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Is death by cyanide the same as suffocation?
Reading this description of cyanide poisoning — http://indianapublicmedia.org/amomentofscience/how-cyanide-kills/ — makes me wonder if death by cyanide is equivalent to suffocation. Is it?

In suffocation or asphyxiation you are actually deprived of breathing oxygen. As a result, the arterial blood oxygen concentration decreases (hypoxemia) which is detected by the chemoreceptors of the carotid body and aortic arch. This induces a neuronal response in the medulla that increases the respiratory rate. Simply put, you get panicked. Prolonged suffocation may lead to seizures, cardiac and respiratory arrest and eventually death.
Cyanide poisoning is an example of histotoxic hypoxia resulting from tissue poisoning by $\rm CN^-$ ions. Unlike other forms of hypoxia where the concentration of oxygen is less in tissues, in cyanide poisoning, the concentration of oxygen is perfectly normal in both the extra- and intracellular fluid. It is the cell that is unable to utilize the oxygen present in/around it. As a result the arterial blood doesn't lose much oxygen during its course to the tissue as the oxygen gradient is not quite steep, resulting in an increase in the $\rm HbO_2$ concentration in the venous blood as well.
Thus your skin gets cherry red, not blue like in the case when you are deprived of breathing oxygen, which occurs due to an increase in the concentration of deoxygenated hemoglobin in the blood.
Here is what happens at the molecular level.
The $\rm CN^-$ ions diffuse into the mitochondria. They have high affinity to the ferrous ion of the mitochondrial enzyme cytochrome c oxidase involved in the electron transport chain (ETC), one of the phases of cellular respiration where $\rm ATP$ is generated from $\rm NADH$ and $\rm FADH_2$. And it is this process that actually requires oxygen. The inhibited cytochrome c oxidase is of no good in transporting electrons, thus no $\rm ATP$ molecules are generated. The oxygen molecules waiting for those electrons remain empty handed resulting in the increase in the concentration of molecular oxygen. Remember, ETC occurs in almost all living cells except a few like RBC which get their major share of ATP from the highly inefficient anaerobic glycolysis. Also, $\rm ATP$ is the energy currency of our body and is required in a wide variety of bodily processes like osmotic balance, nerve impulse transmission, muscle contraction etc. With no $\rm ATP$ your heart and respiratory muscles can't contract, your medulla can't regulate breathing, your kidneys can't concentrate urine and the list goes on. Death is imminent if a high concentration of cyanide gets into your blood.
The symptoms of panic like tachypnea and tachycardia (that result due to low oxygen in blood) are not usually seen unless the victim himself knows he is poisoned. The end effects like cardiac and respiratory arrest, seizures and coma, however, are similar to those of suffocation.
For further read:
The Mechanism of Cyanide Intoxication and its Antagonism

@mindwin it is always recommended to put citations in answers, not only to back-up claims, but also to provide sources for further reading

I'm not a doctor, so I'm not 100% sure about the physiological differences, but on a molecular level there is one:
Cyanide blocks the complex IV of the oxidative phosphorlytaion, which will directly stop cells from consuming oxygen and producing energy needed to survive. This is mechanistically different from suffocation, where there is not enough oxygen in your blood stream to sufficiently power oxidative phosphorlytaion to produce energy (meaning complex IV could work, if it just had more oxygen).
During suffocation - or low blood oxygen - the body can react to the lowered oxygen supply (by increased breathing):

In humans, hypoxia is detected by the peripheral chemoreceptors in the carotid body and aortic body, with the carotid body chemoreceptors being the major mediators of reflex responses to hypoxia. This response does not control ventilation rate at normal pO$_2$, but below normal the activity of neurons innervating these receptors increases dramatically, so much so to override the signals from central chemoreceptors in the hypothalamus, increasing pO$_2$ despite a falling pCO$_2$

The mechanism for these oxygen sensors doesn't seem to be known, so we can't be sure if cyanide would also trigger them, but I think it's rather unlikely. I would also guess that the reflex reaction to low blood oxygen (triggered by these sensors) can additionally induce panic, which would likely not happen in cyanide poisoning. Other symptoms like dizziness, which are a more direct effect of neurons shutting down (or having not enough energy) should be similar.
Edit:
The time it takes you to die is likely to be different as well. Cyanide acts fast - once it is in the cells - but depending on how you 'take' it, it could be similar to suffocation (although, you still might not directly notice the effects).


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Activation of Glycogen Synthesis by Insulin - mechanism and cellular location?
My textbook states the following...
Insulin activates enzymes that convert glucose to glycogen.
Does this conversion occur inside or outside the liver and muscle cells?
If it is inside, does the Insulin act as the primary messenger and activate an enzyme cascade that activates glycogen synthase?

What research have you done to try to find an answer to this question? Have you checked Wikipedia or Berg on NCBI Bookshelf online?

@David I researched Wikipedia and Wikibooks on the synthesis of Glycogen Synthase. It provided no results. I then did the same for Insulin and no results were produed either of significance :)

You didn't look at Berg, though, did you? Anyway, I've given a short answer to your question, leaving you to read further if necessary.

Insulin, like glucagon, binds to receptors on the surface of muscle cells and illicits a response that is transduced to produce changes of phosphorylation in the enzymes controlling glycogen turnover. Unlike glucagon it does not initiate an enzyme phosphorylation cascade, but its binding to the receptor causes autophosphorylation on tyrosine residues, resulting in protein–protein interactions which lead to the activation of various enzymes through subsequent phosphorylations.
I would recommend you go to Berg et al. in NCBI Bookshelf online — rather than Wikipedia — for this kind of thing. It is a best-selling biochemistry textbook which is produced with great care (even if the edition online is out of date). Thus in Section 21.5.2 you will find:

How is glycogen synthesis stimulated? As stated earlier, the presence of glucagon signifies the starved state and initiates glycogen breakdown while inhibiting glycogen synthesis. When blood-glucose levels are high, insulin stimulates the synthesis of glycogen by triggering a pathway that activates protein phosphatase 1 (Figure 21.20). The first step in the action of insulin is its binding to a receptor tyrosine kinase in the plasma membrane. Multiple phosphorylations again serve as the instigation for a regulatory wave of dephosphorylations. The binding of insulin to its receptor leads to the activation of an insulin-sensitive protein kinase that phosphorylates the RGl subunit of PP1 at a site different from that modified by protein kinase A. This phosphorylation leads to the association of the RGl subunit with PP1 and the glycogen molecule. The consequent dephosphorylation of glycogen synthase, phosphorylase kinase, and phosphorylase promotes glycogen synthesis and blocks its degradation.

I am assuming that you are familiar with the pathways of glycogen synthesis and breakdown. (If not, search for this in Berg et al.) At the risk of violating copyright, I reproduce Figure 21.20 below:

You can read more about the insulin receptor in Section 15.4.1 of Berg et al.
Addendum
Insulin also affects glycogen synthesis indirectly by stimulating/activating the glucose transporter, GLUT4. The mechanism by which this is accomplished is less well established than that described above.

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Definition of Cofactor, Coenzyme and Prosthetic Group
This question arises from a student multiple choice question regarding whether certain inorganic ions present in certain enzymes (Cl− in catalyse and Zn2+ in carbonic anhydrase) could be classified as coenzymes or prosthetic groups, and the poster then asked why Cl– was a cofactor for amylase but not a coenzyme.
Expanding this to the general situation, the question becomes:

What is the difference between a cofactor, a coenzyme and prosthetic
group, and where are inorganic ions in this hierarchy?

On the wikipedia page (https://en.wikipedia.org/wiki/Cofactor_(biochemistry)) a coenzyme is defined as a complex oranic cofactor, so Cl- doesn't count. Another thing that doesn't make it a coenzyme (as far as I know) is that the ion is not directly involved in the catalyzed reaction.

@VonBeche cool! Got it now. Answer that below and i'll tick it as an accepted answer. Thanks!

I have edited the question to make it more general, but retained the specific reference to chloride and amylase as other answers have addressed that.

On the wikipedia page (en.wikipedia.org/wiki/Cofactor_(biochemistry)) a coenzyme is defined as a complex organic cofactor, so Cl⁻ doesn't count. Another thing that disqualifies it as a coenzyme is that the ion is not directly involved in the catalyzed reaction. This amylase contains both a calcium ion, involved in catalysis. The chloride is speculated only to be involved in differentiation between substrates, and is absent in other structures.

Why revive a four-year old question?
Although I do not consider nomenclature of this type terribly important, and the high-scoring answer from @VonBeche is reasonable, I decided to add my own ‘answer’ for several reasons. First this is a highly active question, probably because students are required to make this sort of distinction, second because there have been several recent incorrect answers, and third because none of the answers are supported by an authoritative source (I do not regard Wikipedia as necessarily authoritative). However, perhaps the most important reason is to emphasize that, although there has been a recent attempt to produce a standard nomenclature, in actual practice there is no generally agreed terminology for cofactors.
Authority used in this answer
Biochemical nomenclature arises in a haphazard manner from new research discoveries, and only when the dust has settled, so to speak, do committees try to standardize it. I expected to find something in the International Union of Biochemistry and Molecular Biology Recommendations on Biochemical & Organic Nomenclature but those seem confined to enzyme classification. I have therefore used as a starting point ChEBI — Chemical Entities of Biological Interest. This is a “freely available dictionary of molecular entities focused on ‘small’ chemical compounds” published on the EMBL–EBI website, and is part of the ELIXIR Core Data Resources “a set of European data resources of fundamental importance to the wider life-science community and the long-term preservation of biological data”.
ChEBI Definitions of Cofactor, Coenzyme and Prosthetic Group
URL: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=23357
ChEBI Name: cofactor
ChEBI ID:  CHEBI:23357
Definition: An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
ChEBI Ontology: cofactor (CHEBI:23357) is a biochemical role (CHEBI:52206)
A number of compounds are listed as having the role of cofactor, including metal ions such as chloride and organic molecules such as NAD (sub-classified as a coenzyme, below) and FAD (subclassified as a prosthetic group, below)

URL: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:23354
ChEBI Name: coenzyme
ChEBI ID: CHEBI:23354
Definition: A low-molecular-weight, non-protein organic compound participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons.
ChEBI Ontology: coenzyme (CHEBI:23354) is a cofactor (CHEBI:23357)
A number of compounds are listed as having the role of coenzyme (ascorbic acid, coenzyme A, NAD etc.) all of which are organic compounds.

URL: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:26348
ChEBI Name:   prosthetic group
ChEBI ID: CHEBI:26348
Definition:   A tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity.
ChEBI Ontology: prosthetic group (CHEBI:26348) is a cofactor (CHEBI:23357)
A number of compounds are listed as having the role of prosthetic groups (e.g. FAD, haem lipoic acid), but none of them are simple metal ions although they are not exclusively organic (e.g. metal-sulphur clusters).
Ontological interpretation and comparison with Wikipedia Entry
The ChEBI entry on ‘Cofactor’ reproduces the opening paragraph of the Wikipedia page on the subject, relevant sections of which I quote below:

A cofactor is a non-protein chemical compound or metallic ion that is
required for an enzyme's activity as a catalyst.
Cofactors can be divided into two types: inorganic ions and complex
organic molecules called coenzymes.
Coenzymes are further divided into two types. The first is called a
“prosthetic group”, which consists of a coenzyme that is tightly or
even covalently, and permanently bound to a protein. The second type
of coenzymes are called “cosubstrates”, and are transiently bound to
the protein. Cosubstrates may be released from a protein at some
point, and then rebind later.

However, the nature of Wikipedia (anyone can edit it) is such that further down the page under the section on Classification, the following appears:

Cofactors can be divided into two major groups: organic cofactors,
such as flavin or haem; and inorganic cofactors, such as the metal
ions Mg2+, Cu+, Mn2+ and iron-sulphur clusters.
Organic cofactors are sometimes further divided into coenzymes and
prosthetic groups.

The section then goes on to say:

[Bryce 1979] noted the confusion in the literature and the essentially
arbitrary distinction made between prosthetic groups and coenzymes
group and proposed…
…cofactors were defined as an additional substance apart from protein
and substrate that is required for enzyme activity and a prosthetic
group as a substance that undergoes its whole catalytic cycle attached
to a single enzyme molecule.
However, the author could not arrive at a single all-encompassing
definition of a “coenzyme” and proposed that this term be dropped from
use in the literature.

Thus, it would seem that there are (at least) four different ways of classifying cofactors. That from ChEBI does not differ greatly from the second Wikipedia scheme (rather than the one it quotes), but the first Wikipedia scheme — distinguishing between coenzymes and prosthetic groups — certainly does.

Bryce’s suggestion to discard the term coenzyme has not been adopted, but his critique of the general nomenclature is a warning against dogmatism in this area. “Fools rush in where angels fear to tread.”

Nice one David, I think this adds considerably to the answers already posted. I second the emphasis on your phrase Biochemical nomenclature arises in a haphazard manner from new research discoveries, and only when the dust has settled, so to speak, do committees try to standardize it. Exam questions and answers are sometimes woeful when it comes to science, especially (i) in fields where strict nomenclature is not a practical way of life, or (ii) in fields where expertise aids in intelligibility of ambiguous terms, or (iii) within frontier research, where clear pictures haven't yet emerged.

Complex enzymes are made up of protein and nonprotein components. The protein part of the enzyme is called Apoenzymes or Apozyme. While the non-protein part of the enzyme is called Cofactor.
Cofactors are two types based on their chemical properties such as…..

Metal cofactors (inorganic compounds)- Metalloenzymes (Metallozymes) and Metal-activated enzymes

Organic cofactors – Coenzymes and Prosthetic groups

Read more here about the major difference between cofactors and Coenzymes.

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Pharmacokinetics and cell-membrane permeability of Adenosine triphosphate disodium hydrate
【My Question】
(1) Please tell me the pharmacokinetics of this ATP (or Adenosine triphosphate disodium hydrate) when it is administered orally or intravenously. In particular, Does this material has permeability to the Blood-Brain Barrier?
(2) When human cells (for example, fibroblast, MSC,…,) are cultured in a medium supplemented with this material, how much ATP is taken into the cells. (Please tell me about the cell-membrane permeability of this material.)
The known effects of Adenosine triphosphate disodium hydrate are as described below.
【Effects of this medicine】
This medicine increases the blood flow by its vasodilatory effect and activates the metabolism of the body to improves the functions of the organs.
It is usually used to improve symptoms accompanied by aftereffects from head injury; to treat heart failure or chronic gastritis associated with dysfunction of the digestive tract, Meniere's disease, dizziness based on inner ear disorder; to stabilize the accommodative function in accommodative asthenopia.
【References】
http://www.rad-ar.or.jp/siori/english/kekka.cgi?n=1808#
P.S.
P.S. I'm not very good at English, so I'm sorry if I have some impolite or unclear expressions. I welcome any corrections and English review. (You can edit my question and description to improve them)

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Direction of translation/transcription
Perhaps it would not be wrong to say that "translation/transcription goes in the direction of 3' to 5'" or "in the direction of 5' to 3'";that's because these statements are ambiguous, not specifying "XX's".
However, I am confused.
So I would like to clarify by clarifying the "XX's".
My Question;

Are the following understanding correct?

(1) Transcription;
In the case of transcription, the RNA polymerase moves in the 3'→5' direction of the template strand of genome DNA, and the ribonucleotide attaches to the 3' side of the mRNA during synthesis, am I right?
(2) Translation;
In the case of translation, the ribosome moves (relatively) in the 5'→3' direction of the mRNA, and the amino acids are attached to the C-terminal side of the polypeptide, am I right?
(3) Overall;
The genetic code is "the sequence of the complementary strand of genomic DNA read in the 5'→3' direction, with T replaced by U". For example, if the sequence of the complementary strand of the genomic DNA is "5'-ATGTTT...termination codon-3'", the corresponding sequence of the mRNA is "5'-AUGUUU...termination codon-3'", which is "N-terminal - methionine - phenylalanine ...C-terminal" sequence.

The genetic code is a cypher: ATG=Met, UUU=Phe etc and nothing else. See the Wikipedia entry. I am sure the direction of transcription and translation are illustrated in the answers to other questions on this site. Please check. If not try Wikipedia or Berg online at NCBI bookshelf. Happy reading!

AUG, to be consistent  with UUU. The genetic code is a table of mRNA codon / amino acid equivalents, so U. However because one is usually doing conceptual translations of DNA in genomic sequences then one talks about ATG and TTT.

What I want to focus on is the direction of enzymes and synthesis.


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When does the Cas9 nuclease stop?
If I understand correctly, the steps of gene editing with CRISPR-Cas9 are roughly as follows

Cas9 nuclease and guide RNA form a complex.
Cas9+guide RNA complex scans genomic DNA and recognizes the sequences homologous to the guide RNA
Induces a double strand break in DNA upstream of the PAM sequence (only breaks when the homologous sequence of the guide RNA is in the vicinity of the PAM).
Genetic modification using the mechanism of DNA repair (NHEJ, HDR) after double-strand break.

If so, in the gene editing with CRISPR-Cas9 , gene editing is likely to continue as long as the Cas9 does not lose its activity, am I right?
My question

When does the Cas lose its activity?
What was the logic of the experiment that identified the timing? / If the matter itself is unexplored, what kind of experiments could be done to find out the timing when the Cas lose its activity?

As this movie shows, if the gene editing occurs successfully, it will indeed introduce a mutation in the target gene.
However, even if it does,-this is just my guess from here on out- it is likely to remain complementary to the target gene, at least upstream of the guide RNA. However, even if the target gene is mutated, there is likely to remain complementary sequence to the guide RNA, at least upstream of the mutation. So, even if one successful gene edit is completed, I think it's possible that gene editing could happen again in the same location. Moreover, even if the targeted site is successfully edited, there is still the possibility of subsequent off-target editing elsewhere. That's why I think the tools exist to stop CAS.

A guide RNA binds to the target gene that has been bitten by CAS. The strand opposite the strand to which the guide RNA was bound has just been cleaved.
Quoted from this video.
An idea for an experiment to detect when CAS goes quiet
If a single cell colony was created from a gene-edited population and there was genetic variation in the cells born from that colony, then I think that would mean that there would have been Cas9 activity even after the single cell colony was started in culture. Is this idea correct? Could there be a smarter experiment?

Once the cut is made and DNA of interest is inserted will the guide RNA have the same template to bind to?

@ Roni Saiba   Thanks for your comment. Is your answer that the target gene in the template after editing is no longer able to bind to the guide RNA　by mutation occurred on the template side?
But even if mutation does occur, can the guide RNAs still bind to the target gene? The ability to bind may be weakened, but it may still be possible to bind.　Otherwise, there would be no such thing as "Cas that can be deactivated by light" or "a peptide to stop Cas9".

Perhaps the more Chunked downed question might be to create an assay to compare "which method of stopping is more certain to stop the CAS".　If I look for a paper on the means to stop CAS, perhaps I will find the answer to this question. Because such experiments would be necessary to clarify whether peptides or the light (Written in Japanese) can really stop CAS.

the deactivation mechanisms may also have been placed to stop off target activity after the job at the primary site is done. But I am in pure speculation territory now. I'll add an answer if I find enough material with references to convince myself of the mechanism.

@ Roni Saiba Thank you for your help. Maybe the extent of the subsequent CAS rampage may vary depending on what part of the target gene the mutation enters. If I understand it correctly, the way the mutation occurs is a matter of probability. So I think this variation in probability should be taken into account in order to "identify when the CAS will become docile."

Regarding the loss of Cas9 activity, you are already touching on the answer in your question. Cas9 as a nuclease/enzyme is always active, and will continue to cleave double-stranded DNA as long as there are complementary target sites and guide RNAs to guide it there. If the target site is not mutated or completely removed after cleavage, Cas9 can indeed cleave the same site again.

However, even if the target gene is mutated, there is likely to remain complementary sequence to the guide RNA, at least upstream of the mutation.

I'm not sure if I misunderstand the point you are trying to make here, but the introduction of mutations is usually enough to prevent recurrent cleavage of the same site (although studies of off-target effects clearly show that this is not always the case):
Both Streptococcus pyogenes and Staphylococcus aureus Cas9 cleave their target sites between positions -3 and -4, counting from the end of the 20-nt guide sequence (see attached figure below). The double-stranded break can then be repaired either via non-homologous end joining (NHEJ), or via template-driven homologous recombination (HR).

In the former case (NHEJ), double-stranded breaks are sometimes repaired with small errors. These errors usually accumulate near the break site (read about NHEJ to understand why), and such mutations will typically destroy the gRNA recognition site. Note, however, that not all (in fact, very few) NHEJ repair events will result in the introduction of mutations, and "perfectly repaired" breaks both can and will be re-cleaved by Cas9. But since repeated cleavage is lethal to the cell, there is a selective advantage for mutations that prevent re-cleavage of a target site. Also note that the introduction of mutations (and thereby gene editing) via NHEJ is a random process, with no direct control by the researcher.
In the latter case (HR), the DNA template used for repairing the double-stranded break can typically be chosen by the researcher. It can for example be a chemically synthesized DNA fragment or PCR product with at least some sequence homology to regions flanking the cleavage site. But since there is no specific sequence requirement for the region in between the homology regions, this interspacing region can be designed such that it partly or completely replaces the original recognition and/or PAM sequence (violet region in figure below).

Thank you for your answer. I have confused two independent issues; "CAS's own activity" and "Once altered, can other target-genes be altered twice"? I understood the latter one, thanks to your answer. But, I think the first one is still not clear; for example, how many times does it take for a cell to divide to make the CAS docile? How can we measure the 'activity of CAS itself' at a given point in time?

When you write CAS (in capital letters), are you referring to Cas9?

It's not clear to me what you're after with your first question. In what setting do you expect Cas9 to lose activity? Are Cas9 and gRNAs expressed or introduced into the cell via transfection/transformation? Like I tried to point out above, Cas9 itself doesn't lose its activity, and loss of DNA cleavage activity therefore boils down to knowing how long Cas9 and/or gRNAs exist inside the cell, i.e., their "lifetime" or half-life. Bacterial proteins are often very stable in eukaryotic cells and are not actively degraded, but I'm not sure if this is also the case for Cas9.

Sorry the CAS means the Cas9.

To be exact, certainly that depends on how we get Cas9 into the cell . If the Cas9+gRNA complex itself is introduced into the cell, the problem is how long does it takes for all Cas9 to lose its activity from the point of introduction them into the cell. Perhaps it would be more reasonable to use a half-life, as it is difficult to say "the time until everything loses its activity". If you are using a vector expressing Cas9, then all Cas9 will not lose their activity until the last born Cas9 loses its activity.

More important thing is my second of question. It is important to know what experiments are needed to determine "when Cas9 loses its activity" in a given system.　In other words, there are several assays of Cas9 or its analogues (henceforth collectively referred to as CAS) that have been engineered to artificially stop its activity, but how do they prove that CAS has indeed lost its activity?

I see. I will leave it to someone else to properly respond your question, but this sounds like an in vitro rather than an in vivo assay. See for example one of the very first papers by Doudna and Charpentier. A similar assay could be used to demonstrate inhibition of enzymatic activity.

@gaspanic Can you give me a reference of the 'Bacterial proteins are often very stable in eukaryotic cells and are not actively degraded'. It will be helpful for designing future assays.

@RoniSaiba sorry, this is more based on personal experience and communication, so I should probably correct myself by saying sometimes rather than often. But there are techniques for regulating the half-life of proteins via degrons, take a look at the N-end rule for example.

@gaspanic Thank you.


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What is the function of E. coli bacteria in the human gut?
What is the function of the bacterium, E. coli, in the human gut?
I have tried to find the answer by searching the Internet (e.g. here), but have been unsuccesful.

Nonpathogenic E. coli strains are a component of the gut microbiome of humans and many other organisms.
They are commensals, meaning that when they remain in the areas they have evolved to live in, and when they do not acquire virulence factors, they are benign. They live in our digestive tract and basically do nothing to harm us.
In fact, commensal microorganisms like E. coli can be considered part of the innate immune systems of their multicellular hosts. They take up space on the surfaces of the intestines and prevent colonization by pathogens.
Along with the endothelial cells and mucous, commensals form the barrier defenses that are the first line of protection against pathogenic organisms. Basically they are the good neighbors that don't cause problems and they don't leave space for bad neighbors to move in.
Problems can occur if they gain access to areas that are normally sterile. If the intestine is perforated and E. coli gain access to the thoracic cavity, they can become an opportunistic pathogen, as they will not be interacting with the host in a way that can control their proliferation. They can also come in contact with cells that are not expressing the necessary proteins to protect them from E. coli.
You can also end up with the situation where a pathogenic bacteria or a bacteriophage carrying a virulence factor can transfer that virulence factor to the commensal E. coli, turning them pathogenic.
But, for the most part, E. coli are there to take up space that could otherwise be colonized by harmful bacteria.

Commensal bacteria can produce usable metabolites, but I was unclear as to whether or not E.coli specifically provided any symbiotic benefit to the host or if they were simple commensal, space filling organisms.

Some relevant research has been published in the time since this question was asked and initially answered.
The label "commensal E. coli" encompasses a diverse group of strains. Different strains of E. coli, each isolated from the microbiota of healthy mice, have been shown to elicit different immunopathological responses after gnotobiotic colonization.1 Generally, strain-level differences in pathogenic potential are attributed to the carriage and expression of virulence factors 2,3, many of which are mobilizable.4,5 However, I find classifications that rely on the presence/absence of genes to be oversimplified and anthropocentric, and I favor a presentation of E. coli as a genetically and metabolically versatile organism whose activity in the gut is a function of the evolutionary balancing of inter-species interactions with fitness in the intestinal niche.6,7,8

References

Kittana H, Gomes-Neto JC, Heck K, Geis AL, Segura Muñoz RR, Cody LA, Schmaltz RJ, Bindels LB, Sinha R, Hostetter JM, Benson AK, Ramer-Tait AE. Commensal Escherichia coli Strains Can Promote Intestinal Inflammation via Differential Interleukin-6 Production. Front Immunol. 2018 Oct 9;9:2318.
Stromberg ZR, Van Goor A, Redweik GAJ, Wymore Brand MJ, Wannemuehler MJ, Mellata M. Pathogenic and non-pathogenic Escherichia coli colonization and host inflammatory response in a defined microbiota mouse model. Dis Model Mech. 2018 Nov 16;11(11):dmm035063.
Sarowska J, Futoma-Koloch B, Jama-Kmiecik A, Frej-Madrzak M, Ksiazczyk M, Bugla-Ploskonska G, Choroszy-Krol I. Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports. Gut Pathog. 2019 Feb 21;11:10.
Proença JT, Barral DC, Gordo I. Commensal-to-pathogen transition: One-single transposon insertion results in two pathoadaptive traits in Escherichia coli -macrophage interaction. Sci Rep. 2017 Jul 3;7(1):4504.
Desvaux M, Dalmasso G, Beyrouthy R, Barnich N, Delmas J, Bonnet R. Pathogenicity Factors of Genomic Islands in Intestinal and Extraintestinal Escherichia coli. Front Microbiol. 2020 Sep 25;11:2065.
Le Gall T, Clermont O, Gouriou S, Picard B, Nassif X, Denamur E, Tenaillon O. Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains. Mol Biol Evol. 2007 Nov;24(11):2373-84.
Barroso-Batista J, Pedro MF, Sales-Dias J, Pinto CJG, Thompson JA, Pereira H, Demengeot J, Gordo I, Xavier KB. Specific Eco-evolutionary Contexts in the Mouse Gut Reveal Escherichia coli Metabolic Versatility. Curr Biol. 2020 Mar 23;30(6):1049-1062.e7.
Braz VS, Melchior K, Moreira CG. Escherichia coli as a Multifaceted Pathogenic and Versatile Bacterium. Front Cell Infect Microbiol. 2020 Dec 21;10:548492.

E. coli do not serve a human function but live inside our digestive system because our bodies can't prevent bacteria like them from living there.  They live there because they can prosper and reproduce there.  Most strains of E. coli do not cause problems for us, and by being part of the normal bacterial population in our gut they out-compete other, potentially more harmful bacteria and keep them suppressed.  E. coli mainly live in the large intestine, not the stomach.

This is partially incorrect. In addition to regulating the intestinal flora (out competing more harmful bacteria), E. coli play a symbiotic role in the metabolism of carbohydrates and vitamin K


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Why is an A-U bond less stable than an A-T bond?
I have encountered the following fact many times, but have not yet encountered a possible explanation for it. Will you please help me understand the molecular mechanism by which the bond between Adenine and Thymine is more stable than the bond between Adenine and Uracil?
Thanks in advance

Can you add details? Please indicate where you encountered this fact. AU and AT bond comparison in what: Are both DNA, or RNA?

Also have a look at this http://www.ncbi.nlm.nih.gov/pubmed/15977281

I was not previously aware of this assertion, but on doing a little searching found it discussed in the following paper (I'm not sure whether it is open access or not).

Kamya PR and Muchall HM  (2011) "Revisiting the effects of sequence and structure on the hydrogen bonding and π-stacking interactions in nucleic acids" J Phys Chem A. vol 115 pp. 12800-8

From this it emerges that the claim relates to the effect of substituting U for T in DNA, and the paper references previous claims for a stronger AT hydrogen bond. It also references other studies which did not find any difference, so the question was/is contentious. All studies were made on particular stretches of DNA duplex, and the authors' own studies were on a wider range of duplex structures from the protein data bank and (apparently) used more sophisticated analysis. To quote, they concluded:

"H-bonding in AT can be stronger or weaker than that in AU base pairs, depending on the particular choice of nucleic acids used for comparison"

They explain this in terms of the influence of neighbouring bases in the duplex on base stacking, which, depending on the bases (i.e. the sequence), can be enhanced by interactions with the methyl group of T. (There may also be other effects caused by distortion of the base-pairs from planarity in particular cases.) So it would appear that AT base-pairs are not intrinsically stronger than AU base-pairs, but can be stronger in certain three-dimensional contexts.
As a generalization, the premise of the question would therefore appear to be false.


text:
Why are there only 6 molecules of water produced in the synthesis of the fatty acid, palmitate?
The equation for biosynthesis is
1 Acetyl-CoA + 7 Malonyl-CoA + 14 NADPH + 14H+ -> Palmitate + 7 CO2 + 14 NADP+ + 8HS-CoA + 6 H2O
I really don't understand how there is only 6 H2O produced... and not 7?
Every cycle, there is the condensation of one molecule of water.
The first turn yields a 4 carbon molecules. Since palmitate is a 16C fatty acid, and two carbons are added each turn, there should be 6 turns remaining, for a total of 7 turn.
All the other numbers seem right. At first I thought my teacher could have made a mistake but everywhere I look on the net, it say 6 H2O.
Someone has an explanation for this?
Thank you :)
Edit: I found the answer in Voet & Voet yesterday. I add it here in case it can help someone else!
At the end of the biosynthesis, the palmitate is bonded with the Acyl-Carrier Protein (ACP) and it takes an hydrolysis to separate it, hence the missing H2O.

instead of using the biochemical names, use the chemical formulas and write out the balanced chemical equation. Ex. palmitic acid is C16H32O2. Etc.

I didn't think it was relevant since it didn't seem to be a matter of balancing formulas.
I found the answer in Voet & Voet, edited the original post to add it.

I found the answer in Voet & Voet yesterday.
At the end of the biosynthesis, the palmitate is bonded with the Acyl-Carrier Protein (ACP) and it takes an hydrolysis to separate it, hence the missing H2O.


text:
How are probes in capture sequencing synthesized?
In capture sequencing it is common practice to use a panel containing ~10,000 probes. How are these DNA molecules synthesized? I imagine that there is a way to do this in parallel, but I haven't been able to find a reference to this.

Yes, the oligos are synthesized in parallel on a microchip (or microarray). This is commonly based on phosphoramidite chemistry. Various methods can be used to control which areas of the chip are open to attachment of a new nucleotide, including "light control, electochemical, and inkjet printing methods."


text:
What is the effect of temperature and carbon dioxide on the opening and closing of stomata?
I am teaching biology in an academy. The question which I had asked above had been raised by on of my students. I tried my level best to search out the answer to this question but I could not find the answer. I had read a number of answers to different questions from this website. So that's why I thought to Post my question on your website

I like the reference book Plant Physiological Ecology for stuff like this. I know one of the authors is Thijs Pons.
When temperatures become high, plants may close the stomata to conserve moisture. When the stomata are open, usually in daylight hours, the open stomata allow $CO_2$ to enter the leaf. This carbon is needed to form glucose and many other products a plant makes from photosynthesis. Most plants will not open the stomata in the absence of light.
(I use the above text as the reference. I can't give you pages right now, but I was reading this a couple of days ago.)


text:
Comparative effectiveness of antibiotics against colonies and growing bacteria
Appropriate antibiotics usually eliminate bacteria. However are the same antibiotics as effective against bacteria that have grown to form a colony?

I'm not entirely sure what you're asking, but some bacteria can form structures called biofilms, which often allow them to resist concentrations of antibiotics that are normally fatal to individual bacteria.

Usually, if there is a need to take antibiotics, it means there are multiple colonies of bacteria already in the body and as such the express purpose of taking antibiotics is to destroy those colonies.

I have rewritten the title and question, based on the accepted  answer. I am not a bacteriologist so, if necessary, perhaps @WYSIWYG might need to make further modifications.

It depends on the kind of antibiotic. Some antibiotic are bacteriostatic  i.e. they primarily stop the growth while some are bactericidal i.e. they kill the living bacterial cells. Some antibiotics can have mixed effects. Bacteriostatic antibiotics would not be very efficient in eliminating a colony.
Apart from the mechanism of action, there can be other factors that would dictate the efficacy of the antibiotic; these can all be considered under pharmacokinetics/pharmacodynamics:

Degradation/clearance rate of antibiotic
Rate of diffusion of antibiotic inside the bacterial colony (this rate would be less when the cells are inside a big colony compared to when they are disperse).
Community organization and dynamics inside the colony (like user137 said in their comment, certain biofilms can be more resistant to antibiotics)

can bacteriostatic antibiotics kill individual organisms?

@OneFace Eventually because the organisms won't be able to grow, but not directly.


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Does N1-methyl-pseudouridine occur naturally in any RNA?
Pseudouridine occurs naturally in some RNAs. But what about the methylated variant of it, N1-methyl-pseudouridine? The latter is a key ingredient in both the Pfizer and Moderna Covid-19 vaccines, probably due to its relative "potency" in evading immunogenicity to exogenous mRNA itself and its ability to apparently put ribosomes in a sort of "overdrive". (It's use in mRNA therapeutics has been patented by Moderna in 2012 or so.)
Does N1-methyl-pseudouridine occur naturally, in particular, does it occur in RNA?

N1-methyl-pseudouridine occurs naturally in the tRNAs of most archaea. It replaces the ribothymidine found in the TΨC-loop of eubacterial and eukaryotic tRNAs.

Although the enzyme responsible for the conversion of uridine to pseudouridine has been known for some time, it is only relatively recently (2012) that the gene for the methylation of the pseudouridine was reported in a paper, the introduction to which provides a useful background to the topic.
Original References
Pang, H. et al. (1962) J.Biol.Chem. 257 3589-3593
Gupta, R. (1964) J.Biol.Chem. 259 9461-9471

These articles claim it occurs naturally:
Pederson, A layperson encounter, on the “modified” RNA world:

Ironically as to my friend’s concern, N1-methylpseudouridine also occurs naturally (11), a final element in my “case” to him.

N1-Methylpseudouridine substitution enhances the performance of synthetic mRNA switches in cells:

Lastly, as a naturally existing modified base in both prokaryotic (37) and eukaryotic cells (38), our findings imply that m1Ψ might play unique roles in cells.

Both are referencing this paper:

R. C. Brand, J. Klootwijk, R. J. Planta, B. E. H. Maden, Biosynthesis of a hypermodified nucleotide in Saccharomyces carlsbergensis 17S and HeLa-cell 18S ribosomal ribonucleic acid. Biochem. J. 169, 71–77 (1978).

which finds 1-methylpseudouridine in the ribosomal RNA of yeast and human-descended HeLa cells.  (However, if I understand correctly, this is only a precursor molecule that exists temporarily and is then modified further?)
This one is a little more detailed:
Morais The Critical Contribution of Pseudouridine to mRNA COVID-19 Vaccines

One N1-modified Ψ-derivative is N1-methyl-Ψ, a naturally occurring modification found in 18S rRNA (Brand et al., 1978) and tRNA in many organisms (Boccaletto et al., 2018). This N1-methylation is catalyzed by N1-specific Ψ methyltransferase Nep1 found in archaea and eukaryotes (Wurm et al., 2010) (Figure 1). Potentially N1-methyl-Ψ could be more widespread than reported in human RNA, given that the current standard Ψ-detection (-seq) methods, which rely on the use of CMC-modification followed by primer extension (Morais et al., 2021), may not be able to distinguish N1-methyl-Ψ from Ψ (Svitkin et al., 2017). Possibly, therefore, some Ψs thus identified so far (Schwartz et al., 2014) could actually be N1-methylated Ψs.

The Boccaletto reference is presumably this database entry:
which says

Found in phylogeny    Archaea, Eukaryota
Found naturally in RNA types  rRNA, tRNA

and Naturally occurring modified ribonucleosides shows Euler diagrams of m1Ψ occurring in

Archaea tRNA
Eukarya rRNA
but not in mRNA or ncRNA


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Fate of GTP produced in the TCA cycle
As someone already mentioned in one of the following questions, the TCA circuit generates GTP in addition to NADH and FADH2.　The fate of NADH and FADH2 is clear: they are used to pump protons in the electron transfer system.
Why is GTP, not ATP, produced in Gluconeogenesis & TCA Cycle?
However, the fate of GTP seems less clearly described. I have seen a weak statement that "1 mol of GTP can produce 1 mol of ATP," but I do not know when, where, what, and how the energy of GTP is diverted to the production of ATP.
So.

My question;
When, where, what and how GTP generated in the TCA circuit is used to generate ATP

There are direct enyzme-catalyzed pathways for reversible conversions among nucleoside diphosphates and triphosphates, via nucleoside-diphosphate kinases. See also https://archive.org/details/biochemistry200100jere/page/476/mode/2up (link to Berg's Biochemistry from that Wikipedia page).
Note that all of the triphosphates are used for some things in the cell, RNA synthesis in particular, so it's necessary for the cell to be able to generate them all.


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Where is the source of H+ in the matrix that will be pumped during the electron transfer system?　Where does the OH generated at that time go?
In the electron transfer system, it has been mentioned in prior questions that complexes I, III, and IV are proton pumps and that these pumps pump protons from the matrix into the intermembrane space.

Does the formation of water inside the mitochondrial matrix help contribute to the proton gradient during the electron transport chain?
Electron Transport Chain Proton Pumping into the Intermembrane Space
How many protons are pumped out per pair of electrons from NADH in oxidative phosphorylation?

My question.

However, where are the protons in the matrix supplied from?
In other words, where does the OH- generated when the protons are generated in the matrix disappear?
Why is it not biased to the alkaline side to the extreme even though the number of proton is decreasing rapidly due to being pumped out or used to dispose of surplus electrons?

In particular, it seems that the Protons in the matrix are used to dispose of surplus electrons in the electron transfer system by combining with externally introduced O2 to produce H2O, but this seems to result in too much OH-. I would like to know the fate of the excess alkali.
See also,
https://bio.libretexts.org/Courses/University_of_California_Davis/BIS_105%3A__Biomolecules_and_Metabolism_%28Murphy%29/Electron_Transport_System

What "H2" are you referring to? Are you familiar with pH and dissociation of water into OH- and H+ (or H3O+)?

That typ. You're right, it's a proton.

I know that there exists a chemical equilibrium in which the ionization product is constant. Both H+ and OH- should be produced in the process. And if the H+ produced is pumped out, the OH will be left behind.
The protons may be used to dispose of the excess electrons, but in that case they will combine with externally introduced O2 instead of OH-. So there is even more OH- left over.
In the process, it is likely that there will be more and more OH- only.

I'm a bit unclear which part it is you're exactly trying to understand...is it that you're wondering where the "H+" comes from that combines with O2 to make H2O? Or are you wondering about the H+ pumped through the membrane?

Fate? Nothing. There is nothing in chemistry, thermodynamics or  Nature that says a cellular compartment cannot have a particular non-neutral pH. It remains alkaline until the pH gradient is used to make ATP.


text:
Water-soluble vitamins involved in amino acid metabolism in the citric acid cycle
I have never seen anything comprehensively written about the vitamins necessary to metabolize amino acids through the citric acid cycle and gluconeogenesis pathway other than the following diagram written in Japanese. (I added the English translation) The source for this was created by a Japanese health food manufacturer(https://www.orthomolecular.jp/nutrition/vitamin_b/), so it's not completely reliable, but I'm looking for a well-organized diagram like this one.

The abbreviations for vitamins are as follows. However, the active forms of the vitamins are not distinguished, for example, TPP is vitamin B1, FAD is vitamin B2, NAD+ and NADPH are Niacin.

B1: Vitamin B1
B2: Vitamin B2
N: Niacin (vitamin B3)
P: Pantothenic acid (vitamin B5)
B6: Vitamin B6
Bio: Biotin (Vitamin B7)
F: Folic acid (Vitamin B9)
B12: Vitamin B12
C: Vitamin C

The above figure may be summarized as sentences as follows;

(1)Enter the citric acid cycle via pyruvate : Gly, Ala, Cys, Ser, Thr, Trp

Glycine becomes alanine, cysteine, serine, or threonine with the help of folic acid.
Alanine, cysteine, serine, and threonine are converted to pyruvate with the assistance of niacin and vitamin B6.
Vitamins required for the process of converting the Tryptophan into Pyruvate are not mentioned in the figure.
For(1), this is also written only in the Japanese Wikipedia, but since chemical formulas are universal, I give it as a reference.(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%82%A2%E3%83%A9%E3%83%8B%E3%83%B3%E3%80%81%E3%82%B0%E3%83%AA%E3%82%B7%E3%83%B3%E3%80%81%E3%82%B7%E3%82%B9%E3%83%86%E3%82%A4%E3%83%B3%E3%80%81%E3%82%BB%E3%83%AA%E3%83%B3%E3%80%81%E3%83%88%E3%83%AC%E3%82%AA%E3%83%8B%E3%83%B3)

(2)Enter the citric acid cycle via α-ketoglutarate : Gln, Arg, His, Pro,Glu

Glutamine, arginine, histidine, and proline are converted to glutamic acid with the help of niacin, vitamin B2, vitamin B6, and folic acid.
Glutamate is converted to α-ketoglutarate with the help of vitamin B6 and niacin.
For(2),this is also written only in the Japanese Wikipedia, but since chemical formulas are universal, I give it as a reference.(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%82%A2%E3%83%AB%E3%82%AE%E3%83%8B%E3%83%B3%E3%80%81%E3%82%B0%E3%83%AB%E3%82%BF%E3%83%9F%E3%83%B3%E3%80%81%E3%82%B0%E3%83%AB%E3%82%BF%E3%83%9F%E3%83%B3%E9%85%B8%E3%80%81%E3%83%92%E3%82%B9%E3%83%81%E3%82%B8%E3%83%B3%E3%80%81%E3%83%97%E3%83%AD%E3%83%AA%E3%83%B3)

(3)Enter the citric acid cycle via succinyl-CoA: Met, Ile, Val

Methionine is converted to succinyl-CoA with the assistance of F, B12, P, and N.
Isoleucine and valine are converted to succinyl-CoA with the assistance of N and B1.
For(3),this is also written only in the Japanese Wikipedia, but since chemical formulas are universal, I give it as a reference
For the methionine:
(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%83%A1%E3%83%81%E3%82%AA%E3%83%8B%E3%83%B3)

For the Isoleucine and Valine:(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%82%A4%E3%82%BD%E3%83%AD%E3%82%A4%E3%82%B7%E3%83%B3%E3%81%A8%E3%83%90%E3%83%AA%E3%83%B3)

(4) Enters the citric acid cycle via fumaric acid :Phe, Tyr

Phenylalanine is converted to tyrosine with the assistance of N.
Tyrosine is converted to fumaric acid without the need for special vitamin support.
For (4),this is also written only in the Japanese Wikipedia, but since chemical formulas are universal, I give it as a reference;
(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%83%95%E3%82%A7%E3%83%8B%E3%83%AB%E3%82%A2%E3%83%A9%E3%83%8B%E3%83%B3%E3%80%81%E3%83%81%E3%83%AD%E3%82%B7%E3%83%B3)

(5) Directly to oxaloacetate: Asp, Asn

Asparagine and aspartic acid transfer to each other without the aid of specific vitamins.
Aspartic acid is converted to oxaloacetate with the help of vitamin B6
For(5),this is also written only in the Japanese Wikipedia, but since chemical formulas are universal, I give it as a reference;(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%82%A2%E3%82%B9%E3%83%91%E3%83%A9%E3%82%AE%E3%83%B3%E3%80%81%E3%82%A2%E3%82%B9%E3%83%91%E3%83%A9%E3%82%AE%E3%83%B3%E9%85%B8)

(6) Enters the citric acid cycle as acetyl-CoA  (i.e., as a “ketogenic amino acid”)
Ketogenic only :leucine, lysine
Also glucogenic: isoleucine, tyrosine, phenylalanine, tryptophan, threonine

Tryptophan and lysine are converted to acetyl-CoA with the help of B2, P, N, and B6.
Of those exclusively ketogenic, it is not written about what vitamins are needed in the process of converting leucine to acetyl-CoA.
Of those that are also glucogenic, it is not written about what vitamins are required in the process of converting isoleucine, tyrosine, phenylalanine, and threonine to acetyl-CoA.

This is a long introduction, but what I want to accomplish in this thread are as follows;
My questions

What are the Vitamins required for the process of converting the Tryptophan into Pyruvate?
What vitamins are needed in the process of converting leucine to acetyl-CoA?
What vitamins are required in the process of converting isoleucine, tyrosine, phenylalanine, and threonine to acetyl-CoA?
If you notice, I would also like to know if there are any facts that are critically missing or apologized for in the above diagram or summary in terms of amino acid metabolism in the citric acid cycle.

FYI: I could not find any articles written in English that was compact enough for my purposes. Therefore, I would like to share the content of a Japanese university's website with minimal annotations;http://www.sc.fukuoka-u.ac.jp/~bc1/Biochem/amino_met.htm
(1) Groups that enter the citric acid cycle via pyruvate: Gly, Ala, Cys, Ser, Thr, Trp

There is no mention of vitamins in the process of Ala → pyruvic acid.
ASP-(using NADPH2,NAD)→Thr→Gly-(using tetrahydrofolate)→Ser→pyruvic acid
Although not much has been written about Asp, it seems that it also enters the citric acid cycle via pyruvate.

(1)'Amino acids in this group other than alanine (Gly, Cys, Ser, Thr, and Trp) can also become succinyl-CoA.

All amino acids pass through threonine (except alanine)
Serine-(using THF) → Gly → Thr
ASP-(NADPH2, use NAD) → Thr
Thr is converted to succinyl-CoA with the assistance of NAD.
In the process of converting glycine to threonine, acetyl-CoA is produced as a secondary product.

(2) Group that enter the citric acid cycle via α-ketoglutarate: Gln, Arg, His, Pro, Glu

All amino acids pass through Glu
Gln becomes Glu without any special vitamin support
His becomes Glu with the assistance of THF
Pro becomes Glu with the assistance of FAD and NAD
Arg becomes Glu with the assistance of NAD
Finally, Glu becomes alpha-ketoglutarate (α-KG) with the help of NAD.

(3) Groups that Enter the citric acid cycle via succinyl-CoA: Met, Ile, Val

Valine and leucine, with the aid of NAD and FAD, go through similar pathways to methylmalonyl CoA, which is then converted to succinyl CoA.

(+1) For "There is no mention of vitamins in the process of Ala → pyruvic acid." Vitamin B6 (pyridoxal phosphate), surely?


text:
Why are "alanine, cysteine, glycine, and serine" not ketogenic amino acids?
In the figure below,

Purple letters represents both glycogenic and ketogenic amino acids
Brown letters represents glycogenic amino acids, only
Green letters represents ketogenic amino acids, only

https://upload.wikimedia.org/wikipedia/commons/1/16/Amino_acid_catabolism_revised.png
So, the following glycogenic amino acids are also ketogenic;

Threonine, Tryptophan
Isoleucine
Tyrosine
Phenylalanine

However, as can be seen in the figure below, at least the following of these can be converted to pyruvate, which can eventually become acetyl CoA, and in this sense, their carbon skeletons can also be used in the synthesis of ketone bodies.

Alanine, cysteine, glycine, and serine

My question:

Why are "alanine, cysteine, glycine, serine" not ketogenic amino acids, even though they can be converted to pyruvate and thus their carbon skeleton can be used to generate acetyl CoA?

As I understand it, whether it is ketogenic or not should depend on "whether it can be used to synthesize ketone bodies or fatty acids". While pyruvate can be used for glycogenesis directly back through the glycolytic system, some metabolic systems go through acetyl CoA; of course, if acetyl CoA is produced, the carbon skeleton part cannot be used for glycogenesis.
Amino acids that can be converted directly to pyruvate should be able to be converted to acetyl CoA via pyruvate and thus be used in the reaction to produce ketones from acetyl CoA.
Those that must once go through pyruvate (alanine, cysteine, glycine, serine) are not traditionally included in the ketogenic amino acids?
Wikipedia has the following description；
https://en.wikipedia.org/wiki/Ketogenic_amino_acid

A ketogenic amino acid is an amino acid that can be degraded directly into acetyl-CoA, which is the precursor of ketone bodies and myelin, particularly during early childhood, when the developing brain requires high rates of myelin synthesis.1 This is in contrast to the glucogenic amino acids, which are converted into glucose. Ketogenic amino acids are unable to be converted to glucose as both carbon atoms in the ketone body are ultimately degraded to carbon dioxide in the citric acid cycle.

The answer to this question would depend on how one concretizes "degraded directly" in the quoted above.

It always helps to define your terms — so we know what the poster is talking about, and the poster himself does. Please do that — it will probably lead you to the answer to your question.

@David  I added a definition, as far as I know. If there were an additional clause such as "those that cannot become acetyl CoA without going through pyruvate are not included in ketogenic amino acids", then my question would be answered, but I have yet to see such direct language.

I think your definition is incorrect, and I suspect you are not aware of the physiological/pathological context — starvation or diabetes. And what effect does ketogenesis have on acid-base balance? Will expand later if necessary.

Does this answer your question? About the definition of ketogenic amino acid

I now find that your question has been asked before, and that I have already provided an answer from the context of starvation and provision of glucose for the brain. I think it is a much more pertinent answer than the other one, even though it  is losing 0-6 in the scoring stakes. Perhaps you and other readers might wish to reassess it.


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The second law of thermodynamics and the cell (3 questions)?

How is that the cell maintains internal order, yet it discharges heat (disorder) to the surrounding?
If the cell is supplied with materials for metabolism and growth by the surroundings (disorderly environment), then how does that disorder generate order inside the cell?
When we zoom out from a single cell to a multi-cellular organism, will the net value of internal order of cells decrease disorder which would contradict the 2nd law of thermodynamics?
Note:I would appreciate serious informative answers. The questions are important for me no matter how silly they may look like for you.

I think you're neglecting an important point: the 2nd law applies to closed systems, and the cell (or multi-cellular bodies) is not a closed system.  It takes energy from outside to maintain its organization.  Place it in a closed box, and it will die when it has used up its internal reserves.

@jamesqf Alas, Schrödinger's cat was doomed from the beginning.

What research have you done yourself to answer this old chestnut? I entered "life and the second law of thermodynamics"  in my web browser and got a page full of links on this topic, including one that Google had highlighted.

First question: the answer is actually contained within the question.  The cell maintains order precisely by discharging heat.  The second law of thermodynamics states that the tendency of a closed system is to proceed from ordered to disordered.  Since thermal energy is (to our knowledge) the most disorderly form of energy that exists, in any given system where energy is involved, some energy will always be lost to heat.
For instance, if your cell performs the break down of ATP to drive some chemical need of the cell, some of the energy released in the breaking of the bonds in the ATP to form ADP will be lost as heat.  This means that the cell's heat is going up on average, and it must export heat to the environment.  If the heat was held inside the cell, the cell would rapidly become extremely disordered as proteins de-natured, non-enzymatic reactions sped up, and the cell basically self-destructed.
Second question:  I think you've slightly missed something.  Autotrophs (producer cells, such as plants) are the cells to actually "create order" in the biosystem.  They do this by capturing Carbon dioxide and water from the environment, and using light energy from the sun to bond them together and form complex biomolecules - usually carbohydrates.
These carbohydrates are then sent into the rest of the biosystem, where heterotrophs (consumers like me, you and the lion in the zoo) break them down to release their energy for tasks their cells need to do (cellular respiration, catabolism).  As time passes, all that energy is converted to heat and radiated from our bodies, and ultimately by the atmosphere off the Earth (barring excessive greenhouse gases.)
Third question: Not necessarily.  If the multi-cellular organism were a closed system, you are absolutely right.  The chemical energy would rapidly be all converted to thermal energy, and the order would disappear entirely.  However, bodies are not closed systems: they are continually radiating thermal energy and absorbing chemical energy, either from the sun through photosynthesis, or from autotrophs through ingestion and digestion.

A picture is worth 1,000 words:

(Image courtesy of stephsnature.com)

Some pictures may be worth 1000 words, but imho this is completely meaningless, either on its own or in relation to a question on entropy. Doesn't even make good wallpaper.

@David, I thought the image was fairly self-explanatory, but maybe not, lol.  The point is that the energy coming into the system is in the form of light, the energy going out of the system is heat.  As I said in the post, heat is the energy form with the highest entropy.  Therefore, though the entropy in the system is not necessarily increasing, the energy outside the system necessarily is.  Please ping if you want more clarification.


text:
What is a DNA clamp exactly?
I used to think that a DNA clamp is a protein. But today I noticed it doesn't appear in this picture. Then I went to it's Wikipedia page, where it was written:

A DNA clamp, also known as a sliding clamp, is a protein fold that
  serves as a processivity-promoting factor in DNA replication. As a
  critical component of the DNA polymerase III holoenzyme, the clamp
  protein binds DNA polymerase and prevents this enzyme from
  dissociating from the template DNA strand. The clamp-polymerase
  protein–protein interactions are stronger and more specific than the
  direct interactions between the polymerase and the template DNA strand

Which I find a little confusing. For now it seems to me like DNA clamp is a subunit of DNA Polymerase and it doesn't have any function by itself and it is not an actual protein but it binds to Polymerase and becomes functional. Can somebody please clarify this matter to me?!

The reason it doesn't appear in some diagrams is because every diagram needs to achieve a balance between including all known details, and leaving out details to not overload the reader. The clamp isn't essential to understanding the basics of DNA replication, so it gets left out a lot.

Your partly right both ways.  In a sense, the DNA clamp is a protein, in another sense, it's only part of a protein.  What it actually is is what we call a protein sub-unit, which is a protein, but which binds with other protein sub-units to form complex proteins.
In order to understand this, you have to remember what a protein is.  A protein is, in essence, a chain of amino acids.  Those can be short chains, long chains, medium chains: but they're all proteins.  Sometimes, a few short proteins (sub-units) will bind together to form one long protein (protein complex).  This is what happens in the case of a DNA clamp.
Basically, the DNA clamp is (an) independent protein unit(s) which has (have) the ability to encircle the DNA strand and travel along it.  They bind to the polymerase, which is why you don't see them on your diagram.  Their function is, very simply, to make it possible for the polymerase to stay closely attached to the DNA stand.

Sources:

DNA Repair (Amst). 2009 May 1; 8(5): 570–578


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Why do parasitic amoeba lack a contractile vacuole?
Compared to the other amoeba, most parasitic amoeba lack contractile vacuole. I could not get the correct answer as to why these parasitic amoeba lack contractile vacuole.


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Questions about apoptosis

Is apoptosis a part of cell division?
Can apoptosis occur if DNA is damaged beyond repair?

Please show your attempt at trying to find the answer to the question!

Welcome. If this is a home-work question please show some of your efforts in answering it. What do you think the answer is and why?

Homework questions are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy. I am voting to close.

I think this question could basically be summarized as "What is apoptosis?"  I will attempt to give a brief answer to that question, answering the two aspects of the question along the way.
Apoptosis is at its root programmed cell death (PCD).  It is basically when a cell (healthy or not) dies so that it can be replaced.  It is happening all the time in multicellular organisms such as me, you, and the lion in the zoo.  Basically, it allows all the cells to be replaced as the tissues of the body grow.
For instance, as your skin grows, cells in the dermis are dividing to produce a new epidermal layer.  At the same time, cells on the outside are dying (at the stratum corneum) so that the skin does not grow infinitely and we aren't covered with 20 inches thick of skin by the ends of our lives.
The same thing is happening in, for instance, the liver.  As the liver cells split, old ones are also dying.  This allows us to rebuild the liver to its normal size after a surgery in which we remove a section of it.  We simply have to stimulate cell growth so that it counterbalances PCD (apoptosis) and the liver grows to its normal size.
Cell death is initiated, not by the DNA, but rather by caspase activity.  All cells have inactive procaspases which will destroy the cell as soon as they become active.  When what we call an initiator procaspase bonds with a procaspase within the cell, the procaspase is activated, and the signal is spread across the cell.  This initiator procaspase is usually triggered by a death receptor outside the cell.
More reading here


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Motion of Fallopian tube fimbriae
The fimbriae at the ovary end of Fallopian tubes are described as "sweeping" eggs from ovaries into the tubes:

When ovulation is about to occur, the sex hormones activate the fimbriae, causing them to swell with blood and hit the ovary in a gentle, sweeping motion. An oocyte is released from the ovary into the peritoneal cavity and the cilia of the fimbriae sweep the ovum into the Fallopian tube.

Is there more detail known about the "gentle, sweeping motion" of the fimbriae?  For example, is it a single swelling "sweep" per cycle?  Is the motion of the fimbriae against the ovary isolated from or accentuated by other movement of the body?


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In biological nitrogen fixation, the electrons required to reduce dinitrogen to ammonia are provided by which compound?
The reaction is as follows:
N2 + 16ATP + 8e- + 8H+ → 2NH3 + H2 + 16ADP + 16Pi
From where are the 8 electrons coming from?
We know that in photosynthesis, the electrons are supplied by the oxidation of water to evolve oxygen gas. What about here?

Welcome to SE BIology. Please take the Tour and read the Help on asking questions. You will find that you are expected to do some research yourself before posting. I would start with a source that explains the biochemistry of the process — Berg et al online will give you the answer. Then, if there are still specific points you don't understand you should repost explaining precisely what these are. At present I am voting to close your question.


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DNA polymerase in PCR (polymerase chain reaction)
Can the DNA polymerase in PCR (polymerase chain reaction) recognize both DNA and RNA for use as a template?
I want to know is it possible if my primers bind to contaminant RNA and then any DNA polymerase like Taq DNA polymerase use this strand as the template for elongation?

Do you want to know if a PCR reaction is possible with different enzymes for DNA and RNA?

Hi Chris, I want to know is it possible if my primers bind to an contaminant RNA and then any DNA polymerase like Taq DNA polymerase use this strand as template to elongation and continue reaction?

I have edited your question to make it clearer, please roll this back, if this is not ok for you.

No, this does not happen, as the DNA polymerases used for PCR are DNA dependent. This means that they only synthesize DNA when it is bound to DNA. Even if your primers bind to the RNA, the polymerase will not starting new strands here. To use RNA as a template for PCR you first need to reverse transcribe it.

And one more that may 3-HO end of binded nocleotide contaminant(small crashed RNA ) lead to give unwanted fragment?

@M007 I don't get your second question, sorry.


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Who was the first to coin the terms of soft and hard selection?
Soft and hard selection are sometimes used with different definitions. I have been told that at first place hard and soft selection has been defined in the following way:

soft selection: Each deme makes the same contribution to the next generation
hard selection: Different demes make different contribution to the next generation

Who first described these concepts? What was the first paper?

Wallace, B. 1968 "Polymorphism, population size,and genetic load"?

At least in his 1975 paper "Hard and Soft Selection Revisited," Wallace says that he was the first to introduce the terms hard and soft selection in his 1968 paper that I cite above.

@falsum I think you can make an answer from your comment. Thanks

I believe it's Wallace, B. 1968 "Polymorphism, population size,and genetic load" In R. C. Lewontin Population Biology and Evolution. Wallace also discusses his distinction between soft and hard selection in his 1975 paper "Hard and Soft Selection Revisited" (JSTOR link).

Note also Christiansen 1975 who is quite an early paper. Actually I was wondering between the who would be the first to talk about selection softness. Thank you +1


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phosphorous availability to mycorrhizae and parent plant, timing - paper search
I'm researching phosphorous uptake in monocots to develop planting mixes for riparian planting.
I recently saw a paper suggesting (the author lacked proof) that root zone mycorrhizae may solubilize phosphorous from the soil solution out of phase with the parent plant's ability to take up the phosphate, resulting in P loss from the system. Sadly I didn't save the paper and so it is still out there on the net. If this is the true, and the loss significant, then it would be an argument against using mycorrhizal plants in stream-side planting.
Does this ring a bell with anyone? Failing that, what is known about the relative phasing of mycorrhizal phosphorous release and timing of plant uptake, especially in monocots?


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Why would a flower evolve such that a particular pollinator cannot pollinate it?
I went on an interpretive trail today and came across a wild flower sign. It said that some flower species evolved such that they can not be pollinated by humming birds as they are shaped such that only an insect proboscis could get into it. Why would a flower evolve in such a way? Wouldn't it be advantageous to take any pollinator?
An interpreter in the visitor center suggested it might be that the flower wants to save it's limited pollen for pollinators most likely to visit other families of its species. I'm not completely sure I buy this, as a pollinator willing to visit one flower of a species is likely to visit another flower of the same species. That said, I think he might have been on to something. Alternatively, this link made me think perhaps certain pollinators might damage the flower and it would want to discourage them.
This question goes beyond a flower co-evolving such that a particular organism could specialize in pollinating it; I'm curious why a flower would specifically evolve such that it could not be pollinated by a particular organism.

Could you tell us specifically what species you are talking about. Otherwise this is an unclear question.

It's two sides of the same coin, by specialising to have one specific pollinator, you have to exclude others

Probability. A rare flower got a larger chance of successful pollen transfer if the pollinator searches specifically for other members of its species. The previous comment describes one option to achieve that. Typically, what we observe today is the result of coevolution. The pollinator gets access to a food source not accessible to others and the flower gets a specific pollinator.

The interpreter's explanation was also the one that immediately came to my mind. There is also some evidence that high specialization (and therefore low pollinator sharing) increases pollination probabilty: http://www.ncbi.nlm.nih.gov/pubmed/19909087

@James, I was afraid someone would ask that (: I looked a lot online and could not find the species. I believe it was a type of Elephant Flower indigenous to Utah but am not sure.

@rg255, thanks for the comment, but I'm specifically referring to a case where the flower adapted to exclude a pollinator where the adaptation did not benefit a preferred pollinator.

I think the explanation by the interpreter is most appropriate. The definition of species is a particular category of organisms capable of reproduction among themselves. Thus pollen of a particular species must fall on the stigma of the same species. But pollinators visit all species of flowers (as they never visit Biology Stock Exchange, thus ignorant of the definition of species) which bears nectar and the entrance is big enough to let them in.
The flowers in your question increase their chance of pollination by reducing the varieties of flowers a particular pollinator can visit. Lets make it simpler (or even more difficult for those who don't like mathematics!)...
Suppose there lives 4 humming birds and 4 bees in a oasis...both are too lazy to visit other oasis in search of nectar. One morning 4 flowers bloom in that oasis...2 wild flowers you mentioned and 2 wide mouthed flower of some other species.  Now 1 flower of the wild species can be visited by 4 bees (as humming birds can't enter the flower). One flower of the other species can be visited by 4 bees and 4 humming birds. This large number of pollinators for the second type of flower reduces its chance to be visited by a pollinator that visited a flower of the same species. Whereas for the wild type flower the possible number of pollinators are very few (only 4)...so the chance of one bee visiting two flowers of the same species is very common and so is the chance of it getting pollinated.
In this way these flowers increase their chance of pollination by modification of their shape.

I think the OP is asking why a flowering plant might evolve to exclude pollination by some species of pollinators, rather than why it might evolve to special adaptations to allow some specific pollinator

I answered by considering "species" of pollinator...humming birds and bees are examples of species only.

I think this is correct. To repeat but also perhaps flesh out your example, suppose a flower only has enough pollen to be visited by 5 pollinators each day. If a hummingbird only has a 10% chance of visiting another flower of the original flower's species but a bee has a 50% chance of visiting the original flower's species, it is advantageous for the flower to not "waste" pollen on the bird.


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Why don’t different organisms have nucleic acid genomes containing different bases and sugar?
All organisms contain genetic material. Be it DNA or RNA, both of them have a fixed pentose group (deoxyribose and ribose). Also they contain the same types of nitrogenous bases, Adenine, Thymine(or Uracil), Guanine, Cytosine.
What makes ribose and these notrogenous bases so good that among all the molecules in our pre-historic chemical pool, these selective compounds made our genetic material.
Why don't different organisms have different bases/sugars? I understand that we all have a common evolutionary ancestor so the the genetic material will be similar. But mutation is possible, so why is that there are no nucleic acids found naturally that are made of different bases or sugars? Just for example, if we had a hexose like glucose for the sugar instead of pentose..

I've rewritten your title. to eliminate the misleading "predetermined" which is not the right word. I think it reflects your question.

'Why' questions are usually hard in biology and are interesting to think about but rarely useful to ask. :)

@AlexDeLarge is right. They are generally end up as matters of opinion, which strictly makes them off topic. It is more useful to ask something more specific like "Has anyone built artificial polynucleotides with a hexose instead of a pentose, and if so how did its properties differ from DNA and RNA?" That can be answered, but asking about every possible base or sugar cannot.

Everyone is giving you a hard time for this question. But it's a great question! Good for you for asking it.
The answer is that we really don't know why nucleic acids are composed of ribose, as opposed to any other sugars. We don't even know why life on earth only uses L-ribose instead of D-ribose. Or if instead of being carbon-based, we don't know if extraterrestrial life could be silicon-based.
Similarly, two D and L forms of amino acids also exist. (Right handed vs left handed mirror-image molecules that otherwise act the same.) Organisms on earth only use the L-form! We have no idea why. If a meteorite landed on earth that contained D-amino acids, that would really throw scientists for a loop.
(*this link might be of interest to you: https://en.wikipedia.org/wiki/Murchison_meteorite#Organic_compounds)
I'm going to give you a word of advice, and I really hope you get to read this. You are an "out of the box" thinker and the average people will get stumped when you ask questions like this. Ignore them.
If everyone asked grey, imaginative questions instead of following the black-and-white rules they learned, society wouldn't function. But individuals like you help advance society. We need both types of people equally. You happen to be in the latter category. People in the first category will have a difficult time with the questions you ask. Accept and respect them, but continue on and keep asking your questions anyway.
Eventually, you will find people who think like you do. I suggest finding others interested in astrobiology, which is a growing field and that needs people like you in it. Maybe biochemistry or evolutionary physiology too.

People are not giving a "hard time" but correcting a wrong understanding of basic concepts. This is also not "out of the box thinking". At the moment most of your answer is opinion based - please work on this.

This is not an answer to the question. And it's wrong to say that organisms on earth use L-carbohydrates; in fact they mostly use D-carbohydrates. Further, most meteorites contain both D and L-molecules. The selectivity in handedness is, as far as we know, a property of life on earth. Regarding your comments on the open mindedness. It is good to ask questions all the time, but it is better to ask questions that are based on solid science and reasoning. In that sense, pointing to misconceptions is not 'giving a hard time' but helping others to learn.

It sounds like you are confused about how Darwinian evolution "works".  For example, as we survey the current life forms in this biosphere there is absolutely no evidence that these species (or their molecules, which you refer to) are optimized in any way, shape, or form.  All we can state with any certainty is that at some time in the past, during one, or more, selective events, all the species that used ribose, deoxyribose, and the five common bases (A, C, G, T, and U) for their genetic material, survived to reproduce, and contribute progeny to the next generation.
If that putative selective event was different, then perhaps all the pentose-based species would have died off, and we would all have hexose-based genetic material.
We don't know how many different genetic material recipes were tried out before this one "won".
Evolution can only work on, or select, or select against, the current batch of organisms.  It is not an optimization algorithm, it is a filter that lets variants through.
It may well be that our genetic material, for example, replicates faster than the other candidates. That could be a selective advantage, but it doesn't have to be.
So what are you really asking here (since your original question contains incorrect assumptions)?

You are incorrect in your assertion that:

…there are NO nucleic acids found naturally that are made of different bases or sugars

Different bases are found in the anti-codon loop of transfer RNA, in the cap of eukaryotic messenger RNA and in ribosomal RNA, which also contains modified sugars.
You might say that this is pedantic or not to the point, as these variants do not occur in the genetic material. However at least it demonstrates that Nature has ‘played’ with this and decided only to use these fancy Lego bricks for special projects.
I dislike questions of the sort you pose, because any answer tends to be of the form “The structure we have is favoured because it can do this, this and this, which nothing else can do as well.” And, of course, we really don’t know that nothing else can do it — we just assume so because things are the way they are.
With that disclaimer, one might suggest that Mother Nature has shown a willingness to improve on things by moving from RNA genomes to ‘better’ DNA genomes with a different sugar and one different base. (My own explanation of why this is ‘better’ can be found in  answer to Why deoxyribose for DNA and ribose for RNA?.) So although we can’t be sure that another system would not work as well, the fact Mother Nature has stuck with DNA suggests that she has found nothing that works sufficiently better to move to that. (In academic circles this circular argument is expressed in terms of evolutionary advantage.)

David, it is strange that you (as far as I know you) are using personification and anthropomorphism to explain a phenomenon.

@WYSIWYG — It would be anthropomorphism if I wrote about enzymes or bacteria wanting or trying to do something. It was meant as metaphoric humour — oh beware humour in an international context or where you can't see the other's face! You could say it skirts on vitalism or deism — I changed my original 'Nature' to 'Mother Nature' to go with my Lego brick analogy. I wanted to be brief so as not to get sucked into tortuous arguments about the evolution of molecules where one has to discuss enzymes/ribozymes, different genetic codes etc. Perhaps I should have confined myself to a comment.

A small extra note on your question: you are wrongly using the term 'mutation'. Mutation is a process that can work on genes (or chromosomes). As the definition of mutation states:
"The changing of the structure of a gene, resulting in a variant form which may be transmitted to subsequent generations, caused by the alteration of single base units in DNA, or the deletion, insertion, or rearrangement of larger sections of genes or chromosomes."
So mutation works on genes (and their order, sequence, ...), with genes as the 'smallest unit'. It does not work on the molecular structure of genes. If changes in the molecular structure of the pyrimidines/purines are made, these are chemical reactions resulting in other molecules. Which is a completely different proces than 'mutation'.

We all have a common ancestor.  It had a set of genetic mechanisms that worked, and was overall better at surviving than whatever else was available at the time.
Its advantage may have been its DNA/RNA, or it may have been something else and the DNA/RNA just came along for the ride.
At this point you have a planet full of of moderately successful organisms that are all genetically related.  If any completely new organisms appeared, they would be out-competed before they got off the ground.
Now, you can imagine an organism getting a mutation changing the way the genetic code is read. What happens then?  That organism would be unable to read its own genome, and it would die.
What would be needed for a successful switch of code? Let say that we want to use Neoadenine instead of Adenine.
First, the cell needs to produce Neoadenine instead of Adenine.
Second, it needs to produce transfer-RNA that correctly transcribes codons containing Neoadenine.
Third, it needs to change all the existing genes to the new code.
Not only this, but it needs to do all this while not being eaten by its unmutated cousins.
So far, this has happened only once, when either DNA became RNA or the other way around.
The odds of it happening again are small, outside a laboratory dish.


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Which part of the reflex arc takes the longest time?
The reflex arc is composed of 5 parts:
sensory receptors, afferent neuron(s), synapses within the central integrating station, efferent neuron(s) and the effector (includes transmission across the neuro-muscular junction and contractile mechanism - Assuming this is a myotatic reflex).
Which part takes the longest time & why?

I am providing this answer considering myotatic reflex arc (as you have specified in the question).
There are so many factors on which it depends...I have listed as many as I could -
Here the sensory receptor is intrafusal muscle fibres. Afferent neurons are type Ia or type II. Central processing may involve mono- or poly- synaptic junction(s). Efferent neuron is alpha or gamma motoneurons. Effector is intra- or extra- fusal muscle spindle.
Considering the human or animal to be of normal health and condition (absence of hypoxia, pyrexia, high or low pressure and anesthesia) sensory receptor takes the shortest time in reflex arc. Central synaptic junction may be mono- or poly- synaptic. Poly-synaptic junctions take longer time, but still it is shorter than neuro-muscular transmission.
So the competition now is between neurons and neuro-muscular junction. In case of neurons it mainly depends on the length, diameter and myelination (provided the above mentioned conditions about the sample is "normal"). Neuro-muscular transmission speed depends on the length of synaptic cleft, body calcium and chloride level, type of muscle fiber innervated and the type of reflex arc (alpha-gamma co-activation, reciprocal innervation etc) to name a few. So, it can be said that longest time would depend on the reflex arc you are considering, as this will decide the speed of transmission through the afferent and efferent neurons and neuro-muscular junction.

The answer to this question depends which reflex arc was activated, without knowing the exact reflex arc one should assume the answer as multifactorial and relate to this (or similar) table:

(Source: Fundamental Neuroscience for Basic and Clinical Applications,  by Duane E. Haines)

This provides only information on the conduction velocities. Thing is that peripheral sensory transduction, synaptic delays in the reflex arc and in the neuromuscular junction may add considerable amounts of time too, and not to forget the time it takes for the muscle to contract. Conduction velocities are just part of the equation.

@Christiaan In other words, this question could not be answered.

Then why did you O.o ?

@Christiaan I gave a direction... Sometimes it is better than exact answer.

The nerves in the gray matter would expect to conduct slower. Also synaptic transmission is generally slower than saltatory conduction.


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Why not surgically resect the tumor before CAR-T cell therapy? Won't that be more efficient?
If CAR-T cell therapies suffer from tumor antigenic escape, why not just resect the tumor via surgery, leaving behind a small number of cancerous cells, and then wipe them out with CAR-T cells? The small number of cancerous cells may reduce the chance of too many cancerous cells escaping CAR-T cell cytotoxic killing that may cause tumor regrowth.

Can you please make yourself familiar with cancer therapy? Every cancer which can be operated is usually operated to reduce the tumor burden for the patient. And to raise the chances for other therapies to be successful.

To give an appropriate answer is needed to know which type of tumor and the grade of the tumor, because there are specific protocols redacted by medical consensus conferences for each of them.

I second what @Chris said. As it is now, your question is too undefined to provide a good answer. You're touching on interesting subjects, though. Maybe you can either refine your question to be more specific to a type of tumor, or ask for information on CAR-T therapies more generally?

You've deleted all of your previous questions about CAR T cells, which isn't advisable. However, you don't seem to understand much about cancer therapy in general, and immunotherapy specifically. I would strongly suggest finding several good review articles or reliable websites about the type(s) of cancer you're interested in to get an idea of how cancer therapy works in general (surgical resection, chemotherapy, radiation, immunotherapy, combination therapies, etc.), then move on to understanding immunotherapies in general, then you can begin to apply your recent research on CAR T cells.

please read the answer below and follow the links in it, I hope that would resolve this conflict.

CAR-T cell therapy (Chimeric Antigen Receptor-T cell Therapy) is most effective in treating hematological malignancies. Hematological malignancies (known as blood cancers in common parlance) mean the cancers produced due to over-proliferation of hematopoietic stem cells and the liberation of the immature cells into the circulation . Till now all clinical trials of CAR-T cell therapy has seen more and more success. With the development of second, third and fourth generation (also called TRUCK T cells) CAR-T cells the percentage of remission is increasing. But  almost all these advances are in hematological malignancies.
Clinical trials on solid tumors has shown that the "efficacy is not as remarkable as in the case of hematological malignancies".
The question asked was about resection of the tumor before treating with CAR-T cell therapy. This question is valid only in case of solid tumors (you can't resect blood as it is liquid). As I already said this therapy is only used for blood cancer till now, so there is no question of surgery before the therapy.
I think I could answer your query above. If you want to gain more knowledge, then read below -

The best use of this therapy in blood cancers is after hemato-poietic stem cell transplantation (note that it is not surgical resection)
If you ask, why this therapy was not successful in solid tumors, I would recommend to read the review published in Springer with the title "Hurdles of CAR-T cell-based cancer immunotherapy directed against solid tumors".

Recently however there are new developments that are helping to apply this immunotherapeutic procedure in case of solid tumors also and in that case it is usually given after surgical resection.


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How Much DNA do Siblings whose Parents are First Cousins Share?
On average, two siblings generally share 50% of their genome. How much does this increase if the siblings' parents are first cousins?

I have edited the title of your question to clarify that you meant siblings who's parents are first cousins. Your original wording implied siblings of first cousins, who would probably be first cousins themselves.

This is going to be a sum on probability. Good one. I'll follow it.

Before I actually answer your question, let us clear up some problems in your assumptions. The fact that you expect 50% similarity in siblings is a full of several assumptions.
Imagine a case of a simple diploid organism with 2 traits. To restate your assumption, if both the parents are heterozygous in either of the two traits, and the alleles present in either parent for each trait are different (four different alleles possible for each trait), then the probability of getting two children who share 50% of the same alleles is more than any other percentage sharing.
Let us break this down. We'll gradually add complications.
For the 2-trait organisms, let us assume the genotype of the parents to be $\text{AB,EF}$ and $\text{CD, GH}$ where $\text{A,B,C,D}$ are the alleles controlling trait 1. Hence, for their first child, the possible genotypes are $\text{ACEG, BCEG, ADEG, BDEG, }$ and so on.... Since there was no allele match in the parents, each of these genotypes is equally likely.
For the second child, the same possibilities with equal probabilities exist. Now, I computed a matrix which has each possible genotype for child 1 as rows, that of child 2 as columns and the values are the proportion of alleles shared (i.e. common between the two). .
So, all proportions of the sharing is possible between the two kids. But, to find out the most probable configuration, we plot another kind of plot.
Technical note: Although the barplot has frequencies of appearing in the above similarity-matrix, it is equivalent to the probabilities since each genotype was equally likely.
Hence, the case with the two siblings sharing 50% of the genome is most likely for this case. Now, if we expand to 3 alleles, here's the corresponding plot.
It shows, that even if we increase the number of traits (as we gradually approach the human case), the maximum likelihood still includes the sibling-organisms sharing 50% of the genome.
Now, what if the parents already shared some genome? Let us say, the 2 trait organisms already shared 50% of the genome. It is equivalent to say that in the genotypes elucidated above, $\text{A=C, E=G}$. With this assumption, I ran the same kind of simulation to get the following graph.
Another technical note: Although the plot still shows frequencies of appearing in the matrix,the repeats of the same genotype along rows/columns in proportion to their probability of forming will make these frequencies equivalent to probabilities.
So now, the siblings with 75% similarities are the most likely outcome.
Let us now ask, for the 2 trait organisms we are working with, that if the grandparents had zero genomic similarities, and their two kids in-breed, what will their two kids share? For this, we take the probabilities of the first generation (children of the grandparents, sorry for the semantic mashup) for each %overlap, and multiply it with the probabilities of their kids having the various overlaps and plot a final graph.

This shows that they will most likely share 50% or 75% of their genome.
Limitations of this analysis:
 It does not account for linkage of genes. It assumes totally independent assortment of the alleles. It models all similarities to be in alleles of different traits initially and then allows for same diploid pairs, i.e. it does not allow for the observed probabilities of forming a same diploid pair, i.e. case where the similarity (genomic sharing) between two individuals is because of two same alleles for the same trait. It is also blind to any parental imprinting. Homozygosity is not yet incorporated in the simulation, will do in a while.
Below is the two-generation probability simulation for an organism with 4 and 5 traits.
The maximum likelihood of %similarities in genome, as you can appreciate, for a large number of traits would be somewhere around 63-64%.
I shall post the R code in a while, after I format it properly. For computations for greater than 5 traits, I shall write a better engine in a day. Sorry for the improper formatting of the question. Shall rectify in a while.

Note that this analysis is only looking at areas which differ between the two parents.  More than 99% of the genome is identical between all humans.


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What do we call this adjustable platform used to ensure that something is positioned strictly level in a lab?

This is an adjustable platform. Such a platform is used, for example, to make sure that a gel electrophoresis cassette is level relative to the earth. A passage in a procedure description which I'm translating says that the gel caster (the two glass plates between which we will pour the solution) should be put on top of this platform, after which the platform is adjusted "using a level". The text describes a vertical SDS-PAGE procedure.
I wonder what such benchtop lab platforms are called. In my Russian text it is called "заливочный столик" (pouring table, casting table).

I have never in my 5+ years in academic labs seen anyone use an adjustable platform for leveling... In general all tables in a lab should be level checked at installation so using such a platform would be overkill.

I remember using those for agarose gels as an undergraduate, though using them for PAGE doesn't make a lot of sense unless your bench is seriously out of level. Anyways, they can be called levelling tables and are used to promote uniform migration across the gel. Casting table also seems reasonable.