text:
Function of coenzymes: do they act as substrate shuttles?
My biochemistry textbook, "Harper's Illustrated Biochemistry", states:

Coenzymes serve as recyclable shuttles that transport many substrates
from one point within the cell to another. The function of these
shuttles is twofold. First, they stabilize species such as hydrogen
atoms (FADH2) or hydride ions (NADH) that are too reactive
to persist for any significant time in the presence of the water,
oxygen, or the organic molecules that permeate cells.
Second, they increase the number of points of contact between
substrate and enzyme, which increases the affinity and specificity
with which small chemical groups such as acetate (coenzyme A), glucose
(UDP), or hydride (NAD+) are bound by their target
enzymes."

To be specific I don't understand the meaning of the words in bold, above:

what are these so-called small chemical groups?
are they already bound to the enzyme or are they substrates?
what does increasing the specificity mean?

Summary
Co-enzyme is a general term employed early in the development of biochemistry and applied to non-protein components required for enzyme activity. Thus the term is not a chemical or mechanistic description and is of limited contemporary importance. Nevertheless a group of molecules designated as coenzymes, though differing in chemical structure, share the function of being activated carriers for particular chemical groups (not substrates).
The term “shuttle” neither describes, nor is generally applied to, this function: indeed it is reserved for the process of moving molecules back and forward between cellular compartments. This is quite distinct from whether or not the reactivation of the coenzyme occurs within the protein or after dissociation into the surrounding milieu. (Incidentally, the fact that both situations are found illustrates the limitation of defining cofactors tightly bound to proteins as prosthetic groups, and those that are not as coenzymes.)
The basic reason for the other molecular portion of a coenzyme of the activated carrier class is to provide a thermodynamically activated structure — a chemical bond to the group being carried that ensures its reactivity. Other features differ quite widely and may relate to the specific type of interaction of different coenzymes with proteins.
Cofactors, coenzymes, cosubstrates and prosthetic groups
For historical reasons the terminology in this area is generally descriptive rather than chemically systematic, but is best considered first as it has tended to influence perceptions of function (specifically the term “shuttle” in the quotation in the question). The all-embracing term ‘cofactor’ was coined for non-protein components of proteins that were necessary for their activity. There was then a fairly clear-cut distinction made between cofactors that were metal ions and those that were organic molecules. Here the terminology becomes somewhat less clear. Organic cofactors were designated ‘coenzymes’, but then a distinction was made betweeen those which are loosely bound to the protein and those which are tightly bound, the latter being termed ‘prosthetic groups’. Initially prosthetic groups were regarded as a sub-class of coenzymes, but some authors now consider coenzymes and prosthetic groups as a subdivision of organic co-factor, perhaps influenced by the haem prosthetic group in the non-enzymatic protein, haemoglobin. Furthermore, coenzymes such as NAD can be regarded as co-substrates in an enzymic reaction, and it is difficult to argue that they are distinct from co-substrates such as ATP and SAM, which are not generally termed coenzymes. This state of affairs is illustrated in the table below.

Name
Co-enzyme?
Prosth. Gp?
Co-sub.?
Act. Carr.?
Group

NAD, NADP
Y
N
Y
Y
electron

Coenzyme A
Y
N
?
Y
acyl

FAD
Y
Y
N
Y
electron

Lipoic Acid
N
Y
N
Y
electron

Tetrahydrofolate
Y
N
?
Y
1-C unit

Pyridoxal phosphate
Y
Y
N
N
—

Thiamine pyrophosphate
Y
Y
N
N
—

Haem
N
N
N
N
—

ATP
N
N
Y
Y
phosphoryl

S-adenosyl methionine
N
N
Y
Y
methyl

UDPG
N
N
Y
Y
glucose

[Source of designations: Coenzymes — Berg et al., Prosthetic Group — Wikipedia, Cosubstrate — own judgement, activated carrier — general literature]
‘Activated carriers’
It is possible to find a functional chemical communality among many — although not all — of the cofactors and cosubstrates in the table above by considering that they function as ‘activated carriers’ of chemical groups that are transferred to a substrate during the enzymic catalysis. Such groups range from single carbon units to larger acyl and phosphatide groups. It is usual also to include cofactors involved in redox reactions in this category. For species such as NAD and FAD one can argue that the activated group is a hydride ion, although it is necessary to consider electrons as the activated species if one wishes to encompass all redox reactions.
For repeated use of a cofactor it is necessary to reactivate it, which in different cases occurs within the enzyme (e.g. FAD-containing enzymes) or after release in solution (e.g. NAD-containing enzymes). Activated carriers of the former type illustrate that Harper’s statement of the function of coenzymes as “shuttles that transport many substrates from one point within the cell to another” is quite incorrect.
Harper’s chemical explanation of coenzyme structure in terms of stabilizing reactive species is unhelpful and, indeed, misleading as it implies such species are generated in cells. Instead, this should be considered from the opposite viewpoint: that the groups being transfered are more ‘reactive’ than in the target molecules, although the word ‘reactive’ is best avoided as it is ambiguous. The common feature of the molecular structure of cofactors is that the chemical bond between the group that is being transferred and the rest of the molecule is such that its breakage involves a decrease in Gibbs Free Energy sufficient to drive the formation of a stable bond to the target substrate. An illustration of this is the reaction of acetyl-CoA in which it is a thio-ester bond (red) that provides this activation.

Non-catalytic components of coenzymes
One aspect of the structure of cofactors that serve as activated carriers for different chemical groups is obviously the region of the molecule containing the group to be transferred and the ‘activate bond’. Parts of the rest of the cofactor structure will be involved interaction of the cofactor at its binding site on the enzyme, and contribute to the strength and specificity of the binding. That much is self-evident, and is the gist of the second point in the Harper extract in the question, including the emboldened text. The reference to ‘groups’, which the poster did not understand, are those listed in the table above, and encircled by red rings in the composite of co-enzyme structures, below.

It can also be seen how extensive the ‘rest’ of the structure of the coenzyme is in most cases, far more extensive than would seem necessary for simply enabling specific and strong binding. It is also remarkable that in many cases the ‘structural extension’ involves a nucleotide (generally adenosine) diphosphate moiety (yellow background).
Why? The student is warned that what follows is speculation (not original on my part) for which there is — and can not be — any evidence. However, it has been suggested that the nucleotide phosphate moiety is a relic of a postulated RNA world, in which the functional part of the coenzyme was covalently attached to the RNA of ribozymes. When the transition to protein enzymes occurred a nucleotide binding site evolved on proteins to attach the coenzyme, rather than an alternative molecular change, which perhaps occurred in other cases (tetrahydrofolate? lipoate?).
Coenzymes that are not activated carriers
Because of the emphasis above on cofactors/coenzymes that are activated carriers, it seems to me necessary to give an example of coenzyme that does not work in this way. I have chosen pyridoxal phosphate, which is actually covalently bound to the enzymes in which it is a coenzyme. These catalyse quite variety of different types of reaction — the racemization of L-alanine to D-alanine is illustrated — but the important point is that there is no group transfer involved, with the coenzyme being in the same state at the end of the reaction as at the beginning. In this respect it is similar to, say, the catalytic triad of serine proteases, and can be thought of being chemically more sophisticated and versatile for catalysis than a combination of amino acid residues.

[From the Wikipedia entry for pyridoxal phosphate]
…and shuttles?
“The original meaning of the word ‘shuttle’ was as a noun, referring to the device used in weaving to carry the weft thread. By reference to the continual to-and-fro motion associated with that, the term was then applied in transportation to both the vehicle involved, and as a verb, to the motion itself” (adapted from the Wikipedia entry).
The author of the chapter in Harper from which the quotation in the question is taken seems to be using a metaphor in which the coenzyme is equivalent to the shuttle, and the activated group to which it is temporarily covalently bound is equivalent to the weft thread. There are two problems with this. He goes on to say that such shuttles “transport many substrates from one point within the cell to another”. There is confusion about the way that the term ‘substrate’ is employed — rather unusually it appears to be equivalent to what he refers to as ‘species’ or ‘small chemical group’. However the reference to transport from one point within the cell to another is just plain wrong. Some coenzymes diffuse into the containing milieu (usually aqueous) where they are reactivated in a different enzymic reaction, but others stay bound to their holoenzyme. And transfer of groups during chemical reaction can hardly be regarded as transport between points. The second problem is that the term ‘shuttle’ is already in widespread and specific use in biochemistry in relation to surrogate transport of metabolites across membranes such as the inner mitochondrial membrane. This author‘s use of the term is particularly confusing in relation to one particular coenzyme: for NADH in aerobic cells  the malate–aspartate shuttle transfers its electrons from cytoplasm to mitochondrial matrix.

This is a long answer, which is why I started with a summary. I have tried both to answer the poster's question and provide a general perspective on coenzymes in the hope that it will be of wider interest. An answer this long will, no doubt, have deficiencies in fact, clarity and typography. If these are pointed out to me I will endeavour to remedy them.


text:
Why is the retention of ability to synthesize non essential amino acids of negative survival value?
In my textbook "Harper's illustrated biochemistry" chapter 27 it is written that

The existence of nutritional requirements suggests that dependence on an external source of a specific nutrient can be of greater survival value than ability to biosynthesize it. Why?
Because if the diet contains ample quantities of a nutrient, retention of the ability to biosynthesize it represents information of negative survival value, because ATP and nutrients not required to synthesize “unnecessary” DNA-even if specific encoded genes are no longer expressed.

I could not understand the part that I have emboldened.

Seems like a simple word substitution error in editing, and it should read ATP and nutrients are required to replicate the DNA even if that DNA is not expressed. That doesn't fix the argument, but maybe makes it easier to follow.

It’s a very dubious argument in my opinion.
Whenever I see a question on this list arguing that higher organisms could save energy and DNA by such-and-such a hypothetical construct I want to scream. Think ‘junk’ DNA, introns, gene duplication, plant polyploidy and goodness knows how many other apparently inefficient and wasteful aspects of higher organisms that should never have appeared if these arguments held true. And the invalidity of the underlying assumption — that higher animals are competing like bacteria for the most efficient growth — never seems to occur to the proponents.
I‘m no geneticist, but I gather that it is thought that genetic changes can spread in a population even if they convey no advantage, as long as they are not deleterious.
The more I see of Harper, the less I like it. Not a biochemistry book for biochemists, and too many authors with only narrow expertise, lacking editing on what they write.

I totally agree, it's a spurious argument easily disproved by things like loss of ability to synthesize vitamin C - only found in anthropoid apes, guinea pigs, some bats, some birds and teleost fish. If it were about energy it would be much more widespread among frugivorous species.

Good answer. Yes, the argument exaggerates the power of natural selection on things that don't matter any more. There is essentially no selection for or against junk DNA, for instance. The loss of unimportant abilities (like synthesizing vitamin C) is accounted for by genetic drift: "genetic changes can spread in a population even if they convey no advantage, as long as they are not deleterious."

The argument also strongly implies that evolution is a smart, thinking process. When it's far more likely that the ability was just lost because it didn't matter enough (because those nutrients were available in the diets)

The passage is saying that if you get enough of a nutrient in your diet, you don't need to synthesize it.
If you don't need to synthesize a nutrient, you don't need to waste energy on the machinery to synthesize it.
Even if you switch off the process that makes the machinery, even just keeping and copying the instructions for making that machinery is a waste.

I don't see the cost of the synthetization machinery as relevant (in this case), either. There is selection pressure to turn off the production if it's not needed, since leaving it running would consume resources to produce something of which there is enough which thus are not available to produce something that is missing, leaving the next processes which rely on the products unable to run, since it is missing all other raw materials except one being overabundant. This may well make several percent of difference in fitness.
However, the cost of replicating the extra gene just in case someone might need it is an additional burden somewhere around a percent of a percent of a percent of cost: a selection pressure exists, but it is significantly lower. It will still lead to loss of the gene, but it will take thousands of times the number of generations to lose an useless gene compared to a detrimental gene, so it's not a significant effect.
Also consider that a mutation usually changes the gene, it does not remove it, so the cost remains unchanged: the change that makes humans unable to synthetisize vitamin C is merely due to a defective gene, not due to a lost gene.
It's more of a case of "use it or lose it": a mutation that causes loss of the ability to synthesize it would be a disadvantage if the product is not available otherwise. But if it is available from food then there is no deletrious effect: the organism can survive in spite of losing this gene, so there is no selection pressure requiring to retain it. Therefore, a mutation that stops it from working may spread through the population.
Still, the food situation can regularly change (for example, the source being seasonal), so the disadvantage is merely mitigated, thus a selection pressure against it still exists: if during the long time it takes to select against the useless gene a situation occurs where it is useful (like a year with bad weather), it will be strongly enough selected in favor to offset its uselessness.
What is additionally required is a bottleneck in which the population shrinks so significantly that the survivors coincidentally lack that gene to produce it. Since losing the gene was not harmful, lacking it could spread to a sufficient proportion in the population.
Then the founder effect in a subpopulation isolated from the main population would make that gene exceptionless in that subpopulation, coupled with the extinction of the remaining population or speciation of the new subpopulation leads to the species universally lacking that gene.

The question seems confused. Non-essential aminoacids (in the traditional sense, counting only aminoacids that take part in proteins) are only non-essential because we have biosynthetic pathways that make them. Lose the biosynthetic pathway for such a non-essential aminoacid, it becomes essential.

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text:
Use of different biotinylated GTP compounds in molecular biology
In the Cappable-seq technique 3′-Desthiobiotin-GTP can be used to label the 5′ end of mRNA.

However in a commercial technical article on biotinylated-RNA affinity probes I encountered the following biotinylated cap, in which the biotin affinity tag is attached to the 2′-position of the ribose at the 5′ end of the dinucleotide.

This indicates that a 2′-biotinylated GTP had been used, and will be incorporated into mRNA.
What could be the reason for this difference in tag position?

Welcome to SE Biology. Could you please provide some context to your question, which seems rather specialized. You show the structures of two different derivatives of biotin and GTP, which presumably are commercial products (one appears to be from a catalogue). Are you asking what they are used for? And what do you mean by a “typical standalone biotin-GTP?”  And where have you encountered this RNA derivative?  Help us to help you.

Thank you Mr. David for the advices. GTP is a very common structure in biology. If biotin is incubated, then the biotin is bound by the 3' carbon, as shows the second image. If N7 methylated guanosine is incubated with biotin, then the biotin will bound by the 2' carbon, as shows the first image. In this image, the m^7-biotin-GTP has been flipped horizontally and has been added to the phosphate groups, by GTase (RNA Guanylyltransferase). Why this difference in the bounded carbon? I hope to help you. Thanks

You haven't answered my questions. I know all about GTP and about biotin, and — as far as I am aware — that they never occur in Nature covalently bound to one another. The structures you show are clearly of commercial reagents. Where did you encounter these structures? Why do you want to know about them? Is this some sort of homework? Or are you new to some research laboratory? And I see this same question on Biostars. Please only post your questions in one place — cross-posting, as it is called, is not allowed on SE sites as it wastes people's time when a question is asked somewhere else.

Biotinylation requires a catalyst or active group of some sort. If you just mix free biotin and pure GTP, you'll end up with free biotin and GTP, not biotin-GTP.

I apologize for the misunderstanding. I have found these compounds in the Cappable-seq methodology (Ettwiller et al 2016). In essence, RNA guanylyltransferase takes biotinylated GTPs and catalyzes the binding reaction with the diphosphate RNA. Cappable-seq is the subject of my thesis. So yes, these are commercial reagents, the structure of which I do not yet understand, as I told you. Lastly, in biostars I did not receive any reply so I deleted the thread and sent to this forum. Thank you

Ok. I’ll look at it tomorrow unless someone else answers first. It’s never explained, but on SE you have to address comments to people by @theirname unless they are the author of the question or answer you are commenting on.  Look at some other questions to see how it works. That way I get alerted if there is a comment for me.

You are absolutely right Mr @David. It was my omission. Every answer of you is valuable

@MattDMo thank you for this important note

@David regarding cross-posting - I don't see an issue with posting both here and at biostars, because they aren't affiliated with Stack Exchange, and are their own separate entity. Cross-posting to different SE sites is discouraged, but not if they post outside the network. Granted, both sites may share part of their user base, so some people will see the post twice, but that shouldn't be an issue.

@MattDMo — Not a big deal with me, but I thought that was the policy. Is what you say laid down anywhere?

You still do not provide the source of the diagrams. I can see that the second is from NEB and is the capping reagent described in the paper by Ettwiller et al. The second  comes from some page I cannot locate on the Biosynthesis company website. It does not show a biotinylated RNA but a biotinylated dinucleotide cap. Presumably it is generated with some reagent that Biosynthesis sells, and for all I know this reagent is different from that NEB cells for patent reasons. It would probably be able to form 5'-3' bonds in RNA, but you need to find data on the reagent.

@David Yes, the second image is from NEB and the first is from https://www.biosyn.com/tew/RNA-network-analysis-using-biotinylated-RNA-affinity-probes..aspx . So the answer is that these compounds are commercial and are produced in a specific way. Thank you for the answer

@DanK After reading your question and all the comments, I'm still not quite sure what you are asking. Is your question What are the different methodological applications of 3′-Desthiobiotin-GTP and 2′-biotinylated GTP? or Why is 3′-Desthiobiotin-GTP used in Cappable-Seq, and not a different biotin-GTP variant?

I've sorted the thing now, and rewritten the question. If you had followed the link in the legend to Fig 7 in the Biosyn article you could have found the explanation there.

Thank you very much Mr @David for the answer. You have helped me to understand all that I had a question about Desthiobiotin-GTP. The original question was What are the different methodological applications of 3′-Desthiobiotin-GTP and 2′-biotinylated GTP and the functional differences between them?. But in a more general manner, you showed me the whole biochemical background, which I did not know about. Thank you for your time and your informative response.

In the Cappable-seq technique, the aim is to biotinylate primary transcripts at the 5′-cap so that they can be separated by affinity columns, or with affinity beads, of the biotin-binding protein, streptavidin. It would not appear to matter if the biotin linker is attached at the 2′ or 3′ position of the ribose ring, and there may be non-scientific reasons (e.g. cost, availability) for the choice of the  3′ position.
The cap structure in the technical article is adapted from a paper by Bednarek et al. on the synthesis of a variety of such caps, for which one specific use was to pull down complexes of mRNA with eukaryotic initiation factor eIF4e. It turned out that having the biotin affinity tag in the 3′ position of the ribose ring impeded this interaction, to a greater extent than at the 2′ position. Hence the difference.
This is clear from the start of the results section of that paper, in which an additional advantage is also explained:

The affinity tag was attached at the 2′ position of m7G via an amide
bond, which was possible due to the presence of the primary aliphatic
amino group in the starting material—2′-amino-2′-deoxyguanosine—and in
situ biotin activation with
O-(N-succinimidyl)-1,1,3,3-tetramethyluronium tetrafluoroborate
(TSTU). The site for biotin moiety attachment was chosen in a way that
ensures the least possible interference with eIF4E interaction,
because the hydroxyl groups of 7-methylguanosine in the cap-eIF4E
complex are free and solvent exposed [16] (electronic supplementary
material, figure S1). The ability of the cap analogues conjugated with
biotin to serve as substrates for RNA polymerase in an in vitro
transcription reaction was of equally high importance. In this
context, the additional advantage of introducing the tag at the 2′
position is that, similar to 2′-O-methylated dinucleotides, the
resulting compound can only be incorporated into RNA in the correct
orientation (and, as such, belongs to a class of the so-called
Anti-Reverse Cap Analogs or ARCAs).

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text:
How does labelled N from tyrosine appear in phenylalanine if the latter is an essential amino acid?
A certain question (not my course or instructor or even university) goes:

Exposed to regular metabolic activity in a rat liver, a 13C label in tyrosine will not appear as a 13C label in phenylalanine. However, a 15N label from tyrosine will appear in phenylalanine (among other amino acids) under the same conditions.
Explain and show why this is so using appropriate structures and reactions.

Tyrosine metabolism is well-discussed in any undergraduate biochemistry text and takes the following route (courtesy Voet, 5e):
Since phenylalanine hydroxylase catalyzes an irreversible reaction,1 radiolabels ought not to distribute back from tyrosine to phenylalanine. Where am I going wrong?
Footnotes
1: Remember that phenylalanine is an essential amino acid and cannot be synthesized in animals.

What does "Exposed to regular metabolic activity in a rat liver" mean? This phrase seems to apply to radioactive labelled atoms, which is linguistic nonsense. Does the question really say this, or have you garbled it? It smells a little of a trick. And are the rats growing or adult, and did the question say that Phe is an essential amino acid in rats? I cannot find a definitive source for that.

I suspect that the answer might be that there is some phenylpyruvate in rat liver, and that this can be transaminated to phenylalanine using glutamate, the N of which would have become labelled from the Tyr to OH-Pyruvate reaction, but glutamate C would not. This would require that rat liver had enough phenylalanine deaminase to generate phenylpyruvate from dietary amino acids, and that some sort of cycling occurs. I have not provided this as an answer because I don't know if it is true. I can find some papers that suggest these enzymes are present, but the whole things seems rather obscure.

OK, I checked the original paper. The question is just badly phrased.

I simplified the title. A label is a label. We don't need to know what isotope it is, which solves the problem of the superscript.

This isn’t really a question that most people would be able to answer without reading a lot of literature. I suspect the professor of this course taught a case study about phenylalanine metabolism, which would make it an appropriate question for an exam. My guess is the same as @David ‘s: cycling by a transaminase. It’s of note that this enzyme is related to the metabolic disorder phenylketonuria, which make’s it use in a case study more likely.

@canadianer — Agreed. Doesn't look as if there is a suitable deaminase in mammals, but there are reports of a phenylalinine/glutamine transaminase. Of course the reaction would have to be in an equilibrium that allowed the generation of some hydroxy-pyruvate and its reversal, which is perhaps what the "regular metabolic activity" is intended to imply. I don't think data on that are easy to come by. Most of the papers I can find are from the 70s.


text:
Meaning of 5’–3’ in relation to ORFs
I was reading a paper in the journal Molecular Basis of Disease, which stated:

The ORFs are arranged as replicase, and protease and major S, E, M,
and N proteins which follows a typical 5’—3’ order of appearance, are
considered are as considered as major drug/vaccine targets.

(Naqvi, et al., 2020)
I'd like to know what the " ' " means; if it means inch, or something else like minute. I am doing research so I don't know what units are being used.
Source
Naqvi, A. A. T. et al., 2020. Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Volume 1866, p. 165878.

Inch? Imperial units were abandoned in science by the 1950s, and probably before.

I assume you are referring to the "typical 5’—3’ order of appearance".
The correct way to pronounce these is with the word "prime", that is, "Five prime to three prime". These are not units but refer to the directionality of RNA/DNA and the numbers five and three refer to specific carbon atoms arranged in the sugar molecules that make up the RNA/DNA backbone.
RNA/DNA are typically "read" (and always written) from the 5' to the 3' end of the molecule by molecular machinery in the cell, so that's usually the order we read the sequences as well. "5' to 3'" in molecular biology effectively means "beginning to end".

Thank you, and yes I was very confused normally I would have picked a physics topic but this topic of structural virology was interesting especially with whats going on. That is the topic of my paper which is why I included the citation.

In this context, that symbol is read as "prime".

"...a typical 5’—3’ order of appearance..."

would be read

"...a typical 5-prime to 3-prime order of appearance..."

In organic-chemistry, these values are used as a systematic means to denote different Carbon atoms that are part of the same compound. DNA and RNA consist of a sugar (ribose) backbone connected by phsophodiester bonds between the 3' and 5' carbon atoms (source for image).

Since these are the bond sites that link subunits of nucleic acid together into a single molecule, at either end of any given strand there will be an available bonding site, either the 5' or the 3' carbon. So, at the 5' end of a DNA strand, there is an available 5' carbon on the terminal ribose subunit. And at the 3' end, there is a free 3' carbon on the terminal ribose. This determines in which direction the DNA is read. By convention, strands are written from 5' to 3'. In some genomes (especially in viruses and bacteria), there are open reading frames (ORFs) that are found in the 3' to 5' direction, hence the statement given to clarify the nature of these specific ORFs.


text:
Ultra-violet radiation and Bacteria in Petri Dishes
My partner and I are planning on doing a science fair project on how long bacteria can be exposed to UV radiation. We were wondering what the noticable effects would be if we held a UV lamp to bacterial colonies in petri dishes. Would the bacterial colonies shrink?

Welcome to SE Biology. I have removed the word "question" from your title as all titles refer to questions. I also changed "rays" to "radiation". The former may be ok for a science fair, but it is not current scientific usage.

Think about what UV radiation does: It damages the DNA and thus the potential for the cells to replicate. If you blast them when replication is done and over, what do you expect to observe?

First of all, thank you both for editing my question and for the welcome.

I'd expect that the bacteria would no longer replicate.

A more interesting experiment would be to spread plate bacteria and irradiate them before they start actively growing. Then you can compare the effects of no radiation and different radiation on the amount of colonies formed.

I don't know if they would shrink. But, if it is possible for you to do an enumeration (perhaps by hemocytometry, if your school could provide the instruments) and serial dilution, you could test the percentage viability over time by standardizing an arbitrary cellular concentration (in cells/mL) to be spread plated.

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text:
Meaning of ‘NC number’ associated with a gene?‘
Genes in listings etc. often have a number of the type NC_000012.12 associated with them. How should this be interpreted?

I have edited your question so the title is more useful to others, in view of your original misunderstanding and the correct answer supplied by @JITZ.

This particular ID represent RefSeq accession number.
NC_ stands for a genomic molecule representing complete genomic molecule, usually reference assembly. Every sequence has a stable accession number, a version number, and an integer identifier (gi) assigned to it. RefSeq records can be distinguished from INSDC records by the inclusion of an underscore (“_”) at the third position of the accession number.

New sequences are no longer being assigned GI numbers (source) since they were redundant.  Use "accession.version" instead, e.g. "NC_000012.12".

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text:
Why do bacteria use formylated methionine in the initiator tRNA, while eukaryotes do not?
Could anyone suggest an explanation for the evolution of this trait in bacteria? Does it confer any advantage?
It is also exploited by immunity receptors of some eukaryotes for the recognition of bacteria.
In the literature I was only able to find a paper suggesting a possible role in signalling for protein degradation.

Summary
The question is posed in terms which imply that the formylation of the initiating methionine (Met) of protein synthesis was a relatively late evolutionary development for some purpose not concerned with translation, such as allowing regulation of protein degradation.
My answer takes the quite different view that this was an early evolutionary development in translation, arising as part of the system for initiating at a specific codon — AUG. With time, the initiating system became more sophisticated, with the specificity of initiation residing more in a separate initiating Met-accepting tRNAf which evolved to have a distinct structure from the elongating Met-accepting tRNAm allowing it to be distinguished from the latter and other elongator tRNAs.
I postulate that in the line leading to eukaryotes and archaea a mutation subsequently occurred that resulted in a loss of ability to formylate Met-tRNAf, but that individuals with this mutation were viable as initiation had ceased to be dependent on the formylation for discrimination.
Contemporary systems for initiating translation
I constructed the diagram below for an answer to another question, but it shows some of the common features of initiation of protein synthesis in contemporary eukaryotes and prokaryotes. (The reader who wishes more detail on translation is directed to standard text books, e.g. chapter 29 of Berg et al.)

The common features of initiation in eukaryotes and prokaryotes are:
1. The use of  a Met-accepting tRNA with an anticodon that recognises AUG to insert the first amino acid in a protein.
2. That this tRNA, here designated tRNAf (but also designated tRNAi) is distinct from the Met-accepting tRNA used for inserting Met at other points in the protein during elongation.
3. That the (f)Met- tRNAf is recognized by an initiation tRNA-binding factor (I-TBF in the diagram — a non-standard abbreviation) and not by the elongation tRNA-binding factor (E-TBF in the diagram).
4. That the (f)Met- tRNAf is delivered to the P site of the ribosome (otherwise occupied by the growing peptidyl-tRNA), rather than the A site, to which elongator-tRNAs are bound.
5. In many cases the N-terminal Met is removed by proteolysis after translation.
The features of initiation that differ between eukaryotes and prokaryotes are:
1. That the initiating amino acid in eubacteria and mitochondria and chloroplasts  is N-formyl-methionine (fMet), rather than methionine, as is the case in eukaryotes and archaea.
2. The selection of the particular AUG codon for initiation is different in the two cases. In eubacteria and archaea the 16S rRNA binds to a polypurine, Shine and Dalgarno, sequence; in eukaryotes the normal method involves a complex of the small ribosomal subunit and the Met-tRNA ‘scanning’ from the 5ʹ-end of the mRNA (the secondary structure of which is first unwound.
Argument
As the question about the function of the formylation is posed in evolutionary terms, and fMet-tRNA is involved in the initiation of protein synthesis, it seems valid to consider the evolution of this latter process, however speculative that may inevitably be. The following formulation is my own, although I suspect it represents the orthodoxy in this field. This, of course, does not mean that it is necessarily correct.

It seems likely that initially translation lacked signals for start and stop (and probably also protein initiation factors). I will not deal with termination, other than to say it is probably an easier problem, but initiation would seem to require the introduction of two new features:
(i) The designation of a specific initiation codon AUG†, which, for whatever reason, corresponded to one of the existing amino acids, methionine.
(ii) Given that this initiation codon also served for incorporation of Met internally, the development of a system to select one particular AUG for initiation.
It seems simpler to suppose that (i) preceded (ii), and that is what I shall assume, although the following arguments do not depend on this.
In contemporary initiation the problem of competition between initiation and elongation factors for (f)Met-tRNAs has been solved by the evolution of two separate tRNAs that accept Met — one for initiation and one for elongation. These share certain structural features — their amino acylation is catalysed by the same amino acyl-tRNA synthetase — but they differ in recognition by the protein synthesis factors that bring them to the appropriate P or A site on the ribosome. Despite the lack of formylation of Met-tRNAf in eukaryotes, the structural similarity to the eubacterial tRNAf is such that it can be methylated by E. coli transformylase (reviewed here). However, I imagine that this structurally different tRNA took time to evolve, as, indeed did the protein synthesis factors.

My argument is that the formylation of Met-tRNA was the basis of the initial discrimination between initiator and elongator Met-tRNAs, and this could have arisen even before the gene duplication that led to separate tRNAs.

Why would fMet-tRNA bind preferentially to the P site and Met-tRNA to the A site? The amino acyl tRNAs that bind at the A site all have a free α-amino group that attacks the linkage of the peptide to the tRNA in the peptidyl-tRNA in the A-site at the peptidyl transferase centre. The peptidyl-tRNA, of course, lacks such a free α-amino group. In this respect fMet-tRNA, with a blocked α-amino group, resembles peptidyl-tRNA (see diagram below). One can imagine how structural differences in the P site could hinder binding of Met-tRNA, but allow binding of fMet-tRNA. And, of course, fMet-tRNA would not be able to react if bound at the A site, which might also have structural features to hinder its binding.

If subsequently the discrimination became magnified by gene duplication and evolution of a structurally distinct tRNAf, the need for formylation would be diminished, and one could envisage that its subsequent loss in eukaryotes may have had no adverse effects, or was easy to accommodate.
The question does arise why formylation has persisted in eubacteria, even though it is possible to obtain viable mutants lacking the transformylase. This is what the work alluded to in the question addresses. There is a 2015 paper by Piatkov et al. which suggests that N-terminal fMet can be a degradation system in E. coli. Presumably this arose after the divergence of the line leading to eukaryotes and archaea, which developed other systems for regulating protein turnover.
However I would suggest that, assuming that the foregoing is correct, it is an explanation for the persistence of the formylation of Met in eubacteria, and not the reason for its initial appearance.

Concluding Remarks
At present I know of no convincing evidence that proves my arguments and rejects the proteolysis idea regarding the reason for the evolution of fMet-tRNA. This is the problem with ideas about early evolution. It is compounded here by the facts that suggestion of a role in proteolysis only came up recently and that this is no longer the ‘hot’ field it was 50 years ago.
Nevertheless, I find it hard to imagine a system as crucial and sensitive as protein synthesis incorporating a feature like formylation of methionine if it only had a secondary function. In this case it would seem easier to formylate the N-termini of proteins post-translationally, as for other N-terminal modifications like acetylation. Furthermore, the finding that the eubacteria-derived mitochondria still use fMet can hardly be to control protein turnover, as the vast majority of mitochondrial proteins are translated in the cytoplasm and lack fMet.
†Footnote
I am aware that, in bacteria especially, there are other possible initiation codons, notably GUG, although the initiating amino acid is always (f)Met. (This attests to the importance of the tRNA structure in contemporary initiation.) It is simpler just to refer to AUG in the argument.

This answer is in the form of an argument in response to an unanswerable "why?" question. If anyone demands references to support this I can provide them. If you have access to a library with old text books, you can find them all in Adams et al. Biochemistry of the Nucleic Acids.

I demand references. Or, rather, references would be appreciated, especially so that further reading could be done. Interesting answer nevertheless.

@canadianer — Well that was fun. Let me know if there are any particular points which I haven't referenced that you think I should. I can dig them out. Also, if you — or anyone else — have any queries or notice any typos, do let me know.


text:
Was lactose present in the environment before the evolution of mammals?
Are there lactose sources other than dairy products in nature? I tried to search for it but I did not find anything. The question arose because I was wondering whether lactose-utilising enzymes in bacteria evolved only after the appearance of mammals.

Some seem to argue that lactose can be found in some vegetables and fruits too. A common reference to the sources I could find is a paper by Toba et al. (1991) titled Is lactose really present in plants? Unfortunately, the paper is behind a paywall for me so I can't tell whether the answer they give to this question is "Yes" or "No"!

According to Toba et al. per @Remi.b the answer is no.  Reinvestigation of reports of lactose in a few species came up negative.

@BryanHanson Thanks. Do you want to make it an answer or should I (you are probably more able to write an answer as you have access to the article)?

@Remi.b I'll put it as an answer with nod to you.

Is your question as in your title "is there non-milk lactose in Nature?", or is it "did the lactase gene exist in bacteria before mammals appeared?"  As you explain in your reasoning. The two are not necessarily the same.

The main question is the former, however, I cannot see how would it be plausible that lactase gene evolved before it had a substrate available on which it could work, and so before the organism bearing it had a selective advantage over its competitors. Clearly the reverse is not true, so it is possible that lactose was present but there wasn't a bacterium that evolved lactase before mammal uprising.

I think your logic is unsound. The question of the existence of lactose elsewhere in Nature I find relatively uninteresting. What I do find interesting is that enzymes that can hydrolyse lactose are found even in thermophiles (and indeed are being exploited for industrial dairy use). What they are doing in such bacteria is the question I address in my answer.

Preamble
This is an answer to the motivation expressed in the question:

“…whether lactose-utilising enzymes in bacteria evolved only after the appearance of mammals”

rather than that in the title. The presence or absence of lactose elsewhere in Nature will not decide this question.
Answer
The name lactase is applied to the mammalian enzyme that is able to catalyse the hydrolysis of the disaccharide, lactose, to glucose and galactose, allowing the digestion of this milk sugar by the suckling infant. However bacterial and plant enzymes that are normally referred to as β-galactosidases can also catalyse the same reaction.
The role of the β-galactosidases in bacteria such as Lactobacillus lactis that are found in a dairy environment may well be to hydrolyse milk lactose, as may be that of Escherichia coli, found in the human gut. However this is unlikely to be generally true for all bacteria. This is because β-galactosidases are found in a wide spectrum of bacteria, including extremophiles† which cannot possibly have had access to milk lactose.
β-galactosidases are generally members of a group of enzymes termed glycoside hydrolases and have been categorized into a number of families on the basis of sequence similarity. The enzymes in these families differ in their substrate specificity. To explain the existence of such enzymes in bacteria which do not have access to lactase it has been suggested that their natural substrates may be other disaccharides. This is actually the subject of a PhD Thesis by S.A. Shipkowski, who suggests that some β-galactosidases may actually hydrolyse β-1,4 galactobiose:

The significance of this is that the polysaccharide, pectin, found in certain plant cell walls, could be broken down by by other enzymes in the bacteria, yielding galactobiose.
Conclusion
Although the β-galactosidase in certain bacteria may be optimized to hydrolyse milk lactose, the gene encoding it is almost certainly derived from an ancestral glycoside hydrolases gene, the product of which predated the appearance of mammals and was used to hydrolyse other disaccharides derived from polysaccharides originating from various sources.
† It should be emphasized that the β-galactosidase from extreme thermophiles such as Thermus thermophilus KNOUC114 — isolated from a hot spring — hydrolyses lactose well. Indeed, its thermostablity has attracted interest in its development for use in the food industry (Ahn et al. 2012).

The Shipkowski PhD thesis that you linked, it says on the tile page that it was written to fulfill "requirements for the degree of doctor of philosophy"...? What is the relevance of the thesis to philosophy, though?

@ning — Natural philosophy provides the ‘Ph’ in PhD or the ‘Phil’ in D.Phil. I would also quote Shakespear here “There are more things in heaven and earth… than are dreamt of in your philosophy.”.

Here is the abstract from the article that @Remi.b found:

The presence of lactose in Forsythia, Achras zapota and Zizyphus
  jujuba has been reported previously.  We have reexamined its presence
  using gas-liquid chromatography, paper chromatography and high
  performance liquid chromatography.  Although all three plants
  contained glucose, fructose, myo-inositol (except A. zapota) and
  sucrose, lactose was not detected.  Hence, the presence of lactose in
  the plant kingdom should be re-examined.

"Is lactose really present in plants?" Takahiro Toba, Satoshi Nagashima, Susumu Adachi First published: 1991 https://doi.org/10.1002/jsfa.2740540217
So at least this possible source of lactose in plants is disproved.
EDIT: I also searched Web of Science for "lactose AND plant*" in the title field, and there are no articles other than the one @Remi.b found.

This isn't really an answer to your question, being merely a refutation of one source. However if you will post it do NOT post the quotation as an image, but take the trouble to type it out. Images of text are not indexable and discriminate against people with sight defects.

@David Two excellent points, edited accordingly, thank you.


text:
How is the concept of species defined in asexual organisms?
In asexual organisms such as bacteria, archea and some fungi, as well as in some plants where asexual reproduction is the only reproductive strategy, how can we be unambiguous in defining if an organism belong to a different species from another or not?

I have edited your question — there is no English word ‘specie’ (except an archaic word meaning coined money). Both singlular and plural have an ‘s’ (as an observant biologist might have noticed). This is because the word is derived from the Latin singular, species.

Related: How could humans have interbred with Neanderthals if we're a different species?.

The term species is poorly defined anyway- no reason to change the concept based on sexual reproduction. Dozens of definitions.

Defining a species or describing how one species differs from another goes beyond an animal's ability to mate with another. I get the idea that's where you were heading with this train of thought and you're not entirely wrong. An early technique of classification, developed by Carl Linnaeus, relied on the number of stamens a plant had to define a species. Differences in reproductive organs, mating behaviours and gametes are certainly characteristics that can and do help taxonomists to categorize organisms.
Modern taxonomy takes a number of characteristics into account and there a number of different branches of taxonomy that focus on a certain set of characteristics.
Many forms of taxonomy rely on shared descent to classify organisms based on  shared common ancestors. This is called phylogenetics. Taxonomy also uses shared characteristics, rank-based classification and genetics to define species.
Asexual species can also be classified with these techniques but there some challenges associated. Sometimes asexual species have rapid life cycles (eg. bacteria) and therefore evolutionary change can occur rapidly. Horizontal gene transfer can occur transmitting DNA from one species to another and makes the process of classification tricky.
That being said, evolution is a constant process and genomes are constanly changing. Classifying any species that are continually changing is challenging.


text:
Interpretation of picture of human chromosomes

Does this picture show sister chromatids or homologous chromosomes? If they are homologous then what is YY? If they are sister chromatids then do homologous chromosomes ever appear like this (with the centromere)? Do sister chromatids exist only in prophase-I to anaphase-I of meiosis?

The picture can be a bit misleading because it represents 22 autosomes (autosome = non-sexual chromosome) while there are 22 pairs of autosomes (so the homologous chromosome is not represented). And it represents the whole pair of sexual chromosomes (the individual is a male).
homologous chromosome
For each autosome represented, there is another one which would be its homologous chromosome.
Sister chromatids
As you can see, each chromosome looks like an X. The right and left side of this X there are chromatids (two chromatids per chromosome here). The chromatids are attachedf by the centromere.
Note
Please note that 1) chromosomes looks like they are represented here only during the metaphase (when they are condensed). 2) A chromosome is not always made of two chromatids. Sometimes it is made of single chromatid only. It depends on the moment in the cell life cycle.


text:
Why is egg white alkaline?
According to Tiefenbacher,

Egg white is naturally alkaline with an initial pH of 7.6–7.9 but in storage the loss of carbon dioxide by diffusion through the shell
increases the pH of the egg white up to about 9.7 with age.

The loss of $\ce{CO2}$ means loss of $\ce{H2CO3}$, an acid with pKa of 6.3. This reduces acid and in a neutral solution pH would approach 7. Since it goes up towards 9-10, what is the base? Albumin is a buffer in biological systems but I don't think it is that strong a base. What is the alkali causing pH of around 9-10?

This question has attracted some oddly out of character negative attention in the comments; let's keep discussions civil, please. If you want to ask for clarification, do so politely; if you think it's a good question, put your efforts toward an answer instead of a comment.

I have provided a link for your attribution and corrected it to the author of the book that is listed in Google books. Please note that Google is not the author of material found using its search engine.

In the terms of the question, this can be regarded as calcium hydroxide, with the carbonate being in the form of calcium carbonate. Calcium hydroxide is a stronger base (pH of aqueous solution at 1mm = 11.27) than carbonic acid is an acid (pH of aqueous solution at 1mm = 4.68), so that 1mm calcium carbonate has a pH of 9.91. (Values from Aquion)
Calcium carbonate is, of course, the constituent of eggshell, which crystallizes out of solution when it is deposited in the uterus. Its presence within the egg white is presumably a consequence of this.
–––––––––––––
I would add that one does not generally regard there being a particular base balancing the carbonic acid: when the hydrogen ions are removed there is an increase in the free hydroxyl ions and hence an increase in pH. The way the question is formulated only really makes sense if one assumes that the egg white acquired extra carbonic acid to reduce the alkalinity resulting from the calcium carbonate/hydroxide.


text:
What exactly is a DNA molecule?
Are the two strands of the double helix collectively called the DNA molecule, or is each individual strand the DNA molecule?

Been asked before. Try searching to find it. But you won’t find a satisfactory answer, because it’s not a question that concerns molecular biologists. Semantics are not where science is at in the 21st century.

Does this answer your question? Is a DNA molecule a single strand of polynucleotide or two of them linked together?

@Dirigible Kinda. There doesn't seem to be agreement between the answers posted by different users on that post, though one of the users posted a reference from a book, so I'm going with that. Thanks a ton!

@David I found the post, thanks. As you said, no satisfactory answer. Yeah, modern science isn't too concerned with the semantics of stuff, and rightly so, but sometimes there are loose definitions of some things that do confuse me sometimes while reading course material.

I have actually added an answer to that post as the accepted answer is, in my opinion, an unjustified assertion. There is, as far as I am aware, no formal definition of molecule in a molecular biological context — presumably because there is no need for one.


text:
RNA polymerase Sigma subunit: transcription factor, coenzyme, or what?
Studying prokaryotic transcription, it seems that the α2ββ′ω core enzyme + the sigma (σ) subunit comprise the ‘holoenzyme’ required for prokaryotic transcription. In traditional enzyme nomenclature, this would indicate that the α2ββ′ω is the ‘apoenzyme’ and that the sigma subunit is the cofactor or coenzyme. However, I’ve not been able to find any sources that clarify whether or not the sigma factor is indeed a coenzyme (not cofactor since that has to be non-organic), and if not what it actually is and why. Any clarification would be appreciated.

No.
I don’t think anybody would call the sigma factor of bacterial RNA polymerase — or indeed any other protein — a cofactor or a coenzyme, the subset of cofactors that are organic (the original poster is wrong in his declaration about cofactors, or at least one reputable text book disagrees with him).
I could justify this statement by quoting a definition from the section linked above:

“The catalytic activity of many enzymes depends on the presence of small molecules termed cofactors, although the precise role varies with the cofactor and the enzyme.”

by saying proteins like the sigma factor are not small.
However it is more interesting to me, and more useful to the naive reader, to make some general remarks about definitions in biochemistry and molecular biology.
What are definitions good for?
Definitions of terms are useful for scientific discussion or argument to enable those involved to be sure they are talking about the same thing. They often arise at the stage of a field of science when things are crystallizing after a period of uncertainty or lack of clarity. Even so they may lack precision. Cofactor just means “something else that is needed for certain enzymes to work” — biology is not physics.
Definitions are also useful for students and their teachers. They allow students to try to build a rational picture of a subject that is new to them. They allow teachers to systematize a subject (or lazily set rote-learning type MCQs instead of asking students to explain things).
The student new to the subject might find it helpful to consult glossaries such as those in Molecular Cell Biology, Molecular Biology of the Cell and Pearson’s Biological Glossary.
What are the limits of definitions?
The problem in a fast-growing field like modern molecular biology is that the period of resolution — when old men can form committees to give names to things — seldom lasts. Biology is anarchic, and new things come along that don’t fit into the neat pigeon holes that have been so carefully assembled. Nor do the anarchists or revolutionaries care. They find new things, describe them, and then get on with the next experiment. Why spend one’s time reading yesterday’s newspaper?
But the problem for the student comes when he discovers that everything does not fit into the neat categories he’s been taught, that there is a world beyond lactate dehydrogenase and metal proteases.
Sigma factors — what’s the problem in categorizing them?
The “classic enzymes” studied in early biochemistry catalysed simple chemical reactions between small molecules. However catalysis also occurs in more complex polymerization processes like nucleic acid and protein synthesis, that have the complexity of repetition along a polymeric substrate, and the necessity of having a specific start and stop along that substrate. It turns out to do that, that rather than enzymes such as RNA polymerase being a single catalytic protein they are complexed with other proteins that are necessary for certain of these functions. In the case of proteins like the sigma factor(s), this is complicated by the fact that these accessory proteins do not remain permanently associated with the catalytic protein subunit.
The poster, in his title, asks whether the sigma factor is a transcription factor. The answer to this is yes… and no. And calling it a transcription factor doesn’t really help much. Yes, it is a transcription factor because it is necessary for transcription and different sigma factors can impart a certain specificity to bacterial transcription. No, because the term transcription factor is mainly used for the much more specific proteins in eukaryotes that work in a rather different way.
What to call it? A subunit of the enzyme, is sufficient for Berg et al.. An accessory protein might perhaps add something. But don‘t worry too much about naming it, learn how it works.
Postscript: Other fruitless terminological disputes you may wish to avoid

Why is NAD regarded as a coenzyme and ATP a co-substrate?
Why is it epidermal growth factor, not epidermal growth hormone?
Why is it called vitamin D when it’s actually a hormone?
Should the term, molecule, be applied to double-stranded DNA or the individual chains?
How long must an oligopeptide be before it is called a polypeptide or protein?

No doubt there are others that I have missed that can be found in the list archives.


text:
What determines whether a reaction using ATP produces ADP or AMP?
Most reactions using ATP seem to involve:
ATP → ADP + Pi
but in some the reaction is
ATP → AMP + PPi
followed by hydrolysis of the pyrophosphate:
PPi → 2Pi
Is there any principle that determines which ATP-requiring reactions generate ADP and which generate AMP? And is there any reason why the generation of inorganic phosphate does not proceed as follows?
ATP → ADP + Pi
ADP → AMP + Pi

I have edited your question to remove some of the false assertion it contains (e.g. "hydrolyze the pyrophosphate for additional energy") and focus purely on the essential point of whether a reaction generates ADP or AMP. I have also changed the style. Asking how to memorize something is not, I think, a valid question here — asking whether there is a principle behind something is.

Summary
It is the nature of the biochemical reaction that determines whether a reaction of ATP involves hydrolysis of the β- or γ- phosphoanhydride bond. If a part of the ATP molecule is incorporated into one of the products, the choice of bond to be cleaved emerges from the chemistry of the reaction. If the hydrolysis (with a negative free energy change, ΔG) is being coupled to a reaction with a positive ΔG, hydrolysis of single (γ-) phosphoanhydride bond usually suffices, with the production of ADP and Pi. If the free-energy of hydrolysis of the phosphoanhydride bond is being ‘transferred’ to another molecule in order to ‘activate’ it for a specialized group-transfer role (often in the synthesis of macromolecules) two bonds are often broken: the first (β-) transfers the free energy with the production of pyrophosphate, whereas the second (now in the pyrophosphate) is hydrolysed non-productively (free energy lost as heat) to ensure that the overall reaction is irreversible.
Energy considerations in reactions involving ATP
I have discussed some of this at greater length in an answer to another question, however it is important to clarify this at the outset. In considering biological reactions, it is usual to adopt a thermodynamic approach in which the thermodynamical (Gibbs) Free Energy change (ΔG) of the reaction is considered. This is because, to quote from Berg et al.:

A reaction can occur spontaneously only if ΔG is negative.
A system is at equilibrium and no net change can take place if ΔG is zero.
A reaction cannot occur spontaneously if ΔG is positive. An input of
free energy is required to drive such a reaction.

The literature provides values of the standard free energy changes, ΔGo, for reactions, i.e. the values obtained under conditions in which the concentration of all reactants and products are set at the same concentration. The actual free energy change, ΔG, depends on the concentration of reactants and products (mass action effects).
The hydrolysis of the β- and γ- phosphoanhydride bonds of ATP both have a high negative values of ΔGo of ca. –45 and –30 kJ per mol, respectively†.
Use of ATP to drive unfavourable reactions
In many cases the hydrolysis of ATP is coupled to an energetically unfavourable reaction (one with a +ve ΔGo) so that the coupled reaction has overall negative free energy change and hence the energetically favourable reaction can take place:
A → B                    ΔG =  20 kJ/mol (unfavourable)
ATP → ADP + Pi           ΔG = –30 kJ/mol (favourable)
A + ATP → B + ADP + Pi   ΔG = –10 kJ/mol (favourable)

In this hypothetical example, 20 kJ/mol of the free energy of hydrolysis of ATP is used to convert A to B, the other 10 kJ/mol is lost as heat, but makes the reaction essentially irreversible. The energy of hydrolysis of only a single phosphoanhydride bond is sufficient for this, and is achieved by the hydrolysis of the γ bond with the production of ADP. (Hydrolysis of the β bond would ‘loose’ the second bond in pyrophosphate, where its hydrolysis cannot be used productively.) An example is the conversion of pyruvate to oxaloacetate in gluconeogenesis, in which energy is required to form a carbon–carbon bond:
CH3COCOO– + HCO3– + ATP → COO–CH2COCOO– + ADP + Pi
Incorporation of ATP into products
In some cases there is not only hydrolysis of a phosphoanhydride bond, but a chemical component of ATP is incorporated into one of the products. In this case the actual chemical reaction determines which bond is hydrolysed.
In the first type of reaction a phosphate group is incorporated into the product, in which case this will obviously be the γ-phosphate and ADP will be generated. A simple example of this is the hexokinase reaction:
Glucose + ATP  → Glucose 6-P + ADP
The reaction is essentially irreversible as the energy of the hexose phosphate bond is much less than that of the phosphoanhydride bond.
In the second type of reaction the AMP component of ATP (or similar molecules) is incorporated into one of the products, so that the other product must be pyrophosphate. The obvious example is the RNA polymerase reaction, which for our purposes can be represented as:
------ribose-3′OH + ATP → ------ribose--3′O-PO2-O-5′-Adenosine + PPi
ATP and ‘activation’ reactions: rationale for pyrophosphate
In certain reactions of ATP the energy of a  phosphoanhydride bond is being used to created a bond of similar free energy of hydrolysis, which can itself be used subsequently to activate other reactions. In this case the reaction may involve little of no free energy change, so that it would appear to be easily reversible. In many such cases the β phosphoanhydride bond is cleaved, generating pyrophosphate. The rationale for this is that the pyrophosphate is then converted to phosphate in a reaction catalysed by pyrophosphatases, which has a high negative DG and is hence essentially irreversible because the free energy of hydrolysis of the phosphoanhydride bond in pyrophosphate is lost as heat.
A + ATP → B + AMP + PPi     ΔG = 0 kJ/mol (reversible)
PPi → 2 Pi                  ΔG = –33 kJ/mol (irreversible)

The examples often given to explain this are the nucleic acid polymerase reactions, but, although this applies also to them, the nature of their reaction necessitates the generation of pyrophosphate. To some extent this is the case with most other activation reactions, but it may be clearer to consider one in which the component of ATP is incorporated as a temporary intermediate, rather than as a component of the end product. Such a reaction is amino acid activation for protein synthesis:
amino acid + ATP → aminoacyl-AMP + PPi
aminoacyl-AMP + tRNA → aminoacyl-tRNA + AMP
The ‘activation’ is the formation of bond with a high free energy of hydrolysis in the aminoacyl-AMP from the β phosphoanhydride bond. This is then used to drive the reaction forming a bond between the amino acid and the tRNA. The generation of pyrophosphate ensures the effective irreversibility of this key step in protein biosynthesis.
†Possible role of differences of free energy of hydrolysis
The fact that the standard free energy of hydrolysis of the β phosphoanhydride bond is greater than that of the γ phosphoanhydride bond may also be relevant in some cases, as @user1136 has argued in his answer to this question.

DNA polymerase uses this form of the reaction NTP -> NMP + PPi which is followed by a rapid degradation of pyrophosphate for a very important reason. It makes the reaction irreversible (or quasi irreversible). The backward reaction is (practically) impossible because in order for it to take place, multiple compounds must simultaneously reunite in the catalytic site of the enzyme and multiple non-spontaneous processes must occur simultaneously. So, in the case of the DNA polymerase, an important consideration is the irreversibility of the reaction. On the other hand, if your primary goal is to harvest energy (e.g. metabolism), you can catalyze the reaction through a suite of potentially reversible steps.

I agree with you that the hydrolysis of pyrophosphate makes the reaction irreversible, but your explanation of this in the following sentence does not make sense. A reaction is irreversible because of the free energy change. What is this reaction with multiple components you mention. And what do you mean by "harvesting energy"? ATP is "metabolic energy". It's not used to harvest it, surely.


text:
Why are 6 turns of the Calvin cycle needed to make one molecule of glucose?
I‘ve read that 6 turns of the Calvin cycle are required to make 1 glucose molecule.
But, 3CO2 and 3RuBP are used in one cycle and 6 triose phosphate is produced. Only 5 triose phosphate molecules are required for RuBP regeneration. The remaining 1 triose phosphate has 3 carbon atoms in it. Only 3 more carbon atoms are needed, which can be produced again in the next cycle. So, it would seem that, in total, only 2 cycles are needed to produce 1 glucose molecule. Why do most authors write that six are needed 6?

I still think you should state exactly what you mean by a "turn of the cycle", because that is what your (semantic) argument is about. However, as I don't find the answers so far address that point, I have done so myself. But in future, always, always, always clarify your terms. So much time is wasted by people not being clear what they are arguing about.

Question and Scope of Answer
The question is about metaphors and semantics relating to the carbon stoichiometry of the reactions producing dihydroxyacetone phosphate from carbon dioxide. I have decided to provide a clarification of the carbon stoichiometry, ignoring hydrogen and oxygen stoichiometry (even though I find the reduction and energetics more interesting). The answer depends on what you consider the  metaphor “turn of the cycle” means in relation to this sequence of reactions, and is of little interest or importance.
‘Answer’
The so-called dark reactions of photosynthesis produce one molecule of glucose (hexose) from six molecules of carbon dioxide in a two step process.

6 CO2 → 1 C6H12O6

In the first step — the so-called Calvin Cycle — three molecules of CO2 are converted to the triose, dihydroxyacetone phosphate (DHAP).

3 CO2 → 1 C3H7O3PO32–

In the second step, similar to the final part of gluconeogenesis, two DHAP molecules are converted to glucose.

2 C3H7O3PO32–  → 1 C6H12O6

The reason the reactions of the Calvin Cycle are considered a metabolic cycle is that one of the intermediates, the pentose ribulose 1,5-bisphosphate (RuBP), is consumed by reaction with CO2 to give two molecules of triose:

1 ribulose 1,5-bisphosphate + 1 CO2 → 2 3-phosphoglycerate

The problem with the epithet cycle in this case is that it differs from the tricarboxylic and urea cycles where a single molecule enters the cycle and is converted to a molecule(s) leaving the cycle in a single series of reactions regenerating the molecule with which the input molecule first reacted. In the Calvin Cycle,  the initial reaction between RuBP and CO2 has to occur three times for the stoichiometric production of one molecule of the triose, DHAP.
Many diagrams that represent the series of reactions as a cycle tend to be stoichiometrically incorrect (or more charitably, ignore carbon stoichiometry to emphasize energetics etc.), rendering the metaphorical expression “turn” of the cycle almost meanless. This is unfortunately the case for the diagrams in two other answers — one molecule of RuBP and one molecule of carbon dioxide clearly cannot generate one molecule of triose DHAP and regenerate the RuBP.
The diagram below from Berg et al. is stoichiometric as it considers the total number of molecules to produce one of DHAP. (The three arrows to the product, Ribulose 5-P, imply three molecules are produced.) I have modified the diagram by de-emphasizing other aspects of the reactions than inputs and outputs.

Conclusion
If you consider (as the anonymous source in the question and many others do) that each time one molecule of RuBP reacts with one molecule of CO2 a “turn of a cycle” is initiated, then six “turns” (or “rounds” à la Berg) are required to produce one molecule of glucose; if you consider each series of reactions that produces one molecule of the triose, DHAP, represents one “turn of a cycle” then two “turns” are required. I personally would avoid the metaphor, state what happens, and concentrate on the more interesting aspects of the process, which are the energetics and reductions using the products of the light reaction.

@user338907 — Thanks. Corrected.

You're looking at a version of the Calvin cycle that has been simplified to consider 3 "turns" all together as the steps necessary to produce one 3-carbon product. A hint is that you see three CO2 molecules entering rather than one.
You can look for another diagram that has a one-carbon version, like at https://en.m.wikipedia.org/wiki/Calvin_cycle

(image credit: Mike Jones, CC BY-SA 3.0 https://creativecommons.org/licenses/by-sa/3.0, via Wikimedia Commons)
However, arguably this diagram doesn't make clear that 2/3rds of the 3-phosphoglycerate gets recycled back into the Calvin cycle in the abstracted "phase 3".
So yes, you need 2*3 = 6 "turns" of the cycle to make a 6-carbon product. Importantly, though, it's not like there is some singular machine performing this cycle - all the steps are free to proceed on their own independently and simultaneously. The Calvin cycle (and the Krebs cycle in complement) are just the simplification down to the minimum individual reactions.

Please include a diagram in your answer, otherwise only those that already understand will be able to follow. Alternatively, comment and vote to close. The question is similarly incomprehensible.

@David Added; I think the question is pretty clear. Textbooks often say you need "6 runs" through the Calvin cycle to make glucose; this makes a lot of sense because you're taking in one carbon through CO2, so to make a 6-carbon sugar you need to do something 6 times. OP also is looking at a picture showing "3CO2 and 3RuBP is used in one cycle and 6 triose phosphate is produced" - this is equivalent to three runs. That's a handy condensed form because you can consider one "free" triose phosphate to be made per 3 CO2; "free" as in it isn't used up in regenerating the reaction products.

I think you didn't got Calvin cycle properly
For ease of understanding, calvin cycle can be described under three stages; Carboxylation, Reduction, and Regeneration

1.CARBOXYLATION-
It is the fixation of CO2 into stable organic intermediate. it is most crucial step of the calvin cycle where CO2 is utilised for the carboxylation of RuBP. This reation is catalysed by the enzyme RuBP carboxylase which results in the formation of two molecules of 3-PGA.

2.REDUCTION-
These are a series of reactions that lead to formqation of glucose. the steps involve utilisation of 2 molecules of ATP for phosphorylation and 2 of NADPH for reduction per CO2 molecule fixed.The fixation of 6 molecules of CO2 and 6 turns of the cycles are required for the formation of one molecule of glucose.

3.REGENERATION-
Regenration of the CO2 acceptor molecule RuBP is crucial if the cycle is to continue uninterrupted. the regeneration steps require one ATP for phosphorylation to form RuBP...
HERE you see only one molecule of CO2 is being used ... and our product i.e, Glucose is a hexose sugar(6-Carbon)... Therefore, we have to carryout calvin cycle six times...
you can check for cycle on link https://en.wikipedia.org/wiki/Calvin_cycle  ....
HOPE IT HELPS

David, I hope now my answer is complete. Thankyou for your suggestion.

Sorry, but I don't think the diagram addresses the question of carbon stoichiometry, which is what I think the question is about. I have added my own answer now, so I have deleted my previous comments.


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Self-replication in the genome in the seed
Is the genome in the seeds of the plant turned off?  That is, does the DNA in the seed not self-replicate?
My second question is, what are the cells feeding on inside the seed before it is planted?

What makes you think that DNA replication is repressed in seeds?

@user438383 — He doesn’t say he thinks that, he’s asking. Seems a reasonable question, but one which I imagine an Internet search would answer.

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, we expect you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). See also this sites criteria for "homework", which can apply to questions even if they are not assigned as homework. Finally, please only ask one question at a time. Thanks!

I have found that when learning about a new area starting with a relatively accessible and reliable source like Khan Academy is very helpful. Wikipedia is also generally a good starting point and you can then check their references. Online platforms called MOOCs offer free (or very low cost) courses on a wide variety of subjects — two I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

DNA in cells in general replicates when cell division occurs (unless it is a cell that contains many nuclei or multiple copies of its own genome, in which case DNA would replicate as copies are made. Multinucleate cells include things like the mycelium of fungi, and here is an example of a bacterium with thousands of copies of its own genome).
As long as a plant embryo is developing, then the cells are dividing and the DNA is replicated. You might be thinking of the stage of seed dormancy; insofar as during this stage the embryo is no longer growing, cells aren't dividing and therefore DNA is indeed not replicated. I don't know whether we could say the genome is "turned off" however, DNA's role isn't just being replicated, more importantly its role is to be transcribed into RNA which leads to the proteins the cell needs to function being created. I couldn't find whether DNA transcription happens during cell dormancy but it's plausible enough that it is at least slowed down as well. The cells presumably don't have much to do during this period and you wouldn't want them to do much, to conserve energy.
Seeds contain nutrients that can feed the embryo until it can feed itself (for plants that is the moment when they germinate enough to photosynthesize). That is where flour comes from!


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The protostome/deuterostome distinction and why it is important
As I unerstand it, at some point an embryo develops a hole; this hole continues to punch through, and eventually makes an opening at the other side of the embryo. If the original hole becomes the mouth, then the organism is called a protostome. If the second opening becomes a mouth, then the animal is called a deuterotome.
My first question is, is this distinction made only for organisms who have two openings? In other words, would an organism with only one orifice be called a protostome, or would it be neither?
Why is the protostome/deuterostome distinction important? Why does it matter whether embryo develops a mouth from the first or second orifice?

The terminology is really just describing the process in embryonic development that you describe: deuterostome means "second mouth"; protostome means "first mouth."
The significance of these groups is in evolutionary history and cladistics. All of the deuterostomes have a shared common ancestor that is not shared with any protostomes, and vice versa. Regardless of developmental pattern or number of openings during development, no other organism should be given these names (and if it is, and the correct ancestry is determined later, they would be moved out of those categories accordingly).
This is actually really important in biological classification of organisms, and before modern genetic techniques these types of shared characteristics were the best way to determine shared ancestry. Think a bit about what it means for an organism with two openings to differentiate one as mouth and the other as anus: once they are strongly differentiated, there is a huge barrier towards going "backward" and "switching" openings because mouth and anus have very different functions. However, if you go from having one or no openings to having two, before there is specialization, the distinction of which one develops first isn't likely to be that advantageous one way or the other.
Nephrozoa contains the deuterostomes and protostomes, consisting of almost all extant animals. However there are also other animals that are neither. For example, Xenacoelomorpha might be the closest thing to a bilateral animal with only one orifice, though they don't really have a true gut at all.

Thanks for the answer; if I could as a follow up question: In my class we are just focusing on 6 phyla of animals: Porifera, Chordata, Mollusca, Cnidaria, Arthropoda, Echinodermata. Is it possible to say that some of these phyla are completely composed entirely of protostomes, and some of deuterostomes?

@Ovi I can't really help you with your homework more than I already have, but if you see the Wikipedia pages for deuterostomes and protostomes (and most likely your textbook as well...) the answer to your comment question should be quite apparent.

Thanks for all your help; I will check the wikipedia article. Anyways it's not a homework question, I am studying for a test. My book is very short (written by professor specifically for this class) and doesn't seem to answer this question.


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Basic question about phylogenetic trees
The following is an illustration rom my book of the phylogenetic tree of 6 animal phyla (the red stuff is mine):

I think what's causing some confusion is that there are no names/years at the circled nodes.
My first question is, was there an actual population between nodes (ex.) 2 and 3?
I would like to check if my understanding of the tree is correct:
Before node 1, there was a population which split into two populations: Porifera and the population between nodes 1 and 2 which we will call population 1-2. This population is unnamed on the diagram, either because we don't have a name for it, or because members of that population no longer exist, or to keep the diagram simplified.
Next, after some millions of years, population 1-2 split into the Cnidarians and population 2-3. Etc.
Is my understanding correct?
Thank you very much.

Yes, your understanding is correct.
That being said, it is standard to refer to population / species at specific points in time. Also, it is standard to refer to these ancestral populations relative to what they are the ancestors of. For example, we generally don't refer to the population 2-3 (as you named it) but we rather refer to the node/population/species 3 as the Most Recent Common Ancestor (MRCA) of Athropoda, Mollusca, Chordata and Echinodermata. The tree presented here is not complete but all Athropoda, Mollusca, Chordata and Echinodermata are Bilateria while Cnideria and Porifera aren't. Hence, you could say that the ancestor at node 3 is the MRCA of all Bilateria.
Related posts

This intro to phylogeny
If dinosaurs could have feathers, would they still be reptiles?


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Are all tastes just a combination of sour, sweet, bitter, etc.?
For example, can the taste of pineapple be isolated to just a certain amount of "salty-taste-triggering-molecules" and "sweet-taste-triggering-molecules" etc.? Can our current understanding of the gustatory system predict the taste of a new substance (for example we could predict it tastes like chocolate) just based on the amount and ratios of these molecules?

Interesting question.

The brain perceives taste or flavor as a combination of input from taste buds, the olfactory system, and even pain receptors (spicy foods). Other food contents, such as metal, spice, fat, pH, and even dissolved gas content seem to contribute.

While there are 5 types of taste receptor, there are some 2000 olfactory bulbs encoded by 1000s of gene.  As such, it is not possible to predict how something will taste in a simplistic 5-taste combo.  However, this is an area of active research, such that structural models are used to develop taste enhancers, artificial sweeteners etc.
Sources:

http://www.sciencedirect.com/science/article/pii/S0976120913000041
http://health.howstuffworks.com/mental-health/human-nature/perception/taste.htm
http://www.livescience.com/17684-sixth-basic-taste.html


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Is it possible to completely puncture a human hand and have no blood come out?
Illusionist David Blaine sometimes performs a trick where he takes a very long and thin ice pick, insterts it in his hand, and comes out the other side (the palm). However, there is no blood present. Is this possible at all? (Warning: Graphic Content) Here is the video (already timestamped)

Yes, it is possible.
The needle should be passed through Fistula, which is an abnormal or surgically made entry between an empty or tubular organ and the body surface, or between two empty or tubular organs.
According to Magic Secrets Explained >>

This provides us with a reasonable explanation for Blaine's needle
trick. He has a fistula through his arm. He created this fistula to
himself, by repeatedly causing small damage to his arm in the same
direction, probably by actually stabbing a needle into it.
He basically drilled a tube of scar tissue through his arm just so he could perform this one trick.

In order to further cement their logic, they attached another video of a man who had a fistula through his body which empowered him to have swords cut through his body without hurting him.
Fistulas are also incorporated in dialysis, and infact referred to as dialyses’ lifeline. An article by Big D and Me expands more on this plus explains how it also threatens lives.


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MAPK signalling pathway initial conditions
I would like to know the initial conditions and locations of the chemical reagents in the MAPK cascasde.
I'm going to plug this information into a reaction diffusion simulation.
From reading various papers I have gleaned the following:
[MKKK]total = 100nm; [MKK]total = 300nm; [MAPK]total = 300nm

MKKK]total = [MKKK] + [MKKK-P]
[MKK]total = [MKK] + [MKK-P] + [MKK-PP]
[MAPK]total = [MAPK] + [MAPK-P] + [MAPK-PP]

Ras-GTP seems to have an initial concentration of 30 nM and seems to start at the nucleus.

ppMAPK seems to have an initial concentration of 0.

I can't figure out where the rest of the reagents start and what thier concentrations are. People always seem to miss this out from their work...
Thanks

This is probably because it is not important for most people. I did work in this field and it was interesting that proof that the signal came down the cascade (and via which) but not how the concentration were.

@Chris what do you advise doing? Should I make the other reagents equally distributed throughout the system? Should I just make up concentrations?


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Why do crocodiles have a high concentration of lactic acid in their blood?
Crocodilians have high concentration of lactic acid in their blood. This is the cause that prevents them from prolonged intense activity, since prolonged intense activity causes the muscles to secrete more and more lactic acids, up to the stage where the lactic acid level become lethal - even for the crocodile.
So the shortcomings of high level of lactic acid are clear, it restricts activity and endangers the croc to death.
So why in the first place crocodiles have high level of lactic acid? What is the advantage of this?

Remember that not every evolved trait is advantageous. Some can be maladaptive, brought about by selection for another adaptive trait.

Do you have a reference showing that lactic acid is normally high in the blood of crocodilians? Or is it simply that they can tolerate higher levels of lactic acid? The two are quite different circumstances.

https://en.wikipedia.org/wiki/Lactic_acidosis#Reptiles Reptiles, which rely primarily on anaerobic energy metabolism (glycolysis) for intense movements, can be particularly susceptible to lactic acidosis. In particular, during the capture of large crocodiles, the animals' use of their glycolytic muscles often alter the blood's pH to a point where they are unable to respond to stimuli or move.[19] Cases are recorded in which particularly large crocodiles which put up extreme resistance to capture later died of the resulting pH imbalance.[20]
some reptiles can sleep underwater anaerobically.

As far as I can tell from a brief literature search, the explanation for the high concentration of lactic acid in the blood of crocadilians is two-fold:

The lactic acid is generated from the anaerobic muscular activity involved in capturing their prey.

In a gloss from Science Daily a journalist writes:

Concealed below the water's surface, crocodilians stealthily approach animals that have come to drink, spring upon their prey, and drag them into the water and drown them. This powerful burst of activity generates an extraordinary amount of lactic acid in their muscles…

It is maintained at a relatively high concentration in blood so it can be used to acidify the stomach for the digestion of its meal.

I am less sure about this. Certainly the crocodile needs to acidify the stomach, and the scientific article glossed by the Science Daily shows how the lungs are bypassed to allow carbon dioxide to reach the stomach:

During this period of digestion crocodilians divert blood through a special vessel that bypasses the lung, named the left aorta… …when crocodilians are digesting a meal, they chose to shunt and direct CO2-rich blood straight to the stomach where glands make use of the CO2 to form gastric acid and bicarbonate. Consequently this shunt enables crocodilians to secrete gastric acid at a rate that is approximately 10 times the highest rates measured in mammals.

My supposition is that lactic acid also contributes to the acidity, but I may be wrong on this point. If anyone has information about this, I shall be happy to add it to my answer.


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Which horn configuration is more effective as a weapon?
For horned animals, there are two common configurations of cranial horns.

One long horn above the nose (Styracosaurus, Rhino).
Two long horns above the eyes or forehead (Triceratops, cattle, African Buffalo).

In many species, the cranial horns are used as a weapon: both for intra-specific combat (e.g. dueling over mate) and defense against predators.
My question is which configuration is more effective and lethal: 1 nose horn or 2 brow horns?
I suggest dividing the answer into two categories: Ceratopsid dinosaurs and extant mammals.

Why might that be that the vast majority on horned animals are two horned?

In dinosaurs, single-noseed-horned ceratopsids were abundant as well.

My question is about the present, not the past. Did you do any research about this yourself? What did you find out? On this site, failure to present some search result is a reason to down vote and close vote, so if you're done any, it would be beneficial to you to quote and link to it.

Also at play are other components of anatomy: stature, closeness to ground, skull strength, neck muscles, core/limb design/musculature... Not to mention environmental drivers for these adaptations: substrate texture, compaction, slope, etc. In the end, asking which is better isn't really a great biological question. Both evolved in response to ancestral morphological traits adapting to different environments/behaviors. I don't think the question needs to be closed, per se, but I think it's a low quality question as written. I hope the eventual answer includes mention of the issues I raise.

this is pure opinion, what is best is going to depend on the rest of the skull and the rest of the animals anatomy, how it can move and balance. then you have to consider lethal against what? different attacks work differently against different predators.

Note
Since a lot of people are upvoting this (and some downvoting of course), it's worth noting that it's not directly answering the OP's stated interests of dinosaurs etc. However, I think it's probably a more useful answer in general for people interested in horned animals.
Not intended to be the only answer on this question!
Answer
This doesn't fit neatly into your dinosaur vs mammal dichotomy, given the obvious differences in ecology and biomechanics, but I would suggest looking at horned beetles to think more about the effectiveness of horn weapons in different contexts. In some cases both configurations you describe (among others) are present in the same species and vary widely in the same genus.

One review paper here suggests that behavioral variation can account for the presence/absence of horns across species:

Thus, tunneling likely set the stage for the evolution of one-on-one fighting in tunneling taxa, such as Onthophagus, and the evolution of weaponry, such as horns, that is useful in one-on-one combat and in the blocking of narrow tunnels to prevent other males from accessing the female.6,26 Consistent with this scenario, horn possession is widespread and elaborate in tunneling scarabs, where it appears to have evolved independently several times, yet is virtually absent in any other group of non-tunneling scarabaeine beetles.31

One paper cited in that review presents phylogenetic comparative evidence for this view, in the following figure:

These suggest that the horn morph in question (triceratops-style) is useful in intraspecific sexual competition in a physically constrained context yielding single opponents (tunnels). This is somewhat similar to familiar examples in large mammals that do "single combat" mating competition. Direct confirmatory tests of this hypothesis were performed in separate work. There is some evidence in related beetles that this is particularly in response to an environmental stimulus of high beetle population density, and thus intensified sexual competition.
Thus, intraspecific sexual competition appears to be responsible for horn emergence in most cases. One classic study looked for ecological correlates of evolution of various horn configurations in a phylogenetic context, though the results seem ambiguous to me due to the quite small number of taxa. Nonetheless, the study highlighted a possible tradeoff between head horn presence and flying, and the presence of horns on the head in some ecological contexts. So, elaborate or large horns specialize the organism for fighting rather than for other activities.
One likely hypothesis is that mating competition is severe enough to drive an evolutionary arms race, leading to horn innovations that might yield advantages. Agent-based modeling approaches support this general theory, but no one seems to have directly tested this hypothesis with real beetles.


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Effect of heat-treatment of Vitamin C
When it is in the body, does it matter if vitamin C has peviously been heat-treated? Can the body still use it?
For instance, if vitamin C is added to 90 degree celsius water does it matter if you drink all of the water? Will you still gain the vitamin C?

Disclaimer: the denaturation is the process of protein unfolding from their native state. Since vitamin C is not a protein, it cannot denaturate. I think that the word you're looking for is simply "degradation".
Vitamin C can exist either in its reduced form L-ascorbic acid (L-AA) or in the oxidised form dehydroascorbic acid (DHAA). The active (antioxidant) form of vitamin C is the former; however, there are enzymes in our body that can convert DHAA back into L-AA.
In this article, the authors seek to evaluate the thermal stability of both L-AA and DHAA in broccoli. Their results are the following.

Thermal treatments (for 15 min) of crushed broccoli at 30 to 60 degrees C resulted in conversion of l-AA to DHAA whereas treatments at 70 to 90 degrees C retained vitamin C as l-AA.

So, cooking the vitamin C does not alter its structure and your body will still be able to use it. Another reason to eat broccoli, I guess.

Thank you for this information. This is exactly the response I was hoping to get.


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What are the roundish objects in this sketch of a tracheid?
I got this picture from the Wikipedia entry for Tracheid. What are the roundish objects in the sketch?
Also are tracheids sclerenchyma cells?

It's a good idea to do some reading before posting. Your question whether tracheids are cells is answered in the very first sentence of the article that you took the diagram from: "Tracheids are elongated cells…"

The 'roundish stuffs' you are seeing are called 'pits'. The Dictionary of Botany defines a pit as '[a] cavity in the secondary cell wall, allowing exchange of substances between adjacent cells'. The pit itself is composed from a aperture, named the pit cavity and an environing membrane called the 'pit membrane'. The pit is comparatively analogous to the plasmodesmata connecting protoplasts by thin connecting vessels. The difference exists in the presence of pits within the xylem while plasmodesmata arise between other non-vascular cells additionally.
To respond to your second question, where sclerenchyma cells are strengthened, lignified cells, tracheid cells are indeed the 'tracheary' or vascular specialisation of sclerenchyma tissue.
For information regarding the Dictionary of Botany, the website is available from: http://botanydictionary.org/pit.html
Information concerning ground tissue is available from: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/ground-tissue