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Apparent paradox in Glucagon action
Glucagon stimulates glycogenolysis and gluconeogenesis, thus increasing the plasma glucose concentration — so that tissues get enough glucose in the fasting state.
However glucagon also inhibits glycolysis. In this case, what is the point of having high blood glucose if it cannot be catabolized?

Hint: Are there some organs on which glucagon does NOT act (i.e. which do not have significant numbers of glucagon receptors)? Could these organs benefit from the increased glucose levels?

Summary
The apparent paradox is resolved by the fact that not all tissues possess receptors that cause them to respond to glucagon or, more generally, to the same hormone. Where different tissues do respond to the same hormone, the tissue response may differ because of differences between the pathways or particular enzymes within the different tissues. Tissues that use glucose in starvation generally do not have glucagon receptors. In the related situation of response to epinephrine, the glucose utilizing tissue, skeletal muscle, does not contain the particular enzyme isoform that is subject to cyclic AMP-dependent control in liver.
General principles of hormone action in the regulation of metabolism
Metabolism in simple, especially unicellular, organisms is regulated by supply and demand. The mechanisms underlying this are mass action and allosteric activation or inhibition of key enzymes. In more highly developed organisms with differentiated tissues serving specialized functions there are times when this intercellular control must be over-ridden to produce an integrated response to the overall benefit of the organism. This is the rationale for hormonal control.
An integrated response does not mean that each tissue responds in the same way. It means that each tissue responds in a manner that is appropriate for the organism as a whole, given the function of the tissue and its priority (e.g. for rationing of energy sources). A simplified example of how this is achieved is illustrated below.

Tissues 1 and 2 (e.g. liver and skeletal muscle) both contain pathway P1 (e.g. glycogen degradation), but only Tissue 1 responds to hormone H1 (e.g. glucagon) because Tissue 2 does not have the receptor R1, for H1. (SM is the second messenger involved in the signalling, e.g. cyclic AMP.)
Tissue 2 (e.g. adipose tissue) does have the receptor for hormone H1, but responds in a different way because it lacks pathways P1 and P2 of Tissue 1, but contains a tissue-specific pathway P3 (e.g. triglyceride breakdown).
Hormone H2 (e.g. epinephrine/adrenalin) affects Tissue 2 (e.g. skeletal muscle) as well as Tissue 1 (and 3), but the response is only partially similar in that although they share pathway P1, Tissue 2 lacks pathway P2 (e.g. gluconeogenesis).
Differential response to glucagon
Put simply, glucagon is a signal for starvation. Hence the appropriate integrated response is for those tissues (liver and adipose tissue) that can supply energy sources (glucose and fatty acids, respectively), and those tissues with greatest need for the scarcest resource (brain with its requirement for glucose) are supplied it, while those tissues that can manage with the alternative (fatty acid) are made to use it instead.
The brain has no receptors for glucagon (or insulin), so it can utilize the glucose made available by the liver. (Likewise the erythrocytes.)  The main factor preventing other tissues using glucose is that they have insulin-sensitive glucose transporters and the blood concentration of insulin drops in starvation. It is only liver where there is need to make sure that the glucose produced by gluconeogenesis is not glycolyzed.
But doesn’t the paradox remain if we consider epinephrine?
The function of epinephrine is to initiate the ‘fight or flight response’, which involves supplying energy metabolites for skeletal muscle contraction. This involves both the liver, which breaks down glycogen to supply glucose to the muscle through the blood, and the skeletal muscle itself, which breaks down its own stored glycogen. As epinephrine also acts through cyclic AMP, which inhibits glycolysis in liver, why is glycolysis not inhibited in skeletal muscle?
The answer to this is that cyclic AMP inhibits glycolysis by phosphorylating and activating the liver enzyme PFK2, which catalyses the formation of fructose 2,6-bisphosphate, an allosteric activator of phosphofructokinase. Skeletal muscle has a different form of FPK2 which is not affected by cyclic AMP, lacking the regulatory phosphorylation sites. (It is regulated by other metabolites.) Hence in liver, glycogen, through cyclic AMP, causes the concentration of fructose 2,6-bisphosphate to decline and, thus, the activity of phosphofructokinase (PFK) to be decreased, preventing glycolysis; whereas in muscle the concentration of fructose 2,6-bisphosphate does not change.

This regulation of phosphofructokinase by fructose 2,6-bisphosphate is described in sections 16.2.2 and 16.4 of Berg et al. (although they seem to have forgotten about skeletal muscle). However as the overall mechanism and details are somewhat complex, I have produced a simplified summary diagram of my own, above, in which the green lines indicate activation, and the red lines inhibition.


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May two reactions, that share the same reactant, fire at the same moment?
I'm studying metabolic networks from a bioinformatics point of view, but I guess my question is pretty biological so I thought that maybe here I could get the best answers.
So, as the title says I was wondering, if I have one metabolite that is involved in two different reactions as reactant, is it possible that they both start at the same time at a certain point? I'm assuming that, in order to fire, the reactions need a certain amount of that metabolite, so if there is enough concentration to make both start, can the two reactions actually start in the same exact moment? What if the concentration of the metabolite is not enough to "satisfy" both?
Between the lines, are reactions mutually exclusive with respect to the shared metabolite or not?
In my mind, the quickest of the two gets the amount that it needs from the metabolite and the other one will just wait for the latter to have again enough concentration, is this intuition correct?
If you think this question is not appropriate, I will delete it and ask somewhere else. Any suggestion, also books or similar about the topic, is welcome!
I'm a computer scientist and I know just the basics of molecular biology, but I think that my job is mainly speaking to biologists in order to find solutions to different problems, so this is the reason why I chose to write here basically.

As a computer scientist, a little molecular biology is not going to help dispell your incorrect assumptions. You need to read some basic enzymology to find out how substrate concentration affects enzyme reactions and appreciate the stochastic nature of molecular interactions. Try section 8.4 of Berg et al. at NCBI Bookshelf.

What do you mean by "moment"? How big is your time interval? Usually chemical reactions are modelled as Poisson process i.e. in an infinitesimally small time interval, the probability of happening of more than one events tends to be 0. Perhaps you should read about stochasticity in chemical reactions (check out papers by Dan Gillespie). When the amount of a reactant approaches such limits that you describe, the stochastic effects dominate. These reactions can be simulated using Monte-Carlo algorithms. However, your question does not directly concern biology and is hence off-topic.

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Is there a name for the use of sunlight in metabolic processes?
"Photosynthesis" is what is used to describe how plants use sunlight to synthesize sugars, but, I also heard some animals like humans use sunlight in the process of creating vitamin D. Is there a comparable name for when sunlight is used by animals in a metabolic process?

Perhaps you would want to replace "animals" with "organisms". I don't think there would be a special term just for animals.

Photometabolism or photocatalysis would be apt terms and the former would specifically refer to biochemical reactions.
Photometabolism is also used in the context of the light dependent conversion of 7-dehydrocholesterol to Vitamin-D.
A google scholar search with photometabolism returns many peer-reviewed articles that have used this term. Some examples:

Photometabolism of 7-dehydrocholesterol to previtamin D3 in skin.
The photometabolism of glucose by an hydrogen-adapted alga
Photometabolism of Heterocyclic Aromatic Compounds by Rhodopseudomonas palustris OU 11.

"photo-metabolism" also, e.g.here.

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Why are there three stop codons but only one start codon?
I was wondering whether there is any specific reason that there are three stop codons but only one start codon in prokaryotic and eukaryotic cytoplasmic mRNAs.

There are more than 1 start codon. E. coli have 3, for example.

Yes, I just saw that. Though in most cases AUG dominates. Thanks

@David: I guess you didn't read all of my answer. I'm waiting for you to dive into the reasons behind the varying translation efficiency of different start codons. I'm not sure the OP really wants that level of detail for a question like this.

@David: and don't forget to downvote the answers on this question: https://biology.stackexchange.com/questions/9990/why-is-aug-the-initiation-codon

@Fizz — Although not really relevant as a comment to this question, I am obliged for your pointing out another which is certain to have poor answers.

Disclaimer
It is important to realize that it is not possible to answer questions of this sort (the evolution of translation)  in anything other than a speculative manner. Please bear this in mind, especially if you find the speculation below persuasive.
Summary
It is suggested that the redundancy of termination codons is largely similar to that for ‘elongation codons’ decoded at the A-site of the ribosome, although protection against suppressor tRNAs may also be a factor. The consideration here is, therefore, mainly focussed on the question why there is only a single codon for methionine (initiation and elongation), and I suggest this may have been a combination of the late appearance and infrequent usage of methionine, together with the particular requirements for an initiation tRNA at the P-site of the ribosome, where standard wobble is apparently not possible.
Disposing of a Red Herring
Although alternative initiation codons are sometimes used, this usage differs in prokaryotes and eukaryotes, is very limited, and is not seen with the use of methionine in elongation. I would therefore consider this does not invalidate the question, but perhaps rephrase it as:

“Why does the genetic code have only one codon assigned to methionine,
  the initiation codon, whereas other amino acids and termination have
  generally more than one?”

Time of appearance of and extent of use of Methionine
It is generally thought that genetic code initially encoded a small number of amino acids, and that this number increased over time. Methionine is one of the most complex (and energetically expensive) to synthesize (see Wikipedia entry), so is likely to have appeared late. One can argue that most of the codons would have been ‘taken’ (assigned) by that time. This argument is consistent with the situation for tryptophan, the other amino acid which has only a single codon, and which is also synthetically complex. Furthermore, these are the two least abundant amino acids so on can argue that their number of codons reflects their relative usage.
Admittedly, there need only be one stop codon per protein, but it is possible that the mechanism of termination evolved before that of methionine-specific initiation. (Initiation might originally have been from the 5′-end of the mRNA.) There is also the question of protection against suppressor tRNAs, but I shall delay discussion of this until the end.
The unique features of the initiator tRNA
Elongation involves several dozen amino acyl-tRNAs being recognized by an elongation factor which binds them to the A-site of the ribosome, at which 3′-codon wobble occurs where the redundancy of the genetic code allows and the anticodon of the tRNA has evolved appropriately.
In contrast initiation involves exclusive recognition of a special tRNA by initiation factors but not elongation factors, and subsequent binding at the P-site The tRNA has unique structural features that allows it to be N-formylated — structural features that are retained in eukaryotic initiator tRNA, even though there is no transformylase in eukaryotes. (see this SE Question]
This uniqueness may explain why there is only one tRNA for initiation. However one might ask why there is a not a group of methionine codons (e.g. AUA as well as AUG) recognized by the same initiator tRNA through wobble. The reason for this would seem to be that the P-site does not allow third position wobble (as I explain in the answer to a related question), so the initiation met-tRNA would be codon-specific.
Loose Ends
Although perhaps straying a little from the question, one might still ask why there are not alternative elongation codons for Met — e.g. AUA, which could have been ‘stolen’ from Ile, which already has AUU and AUC. In fact in mammalian mitochondria this codon reassignment has happened, but unfortunately does not help explain things. In mitochondria there is only one tRNAmet for both these codons, consistent with the simplification of tRNAs for the small mammalian mitochondrial genome. Initiation requires the formylation of the methionine.
I will finish by returning to the question of multiple termination codons, which are not really consistent with my suggestion that the extent of redundancy reflects usage. Although termination codons, like elongation codons, are recognized at the A-site they are recognized by protein release factors rather than tRNAs. This means that they will be affected differently by a mutation in a tRNA that alters the anticodon. For an amino acid codon, an altered non-cognate tRNA would only cause some misreading and an altered cognate tRNA might be neutralized by wobble or by duplicate or redundant tRNA genes. AS termination codons are not normally decoded by tRNAs, a suppressor tRNA would cause read-through at all the suppressed codons. The presence of two alternatives means that termination would be likely to occur within about 30 codons 3′ to the original termination codon. Variation in the length of the N- and C-termini of proteins is common among related species, and thus need not be deleterious to the cell.
Related SE Questions

‘Wobble’ in Initiation and Elongation — I have contributed an answer to this.
Why is AUG the Initiation Codon? — I will respond to this presently.
Redundancy of the Genetic Code — I have contributed an answer to this.
Initiator and Elongator tRNAs in Translation — I have contributed an answer to this.

Since my initial post of an answer I have added a section considering the possible reasons for multiple termination codons.

The simplest answer is that redundancy has evolved into these codons. A cell would not want a mutation at the stop location and have the protein get excessively large before another stop codon is hit.
Here is a better explanation and if you are very interested in the subject, I would recommend Lehningers Principles of Biochemistry.
Lehninger, A. L., Nelson, D. L., & Cox, M. M. (2000). Lehninger principles of biochemistry. New York: Worth Publishers

it would be helpful if you expanded your answer with some of the material from the link, e.g. "In prokaryotes, E. coli is found to use AUG 83%, GUG 14%, and UUG 3% as START codons. "

But it would also not "want" a mutation in the start codon so that no protein at all was made.

Somewhat obvious, there's weaker selection on the stop codons than on the start codons:

The selection affecting stop codons is relatively weak. In particular, comparison of the strength of purifying selection to that on start codons indicates that purifying selection on UAA is slightly lower than that on GUG and UUG start codons and much weaker than purifying selection on AUG, the primary start codon.

The reasons for this difference are a bit more difficult to grasp... but even for stop codons...

UAA is the optimal stop codon based on its higher proportion in highly expressed genes

On the other hand there's drift ("switches") in the stop codons

Fast-evolving genes generally accrue more stop codon switches than slow-evolving genes, suggesting that the higher evolutionary rate involves also the stop codons.

So come back in a few billion years with the same question on the stop codons.
On the other hand it's fairly well-established that

In prokaryotes, the start codon is one of the major translation initiation determinants: replacement of AUG with an alternative start codon, such as GUG, typically leads to a several-fold drop in the translation efficiency

As for the stop codons:

The causes of the observed preference for UAA as the stop codon, particularly in highly expressed, slow-evolving genes remain unknown. One potentially plausible possibility is that UAA is less prone to formation of stable secondary structures in RNA molecules than UAG or UGA which facilitates the release factor access and is likely to be particularly relevant for highly expressed genes. Furthermore, the frequency of readthrough differs for the different stop codons and is the highest for UGA, at least, in E. coli. Because the deleterious effect of readthrough is the greatest for abundant proteins, the difference in readthrough frequencies could, in part, explain the strong preference for UAA in genes encoding such proteins.

So, in summary, the selection reason for the start codon is fairly well understood, but the reason for the observed preference for UAA as an optimal stop codon (in highly expressed genes) is more speculative, which goes hand in hand with its purifying selection not being as strong as that for the AUG start codon.

I didn’t downvote this answer but your first quote is essentially a restatement of the question: It doesn’t in the least provide a rationale for why this is. The rest of your answer is merely describing facts, again not offering reasons why. I actually prefer the answer you’ve just posted on the related question about AUG.


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How are electrons entering the electron transport chain in cellular respiration energised (excited)?
In photosynthesis, electrons are excited by light energy from the sun (photoactivated).
How do they become excited in human cellular respiration?
I believe it has something to do with NADH and FADH2.

It may be useful to start with a quotation from the Introduction to Ch. 9 of Berg et al. Biochemistry (6e) that addresses the question, more or less as asked. I can’t find a link to the pages in the 5e online so I will transcribe it from my text:

“A principal difference between oxidative phosphorylation and
  photophosphorylation is the source of the high energy electrons. In
  oxidative phosphorylation these electrons come from the oxidation of
  carbon fuels to carbon dioxide. In photosynthesis these electrons are
  excited to a higher energy level by the energy from photons.”

It is important to think about one of the ways in which the excited electrons are used in photosynthesis. To quote from earlier in the Introduction:

“In essence, light is used to create reducing potential.”

What this means chemically is that in photosynthesis the electrons have sufficient energy to reduce NAD+ to NADPH. In the biosynthetic (dark) reactions of photosynthesis the NADPH can be used to reduce carbon dioxide to sugars from which glucose can be produced.
So glucose is a reduced compound and can be thought of as ‘embodying’ the excited electrons, as its oxidation to carbon dioxide generates NADH (from NAD+). Hence:
There is no need for any additional excitation of electrons — that was done originally in photosynthesis.


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How many neurons do we have in our forearm?
I am developing a neural interface, getting signals from the forearm and mapping them to hand gestures. The question we have at the moment is what is the upper bound of information bandwidth that we could tap into, meaning if we were to engineer an electrode so small that we could listen to every single neuron in the forearm, how many neurons could we listen to?

Welcome to SE BIology. Please take the time to take the Tour and find out about this site. After that, the Help on asking questions should be your next call. You need to show that you have done some research for yourself first. What attempts have you made to answer the question yourself?

Your main contributor to the neuron count are going to be touch sensors. The fingertips are quite dense with them.

Yes, I am aware of the homunculus man, but I haven't succeeded in finding any quantitative estimate whatsoever that supports the representation of the homunculus man as having such a high density of motor and sensory neurons in the hands.


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Activated carrier molecules and their relationship to enzymes
I am reading Molecular Biology of the Cell, and one thing I don't quite get is the difference between an enzyme and an activated carrier molecule. I understand that enzymes lower the activation energy for a reaction, and in that sense speed up the rate at which a reaction occurs. I also understand that activated carrier molecules act as a source of energy that can drive unfavorable reactions (like anabolic reactions) forward. But I still don't quite grasp the exact difference. I was wondering if someone could shed some light on this.

I will focus on the meaning of ‘activated carrier molecule’ as descriptions of enzymes abound. In order to do that I need to introduce two other ideas first. I apologize to the purists for tailoring this to the level of the question.
1. Gibbs Free Energy in Biochemical Considerations
There are different ways of considering energy, and in chemistry one may be used to considering bond energy in relation to a particular molecule. However in biochemistry (which is what this question is concerned with) the focus is on the energetics of overall processes. For example “Are the reactions involved in the synthesis of glucose from pyruvate energetically favourable?" or “How can the synthesis of glucose from pyruvate occur if the overall reaction is not energetically favourable?” Likewise for individual reactions, such as the formation of peptide bonds between amino acids.
For considerations of this sort the thermodynamical concept (Gibbs) Free Energy (G) is most useful. This is because the change in free energy (ΔG) during a reaction (or other change of state) indicates whether a reaction can occur spontaneously. To quote from a useful section in Berg et al.

A reaction can occur spontaneously only if ΔG is negative.

So in the reaction sequence just mentioned, the overall synthesis of glucose from pyruvate (gluconeogenesis) has a positive ΔG and is energetically unfavourable, whereas that of the reverse process (glycolysis) is energetically favourable. And likewise peptide bond formation, not surprisingly, has a positive ΔG and is not energetically favourable.
2. How are Energetically Unfavourable Reactions Accomplished in Living Cells?
The question posed in the heading arises from the fact that gluconeogenesis and peptide bond formation occur in living cells, even though taken alone the core reactions that represent the processes are energetically unfavourable. The answer is given in the title of [section 14.1.1. of Berg et al.]

A Thermodynamically Unfavourable Reaction can be driven by a Favourable Reaction

As already stated, it is the ΔG of the overall process that is important, so if a reaction with a positive ΔG is ‘coupled‘ to one of negative ΔG of greater magnitude, the overall reaction can proceed. For example:
A → B           ΔG =  20 kJ/mol (unfavourable)
C → D           ΔG = –30 kJ/mol (favourable)
A + C → B + D   ΔG = –10 kJ/mol (favourable)

If reaction C → D proceeds alone, the free energy is liberated as biochemically useless heat. If it is coupled to reaction  A → B it drives the latter with the balance being lost as heat.
3. The Role of Activated Carrier Molecules in Energy Coupling
Clearly, any coupled reaction can cause water to run uphill, as it were. But in order to continue one needs to regenerate the starting molecules for the favourable reaction. It is more efficient to specialize this regeneration process by using a limited range of specialist reactions with a negative free energy change. One description of the substrates (reacting molecules) of such specialized favourable reactions is “activated carrier molecules”. Alberts et al. define them as:

Small diffusible molecules in cells that store easily-exchangeable energy in the form of one or more energy-rich covalent bonds. Examples are ATP and NADPH.

Berg et al. also use the term, but describe it in terms of the following examples:

ATP as an activated carrier of phosphoryl groups, because phosphoryl transfer from ATP is an exergonic process (i.e. has a negative ΔG)
Nicotinamide adenine dinucleotide (NAD+) is a major electron carrier in the oxidation of fuel molecules. (Although in this case it is the half reaction involving the oxidation of the reduced form, NADH — or NADPH as mentioned by Alberts et al. — that has a negative ΔG).
Coenzyme A… is a carrier of acyl groups (but it is the transfer of the acyl group of acyl-CoA molecules — e.g. acetyl CoA — with the generation of CoA that has a negative ΔG).

Examples of the participation of such molecules in metabolism can be found in the volume referenced, however I would emphasize that it is the specific reactions of these molecules involving the groups (or electrons) that they carry that is important.
And what about Enzymes?
As the poster stated “enzymes lower the activation energy for a reaction”. They are (generally) large proteins catalysts that have no effect on the ΔG, and they are unchanged at the end of the reaction.
Of course they are important for biochemical reactions, they participate in them, and provide binding sites to bring the substrates and activated carriers in juxtaposition so that they can react. But they couldn’t be more different from the small activated carriers.

@user1136 — Whether a reaction proceeds or not depends on the delta G. Only If you start putting numbers in do you have to deal with delta G0. I deliberately didn’t do that to avoid obscuring the basic idea. If the poster reads the links he can, if he wishes, take things further.

@user1136 — I see what your point is. Because as a result of the reaction proceeding the concentration of substrate and product changes, then the deltaG changes. Thus the action of the enzyme, catalysis, has changed the delta G. I think that is more than pedantry, it's casuistry. I wouldn't try it on a class of undergraduate students though.


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Relationship of RNA-binding proteins to peptidyl-prolyl cis-trans isomerase
I am studying a Plasmodium gene, known to encode an RNA-binding protein. However a BLAST search brings up mainly peptidyl-prolyl cis-trans isomerases from other species. Why would this be so?

It's looking an interesting question. Can you kindly add bit more details?

Welcome to SE Biology. Please complete the Tour to find out how this site works. Also read about how to ask questions. It is unclear whether you want are appealing for someone to do your work for you (definitely not the purpose of this site) or information on how to go about it. Assuming the latter, it is impossible to help you without knowing what your gene is. If your Blast search is bringing up PPIs, then I would imagine your gene is a PPI. Show us the sequence comparison, not the tree.

I have edited your question to correspond to what I think your problem is and have provided an answer. If you disagree, you can revert the question but you would need to clarify it. I hope I have not inadvertently answered an assignment rather than a real research problem. If this was a real research problem, you would be advised to believe the evidence of your own analysis in future, and do some research on what they bring up.

Without seeing the sequence of the RNA-binding protein it is impossible to be sure, but the obvious conclusion is:

The RNA-binding protein is a peptidyl-prolyl cis-trans isomerase.

It has been known since 1989 that peptidyl-prolyl cis-trans isomerase is a multiple-function protein, also exhibiting properties of the cyclophilins, proteins which bind cyclosporin A. The post raised the possibility that it may have other activities and a literature search reveals several more recent papers that indicate cylcophilin A can bind certain RNAs. I list some of the titles:
A nuclear RNA-binding cyclophilin in human T cells (1996) FEBS Letters 398 201–205
Molecular cloning, structure and expression of a novel nuclear RNA-binding cyclophilin-like gene (PPIL4) from human fetal brain (2001) Cytogenet Cell Genet 95 43–47
Cyclophilin A Binds to the Viral RNA and Replication Proteins, Resulting in Inhibition of Tombusviral Replicase Assembly (2013) J. Virol. 87 13330–13342
Structure of RNA-interacting Cyclophilin A-like protein from Piriformospora indica that provides salinity-stress tolerance in plants (2013) Scientific Reports 3 : 3001, DOI: 10.1038/srep03001


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How do mRNAs find ribosomes?
After mRNA is released from the nucleus, the next process is its translation by ribosomes. By what physical, chemical or biochemical process does the mRNA reach the ribosome in the cytoplasm?

I didn't understand your thought experiment involving a table... Did you mean 'test tube' or 'dish' rather than 'table'?

Yes, just an assumption. It could be anything a table, a testtube or a dish. Im just trying to understand how the mRNA moves towards ribosome, how it finds the ribosome location?!?

I'm sorry, but I think the edited question is still bad. Your second paragraph is unnecessary and misleading as what you are interested in is what happens in the cell, not reconstituting the situation. Also, mRNA is a molecule — it doesn't know anything — so in science I consider it bad practice to write in a way that suggests otherwise. Finally the cell has a nucleus and a cytoplasm. The term cytosol describes an experimentally prepared cytoplasm from which organelles have been removed. I have edited your question, but the answer is basic — random collision — so I am voting to close.

Thank you @david

Consider also that (i) the nucleus has two membranes, an inner and outer one, and (ii) that the endoplasmic reticulum (ER) is continuous with the outer nucleus membrane. mRNA 'typically' leaves diffuses through pores in the outer nucleus membrane directly into the cytoplasm where free ribosomes are found, but some of it may also get into the ER. where you may also find ribosomes ('rough ER').

please have a look at this article and its images.
R. J. Jackson et al., 2010, Nature Rev. Mol. Cell Biol. 11:113.
https://www.nature.com/articles/nrm2838
In a nutshell, recognition of mRNA by ribosome occurs in multiple steps.Interaction of mRNA with (eukaryotic) initiation factors(eIF) leads to this. eIF4 complex interacts with mRNA and then an intermediate circular mRNA is formed with the aid of ATP hydrolysis.This circular mRNA attaches to the small subunit of ribosome.(the small subunit has a dozen of helper proteins attached to itself.)
After the attachment of circular mRNA to the small subunit , you can say that mRNA has "found" the ribosome as the small subunit would then form a complex with the large subunit and begin the Elongation step of Translation.

The answer to the first part of your question is: diffusion. After transcription and some processing, the eukaryotic mRNA is exported to the cytoplasm. Here it floats around until it meets a ribosome. Binding of ribosome to mRNA is facilitated by proteins called initiation factors (IFs) and the 5' cap of mRNA$^1$.
The second part of your question basically asks about cell-free protein synthesis using an RNA template. This has already been shown to work: one is reminded of the famous Nirenberg–Matthaei experiment$^2$, which ultimately led to the cracking of the genetic code. Nirenberg and Matthaei worked with bacterial cell extracts, but systems based on eukaryotic cell extracts have also been developed$^3$.

References and further reading:

Nelson DL, Cox MM. Lehninger principles of biochemistry. 7th ed (international edition). Basingstoke, England: Macmillan Higher Education; c2017. Chapter 27, Protein metabolism; p. 1077–1126.
Nirenberg MW, Matthaei JH. The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. PNAS. 1961 Oct 1;47(10):1588–1602. https://doi.org/10.1073/pnas.47.10.1588
Chong S. Overview of cell‐free protein synthesis: historic landmarks, commercial systems, and expanding applications. Curr Protoc Mol Bio. 2014 Oct 1;108(1):16.30.1–11. https://doi.org/10.1002/0471142727.mb1630s108

Okay, now it makes sense! Thanks!

Ribosomes are floating around in the cytosol dissociated into subunits, they assemble around the initiation factors bound to the mRNA (and scanning for AUG), depending on the signal peptide and so on during translation they might bind to the ER membrane, after the translation they dissociate and float around again.


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Why is one strand of human mitochondrial DNA designated ‘heavy’, whereas the other is designated ‘light’?

In the Wikipedia article on ‘Mitochondrial DNA’, one strand is designated ‘heavy’ and the other ‘light’. (These are the outer and inner circles, respectively, in the cartoon illustration from the article, above.) What is meant by this terminology, and why do the two strands differ in this respect?

The heavy strand is literally heavier than the light strand. The first, or at least one of the first, observations of this phenomenon was in this paper:
Corneo G, Zardi L, Polli E. 1968. Human Mitochondrial DNA. J Mol Biol 36(3):419-423.
They showed that alkaline denatured mitochondrial DNA separates into two bands upon ultracentrifugation in a cesium chloride gradient:

Human mitochondrial DNA when centrifuged in alkaline CsCl in the analytical ultracentrifuge splits into two bands displaying densities of 1.727 g/cm3 and 1.766 g/cm3, respectively. The two bands appearing in the alkaline gradient correspond to the complementary strands of human mitochondrial DNA with a different GT/CA ratio... However, when an equimolar mixture of them is renatured by heating at 65°C for five hours in 2X SSC, a single band with a density very close to that of the native DNA is obtained. The latter experiment clearly indicates that the two bands correspond to the complementary strands displaying a bias in base composition.

The difference in molar mass (M) is due to a higher purine content (Pu) in the heavy strand (which are heavier than pyrimidines). This can be seen by tabulating the base composition of the RefSeq sequence of human mitochondrial DNA:
               A      T      G      C      Pu(%)   M(kDa)
Light Strand   5124   4094   2169   5181   44      5063
Heavy Strand   4094   5124   5181   2169   56      5174

R script if anyone is interested:
#uses Biostrings
light = readDNAStringSet("mtDNA.fasta")
heavy = complement(light)

comp = function(seq) {
  ll = as.list(alphabetFrequency(seq)[1, c("A", "T", "G", "C")])
  ll["%Pu"] = with(ll, (A + G) / (A + T + G + C)) * 100
  ll["M(kDa)"] = with(ll, (A * 313.2) + (T * 304.2) + (G * 329.2) + (C * 289.2) + 79.0) / 1000
  return(ll)
}

comp(light)
comp(heavy)

Thanks — that improves the answer greatly. Although the "heavy" strand is heavier in terms of molecular mass, it is, of course, worth emphasising that it is the buoyant density of the purines, rather than their mass, that lead to the behaviour that gave rise to the loose nomenclature.

Apologize for comment on this old thread but I think some clarifications needed to be posted.
The response above nicely explains the definitions of the mitochondrial heavy strand and light strand. However, if you really go download human mitochondrial RNA sequence and analyze nucleotide content for both strands, you will find that the strand encoding most of mitochondrial genes (so called "heavy strand") contains LESS G+T than the strand encoding fewer genes (so called "light strand"). Therefore, the outer circle in your figure, which is "heavy strand", is actually lighter than the inner circle in your figure, which is "light strand". This is caused by the discrepancy between the earliest literature describing the mitochondrial genome and the currently accepted definition of the coding strand. You can read more from this paper: PMID: 32148154.
Hope this helps.

Welcome to SE Biology. Please take the time to finish reading the tour, and read the Help on questions. Comments on SE are primarily for asking for clarification or suggesting improvements, and this comment is of the former type. Are you saying that the values of base composition of the two strands presented by @canadianer are incorrect? Or that he has the two strands confused? Though I think that the term “coding strand” is ambiguous for individual genes and inapplicable to most genomes, I cannot see how this nomenclature can affect the distinction of the strands by “weight”. Please explain.

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Caloric Mimicry
I was thinking about natural "zero calorie" sweetners and how these compounds could come to be via evolution. I was specifically thinking about monk fruit. While artificial selection likely played a role in the life history of the modern cultivated variety, this plant still needed to initially possess sweetness traits for humans to select. It seems to me to be an interesting case of mimicry — copy the palatability signal of caloric value of other fruits while not devoting valuable resources to creating equivalent amounts of sugars —because it depends on those other fruits/foods being consumed often enough to sustain the propagating organism. This makes it hard to classify the nature to the relationship in the propagator-mimick-mimicked triangle: the propagator-mimick relationship may be read as parasitic, commensal or mutualistic depending how we consider the value of non-caloric nutritional factors for (reproductive) success. Same can be said for the mimick-mimicked relationship, as both benefit from the strengthening of the sweetness signal, but the true signal might in fact benefit more under complete knowledge on the part of the propagator. As a strategy, it is also very interesting because it requires a generalist propagator in an ecosystem with a certain amount of biodiversity, so it seems more likely for this relationship to emerge in nutrient rich environments than poorer ones.
Can anyone think of other examples and are there any existing examinations of similar relationships in the literature?

Nice idea. Plants generally can afford to be energetically wasteful, so I doubt we will see examples of such a high risk / low reward strategy

Interesting proposition. Mogroside appears to have a very complex chemical structure which I would of thought to be very metabolically expensive to create. Although it is 250 times sweeter than sucrose is there any way to quantify if it is > 250 times less expensive to create, I am sure there are many ways to quantify metabolic expense beyond carbon to carbon comparisons etc?

Synsepalum Dulcificum's fruit contains miraculin which makes acids taste sweet. A small amount of citric acid combined with a tiny amount of miraculin will taste like a lot of sugar.

@KaPy3141: Proteins are expensive (nitrogen) for plants and valuable to animals. Even Drosophila can have sugar/calorie hunger and/or protein hunger. So a plant that mimics a lot of protein using a much smaller quantity of some compound (which could also be a peptide) maybe. But the main parts of the plant that are "designed" to be eaten (the fruit and nectar) aren't very proteinaceous.

@JEJS So it could just be a energetically more expensive strategy that becomes successful in a environment where the propagator, here humans, has evolved receptiveness to sweetness. But since mogrosides can act as antioxidants, maybe the benefits outweigh the costs and the sweetness mimicry is an additional bonus?

@KevinKostlan Interesting. Is that the same as "miracle berry"?

@KevinKostlan: Nice point about Nitrogen. I fully agree: Basically, fruits can be assumed to be nutritiously cost-optimized, while ample access to CO2 and sunlight allow higher 'generosity', in terms of calories (sugars).

Yes, carrion flowers for example mimic the scent of rotting flesh to attract flies which will then carry their pollen to other carrion plants.  With sugar specifically though, I'm not sure it would work as well because I believe the fake sugar in drinks like zero calorie soda are actually just as energetically expensive as natural sugar to produce.  So while a plant producing artificial sweetener might not give us any calories, it still has to expend a bunch of calories to produce it.


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Quantifying Gene Expression
I have found that many studies use the mRNA concentration as a “proxy” for protein activity because there should be correlation between mRNA levels and proteins expression levels. How is protein activity quantified? Which quantity is used? What are protein expression levels?
I am doing some statistical data analysis using this dataset. I would like to understand why they have been interested in measuring mRNA concentration after the cells gamma irradiation (and in general it seems to me that biologists in many experiments are interested in that). I found in this site that discussion about correlation between mRNA concentration (so gene expression level)  and "protein expression level". Therefore I wanted to know what the latter is. Moreover, in the article related to my dataset is written

Very few DNA repair genes displayed significant differential expression in P. furiosus following gamma
irradiation.

And then

the data we reported here suggest that DNA repair proteins in P. furiosus and several other archaea are constitutively expressed and that they may be present in the cell at a level sufficient to maintain the integrity of the cell’s genetic material.

So putting together what the scientists conclude with what MattDMo has answered to me and what is discussed here , I think that I can conclude that "protein expression level" is a measure of the amount of protein actually translated from the mRNA, that then (in this case) will effectively act to repair DNA. Therefore, "protein expression level", as well as "protein activity", indicates the proteins translated from mRNA and that will actively act to repair DNA damages (in this case that we are talking about DNA repair proteins and DNA repair genes).
I have to say that I do not really know well what "DNA repair proteins are constitutively expressed" means, but I think that is that DNA repair proteins have already been translated from the mRNA and therefore they are "present in the cell at a level sufficient to maintain the integrity of the cell’s genetic material" (as they say soon after).
All this makes sense to me if I think about my first objective that was to understand the reason for measuring mRNA concentration. We are interested in it because there should be correlation between mRNA concentration (gene expression level) and the proteins actually translated from mRNA from that specific gene, in order to know which kind of proteins will effectively act in the DNA repair processes (in this case).
I wonder if all this interpretation is correct...

I have deleted my comments as they are now embodied in an answer. I have changed your title to be more general and for reasons I make evident in my answer.

I have now added a postscript addressing the specific circumstances of your work, which are of less general interest than main topic of my answer. (Good questions on answers on Stack Exchange should be of general interest, not a dialogue with the poster.) In summary, "all this interpretation" is not correct. Further, measuring the  mRNA concentration is done because it reflects the extent to which a gene is expressed as mRNA. The topic of interest is gene expression — of which the amount of protein produced is just a part. And the term "protein activity" is meaningless and is not to be used.

What is Protein Expression Level?
This was the original title of the post, which I edited myself because I regard the answer as trivial, but the question as more substantial. To deal with the trivial first:

‘Level’ is not a scientific unit, and can only be used unambiguously
as a scientific term in its English sense in relation to liquids, e.g. “The level of mercury in the thermometer had
fallen.”, “The land is 10 metres above sea level.”
It is used by some people in informal speech or writing to indicate an
undefined quantitation, and because of its very ambiguity is to be
strongly discouraged in scientific communication.

So neither I nor anyone else can say what ‘protein expression level’ is without finding out what the originator of the phrase intended (if indeed he knew) in any individual instance: quantity or concentration of protein, or the rate of its synthesis.
Quantitation
Let us consider some general aspects of a cellular molecule that may require quantitation: Amount, Rate of Synthesis, Rate of Degradation and, where relevant, Biological Activity.
The quantitation of molecules at its most basic is the number species,  or, more practically, their total mass (grams), where possible related to their molecular mass (i.e. moles). The rate of their synthesis or degradation is expressed in terms of the change of their amount in unit time.
In order to compare different systems a reference is needed for the quantitation. This may be per unit volume, per cell, per g cellular protein, per g DNA etc. (However for comparison of similar systems or within one system the reference is often omitted.)
The biological activity of molecules only has meaning if the molecules are, indeed, biologically active (e.g. enzymes). It is expressed in units related to that activity.
Examples of Quantitation for Proteins
The actual units used in quantitation are determined by how one is able to measure the parameter of interest.
Relative amount of protein: You might detect a protein by the intensity of staining of a band on a gel, or by the extent of precipitation using a corresponding antibody. These would have to be calibrated against standards in order to convert raw experimental measurements to g or mole protein. Typical units of relative amount are g/g total protein, g/g DNA.
Rate of synthesis or degradation of protein. You might detect the synthesis of protein by the rate of incorporation of radioactive amino acids into non-radioactive protein, and the rate of degradation by the liberation of radioactive amino acids from pre-labelled protein. Typical units of synthesis would be mg amino acid incorporated per min per mg total protein. (This can be converted to molecules synthesized or degraded per minute, if necessary.)
‘Protein Activity’: The use of this term is not recommended. In chemical terms the activity of a molecule is a measure of its “effective concentration”, and in relation to proteins would only be the concern of biophysicists and the like. Other biologists would associate the term with the biological activity a protein such as an enzyme might have, but as many proteins are structural the term ‘activity’ cannot be applied to proteins generally. Where it is of interest it would be quantified in terms of the nature of the activity, e.g. an enzyme is quantified in units related to the amount of substrate converted to product in a given time.

Quantitation of Gene Expression using Oligonucleotide Microarrays
The two extremes in quantifying gene expression are the detailed study of the expression of one particular gene encoding a protein for which information and tools are available; and general study of the expression of many genes using modern methods that allow the study of many molecules simultaneously. Such methods included mass spectrometry (for small metabolites), two-dimensional gel electrophoresis (for proteins) and microarrays or RNAseq (for mRNA). In general in the latter case one would examine the effect of some agent or condition on the whole spectrum of gene expression.
Let us examine microarray technology as that is the main concern of the poster.

Microarray technology measures the relative amounts of mRNA.

The methodology involves amplifying a mixture mRNA species by reverse transcription to cDNAs, which are labelling with a fluorescent dye. The cDNA is hybridized to immobilized oligonucleotides based on the sequences of the genes in the organism, and the strength of the fluorescence signal is assumed to be proportional to the amount of individual mRNA species in the sample. However the data supplied to the user is the relative image intensity within the experiment, rather than units that allow one to calculate the actual amount of mRNA.
How does these relative amounts of mRNA relate to gene expression?

The relative amounts of mRNA are a relative measure of the rate of synthesis of proteins (3 in dig.), if one assumes that the rate of synthesis of each protein is similarly proportional to the amount of its mRNA (a in dig.) which would be limiting. This is a reasonable assumption in most cases given mRNA is degraded more rapidly than protein. (They are not a measure of the amount of protein — b in dig.)

The relative amounts of mRNA cannot be taken as a measure of the rate of transcription of a mRNA from its gene (1 in dig.) because of the relatively greater effect of mRNA degradation (2 in dig.) on the steady state concentration of mRNAs, and the fact that different mRNAs have different half-lives.

Postscript for the Poster
I have tried to make this answer general, to be of use to more people. As the poster is not a biologist she may still have difficulty in understanding the background to the biological experiments that generated the data she is analysing.
The biological system of interest is gene expression, which encompasses the whole series of events from transcription of genes to mRNA and their translation into protein. The background to this is that there are some genes that are (almost) always expressed, irrespective of physiological circumstances because they are needed to maintain the structure and everyday functions of the cell. This is termed constitutive expression, examples being expression of the genes for cytoskeletal actins or ribosomal proteins. Other genes are expressed (‘switched on’) only when needed (and may be termed inducible). The question here would appear to be whether the genes for the enzymes involved in DNA repair are expressed all the time (constitutively) to deal with normal ‘wear and tear’ of DNA, or whether their expression only occurs in response to some insult knwn to damage DNA, such as gamma irradiation.
As I mentioned, as an experimental scientist, one approach that can be adopted here is to look at the expression of one or two well characterized proteins that are known to be involved in DNA repair. However, there may be proteins involved in this process that you are unaware of, so the modern methods of looking at the expression of all the genes in an organism (if the DNA sequence is known) — oligonucleotide microarrays or, better, RNASeq. These methods measure relative quantities of mRNA in a cell. This is not a proxy for amount of protein or rate of  its synthesis (the term ‘protein activity’ is meaningless and is not and should not be used), it is what it is, but is also a reflection of the expression of the genes that encode the mRNAs. No expression, no mRNA.
You can think of the microarray and RNASeq approaches as a fishing expeditions. If you find mRNAs that are only present after the cell receives a stimulus or an insult, expression of the mRNA has occurred (whether or not the amounts are directly proportional to the rate of synthesis). If the mRNA is synthesised you can assume it is translated into the protein it encodes. In the case of gamma irradiation you might assume any mRNA that shows a large increase in quantity encodes a protein that involved in protecting the cell from the radiation. This will be of scientific interest, especially if it is not what one anticipated.

I have a doubt about the relative amounts of mRNA: they are somehow the log10 ratio between the irradiated sample and the reference sample . So if the ratio is 0, there should be no changes in gene expression (because it is log10(1)=0); if it is greater than 0, it means that the gene expression (amount of mRNA) is increased after irradiation (up-regulation); finally, if it is lower than 0, it means that the mRNA production decreases (down-regulated gene) ?

This is what I have deduced by reading the Wikipedia explanation (indicated by you) and the comments about RadA in fig1a of the article . I think that if I have understood well this case with not irradiated samples and irradiated, I can extend this reasoning to other cases like unhealthy and healthy cells cultures.


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Can the extinct Chinese Paddlefish be revived?
I learned that a rare and unique giant Chinese Paddlefish recently became extinct. I'm wondering if samples of DNA were collected by scientists to allow reviving of the specie in the future.
My quick Google check only revealed one paper that studied DNA of the fish 15 years ago - so there is a possibility that some DNA information exist out there. But is it enough to restore the species?
I'm interested in learning about any organisations or projects that would systematically collect genetic material of all endangered species. Is there a way to ask them about this specific fish?

Informally speaking, there is no real/good way to bring back extinct species. Especially sexually reproducing species; you'd need to revive a male and a female at the very least, and these are markedly different genomes due to unique sex chromosomes.
Some 'bad ways' exist though; in principle, if you found a perfectly preserved nucleus (the organelle that holds genomic DNA of most eukaryotes), it may be possible to insert this nucleus into a sibling or sister species (e.g. wooly mammoth nuclei into denucleated elephant zygotes). This would be the cloning approach. However, you then run into practical issues. You have to guarantee that this embryo will implant itself, which itself is not always the case. The nucleus and chromosomes must also be intact enough (which may not be the case after storing them, e.g. in ice, which may require thawing which often damages cellular structures) to create a rather healthy, fertile organism that will breed at a sufficient rate to restore a stable population. These and many more complications will reduce your chance of rescuing an extinct species to near-zero. Even then, one could argue that it is an incomplete de-extinction because you've only substituted the genomic DNA, and not other parts of the genome (e.g. chloroplast or mitochondrial genomes) which are part-and-parcel of the genetic signature that makes a species a species.
Alternatively, you can create hybrids where fragments of DNA from extinct species are brought into the genomes of similar existing species, by molecular methods such as recombination using CRISPR/Cas9. Here though you are only creating hybrids, not reviving extinct lineages. The extent to which you could do this is also limited and you would have to increasingly troubleshoot why a hybridization didn't work the more host genome you replaced with the extinct species' genome. Transgenesis using individual genes (say, transfering an enzyme into a new organism) is quite plug-and-play, but replacing entire chromosomes would be near impossible to pull off, not least because you would have little insight into why things aren't working - only that they aren't.


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Storing Apples at 30F?
This article about storing apples for the winter says:

You do not want the apples' temperature to fall below 30°F (-1.1°C), however,
  because that will make them freeze and turn to mush when they're
  thawed. Their cell walls will all collapse.
Therefore, apples are best stored somewhere around 30-35°F (-1.1 to 1.6°C), in a humid environment.

I don't understand why you should keep the apples below the freezing point of water. Why would damage only occur below 30°F (-1.1°C)?
Is the article correct?

This temperature range would be a compromise between a very low temperature needed to limit natural decay or decay triggered by micro-organisms (the lower the temperature, the lesser the decay) and the formation of destructive ice crystals.
Only pure water freezes at 0°C (32°F) under atmospheric pressure. But the content of apple cells and cell walls is a rather complex aqueous solution, containing many natural cryoprotectants, among which the fruit's sugars. Therefore, the freezing point of apples might be as low as 30°F.

OK but when it says "in a humid environment" wouldn't the apple be covered in ice (damaging its skin)?

They would be covered in ice if the air were saturated with water. In this case humid means that a dry environment has to be avoided. e.g. keep 80% relative humidity.

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Effects of Great Pacific Garbage Patch to Phytoplankton?
I was wondering if the decrease in light received by the area comprised by the Great Pacific Garbage Patch (GPGP) could affect Phytoplankton enough to reduce its potential in that area as a carbon sink.
I mean, it is an area that gets plenty of sunlight, but compared to the overall size of ocean coverage it is not that much and maybe the cover is not intense enough to reduce completely photosynthesis in that area, so maybe the effect is negligible.
I couldn't find any article reviewing this.  If someone can point me to some literature at least.
I found this: https://www.researchgate.net/publication/325022723_Impact_of_microplastics_on_phytoplankton
But I find these results hard to interpret and was hoping more for an ecological studies.
Rephrasing the question for clarity: how much does the GPGP effect C02 capture by effects of disrupting phytoplankton?

PS: Back of envelope calculations:
with a GPGP area of 15e6 Km^2 (source wikipedia)
and a total ocean area of 360e6 Km^2
we have lost 4% of CO2 capture from plankton. But if plankton captures 30-50% of all CO2 emissions, then we lost 2% of all of our carbon capture potential.
But more so, if we assumed that tropical phytoplankton captures more CO2 than from other regions (suppose all of it), then with about 40% of oceans in the tropics we have:
15/(360*0.4) ~ 10% CO2 capturing phytoplankton lost
which would yield 3-5% reduction on our total carbon capture capacity (I am taking this number as a maximum possible impact )
This, to me, seems like a pretty important number, so I must assume that either:
(1) tropical phytoplankton does not contribute majorly to CO2 capture, so its loss would not be impactful
(2) this is very difficult to study and model
(3) some other reason I haven't thought of
In any case, thank you for your attention!

Do you have a source to support your claim of losing 4% of carbon dioxide capture from plankton (phytoplankton)? Is this a hypothetical figure?

completely hypothetical, just trying to do basic estimations since I don't have any information.


text:
What was the evolutionary reason for cross lateralization of the brain?
In the human brain the right hemisphere controls the left side of the body and the left hemisphere controls the right side of the body. What led to this development? Why doesn't the left side of the brain control the left side and vice-versa?

The theory developed by Cajal more than a hundred years ago hasn't been challenged, according to a recent article in Molecular Neuroscience. Making it simple:

At a certain point in the phylogeny, decussation is favored for the optical pathways. Since the images are inverted on the retina, the crossing is necessary in order to build a coherent and continuous image on the cortex.
Decussation of the motor pathways appears next, and it is supposed to make the flight response more efficient. If a danger is perceived visually at the left hand side of one's body, it is processed in the right hemisphere and the motor signal is sent to the left hand side muscles, which are the one that can propel the body to the right, thus escaping the danger. The efficiency resides in that the interpretation of the danger and the signal for the reaction happen in the same hemisphere.

Your DOI link is broken. Can you add a link to PubMed instead?

@MattDMo I changed the link to a PubMed one.


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Lyonization vs Genetic Imprinting
Lyonization is the process in which there is inactivation of an X chromosome in females. This process is implicated in mosaic forms of turner's syndrome (in this case the altered X chromosome is Lyonised, thus allowing the normal X Chromosome to express itself).

Is Lyonization considered as a form of genetic imprinting? What is the difference between the two (if no)?
Lyonization is a random process (according to the extent of my knowledge which X chromosome is inactivated is not predicatable). Is genetic imprinting also random?
Is there any known aberration of Lyonization in males? (meaning the single X Chromosome or Y Chromosome gets silenced)

A bit related: http://biology.stackexchange.com/questions/27681/what-effect-does-the-barr-body-have-in-relation-to-female-turner-syndrome

I use the term "X-inactivation" instead of "lyonization". Anyway, X-inactivation is a very specific process by which an entire X chromosome (or equivalent sex chromosome) in a female mammal is completely silenced.

"Imprinting" is typically applied to single genes, wherein genes inherited from a specific parent are always epigenetically silenced. The genes are usually autosomal. Thus, we're talking about scales : entire sex chromosome composed of thousands of genes (x-inactivation) vs single genes (imprinting)

The choice for which X-chromosome is inactivated is sporadic and different in different cells within the body. It is controlled by opposing expression of different non-coding RNAs (XIST on the inactive X and TSIX on the active X).

Imprinting is very specific to the allele that is inherited from a specific parent (for example, some genes are paternally imprinted, while others can be maternally imprinted).

Males with aberrant X-inactivation will lack any expression of genes carried on their single X-chromosome, a condition that will not result in a viable fetus. However, whether there are aberrant X-inactivations in single cells or tissues of ageing adult males....perhaps likely yes, given all the other aberrant somatic mutation events that occur over the course of life.

I guess, we are talking about mammals here (because in other organisms leveling up of expression on sex chromosomes happens differently: e.g. in flies females express both X chromosomes, while fly males express their single X at twice as high level).
In embryo proper the decision of whether to inactivate maternal or paternal X seems to be at random. This inactivation adjusts level of expression of genes on X to be in the same ball park as on autosomes and in the same ballpark between males and females. Neither farther nor mother cares about which copy of X gets inactivated in individual cells of an embryo.
When we say that a gene is imprinted, that means only one copy of the gene is expressed  but, to the contrary of what happens with X, maternal or paternal origin of the expressed copy is predetermined (so there is no randomness in which copy is inactive). Imprinting is usually a property of genes expressed during embryonic development and it is related to tug of war between farther and mother's interests: the farther "wants" embryo to take as much resources from the mother as possible (so paternal copies of some genes tend to be highly expressed), while mother wants not to give too much to one embryo, so that she can raise many more progeny (so maternal copies of some other genes tend to be highly expressed). This whole thing is interestingly described Matt Ridley book The Red Queen: Sex and the Evolution of Human Nature.
Note, that to confuse matters a little bit, in placenta of female embryos it is always the paternally inherted X that gets silenced, so the whole X chromosome is imprinted in extra-embryonic tissues of female embryos.
And in males X chromosomes do not get inactivated, since many genes are present solely on X chromosome and not on Y, so inactivating the only copy of X chromosome is lethal.


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Gene frequency — database/site
Is there any free database when one can check the gene frequency in a healthy population? For example I would like to check it for genes like BIN1, CLU or CR1. On the English Wikipedia I found a gene frequency for APOE gene (for example: 79% for e4 and 7% for e2), and it was linked to the specific publication. I wonder if one need to look for specific publication when looking for information like that or there is any database with such information available?

I believe SNPedia has frequency information, but I don't know the breadth of their database. Not a biologist.

@MelanieShebel Thanks a lot, gonna check that!

@Mary Are you talking about a specific species?

You can find some, but not all, gene frequencies in a range of populations at The Allele Frequency Net Database - Allele, haplotype and genotype frequencies in Worldwide Populations.
However, your question is broad genes have a lot of variation within them, the most basic being Single Nucleotide Polymorphisms (SNPs) and you've already been pointed to one source of information (SNPedia which is new to me) but you can look at the variation of allele frequency of SNPs in different populations by looking at dbSNP1.  Note they have a subset for variation associated with clinical phenotypes.

1 This may be the source on which at least some of SNPedia is based as dbSNP has been around for a very long time.


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If stomatopod crustaceans do not have myelination, why is their reaction so fast?
As far as I understand, there are only two known ways of achieving fast nerve signal transmittance (and hence fast reaction time) in animals larger than ~10 cm: either myelination (as in vertebrates) or really thick neurons (like in cephalopods). However, stomatopods are both quite large and have devilishly fast reaction fitting their predatory lifestyle. They are definitely swifter and more "alive" than lobsters or crabs of the same size (who are all sleepy and slow). However, I have never seen it mentioned that stomatopods have myelination. In fact, this page claims that mantis shrimp (stomatopoda) are not among the few crustaceans that have evolved myelination. Is there any research on how they manage to be so fast? Do they maybe have thick neurons like cephalopods? Or do they have another solution to nerve transmission?

Are you sure these animals have a fast reaction time? Or do they just move quickly or have a specialized high-velocity movement? These are not the same thing. Reaction time measures the time from some stimulus to the start of movement. It does not relate to the speed of the movement.

Yep, I'm pretty sure. Just the fact that stomatopods are successful predators (which no decapod of same size has managed to achieve), and their rapid raptorial abilities show that they have a fast reaction time. Here is just one example video where the stomatopod is the live and active one while the decapod takes a couple of seconds to even choose a strategy (let alone put up a fight). And just overall, stomatopods seem to exhibit almost vertebrate-like reaction and ability to assess the environment.

I do not see any fast reaction times in your video. The stimulus (crab) is very slow moving, so there is nothing to react to quickly. It's just a fast motor action.


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What is the reason for the discrepancy between the total number of non-N bases and the total length of the human genome assembly on the NCBI website?
I've been digging into the human genome assembly data and I've stumbled upon a discrepancy that I couldn't resolve on my own. I'd appreciate any insights or explanations from the biology community.
According to the NCBI website:
https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh38.p14
the total non-N base count (bases other than A, T, G or C) for the GRCh38.p14 assembly is 3,137,300,923. However, when I add up the total lengths of all the chromosomes, I get a total of 3,099,734,149. This leaves a discrepancy of 37,566,774 bases.
I've checked the data for alternate loci, FIX patches, and NOVEL patches, but they don't seem to account for the entire discrepancy. I've also looked into the RefSeq and GenBank databases, but I couldn't find any information that would explain the difference.
Can anyone help me understand where the extra 37 million bases are coming from? Is this a known issue, or am I missing something obvious?
Thanks in advance for your help!

I'd suggest directly contacting NCBI to resolve this. They have a somewhat funky ontology. It might help to understand how you did your math for adding up CHR lengths/alts/etc.

You might also ask our sister site Bioinformatics SE by requesting migration to that site.

I had to do a search to find out what non-N bases are — it isn't at all obvious from the name — so I modified your question to include an explanation.


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Open Reading Frame problem
Problem
An mRNA of 999 bases codes for a protein with 300 amino acids and the open reading frame (ORF) starts from base 38. If the base at position 903 is deleted the length of the ORF increases by 3 bases. Which base is present at position 942 of the original mRNA?
a) A
b) U
c) G or A
d) Cor U
My reasoning
Since the ORF starts from the 38th base, the first 37 bases form the promoter sequence. Further, since there are 300 amino acids, the orf would have 900 (+3 +3) bases including the start codon AUG and stop codon, UAA/UAG/UGA.
Therefore the ORF would be 906 bases long, from the 38th base to the 943rd base.
So, the codons, (38,39,40), (41, 42,43),...., (902,903,904),..., (941, 942,943) code for amino acids.
If the base at the 903rd position were deleted, there would be a frameshift mutation, and all the bases after 903rd place would shift leftward by 1 place.
I do not understand how this leads to the increase of the length of the ORF by 3 bases.
Because, the deletion of 1 base would cause the length of the ORF to change by 1,4,7,... bases, but not by 3 bases.

The mistake in the original poster’s reasoning is to calculate the ORF as 906 bases. In fact, as normally defined, it is 903 bases — the amino-acid coding portion (300 x 3 = 900 bases) plus the termination codon (3 bases).
The initiation codon (normally AUG) encodes the amino acid, methionine!
Hence the end of the ORF is at base 940 (37 + 903) — the termination codon consists of bases 938–940.
We are concerned with the base 942, at a position +2 from the termination codon, and this will change to position +1 (941) after a single base deletion that abolishes the normal termination codon.
For the original bases 942–944 to become the new termination codon 941–943 (as the increase in ORF requires) this region must become a termination codon UAA, UAG or UGA — in each case starting with ‘U’ at new position 941.
So the answer is (b).
NB
Bases 1–37 are not the mRNA equivalent of the DNA promoter, which is not transcribed. They have a function in their own right, and are referred to as the 5' untranslated region of the mRNA.


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Sabouraud dextrose agar breaking?
I recently started growing some Geotrichum Candidum (GC) on Sabouraud dextrose agar (SDA) beds. The SDA was poured into sterilized petri dishes. After setting the plates in a cooler (20 C) for a day, I then inoculated the plates with a tiny smidge of GC. The GC is growing happily in that environment.
However, today on day 3, I noticed a crack across the SDA like shown in the picture below.
What does this mean? Did I prepare the plate wrong? Or is my GC just a bit naughty and somehow burrowing into the SDA?
Please note I am not a trained biologist, I've learned the skills I require for my activity from online resources and advice.

It could just be the agar drying out.

My initial thought. The cooler is at 80 % relative humidity though. Isn't that enough?

I suppose evaporation can occur at any relative humidity less than 100%. Is the agar shrinking in terms of thickness and/or peeling away from the side of the plate? These are also signs of desiccation.

I see no signs of desiccation on the surface nor on the edges of the agar.

After closer inspection it seems to be desiccation. I've added a 1/4 teaspoon demineralized water in the lid (inverted dish).

@neydroydrec If that turns out to solve your problem, can you please add it as an answer to your own question? Then  it will help the next person with a mysterious crack in their agar.

Sure. Waiting for results.

I cannot be entirely sure about the cause as I have not been able to reproduce this situation subsequently, but based on the comparison of what I did before and do now, it seems the cause was the wrong dosage of agar per water, i.e. an excess of agar.
Hoping this may help others.


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In the absence of natural enemies, does evolution eventually create natural enemies?
I wonder if there is experimental evidence on this (either from computer simulations or perhaps cases of isolated species like on the Galapagos Islands).
Imagine the hypothetical situation of a group of individuals of the same species that becomes isolated from all others. I know it's not a very realistic scenario because life is pretty much everywhere on Earth, but maybe experiments could be done in the laboratory.
So we have, for example, 100 or 1,000 or so individuals of the same species (any species, from any domain and kingdom of life) that is isolated from all other life. I know this group would undergo several speciation events (I think I've read about experiments like this and I think it's not really debatable, but is likely to be universally agreed upon by evolutionary biologists), but would this group eventually evolve natural enemies (e.g. a predator-prey or host-parasite or similar relationship)?
I think limited resources would certainly result in different competitors evolving, with some competitors fitter than others, but I'm not sure about enemies. I'm thinking that given adequate time, full-blown enemies would be almost certain to evolve, but that's just a guess.
A more specific example might be to take a single ant colony or honeybee colony and isolate it in a laboratory and study it over hundreds of generations or more.
I did some searching on this, but didn't find anything closely related to this question.
For more context, I started thinking about this question while reading this article.
Thanks in advance for any thoughts on this.
Edit: assume in a lab experiment that non-living nutritional sources (e.g. sugar water) were supplied in a measured way.

I’m voting to close this question because unfortunately this is a speculative question, even if the answer is likely yes, it is still speculative and unable to be answered with evidence from the literature.

I'll add a comment here to partially answer this question - if you take reductio-ad-absurdum as an argument: Imagine the beginning of life on this planet - at some point there must have been 1 animal species, assuming all animals are descended from this species, now there are thousands, some of which are predators... so, yes?

True that, but I'm seeking experimental evidence (either in silico or in vitro) published in the last 20-40 years or so. For example, the 1952 Miller–Urey experiment was in vitro & although it didn't involve life, it was in vitro & insightful in that only water, methane, ammonia, and hydrogen started the experiment. But at least 3 amino acids were identified in the resulting solution: glycine, α-alanine and β-alanine. In 1996, Miller said: "Just turning on the spark in a basic pre-biotic experiment will yield 11 out of 20 amino acids." So they've been doing experiments like this for ~70 years.

Also, here's an oversimplified experiment in silico where some experimental parameters do not lead to natural enemies, no matter how many generations are allowed to pass: https://ncase.me/trust/


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What fraction of sites are expected to be polymorphic?
Question
Consider a very long (eventually infinite) DNA sequence of neutral sites. Consider a panmictic population of constant size $N$ with a per site mutation rate of $\mu$ where all individuals have the exact same fitness.
What is the fraction of sites that we'd expect to be polymorphic in the population (SNPs)?
Motivation behind this question
I am asking this question to verify the results of simulations I run. For example, I run a simulation with $x$ ($x$ will be varying below) neutral sites, with a per-site mutation rate $\mu = 10^{-9}$ and a population size of $N=100$. I run the simulations for 10,000 generations. There is no recombination. When the number of sites:

$x=10^3$ I get 0 SNP
$x=10^4$ I get 1 SNP
$x=10^5$ I get 3 SNPs
$x=10^6$ I get 25 SNPs
$x=10^7$ I get 238 SNPs

Is there a bug in my model or is it what we'd expect given the parameters?
In the human genome, 1 out of 300 sites are polymorphic (SNPs) (ref.). This is a frequency of SNPs that is 100 times greater than what I observe in my simulations. Note however, that the assumption of neutrality and out demographic assumptions would not perfectly hold and this result could pretty far off neutral expectation. My goal is not to reproduce something that look like the human genome but only to reproduce the neutral expectations for the moment.

Have a look at https://en.wikipedia.org/wiki/Tajima's_D. It provides an estimate for the number of segregation sites for a population under a neutral mutation model.

@putnampp Sounds interesting indeed. Does it mean that the expected number of SNP's in a sample of size $n=N$ (I sample the whole population) is $E[S] = 4N\mu\sum_{i=1}^{N-1}\frac{1}{i}$? Therefore, in my case $N=100, \mu = 10^{-9}, E[S] ≈ 1/481939$. Therefore, out of $10^7$ sites I'd expect to have $20.75$ SNPs. Is that right? This is 10 times less than what I observe.

I would agree with your comment. If you were to use the entire population as your sample size you would expect to find roughly the number you suggest. I've written some example simulation software that is capable of performing such evolutionary scenarios (Clotho). You could also check your numbers against MS.

Ok, sounds good. I'll have a look at clotho. If you want an make a short answer out of your comments by repeating the calculation I made. And you'll hopefully get enough reputation to comment in the future thanks to this answer! I'd welcome you link the paper describing clotho as well. Thanks! I've got to understand why I have so much polymorphism now!

Reiterating the above comments. Have a look at Tajima's D. It provides an estimate for the number of segregation sites for a population under a neutral mutation model.
The general form of the estimation for a diploid population is $E[S]=4N\mu\sum_{i=0}^{n-1} \frac{1}{i}$.  Here the mutation rate of is per-genome not per-site, so $\mu=L * 10^{-9}$ where $L$ is the genome size. Estimating the segregation sites of an entire population of $n=N=100$ with genome size of $L=10^{7}$ where each site has a per genome mutation rate of $\mu=10^{-2}$ one would expect that $E[S] \approx 20.75$. So, your numbers seem higher than expected.
I've written some example simulation software that is capable of performing such evolutionary scenarios (Clotho manuscript). Similarly, you can check your numbers against a population generated using MS.

The fraction of polymorphic sites that exist in a population is dependent on the biology of the organism. For instance, you would expect to find different rates of polymorphism in related plants that have different breeding systems, e.g. in Silene [1]. Past bottlenecks are also expected to decrease polymorphisms [2]. So, the answer to your question would depend on the exact species and population that you are looking at.

Thanks for your answer. Yes, I am well aware that pattern of selection (frequency-dependent, purifying selection, spatially or temporally heterogenous environment, LD, etc..) as well as demographic patterns (bottleneck, population structure, range expansion, etc..) affect these polymorphism. I am interested in a theoretical predictions assuming a whole bunch of things. I made those assumptions a bit more obvious in my post.

we included a script to calculate this in supplemental material
http://onlinelibrary.wiley.com/doi/10.1111/mec.13034/full
....single segregating site per locus or up to a maximum of four SNPs, as is expected for short-read genomic data (see attached R script for estimation).

Could you tell a bit more about the method? It's more of a comment now.


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Why does an complete molar pregnancy not result in a clone?
Complete molar pregnancy is one where an ovum devoid of nucleus is fertilized by a sperm after which the haploid set of chromosomes double to form a diploid set.
As far as my understanding extends if the sperm had Y chromosome the embryo will not survive.
However if the sperm has X chromosome the zygote will survive to have the 46 XX karyotype and will start to grow as molar pregnancy (which is basically trophoblastic tissue with no fetal parts, as answered by Anongoodnurse).
Why is there no proper fetus? Why can't a "female clone" of male parent form instead? Where is the defect as such?

The Question pointed out by WYSISYG contains data only from animal studies. Although it answers my question, I want more data obtained from study of human trophoblastic tissue (from the molar pregnancy).  Papers on imprinting which are linked in those questions have no mention of molar pregnancy although Prader-Willi and Angelman syndromes are mentioned (as cases seen in humans).

Oops, I corrected my question thanks to anongoodnurse. I mixed up complete and partial moles with each other.

Imprinting issues: possible duplicate of Does a man contain all the genes needed to make a woman? and Could a sperm be altered to contain a female's genetics?

"However if the sperm has X chromosome the embryo will survive to have the 46 XX karyotype and will start to grow as molar pregnancy."

Complete molar pregnancy is diploid, and there is no fetal tissue identifiable. It is a disease of the placenta, a uterine tumor (cancerous in some cases, non-cancerous in others); fetuses do not develop from such pregnancies, not haploid or diploid (though they are usually 46, XX). A male haploid 23,X replicates, but only trophoblastic (what should be the placenta) tissue results.
Partial molar pregnancies are triploid, and a fetus can sometimes be identified. However, it is non-viable, as polyploidy is non-viable in humans. Even if it were, the abnormal placenta could not support it.
Molar Pregnancy
p57KIP2 immunohistochemistry in early molar pregnancies: emphasis on its complementary role in the differential diagnosis of hydropic abortuses

This should be a comment rather than answer. It does not answer the question in any way.

Yes this should be converted to comment.


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Enlargement of joints in osteoarthrosis
If osteoarthritis (osteoarthrosis) is a degenerative condition, where the cartilage in joints wears down, what causes the joints to become inflamed? I'm reading through a book called Understanding Disease: Arthritis by Steven Tiger, and it mentions that Heberden's nodes are caused by osteoarthrosis. if things inside the joint are wearing down, why does it get bigger?

Osteoarthritis results from the gradual degradation of articular cartilage. When the cartilage is damaged extensively, e.g., all the way through the cartilage and into the bone, an inflammatory response ensues in the bone. This often happens when bone is rubbing against bone.
One of bone's responses to injury and inflammation is the production of new bone. In this case, the bone, called osteophytes or bone spurs, is produced pathologically (i.e., not like the bone laid down normally during growth). Heberden's nodes are the names given to these osteophytes at the distal interphalangeal joints, but the process is basically the same at other joints in the digits, ankle, etc.


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Which molecular changes make certain SARS‑CoV‑2 strains more contagious?
Articles  often state that certain SAR-COV-2 strains are more transmissible, e.g:

Most studies indicate Delta is 50-60% more transmissible than the
Alpha variant

How dangerous are covid-19 Delta and Delta Plus variants?
I believe that these studies are all based in statistics of people infected — that higher transmissibility has something to do with changes in the virus attachment and entry into human cells — but without much further detail. Is it known which changes lead to a virus strain becoming more contagious, and whether one can predict that when certain molecular changes appear in a virus strain it will be more contagious, or is our knowledge based solely on observation?
Is it known which molecular changes make certain SARS‑CoV‑2 strains more contagious?

Aside from changes in virus attachment and entry, other changes affecting transmissibility would include those affecting number of viruses given off by the infected and in what form (e.g. aerosolized), survival of the virus outside an infected individual, mutations affecting course of disease once virus enters a cell, and so forth. Some of those mutations can be studied in the lab in animal models or in tissue culture. Mutations affecting structure such as in the S protein can be modeled and can be tested to see if convalescent serum or monoclonal antibodies will still bind to them.

There are many approaches as described above -- it's worth looking into them if you're interested.

Pablo, two things. 1. Infectologist is not an English word. 2. Questions of the sort “Do experts know?” are unnecessarily contorted. This site is for questions about biology, not biologists. Your title would be better if you deleted the first three words. Likewise in your last sentence.

@RoniSaiba The  important thing is not whether virologists know, but whether it is known on the basis of peer-reviewed published science that is supported by other findings. The paper could be published by a Nobel Laureate or an Undergraduate student. Emphasis on status has no place in science. I therefore feel obliged to edit the post in the way I hoped the poster would. He will not learn if you do it for him, especially if you do it wrong.

@David sure. Feel free to edit as you see fit. "Infectologist" was too much of an eyesore so I suggested an edit.

We can only see this in retrospective. So here are some mutations that have enhanced the transmissability of the virus:

ORF1b:P314L in combination with S:D614G (Pango lineage B.1 and all subsequent lineages)
S:N501Y Most prominent mutation of Alpha, Beta, and Gamma. It often licences S:E484K which on its own does not seem to boost transmission.
S:P681R The key mutation in the Delta variant, enhancing the Furin cleavage site

In order to be efficient the mutations need to be embedded in a fitting virus, the same mutation may enhance transmission for a certain variant, but being inefficient in another variant with different co-mutations.

To improve this answer, you could 1) provide links to references for your points. 2) discuss why retrospective analysis is not the only method we can use to see these sorts of things, and 3) what sort of changes are seen in similar viruses that also lead to enhanced transmission (cough polybasic cleavage site cough).


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Why can a zygote develop into all different types of cell, whereas a differentiated cell cannot?
A cell formed by the fertilization between two gametes has all the DNA and can lead the development of a human person (or other animals in other species). But other cells in a human person has also all the DNA (like skin cells), yet they don't lead the development of organs, bones, etc. What is the difference between the zygote and cells from any part of the body from a developed person that one can lead to the development of a person and the others can't in spite of all of them have all the DNA? Does it have to do with the enviroment/surrounding those cells are in, is there any structural difference between the zygote and the other cells or how is it?

You may want to ask for basic sources/reading for embryology and development, since answering this question will require restating everything about cell differentiation. As it is it will be flagged as too broad becasue you are asking many different questions.

I disagree that answering this question requires anything as complicated as that; I think swbarnes has already answered the question sufficiently in just a few sentences.

Developmental biology is a huge field that we are still working on a lot.
DNA is only half the story.  The other half is gene expression; what subset of the DNA a cell is using at any time.  Your lung cells have the gene for insulin, but in lung cells, that gene is dormant.
The short answer is that in general, a mature cell is using the subset of its DNA that it needs to do its job and can't just change its gene expression to become a different kind of cell.   Cells that do become less like adult cells and less specialized can become cancerous.

The question in the title — too broad for SE Biology in my opinion — is "Why", not what happens. Saying genes get switched off in differentiated cells doesn't explain why, or why one cell becomes liver and another muscle. Better just to comment if this is all you have to say.

@David I don't think the OP was going for an existential "why" here: see the two questions that are the last two sentences of the OP. This answer, while simplified and missing other special attributes of a zygote, I think does answer those questions succinctly, especially the original title before you edited it which was directed toward the presence of the same overall DNA.


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Why do universal recipients (AB blood group) not react to antibodies in the blood of O-group donors?
While studying compatible blood groups, I found that we only consider the antigens on red blood cells (RBCs) and not the antibodies present in blood plasma. For example

“an AB blood group person can receive blood from persons of any blood group as there are
  already both antigens, A and B, on the RBCs.”

But why don’t we consider the antibodies already present in the plasma from people with different blood groups?
For example, the O blood group has both anti-A and anti-B antibodies. If this blood is given to an AB person who has antigens A and B, do the antibodies of O not react with the antigens of AB?  Or, in other words, how is a person with the AB blood group a universal recipient if he has both antigens(A,B) in the blood, which can react with antibodies(anti-A and anti-B) present in indiduals of other blood groups (A, O, B)?

Always remember that plasma is not given while blood transfusion. So if you are giving only RBC of O blood group to the person having AB Blood group it will not react.

Although I answered this question, an older similar question has just surfaced for some reason. (The answer there is also more comprehensive than mine, and some comments more authoratitive.) I therefore flag this as a duplicate and have deleted my answer. (I may add something to the older question.)


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What is this cocoon (if that is what it is)?
I found this cocoon (or what I think looks like a cocoon) in an urban hedgerow in Upper Bavaria, Germany in early October (begin of autumn).
Around was a web, but no inhabitants were there.
Its diameter was about 3 cm and its opening showed towards the sky.
Thank you already for hints! :)

I guess, I figured it out: it seems to be an abandoned cocoon of a wasp spider (Argiope bruennichi).
Images for comparison are found on Wikimedia Commons and on iNaturalist.
Only thing that puzzles me is that usually the spiderlings overwinter in the closed cocoon and it was opened already in autumn (and the hedgerow is - unfortunately - neatly cut each autumn, so it is impossible the cocoon was there since the last year).
Anyway, I guess someone might have preyed on them... ¯_(ツ)_/¯


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Is the formula of cyclic adenosine monophosphate (cAMP) $\ce{C_{10}H_{11}N_{5}O_{6}P}$ or $\ce{C_{10}H_{12}N_{5}O_{6}P}$? Does it matter?
For some reason, half the sites on the internet say that there are 12 hydrogen atoms in one molecule of cAMP, and the other half claim 11.
Who is correct?  Does a single, free, unbounded and unresolved cAMP molecule in isolation possess 12 hydrogens, and in all other cases have 11? I am confused.

OK. Despite my reservations I have provided an answer as there was some interest in the question. As you are more active on physics and chemistry SE sites I'm a little surprised that you didn't see the answer yourself.

Without links to, or presentation of, examples of the two formulae it is not possible to be sure that the following explains the particular experience of the poster, but nevertheless I provide it as there has been some interest in the question
The chemical formula depends on the actual molecular structure
This statement may seem obvious, but certain molecules can exist in different states — in biochemistry acids and bases especially can be ionized or not.
If one consults the catalogue of a chemical company, one finds the following diagram of one type of cAMP that they sell in powdered form, in which the phosphate group is shown protonated:

The chemical formulae is given with 12 hydrogens, to reflect this: C10H12N5O6P.
If one consults the Wikipedia entry for cAMP, one is provided with chemical information in the standard form used in Wikipedia, with the phosphate group shown ionized in the diagram of the molecule:

The chemical formulae is given with 11 hydrogens, to reflect this: C10H11N5O6P.
Does it matter?
It matters if you are in the laboratory and preparing a solution of cAMP at a particular concentration. In this case the error would only be about 0.3%, but if it were a salt of an acid, that would have a greater effect. Use the MW written on the label of the bottle.
It matters if you are doing metabolomics and identifying species by their molecular mass, but the species present will depend on how the experiment is done, and one is unlikely to be dealing with this oneself — your software will identify the species for you.
So, in practice, not very much. But in general it matters a lot that one thinks about the ionization state of molecules in solution in biochemistry, and understands how this will vary with the pH.


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How does estrogen influence collagen synthesis?
Through what mechanisms does estrogen interact with collagen synthesis? Especially in the context of elevated estrogen levels and genesis of purpura simplex .

Questions that show no research are generally not well received in this site (they may be closed as homework). Please see here for help. The moderators are strict about effort put into research before asking a question. So please include what you found in your search for the answer in the post to get good answers.

You should look this up yourself, this is basically asking someone to do a very specific piece of reading and interpret it for you... unless you can provide some of the background info and point out points you don't understand or are interesting for discussion.

Is this a homework question?

this is a very vague question - but one that is easily addressable if you go to http://www.ncbi.nlm.nih.gov/pubmed and search for estrogen and collagen. There are numerous effects that aging and estrogens have on collagen synthesis and metabolism.