation steps in the TCA cycle, and in fact can use 2-carbon substrates like acetate (that enter through acetyl-CoA) for gluconegenesis and growth. (https://en.wikipedia.org/wiki/Glyoxylate_cycle)

Yes, but I think the OP is already aware of this; see the last paragraph of the question.

The main point is specified above - that Krebs is a cycle. It starts with a 4-carbon molecule (oxaloacetate), adds 2 carbons (acetyl from acetyl Co-A) to make a 6-carbon  (citrate) and burns off 2 carbos as CO2 in a set of steps until it gets back to the 4-carbon starting point (oxaloacetate) to add another Acetyl.
If you siphon off any of the components of that cycle there's no feed to the next step and the cycle stops.
the second point is that Krebs cycle enzymes are inside mitochondria, and gluconeogenesis enzymes are outside in the cytosol. It is within Mitochondria that Acetyl is snipped off fatty acid chains (i.e. 2 carbons at a time) and linked to CoA and enters Krebs.
As a general point, most molecules cannot exit (or enter) mitochondria without a specific protein that will carry that specific molecule across the membrane, so there has to be a specific gene for that function.
So any specific molecules in Krebs have to have a gene to exit the (two) mitochondrial membranes. Humans don't have genes for that.
(NB - you can generate a small amount of glucose from fat from (a) the 3-carbon Glycerol that joins 3 fatty acids together and (b) the few odd-number fatty acid chains that will leave a 3-carbon molecule after a load of 2-carbons are snipped off)

Welcome to Biology.SE! This looks like a good answer, but answers are much more likely to receive a favorable response if you cite supporting references (primary literature is best). This allows non-experts to verify your answer and provides a starting point for further learning. A good example of how to format references. (NB: Standards have increased from when the accepted answer was posted.) ——— You may also want to take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site. Thank you!

(+1) As I understand things, the basic problem is that for each acetyl-CoA (a two-carbon compound) entering the TCA cycle, two carbons are lost as CO2 for each round of the cycle. Thus there can be no net synthesis of any carbon compound from acetyl-CoA via the TCA cycle. This is not true of the glyoxylate bypass where the CO2-losing steps are effectively bypassed, and this pathway is often a prerequisite for growth on acetate as sole carbon source (This is what so impressed Hans Kornberg).

See Tricarboxylic Acid Cycle and Glyoxylate Bypass, for example.  Plants (and bacteria) can make glucose from acetyl-CoA if they have the enzymes of the glyoxylate pathway. More can be found in Kornberg's papers (Hans Kornberg, that is) on the glyoxylate cycle.

Please do not refer to the Krebs Tricarboxylic Acid Cycle as "Krebs". This is not standard practice (I have never heard it before) and appears disrespectful to the memory of Hans Krebs (although I imagine that was unintended). "The Krebs Cycle" is acceptable, although people use the name "Tricarboxylic Acid Cycle" or "Citric Acid Cycle" because Krebs was also responsible for elucidating another metabolic cycle — "The Urea Cycle".

Your emphasis on loss of C2 via carbon dioxide is a useful clarification/extension of the accepted answer. However, your remarks about mitochondria are incorrect. Oxaloacetate (OAA) is a constituent of the TCA cycle and is normally produced from fumarate in the mitochondrion. In "normal" oxidative metabolism it condenses with Acetyl CoA to complete the cycle. However if there is direct or indirect input of OAA from amino acids it can act as a gluconeogenic precursor through conversion to PEP by PEP carboxykinase. To do this it is exported to the cytoplasm as malate via a malate transporter.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Please help me identify this plant. Is the fruit edible?
When free, could the experts here please help me identify this plant.
Location: Puget Sound, Washington State, US
Height: 3-4 feet
Date: July
Is the orange colored fruit edible?

This is a huckleberry or related vaccinium, Vaccinium parvifolium probably.
It looks unripe to me. I'd wait till August or September.
Some are unpalatable/sour but they are nominally edible.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Triosephosphate isomerase deficiency

Triose phosphate isomerase deficiency, a rare condition, is the only glycolytic enzymopathy that is lethal. This deficiency is characterized by severe hemolytic anemia and neurodegeneration.

How can I relate this enzyme deficiency to hemolysis?

My attempt:
1- Accumulation of DHAP is causing intracellular fluid to be more osmotic leading to cell bursting.( Then why don't we see the same in outer cells?)
2-Lack of glucose may lead to less ATP production, Na/K pumps work less, thus disturbing membrane potential, which finally may cause hyper-osmic ICF and then henolysis. ( But why don't RBC take twice the amount of glucose?)

Source: Biochemistry 8th edition by Jeremy M. Berg John L. Tymoczko Gregory J. Gatto, Jr. Lubert Stryer


text:
Hematuria due to Nitric Oxide

Drug interactions between properly dosed NO and other medications are not expected, but side effects may include noisy breathing, hematuria, or possibly atelectasis. (pg.no:577; Goodman and Gilman Pharmacology 13e)

What is the basis for this hematuria?  Is it because of platelet inhibiting activity of Nitric Oxide?


text:
Why some eggs are bile stained?
Why eggs of some helminths( Diphyllobothrium latum, Trichuris trichiura, Ascaris lumbricoides etc)  are stained with bile while eggs of other helminths( Hymenolepis nana, Enterobius vermicularis etc.) are not?

Some sites say that its because, more the lipid content better is the staining with bile of egg, then how eggs of ascaris are bile stained whose outer shell is made of proteins?


text:
How lymphocytes in lymphatic system get oxygen?
We know that the gas-transporting protein hemoglobin is absent from the lymphatic system. So, how does gas transportation takes place in lymphatic system? Is mere diffusion from surrounding blood vessels sufficient for lymphocytes and lymphatic endothelium to survive?

Besides carrier transport of oxygen and/or other gases that hemoglobin binds in the blood, there is also dissolved oxygen present in the plasma - this would also be present in the lymph fluid despite a lack of hemoglobin. With the complex network of arteries/arterioles/capillaries that deliver oxygen to tissues, do you think that lymph transport of gases is even important?

@Vance Yes , I think it's important because how does the cells forming lymph vessels(endothelium of vessels), lymphocytes in vessels and nodes get the required amount of oxygen?

@JM97 Dissolved gaseous oxygen moves fairly freely over short distances...lymph vessels will never be far from other vessels, including capillaries. So, essentially the lymphatic vessels are fed the same way as any other organ tissue.

@BryanKrause what about lymph nodes?

@JM97 Lymph nodes are highly vascularized.

So oxygen dissolved in lymph will support myriad of lymphocytes of lymph node? I don't think that's sufficient considering the very large density of lymphocytes in the node.

@JM97 Lymph nodes are highly vascularized, as Bryan Krause said. That means lots of RBCs delivering lots of oxygen to the node and all of the cells contained therein. It doesn't matter if you think it's sufficient, in reality it is.


text:
Fatty acid oxidation in adrenal medulla?
Why adrenal medulla can not utilise fatty acids for generation of energy?
What could be the benefit for not having ability to use fatty acids?
Refrence 1
Refrence 2

Does it have something to do with feedback mechanism?

Interesting question. Do you have a reference showing that fatty acids cannot be used? The adrenal medulla is basically a specialized nervous tissue, and neurons are usually considered to be unable to oxidize fatty acids, but other cell types in the CNS do oxidize fatty acids, see for example https://www.hindawi.com/journals/bmri/2014/472459/

but the blood brain barrier is not present in adrenal medulla.

I was hoping for a reference to actual experimental data, rather than just somebody else claiming the same thing. I did find some textbooks that repeat this statement (without reference), so perhaps it's valid, but textbooks can also be inaccurate ... Also, the blood-brain barrier does allow fatty acid transport (contrary to statements in some textbooks :), see for example https://www.ncbi.nlm.nih.gov/pubmed/17901540  See also my related question http://biology.stackexchange.com/questions/34159/why-is-the-brain-dependent-on-glucose

Also, we should consider the possibility that there is no benefit. Some features of biology are not good for the organism, but evolution just hasn't come up with any better solution.


text:
Absorption of digested food in small intestine
My book says

glucose , galactose and amino acids are transported into cells of villi via secondary active transport(sat). Fructose is transported by facilitated diffusion(FD) .short chain fatty acids , vitamins diffuse into cells of villi. From there all these are transported to blood by FD.

This site says the reason for using SAT: http://www.phschool.com/science/biology_place/biocoach/biomembrane1/glucose.html
But I want to know why fructose, vitamins and short chain fatty acids do not need S.A.T. and travel via FD (or just diffusion)?dont they get reabsorbed into small intestine ?

In general:

Hydrophilic/polar/charged molecules require some kind of assisted transport across a membrane
Hydrophobic/nonpolar molecules can easily diffuse across a membrane

Glucose, galactose, and amino acids are hydrophilic. Fructose, fat-soluble vitamins, and short-chain fatty acids are hydrophobic.
Glucose and galactose have similar structures (aldose/pyranose) and are both hydrophilic. Fructose has a slightly different structure (ketose/furanose) which affects the way it is transported. Basically, it has a ketone (rather than an aldehyde) so it is relatively less reactive/polar. Because it is hydrophobic, it can diffuse across a membrane more easily.

"Since the concentration of fructose is higher in the lumen, fructose is able to flow down a concentration gradient into the enterocytes, assisted by transport proteins." (Wikipedia) Based on this statement, it seems that the lumen maintains a higher [fructose], relative to the enterocytes.
As explained in your link, glucose is mediated via SAT to ensure one direction of transport: we want glucose going only INTO our bloodstream. The [glucose] in lumen decreases after a meal, but we want glucose to keep being absorbed (hence SAT).. Also, unlike fructose, glucose and galactose are highly regulated for use in glycolysis, so it is important to keep glucose in the appropriate cells. In particular, because of its structure, fructose enters glycolysis after the "rate-limiting" phosphofructokinase step in glycolysis.
Quick notes on fat-soluble vitamin and short-chain fatty acids: they're both relatively small and hydrophobic. Short-chain fatty acids can easily diffuse across a membrane, which is also made of lipids. (I recommend reading about hydrophobic effect if you want to know more about this).. Larger fatty acids require shuttles because of their size.
Regarding "reabsorption" into the small intestine:
Diffusion is the result of the random motion of particles. The more collisions in a higher concentration region eventually leads to a net movement "down a gradient." Using this logic: at some point, yes, the molecule may go back out into the lumen or go back in ("reabsorb") because it basically follows the gradient.
(I may come back to this post after learning more about it in a few months.. I used most of my answer based on what I learned in nutrition, o-chem, biochem)
Read more here about fructose metabolism


text:
What is preliminary work in a biological investigation?
Here is an example of preliminary work that confuses me (from an A level Biology exam question). Please help me by providing an explanation of preliminary work in the generic sense, then use the example below.

A company is in the process of developing a new stain-removing washing liquid.
  They want to include a protease enzyme to digest the proteins that are responsible for some stains on clothes. Plan an investigation to discover the optimum concentration of protease to use in this new stain-removing washing liquid.'

Here are the answers suggested as the preliminary work:

see if proposed method will work / will provide
  measurable results
to check for suitable conditions for digestion
  e.g. temperature, pH
select timescale (for measuring stain digestion)
idea of selecting a range of protease concentrations
check if the type of {protein / stain} is affected
select suitable dependent variable for measuring {digestion / removal / eq} of the {stain / protein/ eq }

Now, in my process of understanding what preliminary work is, I want to
question is there any other preliminary work that could be done on this investigation? Seems like there is a lot more to prepare for such an investigation. For example, at first sight, I suggested that secondary research needs to be carried out in order to identify the mean amount of stain and its distribution around that mean. Then that will be the suitable substrate concentration to be used. I also mentioned researching the type of proteases that the company wanted to use, alongside carrying out the preparation of the range of concentrations of enzymes that need to be used.


text:
What determines the differences between differentiated cells?
Given two multi-cellular species with obviously different phenotypes. The reason for the different phenotypes reflects their different DNA.
However two types of cells in an adult organism may have clearly different phenotypes (e.g. morphology), but the same DNA, with a different set of genes expressed.
To explain this it would seem that there must be some molecules to modulate the expression of the DNA in different cell types. In my reading I have found one such type of molecules the presence of which is prerequisite for one type of differentiation – modification of histons – methyl, phosphate, acetyl, ubiquitin. Another class of molecules is the transcription factors.
My question:
What would one look at to tell the differentiated type of a cell (ignoring its phenotype)?

Addendum: After having delved a little bit deeper into the topic of epigenetics, I'd like to suggest as a possible answer: it's the histone code one has to look at, something like: how the DNA is wrapped around which sequence (!) of (modified) histones.

I read the question a few times but I can't understand it. What do you mean by a species [.] in the sense of Darwin? What do you mean by a species of differentiated cells?

The two following two posts will likely help you. Why is a heritability coefficient not an index of how “genetic” something is? will tell you about what causes phenotypic variation (environmental variance, genetic variance, epigenetic variance, .... and all covariances).

How could humans have interbred with Neanderthals if we're a different species? will teach you about the difficulties and subtilities behind the concept of species.

@Remi.b: Thanks a lot for having tried to understand my question. I've got to admit that I obviously didn't manage to make clear what I mean. Possibly it's not even clear to myself? Another try: "Individuals of the same species share considerable portions of their DNA (next to having the same phenotype). What do individual cells in the human body of the same cell type have in common (next to having the same phenotype as cells) but not with other cells in the same body?"

This question may seem unclear, because of the non-biological background of the poster and the misuse of "species" in relation to cells. However, it is actually a very basic and important question. Put simply to a modern biologist one could say "If muscle cells and liver cells have the same DNA, what causes them to have a different morphology, i.e. what causes them to express different genes from the DNA?" The question hints at some of the reasons in mentioning modification of histones. The problem with answering the question is that it is very broad, and there is a lot we don't know.

@David: I understand, "species" is not to be used related to cells. But I'm quite sure to have heard of "populations of cells". Is "cell type" an acceptable term for "species of cells"?

I have modified and simplified your question in an attempt to focus it and prevent it being removed as unclear. Yes "cell type" is the term used. If you don't like my changes you can revert them. The problem now is that you have (partly) answered the question yourself. Unless someone (not me) has a reference to a good review or can write a good thumbnail account, I'm not sure where we can go from here.

You saw that part in your wiki link that the "histone code" is just a hypothesis?  The development of the anterior-posterior axis in fruit flies is pretty well explained with RNA gradients, and not so much histone positioning.  Here's a hint, RNA seq is a much more common application than CHiPseq on histones.

@swbarnes2: I did. RNA seq and CHiPseq seem to be hard stuff for the novice.

Well, you are not asking a question that can be answered by a novice in biology, either.  Scientists asking "How are these tissues different" are generally not starting with CHipSeq; they do RNAseq, or 10 years ago, microarrays.


text:
Drake's Law. What is the genome-wide mutation rate and what are the estimates?
Drake's rule
Drake's rule states that the genome-wide mutation rate is more or less constant across all species — from E.coli to the house sparrow.
Data
From what I think being Drake's original paper (table 1, page 4) on the subject (see here) is at the order of $3\times 10^{-3}$. When I look at this paper, I see that the genome-wide mutation rate is roughly around 30 for human. When I look at this paper, they cite some other papers suggesting a genome-wide mutation rate in the order of 0.1 to 1 in multicellular eukaryotes and typically at the order of 1 for vertebrates. Finally, when I look at this speech (at the 60th minute), it seems however that the genome-wide mutation rate in human is 2.2.
What is going wrong?
Do I mix-up different concepts or are there some very contradicting estimates depending on the article we look at? Isn't the genome-wide mutation rate, $U$, which is just the number of de novo mutations transmitted to one offspring on average? What is a correct estimate of $U$ for human for example (1, 2.2 or 30)?

I don't think it is right to assume that genome wide mutation rate is same for all organisms. We know now that mutation rate depends a lot of biochemical milieu of the cell and efficiency of proofreading mechanisms.

There are so many things that are implied in this paper, not explicitly said.
The mutation rate here detected seems to be the emergence of chain-terminating (CT) mutations, which truncate protein coding genes, usually just one gene in a bacterium or phage, which would be possible to observe from inspecting a plate to see which colonies die or survive.
This is only a specific kind of mutation, but Drake assumes that its frequency is related to the overall mutation rate.  Which is probably fine.  Mutations we infer from this work arise spontaneously from a similar mechanism in all organisms.  This is just ionizing radiation for the most part.  So at a first glance we still believe this.  That there are no specific mechanisms for mutation.  Since this is usually ionizing radiation we would expect that the rate would go up when there's more radiation around and it most certainly does.
There are lots of reasons that animals and humans would have a smaller rate.  Drake is including in the paper the involvement of DNA repair mechanisms in the experiment as they are intrinsic to the survival of the yeast and bacterial cases and the phage may also enjoy the benefit thereof.
In some organisms there is a lot more DNA repair possible.  So that would mitigate the mutation rate in some cases like Deinococcus radiodurans.
Metazoans and diploid organisms which undergo meiosis for sexual reproduction have other methods for reducing the number of mutations they pass on.  Meiosis and recombination will allow the removal of many mutations by competition in gametes.  Since there are two copies of each chromosome, mutations are constantly being competed against their unmutated versions as gametes.  Then eukaryotes have their own repair enzymes and conditions.  Then lastly recombining into diploids, they also show mutations less often.
For these reasons and others, the mutation rate being even across the genome does not mean that that the mutations accumulate evenly.  Mutations still tend to accumulate in regions where positive selection is operational.  Here is an excerpt from a recent genomic comparison of five strains of rice:

Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia.


text:
Shape of feces in herbivores
Why do some herbivores like sheep, cow, and others excrete feces in a pellet (or biscuit or other) shape, while other species including humans do not do so? What is the reason for such an adaptation in herbivores? Is it beneficial to them, and if so, how?

I don't think it is an adaption, but the that diet plays a dominant role. The feces of cows in intensively fertilized agricultural fields, with grasses rich in protein, has no shape at all. See picture below.

The feces of cows in natural areas has much more structure. (image has copyright, so can only link)

Please have the courtesy to explain your downvote?!


text:
Dorsal root fibres
How can dorsal root fibres be unmylinated though are responsible for conduction of pain and temperature? How is their conduction so fast without even being myelinated? Is presence of only one axon( indicating that a single axon travels from skin to dorsal root ganglion) enough for such fast conduction?


text:
Iron deficiency anemia
It is said that iron deficiency anemia is characterised by microcytic-hypochromic RBCs. I would like to ask how iron deficiency causes decrease in the volume of RBCs? If the volume is decreasing because of low hemoglobin, then why  does the concentration of hb too decreases causing hypochromic RBCs? Why don't they decrease in same pace?

@anongoodnurse please see the bold text in the question.

Still think it's a dupe (bolding didn't change anything.)

@anongoodnurse there question is just about size but I want to know if the size is decreasing since hb has less concentration then why do it's concentration too gets decreases in the new rbcs? Shouldn't the concentration be same since volume is decrased? So why don't they decrease with same pace?


text:
What's so special about Chassaignac tubercle?
1-How does massaging of carotid artery at chassaignac tubercle( anterior tubercle of transverse process of C6 vertebra ) can relieve the symptoms of Supraventricular Tachycardia?
My attempt: I think by massaging carotid artery we are somehow stimulating the satellate ganglion present at level of c7. Or, I think, by massaging the carotid artery we are increasing BP, thereby affecting the baroreceptors and somehow this relieves the symptoms of supraventricular tachycardia.

2-Why can't the same massage be done at level of other cervical vertebrae?

It's not the vertebra that is important, but the carotid artery, and where it is most likely influenced by massage. There are too many interfering structures at C1/2; I believe C3-5 is ~ normal. Some guidelines indicate midpoint between the angle of mandible and the superior border of thyroid cartilage (so about C4-5), others just below the angle of the mandible (C3). C6 seems to be well below the carotid sinus to me. If you can refocus your question (not where and why) and show some research, I'd be happy to answer your question.

@anongoodnurse Unfortunately  I could not find any reason by doing research. All the websites I saw only state the fact but didn't explain and my textbook too.

OK, then I won't post an answer. Sorry I could not help you, but I really prefer to help those who post according to our guidelines when possible.. :(

Is it related to stellate ganglion ? Or it's just because massaging increases BP thereby affecting the baroreceptors??

Please edit your question to reflect the new information. Thanks!

Ok, I'm busy at the moment, but I will answer today. :)

The reason massaging the carotid artery can relieve symptoms of supraventricular tachycardia is because by massaging the artery, as you point our yourself, you artificially increase BP within the carotid artery, this activates a reflex (via the glossopharyngeal nerve) that lowers bloodpressure by reducing the heart rate via the vagus nerve, by increasing the refractory period of the AV-node, so the heart rate drops.
It should be noted though, that it can be a bit dangerous to play with these reflexes in some patients, especially because massaging the carotid arteries can lead to an embolism in older individuals with atherosclerosis, or in some patients, it can lead to asystole or ventricular fibrillation (i.e. cardiac arrest).
It's not really about which vertebra is at the level you are massaging, rather it's about being near the carotid sinus, which is where the baroreceptors are located, and that might vary between individuals and how you position the head etc.

Welcome to Biology.SE! This looks like it could be a good answer, but non-experts have no way of verifying your post. Consequently, answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. This is a good example of how to format references. ——— You may also want to take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site. Thank you!


text:
Why are sutural bones more common in lambdoid suture?
Why are sutural bones (Wormian bones) are more commonly present at lambdoid suture? Is the tortuous nature of lambdoid suture a reason for that?

Evidences for my claim:

They(sutural bones) occur most frequently in the course of the lambdoid suture, which is more tortuous than other sutures. They are also occasionally seen within the sagittal and coronal sutures. (1)

They are commonly found in the lambdoid suture and fontanelles but are occasionally seen in other sutures especially the coronal, squamosal, and sagittal sutures. We examined 25 dried human skulls with the aim to find out the occurrence and variations of Wormian bones, and surprisingly we found Wormian bones in the coronal, squamosal, and sagittal sutures in 6 skulls. These are uncommon sites of occurrence of sutural bones as reported in the literature. These findings prompted us to report these cases as their presence can lead to confusion in diagnosis in cases of skull fractures.(2)

Sources:
1- https://en.wikipedia.org/wiki/Wormian_bones
2- https://www.ncbi.nlm.nih.gov/pubmed/22117248

Is the question now more clear?


text:
Changes in spongy urethra during tumescence
How does the columnar cells of spongy urethra expand during tumescence(erection of penis)?
If we assume that the urethra has the length, long enough to sustain tumescence without expansion of cells, then will it form wrinkles on retraction just like skin? Probably latter should not be the case, since accumulation of urine would then take place in the grooves of those wrinkles.


text:
How to decide which protein structure to use from multiple entries in the Protein Data Bank?
I am trying to analyze the structure of SARS-CoV-2 spike protein. There are thousands of entries when searching for it on RCSB website. I have narrowed it down to 2 best matches (6VXX and 6XR8). For 6VXX, it is one of the first structure to be reported on RCSB website. The structure is heavily cited (>10000) but possess 5 point mutations, and sequence coverage is 14-1211. On the other hand, 6XR8 is cited less (>1000) in comparison with no mutations and sequence coverage 1-1273. I want the original strain with closed pre-fusion conformation. How to decide which structure to use for downstream application?

What downstream application did you have in mind? which structure to use is going to depend on that.

@timeskull I want to mutate some regions of the protein to see how it changes the binding dynamics with ACE2 protein and antibodies.

Mutations compared to what? The CoV spike is highly mutable as this is part of the immune evasion strategy. You should use one that suits your purpose. The first published usually has the most references simply because of time, it doesn't mean it is the "best" one to use, much like first answers on here tend to be more upvoted than later because they have had more time for exposure, even if the answer is incorrect.

@bob1 Mutations compared to the canonical sequence (UniProt ID: P0DTC2). Yes, there are multiple structures for the same protein (same amino acid sequence) with no standardization on RCSB.


text:
Why do highland/alpine plants require a drop in night temperatures to thrive?
There are mountain plants which require a drop in nightly temperature (many Nepenthes, Heliamphora and orchids for example). A non-specialist explanation is that the plants die of "starvation" if you do not provide cold nights, that During warm nights they metabolize their stored energy reserves much faster than they're adapted to do in natural environments, leading to overexpenditure and eventual death.
Is that plausible and if so can it be expressed in scientific terms?
Would extending the photo period be a simple way of counteracting this?

What research have you conducted to try to find an answer? As you have credit from another SE community you will be aware that this is requirement for posts.

There's a possibility this might fit on [gardening.se] if it doesn't work here. Nonetheless, interesting question, perhaps show your attempt to answer  - anything you found on the subject and where it lead you.

There's this paper (https://www.pnas.org/doi/10.1073/pnas.0914299107) that finds starch accumulation during the daytime is basically linear and more importantly, the plant then proceeds to use up those stores until dawn when they're basically depleted. I had already assumed that because it makes sense for an equilibrium state to evolve. This seems to support the logic behind the starvation hypothesis, I haven't found anything looking at the starch degradation in alpine plants however. I really want to know if there are metabolic processes that can't happen at all without a temperature drop.

At first, I also thought that it might be an equilibrium problem for metabolites and revcheckd the Michaelis-Menten equation.
However, the metabolic reaction stops (or appears to stop) because
-All enzymes are lost or inactivated.
-All substrates are lost.
-The enzymatic reaction reaches an equilibrium
All of the substrates are lost.
If the temperature is around 10°C, the enzymes are not completely deactivated. Nor is the enzymatic reaction in equilibrium, since the starch will continue to be broken down until dawn.
So I thought there is not enough CO2 in the material.

That's an interesting explanation.
I don't know of a definitive paper, so I write here only a guess.
Perhaps in alpine plants that are stressed by high temperatures at night, abscisic acid is produced and the stomata close, preventing CO2 uptake and photosynthesis.
CO2, the material for photosynthesis, is taken up by the leaves by opening the stomata at night.
Abscisic acid, a plant hormone that closes these stomata, appears to be synthesized in response well to stress responses.
https://www.frontiersin.org/articles/10.3389/fpls.2016.00571/full
In common plants, it seems to be synthesized in response to dryness, high salt concentrations, and low temperatures, but alpine plants may have a mechanism to recognize high temperatures at night as stress.
About abscisic acid, it is still under research, especially its receptors and signals.


text:
Double stranded RNA Single stranded DNA
I have seen in textbooks referring to ds RNA and ssDNA.
How a RNA can be double stranded and likewise how a DNA can single stranded  and if they do exist why are there names not interchanged?

The main differences between RNA (ribonucleic acid) and DNA (deoxyribonucleic acid) is that DNA contains a hydrogen atom where RNA has a hyroxyl (-OH) group and RNA's uracil is substituted for DNA's thymine.  The below image shows several deoxyribose molecules bound together, and off to the side, a ribose molecule. It is the OH group on the bottom right of the ribose molecule that is exchanged for a hydrogen in deoxyribose.

The structures of RNA and DNA are almost identical, so there is no reason why you can't have double stranded RNA. Similarly DNA can be single stranded. In fact, for DNA replication and transcription, the DNA strands must be separated. dsRNA and ssDNA are most commonly found in viruses. Check out these lecture slides for more about them: http://www.columbia.edu/itc/hs/medical/pathophys/id/2009/viruses2Color.pdf

"DNA contains one less oxygen atom" — please edit your answer to be more precise. The naive reader would have no idea what you mean, and the difference between ribose and deoxy-ribose is what produces different structures of dsDNA and dsRNA.

edited for clarity, though the reason I added the image originally was to provide the reader with a fairly self-explanatory comparison.

Complementary base-pairing is possible for RNA
As the poster is no doubt aware, the double-stranded structure of DNA is stabilized by A–T and G–C base pairs. He will also be aware that in transcription of DNA to RNA (in which A is replaced by U) A–U base pairing occurs. Hence, there is no physico-chemical reason why dsRNA cannot occur between suitable complementary strands.
Viruses provide examples of single- and double-stranded DNAs and RNAs
As is mentioned in another answer, the genomes of bacterial and eukaryotic viruses provide examples of dsDNA, ssDNA, dsRNA and ssRNA.
It takes two to tangle
Whether or not a particular DNA or RNA is double-stranded or single-stranded in Nature depends on whether both complementary strands are present. That depends on biology, not chemistry. Thus, a virus that is single stranded has evolved a replicative strategy whereby many copies of one strand are copied from a few copies of the complementary template. In double-stranded viruses (and organisms) the replication method starts with a double-stranded genome and makes a copy of each at the same time, resulting in equal numbers. (They are also synthesised in a way that allows them immediately to hydbridize.)
Nature is full of black swans
The fact that most DNA encountered is double-stranded and most RNA encountered is single-stranded, just reflects the nature of the genome and translation apparatus of cellular organisms. But transfer-RNA and ribosomal-RNA (and mRNAs) have double-stranded helical portions, and there are a variety of less abundant species of RNAs with individual functions that may involve helix formation. And, of course there are also DNA/RNA hybrids, for example the Okazaki fragments that occur during DNA replication.

why not link to your answer to "Does dsRNA exist in eukarotic cells?" https://biology.stackexchange.com/questions/95306/does-double-stranded-rna-dsrna-exist-in-eukaryotic-cells/97593#97593

I'll try a third pedagogical approach, the above answers are sufficient.
The typical college-entry level textbooks on biology will state that DNA is double-stranded and RNA is single-stranded. This is misleading later on, especially when you encounter an instance of single-stranded DNA and double-stranded RNA.
The posters above have already answered your question well - dsRNA and ssDNA exist all over the tree of life. However, I'd like to emphasize that they also exist transiently all the time in every single cell...
3 critical examples:

DNA must unwind and become single-stranded for DNA replication.
The same is true for transcription.
RNA has a tertiary structure too. Ribozymes rely on this. However, the most abundant RNA species in all cells is ribosomal RNA. It forms these structures:

These are 'single-stranded', but are capable of dimerizing with another RNA species if there is sufficient complementarity between local regions. Below you see many RNA hairpins and loops and locally these are double-stranded, even though it's a single molecule.
In situ hybridization is also another common technique in biology, it takes advantage of pretty much all 'exceptions to the rule' you mention. Nowadays, RNA is increasingly probed. Here is a simple diagram of how it works:

If they do exist why are there names not interchanged?

The names for RNA and DNA are not interchanged because they are different chemically! They just share features, most notably the ability to complement and hybridize to themselves and other nucleic acids, given enough complementarity.


text:
How does carbon dioxide diffuse into red blood cells?

Carbon dioxide diffuses out of the tissues and into the blood, where it is dissolved in the plasma. While some of the carbon dioxide remains dissolved in the plasma, most carbon dioxide diffuses into our red blood cells. In the red blood cell, some carbon dioxide binds to hemoglobin, forming what we call carbaminohemoglobin.

Do any other gases also diffuse into the red blood cells. If not, why does only carbon dioxide get into the red blood cells?

The red cell membrane is highly permeable to gases because the molecules of gases are small, uncharged, and soluble in lipids, such as those of a bilayer.The effect of 4,4′-diisothiocyanato-stilbene-2,2′-disulfonate on CO2 permeability of the red blood cell membrane Remember red blood cells are  cells like any other cells only that they have hemoglobin and no nucleus. Because they have an ordinary cell membrane, it follows that the laws of diffusion which apply in gases and other cells will also apply with gases and RBCs. Oxygen is the major gas which gets into RBCs, so is carbon monoxide and others

Hi welcome to Bio.SE, and thanks for contributing an answer! We generally like to see answers contain citations or other indication of sources of support for answers. Links, pictures, etc. also enhance posts. We're trying our hardest to be better than low-quality sites like Yahoo Answers and Quora, so any effort you can make to shift your post from looking like an "unfounded" personal opinion to a well-supported claim would garner you more upvotes and reputation on our site. Please take a moment to use the "edit" button below your post to indicate research effort and some citations. Thanks!!

@Moyo Freeman , can you just explain me the paper  in brief.

@Dhruva, the paper involves inhibiting trans-membrane transport proteins (Band III or capnophorin) in RBCs and then checking if they have an effect on the movement/transport of gases across the membrane.


text:
Accessing the recombination map of Drosophila melanogaster
I'm looking for some information on the data of a recombination map of Drosophila melanogaster. In 2012, an extensive study by Comeron et al. appeared saying that they had reconstructed a recombination map for D. melanogaster. I want to access the data files themselves, and the Data Availability section of the paper included:

Estimates of recombination reported in this study are publicly
available, for any genomic region or gene in D. melanogaster, from
www.recombination.biology.uiowa.edu and www.recombinome.com.

So two websites are listed for where the data can be accessed. But neither site exists anymore. A data file can be downloaded from Comeron's work on FlyBase here. The problem is, however, this data file only seems to list crossover (CO) recombination rates in windows, but not the same thing for gene conversion (GC) recombination rates, despite both being reported separately in the paper. So this makes me think that there's a lot of supplementary files from Comeron's paper not saved here on the FlyBase page. I found another indication of the limited access there seems to be of Comeron et al.'s original files. Reading this 2019 paper which appeared to make use of Comeron et al.'s recombination map data:

The resultant D. simulans recombination map was used in parallel with
the D. melanogaster recombination map produced by Comeron et al.
(2012), downloaded from the D. melanogaster Recombination Rate
Calculator (Fiston-Lavier et al. 2010, last accessed April 19, 2019 ).

So the paper for the Recombination Rate Calculator (RCC) was published in 2010 to introduce this web tool. And when the Comeron et al study came out in 2012, the website incorporated that papers data. And that's how this 2019 paper is accessing that data, ie via the RCC website. The RCC website is old and not updated, as you can only query recombination map coordinates in Release 5 of the D. melanogaster genome. But when you do submit a query for the recombination rates of regions of the Drosophila genome to the website, you suddenly get these additional columns of information referenced back to the Comeron et al. study: minimum, maximum, and average recombination rate over the genome. This is not listed in the FlyBase file at all, and the RCC website doesn't specify if this is CO or GC recombination rates. Also, from what I can see you can't actually download the supplementary data files from the RCC website for yourself either.
So, how can I actually access the full supplementary data from Comeron et al.'s original recombination map study of Drosophila? It doesn't seem that there is any sort of full access from the sources listed in the paper, or FlyBase, or the RCC website. If any additional recombination maps have come out since and the data files are available, I'd be happy to use those as well.
EDIT: FlyBase unfortunately doesn't have additional files to those I've found. The Comeron lab also lost some info when those websites went defunct, but will attach some of the per-chromosome recombination amp files to the website in R5 and R6 coordinates.

We don’t know. Write to the authors of the paper, and if they don’t reply, try writing to FlyBase, which provides excellent professional support.

@David Thanks for the suggestion, I've sent FlyBase an email and will update if I get what I'm looking for.

Yes, the original links stopped working, apologies. I have now added a file/link in my current website with per-chromosome recombination maps in R5 and R6 coordinates.
https://comeron.lab.uiowa.edu/recombination-rates
Josep

Josep Comeron is still at the University of Iowa Biology Department, and his lab has its own website. Browsing around, I found this page on recombination rates, but no apparent way to access the data. His contact information is available on both the UIowa Biology Dept. page and his lab site, so I suggest emailing or calling him directly to see where the information you're seeking is currently available.
I tried to use the Wayback Machine to see if the data from either recombinome.com or the uiowa.edu was archived there. recombinome.com has been crawled repeatedly, but clicking on some random results from 2013-2015 only gave the main page, with no links to the raw data. www.recombination.biology.uiowa.edu was never archived.

I originally encountered the same issue trying to access those sites with the Wayback Machine unfortunately.


text:
Detrimental effects of fructose in fruit on the liver?
Fructose is mostly broken down by the liver. During this breakdown, the liver also creates fats (by the process of lipogenesis) which over time can get accumulated in the liver and give rise to nonalcoholic fatty liver disease.
Now, fruits contain fructose. So, here is my question: "Will eating lots of fruit lead to fatty liver disease?" If yes, how much fruit consumption is too much? If no, why not? What about lipogenesis, then?
I got the above information from this article by Harvard Medical School.

Moderation in all things, and all things in moderation.

There is insufficient evidence to claim that high consumption of fructose, when part of isocaloric diet (no weight gain), is a risk factor for non-alcoholic fatty liver disease (NAFLD).
Fructose Consumption, Lipogenesis, and Non-Alcoholic Fatty Liver Disease (PubMed, 2017):

...the available evidence from human epidemiological and
  interventional studies does not support the hypothesis that
  fructose, when consumed in isocaloric amounts, causes more liver fat
  accumulation than other energy-dense nutrients. The observed
  prosteatotic effect of fructose in hypercaloric trials is likely
  confounded by associated weight gain...

Effect of fructose on markers of non-alcoholic fatty liver disease (NAFLD): a systematic review and meta-analysis of controlled feeding trials (PubMed, 2014):

Isocaloric exchange of fructose for other carbohydrates does not
  induce NAFLD changes in healthy participants.

Consumption of fruits, if part of isocaloric diet, is also not likely associated with NAFLD.
No association between fruits or vegetables and non-alcoholic fatty liver disease in middle-aged men and women (PubMed, 2019):

No obesity-independent association was found between fruit or
  vegetable intake and NAFLD.

The main source of dietary fructose are probably soft drinks, not fruits, anyway:

Popular soft drinks can contain 60-70 g fructose per liter (ScienceDirect, Fig. 2).
Four apples (150 g each) contain 36 g fructose, which is more than in most other fruits (USDA.gov).

And finally, even if there is abundant evidence that fructose stimulates lipogenesis in the liver, this does not automatically mean that it stimulates the development of NAFLD (according to the first source above).

There is sufficient evidence to apply the precautionary principle, however.


text:
The correlation between a leaf's age and its length in the initial stage of growth
I am building a machine learning algorithm which predicts the age of a leaf before its maturity period based on its measured length or area. I would like to know whether there is a mathematical relation to describe this or a repository of data on this topic.

Your question is very broad. Please narrow it down to a specific issue that can be answered in a few paragraphs. Moreover, we expect you to show some research from your part.


text:
Three foramen lying in one vertical plane
In the human skull we can see that 3 foramina named as supraorbital notch(foramen) , infraorbital foramen and mental foramen share a common vertical plane.
Is there any surgical significance of for such a geometry or its just a coincidence?

Well, your cranial nerves all leave the brain just off center on both sides..

Many a times surgeons make use of geometries, so I ask the question. As far as I know all those foramen contain blood vessels too in addition to nerves.

Why pick only those three? Include all the foramen (like the foramens magnum and spinosum) and you'll see that they are oriented by function, not some forced geometric orientation.

I think you have taken it in a different way. My question does this geometry is made use by surgeons. It's made clear in the comment to theforestecologist.

@JM97 If that's what you mean, you should edit your question.

yes, edited. have a look at it.

Can you explain what you mean by "surgical significance"? They lie in roughly the same plane because humans have flat faces, and that fact might be useful. It's not clear what the question is.

I want to know whether this geometry is exploited during any surgical procedure or in craniometry.


text:
Mental Symphysis
Why dow we consider mandibular symphysis(symphysis menti) as type of Amphiarthrosis that too of symphysis variety, eventhough it lacks movement and cartilage at joint?
Why don't we consider as Synostosis (a type of synarthrosis)?

Why downvote???

What is the source saying that the mandibular symphysis is an amphiarthrosis?

All symphysis are amphiarthrosis. See https://en.wikipedia.org/wiki/Symphysis

Maybe wikipedia is wrong and/or incomplete.

No, many different sources too say so. See this: https://www.google.co.in/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwiRwqzUjvzTAhVJP48KHVO6AaQQjhwIBQ&url=http%3A%2F%2Fwww2.highlands.edu%2Facademics%2Fdivisions%2Fscipe%2Fbiology%2Ffaculty%2Fharnden%2F2121%2Fnotes%2Fart.htm&psig=AFQjCNFTkbPWP72aNKaHrWWFUht_we-hqw&ust=1495288708303622

Lots of vertebrates have unfused mandibular symphyses.

Hmm, that makes sense.


text:
Curved membrane effect

Curved Membrane effect: Movements of the  tympanic membrane are more at the periphery than at the centre where malleus is attached which provides some leverage. This is called as curved membrane effect.

I am unable to comprehend how movement is more at periphery than at centre.
Practically movement is more at the centre as can be seen from  this  .gif or from following image:
So, why it is said that movement is more at periphery?

Why down vote??

"...as seen from the gif" Is the gif not accurate in showing the curved membrane effect?

Yes, see a better picture here http://doctorlib.info/physiology/medical/medical.files/image540.jpg


text:
Why bipolar neurons in retina transfer information via graded potentials?
Why should bipolar cells prefer graded potentials to action potentials?
My attempt:
I know that graded potentials are better in processing information since stimulus is directly proportional to response generated unlike action potential where the response is always same.
Reasons:
But I don't understand its need in bipolar cells , because graded potentials  have already been generated in rods and cones. Also the final message coming out of eye is in the form of action potentials from ganglion cells. If graded potentials were of that importance then why they do stop at bipolar cells and continue as action potentials in the later pathway?
Finally, graded potentials are slower than action potentials so latter should be preferred in places like eyes where response is needed to be quick.

"where response is needed to be quick" - note that vision (in vertebrates) is actually incredibly slow.

Relatively it maybe slow but in absolute terms it's still fast. Quick response from rods help a lot in activities like fast car racing, gaming, hunting etc


text:
How urination prior to blood test may give error?

Source: Textbook of  Practical Physiology, 4th Edition

according to it urination within 30 minutes is a precollection factor that may alter the results of blood test.

I am unable to comprehend how urination could affect the blood sample. Urination will just result in excretion of urine already formed and stored in the urinary bladder, so how its loss could lead to error in blood sample?

This is new  to me and rather baffling. I can't imagine how emptying your bladder affects a blood test. The entire first section of the text is about hematology and covers the subjects in a CBC, nothing else.

Please don't post text as a picture. It's harder to read and cannot be searched.

What is being sampled from the blood?

It's just a general guideline. However we mostly do CBC.


text:
Is Ellman's reagent specific for low molecular weight proteins and thiols?
Is it still possible to quantify cystein rich low molecular weight proteins such as Metallothionein in a given sample using Ellman's reagent if the sample is contaminated with some high molecular weight proteins?

It's specific for thiols in general. If the contaminating proteins contain solvent accessible thiols, DTNB will react with them.

Doesn't even need to be a protein. People in my lab often make large polymers with some thiol modifications. The thiols are quantified with Ellman's Reagent.

@user137 Yes certainly; I confined my answer to the question.

@canadianer How can we determine if the contaminating protein contains solvent accessible thiols?

@k.shekh First of all, it should be rather trivial to purify your low molecular weight protein from the contaminating high molecular weight proteins. I think that by far would be the best solution. If for whatever reason that’s not possible and you know the identity of the contaminating proteins, you can search the literature (including primary protein sequences) for information on the cysteine content. If the identity is unknown, you would need to make the determination yourself. I have had success labelling thiols with maleimide conjugated fluorophores and then visualizing them in a gel.


text:
What is measured by electroencephalograms and local field potentials?
In the Scholarpedia article on local field potentials (2013), I read:

The current view is that EEG and LFPs are generated by synchronized
  synaptic currents arising on cortical neurons, possibly through the
  formation of dipoles (Niedermeyer and Lopes da Silva, 1998; Nunez and
  Srinivasan, 2005).

There are three things I do not understand:

What does "on neurons" mean? Why not "in" or "around neurons"?
I assume that what is measured is the electric potential in an electric field that is generated by charges (the ions). So only the changes of the measured potential are due to currents, the potential itself (at any given point in time) is only due to the distribution of charges. Is that view correct? Independent of the nature of the charges.
What exactly are the above mentioned dipoles? Of which are they formed and what is their size? (At least, the article says "possibly generated through the formation of dipoles".)

Does all this sum up to the picture that it is all and only about the ions that pass through the ligand-gated channels at a synapse and the electric field and potential generated by them, the contribution of all other charges being cancelled and filtered out?

[I give this as a sketchy answer being aware that it might be nonsense. So feel free to downvote in this case. I should have mentioned - thanks to Bryan for having remembered me - that this answer has been inspired by Buzsáki/Anastassiou/Koch's article on The origin of extracellular fields and currents and just tries to sketch the mental image this article evoked in me.]
I assume that what is actually measured by an EEG electrode is an effective dipole moment in the upper cortical layers underneath the electrode (which decays with $1/r^2$). The way this dipole moment is created by "brain currents" is the matter of this answer.
There seem to be some premises under which a measurable EEG signal (= a dipole) can be detected:

The presynaptic action potentials must arrive highly synchronized. (Additive superposition.).
The apic dendrites of the pyramidal neurons that give rise to the dipole must be vertically oriented (pointing to the skull, resp. the electrode). (Orientation of the dipole.)
The sodium potassium pumps trying to restore the rest potential are unevenly distributed, i.e. mainly located at the soma. (Breaking the symmetry.)

This is the situation for the neuron (gray) at rest:

The dipole then forms as follows in three steps:
Step 1: An presynaptic action potential releases neurotransmitters that open ligand-gated ion channels causing sodium ions to enter the neuron.

Step 2: The extra sodium ions wander quickly to the soma. This happens passively, i.e. driven by repulsion and diffusion. At the end of step 2, all ions inside the neuron are distributed approximately evenly (i.e. not giving rise to an inner dipole).

Step 3: At the soma sodium ions are pumped out of the neuron. During this step equidistribution of ions is maintained inside the neuron (still no dipole inside the neuron).

In the extracellular medium, we now have an observable dipole.
Summary: What is measured by an EEG are not directly "brain currents" but an effective dipole moment that results from three different currents on different time scales:

Ions passing the membrane of apic dendrites into the neuron. (Slow.)
A net flow of ions wandering from dendrite to soma (driven by repulsion and diffusion). (Fast.)
Ions leaving the soma, e.g. by sodium pottasium pumps. (Slow.)

I'll come and post a more researched answer; this one is mostly not nonsense, but I think you can do better if you rely on actual published work rather than conjecture. :) http://www.nature.com/nrn/journal/v13/n6/full/nrn3241.html is a good paper. Great question, though.

I read this paper, and my answer was inspired by it. I just tried to sketch my understanding, i.e. my mental picture it evoked.

Isn't it something like a miraculous accident, that the apic dendrites are arranged vertically in the topmost layers of the cortex? Otherwise we wouldn't be able to record EEGs?

And without EEGs we would know much less about the workings of our brains. Compare this to the miraculous accident of fine-tuned natural constants that guarantee a stable universe giving rise to the evolution of brains: https://en.wikipedia.org/wiki/Fine-tuned_Universe

@Bryan: I am looking forward to your answer!

Even though this image is to depict the neuronal origins of the fMRI hemodynamic response, doesn't it also depict quite well the neural origins of the EEG response:

from Scott Huettel, Neuroimaging the Aging Mind, p. 14

1) Is on neurons because here neurons are considered as population, in this case the cortical neurons.
2) Yes this point of view is correct since the electric potential is generate by charges present outside and inside of the cell. Is the movement of this charge that could generate the electric field.
3)According to wikipedia

An electric dipole is a separation of positive and negative charges.
  The simplest example of this is a pair of electric charges of equal
  magnitude but opposite sign, separated by some (usually small) distance

In this case the cortical neurons have some zone where they are positive charges and other zone where they are negatively charged give to them the propriety to be considered as dipole.
The ability to generate a potential by neurons is due by the ions that pass through the channel that could be voltage-gate (open when a specific potential is reach) or ligand-gate (active in presence of a ligand). Depending on the concentration of a specific ions found inside and outside of neurons, this ion can exit or enter the cell if the correct channel is open.
Hope this could help you.

I guess it is not the movement of the charges that generates the electric field but a) their mere presence and distribution or b) that generates the dynamics of the field.

@HansStricker yes is the distribution of the charges that determine the electric field in this case the membrane potential. The fact that after a signal the charge will be able to enter or exit from the cell, generate the potential.

Thanks for the answer, but to be honest: it didn't really help clarifying things. (E.g. I didn't ask what a dipole is, but what it is formed of.)


text:
Is co-transport within a cell active or passive transport?
ATP is used to actively transport H+ out of the cell against the concentration gradient. The H+ & sucrose cotransporter, for example, then uses this proton gradient for transport. H+ goes back into the cell with the gradient (passively) with concomitant sucrose transport across the membrane. Is this active or passive transport?

Co-transport, also called secondary active transport, is a form of active transport because it is using the energy from one concentration gradient to transport another molecule across the membrane against its concentration gradient. The concentration gradient which drives this process requires energy to set up in the first place, which is why co-transport is considered active.


text:
Do RNA modification proteins bind to specific repeats on the RNA polymerase II CTD?
The C-terminal domain (CTD) of human RNA polymerase II has 52 repeats of a similar heptapeptide sequence.
Will the RNA modification proteins only bind to some repeats at specific locations on this (e.g. the 1st repeat/the 10th repeat/the last repeat, etc), or will they bind randomly to any of the repeats?
If they bind to specific repeats, how can this specificity achieved?
If they bind to any of the repeats, then it would seem to me that several molecules of an RNA modification protein could be bound to a single RNA polymerase II CTD. Does this happen?

Part 2 last question. Lock and key is not the only mechanism for ligand recognition/binding. Induced fit models don't require fixed structures. In fact, the CTD is disordered. Also, please create separate questions for let's say protein binding, and then another for specificity. As it stands now, few would dare to undertake the monolithic task of answering this question.

What research of your own have you done to try to answer this question?

I've edited your question to clarify it a little etc. If I have changed your meaning, please say so and edit it accordingly.

@David Wikipedia

The entry in the Wikipedia article on RNA pol is just a couple of paras, and the references cited are all over ten years old. This tends to be the problem with Wikipedia — all entries are by individuals and after the first burst of enthusiasm people pass to other things and there is no incentive to maintain them. It's difficult if you haven't got access to a university library, but one needs to try harder for more recent review articles.

In attempting to answer questions about protein structure, the first port of call (which one might expect the questioner to have also visited) is the Protein Data Bank — the global repository of such structures. There one can search for RNA Polymerase II CTD, look for complexes with other proteins, find recent publications in which they are reported, and consult them to find the state of knowledge of a topic.
Knowing nothing of the protein in question, I adopted this approach, and after looking at a few proteins and a few papers the following points seemed to emerge.

The CTD has a series of 7-amino acid (heptad) repeats — in mammals 21 of these are consensus(YSPTSPS), and 31 non-consensus (K7, rather than S7).
Further heterogeneity is afforded by phosphorylation (especially) and also glycosylation and proline isomerization, together with modification of the lysine of the non-consensus repeats.
It is thought that different post-transcriptional modifications are responsible for differential activation of 5′-capping or 3′-processing enzyme activities.
The CTD is disordered (unresolved) in the crystal structure of RNA Polymerase II, indicating that in the protein itself it does not adopt a fixed structure.
There are no structures of the CTD complexed to proteins it activates, so the question cannot be answered definitively.
There are structures of proteins complexed to short peptides (10- to 19-mers) based on the repeating sequence. These suggest that the structure of CTD in the complexes may be a spiral bound by specific interactions in a groove. The spiral formation may involve hydrogen-bonded β-turn motifs. A deduced structure from one such study with a 10mer is shown, together with indications of specific protein–protein interactions.

(Phosphorylated 10mer based on CTD complexed to the conserved CTD-interacting domain of mRNA processing factors RPRD1 and 2 — Adapted from Ni et al., Nature Structural and Molecular Biology (2014) 21, 686–695)
Concluding Remarks
The question contains two invalid assumptions — that proteins that interact with the CTD should interact with a single repeat, and that repeat should have a compact structure. Nevertheless, the functionality of the repeats and whether there are multiple interactions are valid questions. It appears from discussion in the paper by Ni et al. that the interacting unit is a 24-mer that binds to a dimer of the interacting protein (CID), and they propose that for phosphatases (and I presume protein kinases)15 molecules interact with the CTD at once.
What the situation is with 5′-capping or 3′-processing enzymes is another matter. There will only be one mRNA emerging from the RNA polymerase, so multiple binding would appear to make no sense. How much of the CTD is needed as rope to attach the processing enzyme soap? Does the soap slide along the rope? One would hope that eventually such questions would be answerable by molecular visualization techniques (see e.g. this BioRxiv preprint).

The question is asking about "repeat specificity" (i.e, will the binding of a specific protein on the CTD only happen on some specific repeat, or randoms on any repeat), not the specificity of the binding to a repeat. I'm not sure whether you get this?

@jw_ David mentions that the structure of CTD complexed with its binding partners are not known (yet). In absence of this data the only way you can check specificity is by painstakingly deleting 51 repeats, while ensuring you maintain a similar conformation with the filler sequence you have entered. As you can see it is an extremely complicated thing to achieve. As such, I think this question is not likely to get a definite answer in the near future.

@RoniSaiba I just realize that every result in biology come from real experiments (tons of work)

@jw_ I live in a different time zone from you and posted without "wrapping my answer up", which I now have done. I believe it addresses your question.


text:
What are primary reasons for the failure to localise/anchor sequences in genome assemblies?
My question concerns the incorporation of individual sequence reads into chromosomes during gene sequencing projects, especially those with larger genomes such as Drosophila melanogaster or Homo sapiens.
There are some sequences or short contigs that it has not yet been possible to incorporate into the larger chromosome assemblies.
What are the reasons for this failure?

I'm going to re-interpret this question slightly to make it easier to answer:
"Why do genome assemblies frequently consist of large numbers of short contigs rather than a relatively small number of long chromosomes (or full replicons of other types)? And how could I make my assembly better?"
De novo sequence assemblies (usually) consist of a set of contiguous sequence fragments ("contigs") that have been derived from shotgun sequencing by some heuristic. If sequence assembly did a perfect job, we would expect that these contigs would be full chromosomes. Instead, what we observe is lots of sequence fragments with uncertain relationships to one another. In this common case, we think that some of the contigs could be stitched together ("localized", "anchored", "scaffolded") meaningfully into chromosomes, but we aren't sure how.
For de novo sequence assembly, there is no ground truth to compare to. So all of the information for generating assemblies comes from the starting sequences (which are usually "reads", small shreds of sequence that come off of a sequencing instrument). The heuristics that generate contigs from reads consist of finding overlaps between different starting reads and trying to extend them into the largest possible partially overlapping groups of reads, using some assumptions about rates of error in the sequence of the reads (and other variables). See wikipedia or this paper (figure inset) for a little more information on this.

It turns out that there is a body of statistical theory that governs how large these overlaps will be, and therefore how big/complete your contigs will be. This body of theory says that the size and number of contigs is predictable to some degree from the size of the genome you're trying to assemble, the length of the reads, and the number of reads you have.
Some genomes, like maize, wheat, or the human genome, are also harder to assemble because they are "repetitive". This means that there are lots of very similar sequences in different places in the genome. So when you take a read from one of these places, you are uncertain which one of these very similar regions it comes from. These repetitive regions are hard to resolve unless you have very long reads or some parallel information, so they also lead to gaps in sequence. Such regions will also tend to be "collapsed", meaning that you only have one contig representing a repeat that should actually be present as several contigs with different locations in the assembly.
Sources of parallel information that are helpful are proximity ligation (methods such as Hi-C), genetic maps from crosses, or optical mapping. These orthogonal sources of information express relationships between contigs in terms of their closeness on a chromosome. Here is a paper with more information on these topics. Recently, long read technologies such as PacBio or nanopore sequencing are starting to read through large repeats, but they are still usually not reliable enough to fully assemble even smallish genomes "telomere-to-telomere".
So, if there is a recipe for localizing/anchoring/scaffolding fragmented assemblies, here is roughly what can be done:

get more reads
get longer reads
get orthogonal information about contig placement (e.g. proximity ligation, genetic maps, a closely related assembly, etc.)

Hope that helps.