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Help with analogy: Competition among similar species
I'm not from this field, but I'm trying to make a biology/ecology analogy for companies with similar products competing for the same market segment.
I was thinking of using the competitive exclusion principle to illustrate that the products will have to each find their own niche, or disappear from the market.
In a market, when opportunity arises (lots of capital available, and interest from the consumer side for an new product) many competing products spring up, and then we slowly arrive at an equilibrium similar to the exclusion principle mentioned before.
My question is this: Is there a similar "opportunity stage" of this process in nature? Like an increase in resources available that drives many different species to "appear" and compete for the newfound wealth?
Pointers to Wiki articles etc. for further research will be appreciated.

The Cambrian explosion may be an example of what you are talking about: https://en.wikipedia.org/wiki/Cambrian_explosion

Here are some definitions of interest to you

Ecological succession is the process of change in the species structure of an ecological community over time. The time scale can be decades (for example, after a wildfire), or even millions of years after a mass extinction.
A seral community (or sere) is an intermediate stage found in ecological succession in an ecosystem advancing towards its climax community. In many cases more than one seral stage evolves until climax conditions are attained.1 A prisere is a collection of seres making up the development of an area from non-vegetated surfaces to a climax community.
In biology, a disturbance is a temporary change in environmental conditions that causes a pronounced change in an ecosystem. [..]  Because of these and the impacts on populations, disturbance determines the future shifts in dominance, various species successively becoming dominant as their life history characteristics, and associated life-forms, are exhibited over time.
Ecological facilitation or probiosis describes species interactions that benefit at least one of the participants and cause harm to neither.1 Facilitations can be categorized as mutualisms, in which both species benefit, or commensalisms, in which one species benefits and the other is unaffected. Much of classic ecological theory (e.g., natural selection, niche separation, metapopulation dynamics) has focused on negative interactions such as predation and competition, but positive interactions (facilitation) are receiving increasing focus in ecological research.


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(A)sexual reproduction of plants
Are all plants capable of sexual reproduction? Some can do asexual reproduction as well but I haven't found any plants that aren't capable of sexual reproduction. Is it correct to say all plants are capable of sexual reproduction?

No, it's not. There are common plants that can only reproduce asexually.
It's likely you can buy produce from several plants which are unable to do so at your local supermarket. The most famous example is, of course, the banana which is a sterile mutant and all bananas of a particular variety are clones, but some seedless varieties of grapes and oranges would also count (although most seedless fruit you find in the supermarket are actually produced with hormonal treatments rather than being asexual varieties).
These plants are examples of artificial selection but there are also examples of plants that have lost the ability to sexually reproduce in the wild. The evening primrose is a good example, with some 30% of species in the genus Oenothera having evolved to be asexual (Hollister et al, 2015), but this is not the only example. It is likely that, just as in animal species, asexuality has short (on an evolutionary timescale) term advantages but results in lower fitness in the longer term.

How come bananas lost their ability to reproduce sexually?

Because bananas with seeds are nowhere near as edible, humans have selected the varieties without for cultivation.

Did some plants also lose their ability to reproduce sexually due to natural (non-human) circumstances?

@Koekje: Yes, see updated answer.

Thanks 1000 times for answering my questions! (I've been looking on the internet for at least 2 hours without finding any evidence for plants that solely reproduce sexually)

So it turns out that what I said about seedless fruit in the supermarket is largely incorrect, while some are produced from seedless varieties most are produced with hormonal treatments that induce normal seeded plants to produce seedless fruit and these plants can reproduce normally when allowed to do so. Bananas are an exception to this, and really are obligately asexual.

Does "heterosis" fit into your context? From Hollister who you link to I got, e.g. Dorken, M.E. and Eckert, C.G. (2001) Severely reduced sexual reproduction in northern populations of a clonal plant, Decodon verticillatus (Lythraceae). Maybe "banana" is just an example for all sorts of plant losing their capability when: inbreeding. "Obligately" could even, conversely mean: all other forms extinguished.

Actually, I think you might be referring to apomictic plants.
Apomictic plants are those plants that are unable to complete the normal process of sexual reproduction and have to use another alternative pathway to produce an embryo. One way out is through asexual reproduction, and another is called Agamospermy.
Agamospermy is basically the process of formation of seeds without sexual reproduction. Agamospermy is further of two types, sporophytic agamospermy and gametophytic agamospermy.
In sporophytic agamospermy, the embryo is directly formed by diploid sporophytic cells such as those of the nucellus of the ovule, and this is also known as adventive embryogeny. More often than not, in adventive embryogeny, multiple embryos are formed(this is called adventive polyembryony, but i will not go into that for now).
However in the case of Gametophytic Agamospermy, the nucellus cells first develop into a diploid egg cell( the egg cell is normally haploid, however, in this case meiosis is not possible so egg cell has to be diploid). This diploid egg cell now undergoes parthenogenesis(i.e, formation of embryo without fertilisation or syngamy) to produce an embryo which is a clone of the parent.
Now coming to the examples. Apomixis is really well marked in Citrus plants like oranges, lemons, etc and also in Mango.
Also, some varieties of apple are known to show parthenogenesis(DO NOT confuse with parthenocarpy!!)

Even Rubus shows the same.

Refering to question, are those plants not capable at all of sexual reproduction; have they completely opted out of or lost their sexual way of reproduction?
I think your definition of "sexual reproduction" is based on gametes as special cells being a prerequisite. Some authors may consider Apomixis sexual reproduction as the term implies crossing over of genes. I think the  question: "Can parthenogenesis be considered sexual reproduction?" pretty much relates to your answer.

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Why does chromosome inversion happen?
I read that chromosome inversion is a type of genetic mutation.

Why does inversion happen? What is the purpose?

I also read that if genes do not match up during cross over between inverted chromosome and non-inverted chromosome could cause birth defect.

Then would that make chromosome inversion fall under harmful mutation?

In addition, there are two types of inversions: paracentric and pericentric. The difference between these two inversions is that one of them invovles centromere and the other one does not.

What is so important about centromere?

And lastly,

Does inversion happen before humans are born, or after they are born? When does it happen?

I apologize if my questions are vague. I do not have much background information on chromosomes.

If you are free I suggest you to red this excellent piece which answers few of your questions - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946949/

Why does inversion happen? What is its purpose?

Like many other mutations, inversion is generally a neutral mutation. Many inversions, especially those which are between small, intergenic regions, evolve neutrally by drift alone. However, selection can, and does, occur when:

inverions create structural problems with meiosis, like pericentric inversions
a breakpoint disrupts open reading frame or alters gene expression
inversion carries one or more selected alleles

Thus, inversion does not necessarily yield any advantage, but it usually does not cause any harm either (Kirkpatrick, 2010).

Can chromosome inversion fall under harmful mutation.

No mutation is useful or harmful by default. It depends on what effect it gives in every case. Similar is the case with chromosome inversion. It is mostly a nuetral mutation, occasionally harmful, and rarely useful for the individual. Thus, in a way, it can be classified as a neutral mutation.

What is so important about centromere?

The main point to ponder is how the two types of inversion affect daughter cells, especially during meiosis. For introduction, in a paracentric inversion, the centromere is not involved, while it is in pericentric inversion.
Now consider paracentric inversion during meiosis. Start with a diagram:

Due to a paracentric inversion during a crossover, formation of a dicentric bridge and an acentric fragment takes place. While the acentric fragment, due to lack of a centromere, is lost from the genome, the dicentric bridge forms such structure that the two remaining chromatins lie farthest apart. Eventually, due to tension, the homologous chromosomes break apart, leading to formation of chromosomes lacking certain genes. This makes the gamete and/or the zygote inviable, and reduces the recombination frequency.
Now, while very similar thing happens in pericentric inversion, the mechanism is a bit different. Again, see the diagram first:

Since the centromere is also involved in inversion, the genes on both arms of chromosomes are, as a result, inverted. When crossover takes place, both homologous chromosomes receive two copies of one fragment and no copies of the other. As a result, again, the gamete and/or zygote is inviable and the recombinant frequency is reduced (Griffiths et al, 2000).

When does chromosome inversion happen?

Just like all other mutations, chromosome inversion can occur at any stage of life in an individual. It is not limited to meiosis, it can occur in any replicating cell in the body. However, the phenotypic effects are most prevelant when it occurs during meiosis, since it can easily lead to defected or inviable progeny.
References:

Kirkpatrick M (2010) How and Why Chromosome Inversions Evolve. PLoS Biol 8(9): e1000501. doi:10.1371/journal.pbio.1000501
Griffiths AJF, Miller JH, Suzuki DT, et al. An Introduction to Genetic Analysis. 7th edition. New York: W. H. Freeman; 2000. Inversions. Available from: https://www.ncbi.nlm.nih.gov/books/NBK22042/

@gerardo I couldn't think of a better word ;) thanks though

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Is cancer caused by vitamin B17 deficiency?
I have read in an article on the internet that cancer is caused due to deficiency of vitamin B17 which has been removed from our diets long ago in the western food. But some people say that vitamin B17 does not work. So, is it deficiency of vitamin B17 which causes cancer i.e. can this vitamin really be used to cure cancer?

It is mentioned as cancer quackery in this paper which you might find useful.

@user39315 Please open new questions, and do not ask in the comments.

@Kiritee I see we just found the same paper :-)

https://en.wikipedia.org/wiki/Amygdalin

I'm voting to close this question as off-topic because it's not about biology.

I have no idea why it was not closed or migrated before. I would suggest migrating it to skeptics but it is too late. I find this type of question comes in the category http://biology.stackexchange.com/help/dont-ask. Did you really post this expecting an answer Yes? The motley crew on this list have some special insider knowledge about cancer cures denied to the rest of mankind? That I am going to say, Yes there is a medical conspiracy, I met a man in the pub last week and he told me that his brother-in-law...? Allowing this kind of non-question really drags this site down.

@david I would disagree with your last point. Since this is a conspiracy, it is indeed better to have an answer regarding why those claims are false and why amygdalin is indeed harmful rather than useful. For the question title, I agree that it could be framed better.

@another'Homosapien' — that assumes these posters are open to rationale argument. It's like politics or religion — did you ever get anyone to change their mind on these topics by arguing with them? And this is a question and answer site. Allowing this sort of crap is like a SE site in geology or the like fielding questions from flat-earthers all the time. Remember what they say about not feeding the trolls.

Its not about the trolls. I meant it would be useful for the ones who don't know about this matter; if they read this post and get to know the truth behind the conspiracy, then how can't it be better?

If you wish medical information or advice I would suggest you do not come here. The British, NHS Choices site (http://www.nhs.uk/Conditions/Pages/hub.aspx) or the US NIH Health Information (https://www.nih.gov/health-information) are reputable sources. If there is a conspiracy, of course, these sites will be part of it. But then, perhaps Elvis has really become a Tibetan monk.

Short Answer: No.
Background: First of all, there is no such thing as vitamin B17. The compound, amygdalin or laetrile, which is referred to by this term, is not a vitamin1. Amygdalin is indeed a cyanogenic glycoside (like glucosinolates, see this answer) which is poisonous to organisms including humans, because it forms cyanide which is toxic2. See this image for its structure:

The notion that amygdalin is a vitamin started when Ernest Krebs Jr., inventor of 'laetrile' (a modified form of amygdalin), rebranded it as a vitamin to get around the new FDA drug regulations and get it approved as nutrient supplement instead of pharmaceutical3. Ernest Krebs Sr., in 1920s, formulated a theory that amygdalin could kill cancer cells4 and the notion was carried forward by his son, though Ernest Krebs Sr. himself considered amygdalin as too toxic for human consumption. This view received a huge uplift when, in 1973, a public relations officer at Sloan Kettering Hospital, which was given the task by the NIH of performing a series of laetrile trials, alleged a cover up of, and leaked, data that claimed potential for laetrile as an anti-cancer agent5, though nobody else was able to reproduce the same test results in a series of followups. Yet, perhaps the most prominent force which still keeps this myth alive is the book World Without Cancer: The Story of Vitamin B17 by G. E. Griffith (interestingly, reviewed by 'Dr.' Ernest Krebs Jr.). According to all these reports, laetrile might work in following ways6:

malignant cells have higher levels of $\beta$-glucuronidase and lesser levels of rhodanase, because of which they are more susceptible to effects of laetrile.
malignant cells have higher levels of $\beta$-glucosidase (different from $\beta$-glucuronidase) and lesser levels of rhodanase, because of which they are more susceptible to effects of laetrile.
cancer is due to deficiency of vitamin B17 (laetrile) and vitamin B17 is required by cells to restore health (though there is no evidence for this).
cyanide released by laetrile has a toxic effect beyond its interference with oxygen utilization by cells. According to this theory, cyanide increases the acid content of tumors and leads to the destruction of lysosomes. The injured lysosomes release their contents, thereby killing the cancer cells and arresting tumor growth.

Laetrile is even supposed to raise the red count in blood, be of value in treating sickle cell anemia, treat parasitic diseases, help regulate intestinal flora, cause lowering of blood pressure in cancer victims and provide relief from arthritis3.
However, all clinical tests have concluded that laetrile is poisonous to humans (and other organisms) due to cyanide poisoning and thus, its effect in cancer treatment is unambiguously negative6,7,8. In fact, use of laetrile has even led to a number of deaths9.
In reality, when amygdalin is ingested, the enzymes  $\beta$-glucosidase, emulsin and amygdalase hydrolyze it into gentiobiose and L-mandelonitrile. Gentiobiose is further hydrolyzed to glucose, whereas L-mandelonitrile is converted into benzaldehyde and hydrogen cyanide, which causes cyanide poisoning2. The concerned process looks like10:

If the quantity of cyanide generated is under the acceptable daily intake limit (0.05 mg/kg body weight)11, then it can be handled easily by enzymes, like rhodanase which converts toxic CN- to non-toxic SCN- ion12. But this quantity is often beyond the limit; a single apricot seed contains about 0.5 mg cyanide13. Hence, it results in cyanide poisoning.
Thus, the so-called vitamin B17 cannot cure cancer.
References:
 1. Lerner IJ (1981). "Laetrile: a lesson in cancer quackery". CA Cancer J Clin. 31 (2): 91–5
 2. Wikipedia contributors. "Amygdalin." Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 10 Mar. 2017. Web. 11 Apr. 2017.
 3. United States, Food and Drug Administration. “Laetrile, the Commissioner’s decision” 1978
 4. (1991), Unproven methods of cancer management: Laetrile. CA: A Cancer Journal for Clinicians, 41: 187–192. doi:10.3322/canjclin.41.3.187
 5. WADE, NICHOLAS (1977). Laetrile at Sloan-Kettering: A Question of Ambiguity. Science, 198, 1231-1234.
 6. Ellison NM, et al. “Special report on Laetrile: the NCI Laetrile Review. Results of the National Cancer Institute’s retrospective Laetrile analysis.” N Engl J Med. 7 September 1978.
 7. Milazzo S, Horneber M. Laetrile treatment for cancer. Cochrane Database of Systematic Reviews 2015, Issue 4. Art. No.: CD005476. DOI: 10.1002/14651858.CD005476.pub4.
 8. Milazzo S, Ernst E, Lejeune S, Boehm K, Horneber M (2011). "Laetrile treatment for cancer". Cochrane Database Syst Rev (Systematic review) (11): CD005476. doi:10.1002/14651858.CD005476.pub3. PMID 22071824.
 9. Editors of Consumer Reports Books (1980). "Laetrile: the Political Success of a Scientific Failure". Health Quackery. Vernon, New York: Consumers Union. pp. 16–40. ISBN 0-89043-014-4
 10. Amygdalin - TradMPD
 11. FAO Meeting Report No. PL/1965/10/2;
    WHO/Food Add/28.65;
    Evaluation of the hazards to Consumers resulting from the use of
    Fumigants in the protection of foods
 12. Cipollone R, Ascenzi P, Tomao P, Imperi F, Visca P (2008). "Enzymatic detoxification of cyanide: clues from Pseudomonas aeruginosa Rhodanese". J. Mol. Microbiol. Biotechnol. 15 (2-3): 199–211.
 13. S Krashen. Are Apricot Kernels Toxic?. The Internet Journal of Health. 2008 Volume 9 Number 2.

+1 Great answer. It's cool how your answer and my answer here are actually saying the same thing in terms of how laetrile/amygdalin is useless as cancer medication, but with slightly different narratives and lines of evidence (and also references).

@AlexDeLarge thanks for appreciation! I first thought of answering that question, but then I saw this question and thought it would be better to answer this one ;)

Short version: This is nonsense, cancer does not arise from nutritional deficiencies.
Long version: The substance is called Amygdalin, a poisonous cyanogenic glycoside. It can be found in higher concentration in the kernels of several plants including apricots, plums, bitter almonds, peach, plum. The semisynthetic, modified form is called Laetrile. Taking up this substances with the oral route can lead to cyanide poisoning up to death due to the release of cyanide from the molecules.
There is nothing like a vitamin B17 (which suggests that the substance is an essential vitamin to the human body), this has been invented by cancer quacks. None of the two substances have shown any activity in clinical cancer trials. See references 1 and 2 for details. The second is a systematic review of the Cochrane Foundation which analyses all available articles on this topic.
References:

Laetrile: A lesson in cancer quackery
Laetrile treatment for cancer

As far as toxicity of laterite is concerned, all currently approved neoplastic agents have enough toxicity and patients succumb to the effects of such more than the disease itself.  Not to mention the extravagant cost. There definitely needs more in depth analysis on the disease process to find a simple cure. This disease appears to go beyond genetics alone.  A few viral and bacterial variants have been discovered hpv and h. Pylori when earlier it was denied that it is caused by any microorganism.

Welcome to Biology.SE! Please add some references to your answer.

Cancer is not a simple disease and there won't be a simple (meaning always working) cure. There has been quite a lot of success lately with targeted and immune therapies - cancer treatment is by far not only chemotherapy.


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What inactivates pepsin in infants?
In infants, rennin helps in digestion of milk. Pepsin is also present in their stomach.
Why do infants need rennin for milk digestion, at the first place? Why does pepsin not act on the milk proteins in infants? Does the production quantity of rennin play a role in inhibiting the action of pepsin?

EDIT: Thanks a lot to @abukaj for pointing out the mistake in my answer (and to @paracetamol for asking such a beautiful question). I am rewriting my answer to incorporate the (hopefully) correct background knowledge this time.
NEW ANSWER: As @paracetamol and @AlanBoyd (in their answer) pointed out the lack of credible support for the claim that infants produce rennin/chymosin, the previous answer attributing the digestion of casein in infants to chymosin had to be corrected. So, lets now look at the other possible candidates for casein (or, more specifically, $\kappa$-casein) digestion in infants.
As Martin et. al. (2016) claim, milk casein has some bioactive roles, such as forming masses with calcium and phosphorus1. Also, infant milk formulas mostly have higher casein content than human breast milk, making the former harder to digest than the latter. Back to the digestion point, human breast milk is known to contain many proteases in itself, including anionic trypsin, elastase, plasmin, cathepsin and kallikrein, while prothrombin has also been identified in human colostrums2. In fact, Ferranti et. al. (2004) also identified fragments of casein created by plasmin cleavage3. However, Chatterton et. al. (2004) were able to detect $\beta$-casein after 1 hour of in vivo gastric digestion in 8 day old infants, but not in 28 day old infants, suggesting the increase of digestive capacity of the infants4. This increase can be attributed to the development of gastric acid production system in the infants. For the case of newborns, Nakai and Li-Chan (1987) suggested that Pepsin C, also called gastricsin, can hydrolyze casein at the pH range of 4-5 (the lowest pH newborns can reach)5. However, the buffering effect of human and bovine milk proteins does not allow the gastric pH to reach the optimum pH required for activity of pepsin A and pepsin C.
How, then, is casein digested by infants at all? This is summarized (to some extent) by Chatterton et. al. (2013), according to which, although gastric pH is unable to reach the optimum pH for pepsin activity, it is sufficient for minor initial digestion of human milk proteins. This causes the release of glycomacropeptide, the C-terminal portion of casein. The combination of this initial digestion and the gastric pH, close to the pI of caseins (~ pH 4.6) causes precipitation of caseins and slowing down of their digestion. The casein peptides, on the other hand, are absorbed into plasma where they show a number of biological activities, including inflammation modulation and blood pressure regulation6.
Thus, even though infants lack chymosin and a fully mature digestive system, this is compensated by a combination of proteases in breast milk and the slower digestion process until the digestive system of the infants develops completely.
source
References:

Martin CR, Ling PR, Blackburn GL. Review of Infant Feeding: Key Features of Breast Milk and Infant Formula. Nutrients. 2016;8(5):279. Published 2016 May 11. doi:10.3390/nu8050279
Dallas DC, Underwood MA, Zivkovic AM, German JB. Digestion of Protein in Premature and Term Infants. J Nutr Disord Ther. 2012;2(3):112. doi:10.4172/2161-0509.1000112
Ferranti, Pasquale & Vittoria Traisci, Maria & Picariello, Gianluca & Nasi, Antonella & Boschi, Velia & Siervo, Mario & Falconi, Claudio & Chianese, Lina & Addeo, Francesco. (2004). Casein proteolysis in human milk: Tracing the pattern of casein breakdown and the formation of potential bioactive peptides. The Journal of dairy research. 71. 74-87.
Chatterton DEW, Rasmussen JT, Heegaard CW, Sørensen ES, Petersen TE. In vitro digestion of novel milk protein ingredients for use in infant formulas: research on biological functions. Trends in Food Science & Technology. 2004;15:373–383
Nakai, S. and Li-Chan, E. (1987) "Effect of Clotting in Stomachs of Infants on Protein Digestibility of Milk," Food Structure: Vol. 6: No.
2, Article 8.
Chatterton, D. E. W., Nguyen, D. N., Bering, S. B., & Sangild, P. T. (2013). Anti-inflammatory mechanisms of bioactive milk proteins in the intestine of newborns. The International Journal of Biochemistry & Cell Biology, 45(8), 1730–1747

@mesentery Pepsin can too digest casein, but at lower pH, and yes, chymosin is just another name of rennin...I'll add that part. Quite clever BTW :D

Are you sure infants produce chymosine? Please see: https://biology.stackexchange.com/a/65017/33294

@abukaj oh boy, thanks for pointing this out. I've edited the answer, feel free to let me know if you find another error(s) :D

Milk contains a protein called caesin which gets digested in an adult body with the sole help of pepsin.But pepsin requires lower pH for digesting caesin. Since infants are basically fed on milk and they have a higher pH which makes pepsin incapable of digesting caesin in their body.Therefore infants need an enzyme named renin for this purpose.

Hello Pooja. Can you please add some references to support your answer? Good references include peer-reviewed articles, books and websites of scientific organizations. I should also point out that you have not added anything more than what is already mentioned in the existing answer. Moreover, the picture you have put is irrelevant. You should remove it.


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Why do some vegetables taste bitter?
Bitter gourd, cucumber, etc. are bitter to taste. Which chemical causes bitterness in them?
I found these when I searched online: this says that it is because of calcium, while this and this talk about physical effects.

As far as I know the maximum bounty is 500. It's easy to give away 500 when you have > 5000, not when you have < 1000...

@another'Homosapien' that's not the point in my commentary. The point is that giving 50 when you have < 1000 is good enough to my taste.

@another'Homosapien' Good, so he/she is, indeed, generous.

Actually, Bitter vegetables are composed of Sourmoi, which came from the word sour

Bitter taste is sensed by bitter sensitive gustducin receptors (T2R family). There are different types of bitter receptors and they can be triggered by different kinds of ligands. Different classses of phytochemicals that can trigger bitter taste, are reviewed by Drewnowski and Gomez-Carneros (2000).
The bitter tasting phytochemicals include phenols, terpenoids, alkaloids, flavonoids, glucosinolates and isothiocyanates.
Drewnowski and Gomez-Carneros' review (2000) and @anotherHomosapien's answer provide examples for these different classes of compounds. I guess they have missed alkaloids; so I give some examples: theophylline, theobromine (from chocolate) and caffeine (from coffee); these all are isomers of N,N'-dimethyl xanthine and taste bitter. Many alkaloids are toxic. Different bitter tasting alkaloids are reviewed in this chapter (Fattorusso and Taglialatela-Scafati, 2008. Chapter 3. Modern alkaloids. Weinheim: Wiley-VCH. ISBN:9783527621071).
High amount of salt may also taste bitter. The sensation of high salt concentration is transduced by amiloride-insensitive channels which are different from the amiloride-sensitive ENaC which sense low sodium concentration. Amiloride insensitive channels can also sense cations other than sodium. This taste is aversive in contrast to that due to low sodium concentration. Some of the bitter sensing taste cells have amiloride-insensitive channels (Lewandowski et al., 2016). However, I cannot comment if these channels elicit a bitter taste response.

Nice answer, +1! I totally forgot about amiloride channels ;)

Nice question! Many vegetables taste bitter because they contain compounds known as phytonutrients (Greek phyto = "plant"). There are more than 2500 phytonutrients known, and the most important (and common) ones are categorized as1:

Carotenoids: they are the ones that give red/orange/yellow color to some vegetables. They are mainly antioxidants, but some of them, like $\beta$-carotene and $\beta$-cryptoxanthin, are good for eyes as they can be converted into vitamin-A, whose derivative forms a part of phototransduction cascade.
Ellagic acid: it is found in a number of berries, such as strawberries, raspberries, pomegranates, etc. and has been shown in vitro to be helpful in slowing the growth of cancer cells and aid liver in neutralizing cancer-causing chemicals.
Flavonoids: they are found in a large variety of plants and constitute a large number of phytonutrients. Some flavonoids, like catechins, hesperidin and quercetin are very good for health. For example, see this answer for effects of catechins on the body.
Resveratrol: it is found in grapes, red wine, etc. and shows antioxidant and anti-inflammatory effects. Some researches have also concluded that it may reduce risk of heart disease and certain cancers.
Glucosinolates: these are found in cruciferous vegetables, like sprouts, cabbage, etc. and help checking formation and growth of cancer. This is the one we're talking about, so I'll continue about this below.
Phytoestrogens: they can exert estrogen-like effects on the body because of their structure, and even block body's natural supply of estrogen. Isoflavones can also reduce risk of endometrial cancer and bone loss in women. They are also found in a large number of plants, including soybeans, oats, barley, rice, apples, carrots, etc. (see full list here).

Another category, alkaloids, has been discussed by @WYSIWYG in their answer. These are all made naturally by plants as a part of their defense mechanism against insects and pests. This, in part, explains why they are bitter.
Coming to main point, glucosinolates are organic compounds that are responsible for bitter taste and pungent smell of many cruciferous vegetables. They are derived from glucose and amino acid, and contain sulfur and nitrogen as constituents. When they are cooked, chewed, or otherwise damaged, an enzyme myrosinase cleaves the glucose molecule, while the remaining molecule converts into isothiocyanate, thiocyanate and nitrile2, which cause the bitter taste and pungent smell (think of the isocyanide test you performed in grade XI and the smell it produced ;) The reaction looks like this:
source
A special glucosinolate, sinigrin, has been shown as responsible for the bitterness of Brussels sprouts and cauliflower3. Also, high concentration of glucosinolates are toxic to humans as well as other animals, though tolerance levels vary even within the same genera (Acomys cahirinus and Acomys russatus)4. So, that partly explains why these compounds are bitter.
Talking about the anti-cancer properties of glucosinolates (going a bit off-topic just so that you know why these are good for you), two of the main compounds that are responsible for such effects are sulforaphane and indole-3-carbinol. Sulforaphane (in which R- becomes C5H11OS- in R-NCS), for example, is derived by the action of myrosinase on glucoraphanin (again, a glucosinolate). It has been shown to have anti-cancer properties. For example, Li et al, 2010 have shown that sulforaphane prevents breast cancer by inhibiting breast cancer stem cells and downregulating the Wnt/$\beta$-catenin pathway (yeah, there is something like cancer stem cell!). In another research, Hsu et al, 2011 showed that sulforaphane prevents prostate cancer by inhibiting HDACs (histone deacetylases, which interfere with normal functioning of tumor suppressor genes) and DNA methylation. This example was just to mention about the anti-cancer properties of glucosinolates in general.
Another class of compounds, called cucurbitacins, are produced in plants of Cucurbitaceae family. Unlike phytonutrients, cucurbitacins are considered a type of steroid since they are derived from cucurbitane and stored as glycosides5. Their derivatives are also found in other families like Rubiaceae, Rosaceae and even some marine mollusks, and, much like glucosinolates, they are also produced for defense against herbivores.
However, it is not sure whether only glucosinolates are the only compounds responsible for bitterness of vegetables. A study suggests that increased levels of calcium can also be responsible for bitterness of vegetables6, although its evolutionary cause and mechanism of action are unknown yet. Also, it may even depend on the person(!). If you are a supertaster (which has high chances to be true if you're woman or from Asia, South America or Africa), you will tend to be highly sensitive to bitterness of Brassica oleracca cultivars, such as kale, Brussels sprouts or cabbage7,8. Sensitivity to coffee, green tea, mushrooms, etc. is also known to increase. You can view a full list on Wikipedia.
References:
 1. Phytonutrients - WebMD
 2. Burow, M; Bergner, A; Gershenzon, J; Wittstock, U (2007). "Glucosinolate hydrolysis in Lepidium sativum--identification of the thiocyanate-forming protein.". Plant molecular biology. 63 (1): 49–61.
 3. Van Doorn, Hans E; Van Der Kruk, Gert C; Van Holst, Gerrit-Jan; Raaijmakers-Ruijs, Natasja C M E; Postma, Erik; Groeneweg, Bas; Jongen, Wim H F (1998). "The glucosinolates sinigrin and progoitrin are important determinants for taste preference and bitterness of Brussels sprouts". Journal of the Science of Food and Agriculture. 78: 30–38.
 4. Samuni Blank, M; Arad, Z; Dearing, MD; Gerchman, Y; Karasov, WH; Izhaki, I (2013). "Friend or foe? Disparate plant–animal interactions of two congeneric rodents". Evolutionary Ecology. 27 (6): 1069–1080.
 5. Jian Chao Chen, Ming Hua Chiu, Rui Lin Nie, Geoffrey A. Cordell and Samuel X. Qiu (2005), "Cucurbitacins and cucurbitane glycosides: structures and biological activities" Natural Product Reports, volume 22, pages 386-399
 6. Tordoff MG, Sandell MA. Vegetable Bitterness is Related to Calcium Content. Appetite. 2009;52(2):498-504. doi:10.1016/j.appet.2009.01.002.
 7. Dinehart, M.E.; Hayes, J.E.; Bartoshuk, L.M.; Lanier, S.L.; Duffy, V.B. (2006). "Bitter taste markers explain variability in vegetable sweetness, bitterness, and intake". Physiology & Behavior. 87 (2): 304–13.
 8. Drewnowski, Adam; Henderson, Susan Ahlstrom; Levine, Alisa; Hann, Clayton (2007). "Taste and food preferences as predictors of dietary practices in young women". Public Health Nutrition. 2 (4).
 9. Li Y, Zhang T, Korkaya H, et al. Sulforaphane, a Dietary Component of Broccoli/Broccoli Sprouts, Inhibits Breast Cancer Stem Cells. Clinical cancer research : an official journal of the American Association for Cancer Research. 2010;16(9):2580-2590. doi:10.1158/1078-0432.CCR-09-2937.

If these things are bitter because they don't want to get eaten, why are fruits so sweet?

@MasonWheeler you might be interested in this. I didn't really mean 'they don't want to get eaten', they want to protect themselves from infection, and it might be mere coincidence that they are toxic to us too.

@AlwaysConfused oh didn't notice that! I was more focused on a general answer ;)


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Why do we feel sleepy when we wake up
Why do we feel sleepy, tired, and feel like we need to sleep more when we wake up? (Like, is there a special chemical in the brain that causes that?).
Are there any ways to wake up without feeling such things?

Possible duplicate of http://biology.stackexchange.com/questions/6829/why-do-we-feel-tired-if-we-sleep-excessively?rq=1

It is not tired by sleeping excessively, the question was why do we feel sleepy when we just wake up from being asleep.

Let say you are hungry and I stop you in the middle of your lunch. With high probability... you will be still hungry %))

I don't know if anyone else experiences this, but for me I always wake up six hours after falling asleep (and that's usually as soon as my head touches the pillow). At that precise moment when I wake up, I'm wide awake. Any sooner I feel sleepy and any later I feel groggy.


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Why is GTP, not ATP, produced in Gluconeogenesis & TCA Cycle?
In both gluconeogenesis and the TCA cycle, there is a point in each that GTP is produced instead of the usual ATP. My question is why GTP and not ATP for these 2 specific steps?

I've added to your title to put the focus on GTP. It's a good question. I must say I've wondered about it myself and never seen or come up with answer, although I haven't put much effort into doing so.

Welcome to Biology.SE. This is a good question, maybe you are interested in this question about why ATP is the preferred energy carrier.

Nice question. Beginning with Krebs cycle, there is actually no specific answer as both GTP and ATP are produced. First, see this article for why GTP is the more frequent product:

It may be that at the beginning, both GTP and ATP were equally available for energy and that the succinyl CoA synthetase reaction happened to choose GTP and that reaction is still with us today, billions of years later, even though we run the TCA cycle clockwise (forward) instead of backwards.

So, actually both ATP and GTP can be produced. And indeed both are produced, depending upon the organism. See this article:

A step with significant variability is the conversion of succinyl-CoA to succinate. Most organisms utilize EC 6.2.1.5, succinate–CoA ligase (ADP-forming) (despite its name, the enzyme operates in the pathway in the direction of ATP formation). In mammals a GTP-forming enzyme, succinate–CoA ligase (GDP-forming) (EC 6.2.1.4) also operates. The level of utilization of each isoform is tissue dependent. In some acetate-producing bacteria, such as Acetobacter aceti, an entirely different enzyme catalyzes this conversion – EC 2.8.3.18, succinyl-CoA:acetate CoA-transferase. This specialized enzyme links the TCA cycle with acetate metabolism in these organisms. Some bacteria, such as Helicobacter pylori, employ yet another enzyme for this conversion – succinyl-CoA:acetoacetate CoA-transferase (EC 2.8.3.5).

So, there is no strict rule that only GTP will be produced instead of ATP at that step. And, afterall, it does not matter much as both of them carry equal energy.

Now coming to Gluconeogenesis, GTP is hydrolyzed by the enzyme Phosphoenolpyruvate Carboxykinase or PEPCK. This enzyme can also work with both ATP and GTP, depending on the sepcific type of enzyme. See this article (links added separately):

It is classified under EC number 4.1.1. There are three main types, distinguished by the source of the energy to drive the reaction:

4.1.1.32 - GTP (PCK1, PCK2)
4.1.1.38 - diphosphate
4.1.1.49 - ATP

Thus, there is no strict protocol for using specific energy carrier in the process, both ATP and GTP can be used in the reaction. Its just because GTP is more frequently used that it is mentioned instead of GTP/ATP in the reaction.

I would say it is not known if the GTP/ATP distinction is important -- maybe it really doesn't matter, since the two can be interconverted -- but maybe it does.The kinetics is probably different since the GTP concentration is typically an order of magnitude smaller than ATP. Maybe there is some compartmentalization effect that we don't understand, as with NAD/NADP.  It's curious that major anabolic processes use GTP (protein synthesis, gluconeogenesis), while other energy-demanding processes (pumps, motor proteins) use ATP ...

@roland this is a valid point, there is still a lot more that remains unknown. But on searching, I found that this distinction (GTP/ATP) is limited to just the different types of enzyme: different types of same enzyme use different molecules. So maybe it is that during evolution, enzymes either learnt that GTP is also useful or they tried to rely as much on ATP as possible. But I'll add more details when I find them :)


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Why is DNA double stranded and RNA single stranded?
Why is DNA present as a double helix structure and RNA as a single helix? What causes the difference between them? What are the practical physiological differences between dsDNA and ssRNA? How are the key biophysicochemical features responsible for those differences? What is the role of these differences? Also, why is DNA preferred over RNA as the genetic material?

where is your question?

why the DNA double helix and RNA single? What make the difference between them? why they are not the same? what the role of the differences?

Though these are too many questions, and these are all too basic, I will post an answer. Please edit your question to make it easier to understand.

I don't have any problem with answer of question all them perfect. thank you

answer of this question I wanted (Why is DNA preferred over RNA as genetic material?) and you answer

I have added this also in my answer.

Though this is a basic question (a few google searches will provide all answers) and you have asked a lot of questions, I shall answer them one-by-one.

Why is RNA single stranded (and not double stranded like DNA)?

dsRNA is less stable than dsDNA.  See this: http://en.wikipedia.org/wiki/RNA#Structure. An important structural feature of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar. The presence of this functional group causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA. This results in a very deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone.
RNAses are very common.  Most critically, in biological systems, the presence of dsRNA is a signal of viruses and active transposable elements, so ssRNA is an easy way for the host cell to distinguish foreign elements.  Yes, that was an oversimplification and ignored functional dsRNA, but even then, dsRNA likely evolved from systems to foreign elements.1

Why is DNA double stranded (and not single stranded like RNA)?

Firstly, the 'information' part of DNA is the nitrogenous base, as opposed to the pentose sugar or the phosphate residues. In a single-stranded molecule, this important part would be exposed to the cellular environment, providing more opportunity for it to be mutated by the various chemicals there. In a double-stranded configuration, however, the two nitrogenous bases are locked within the complex, facing each other in the centre of the molecule. This organisation helps to safeguard them from local mutagens.
Secondly, having two complementary strands facing each other fundamentally means having two copies of the same thing placed right next to each other. This allows for proof-reading. George C. Williams summarised this beautifully in his pithy passage (from "The Pony Fish's Glow" (1997)) (recall that adenine [A] on one strand should always bind to a thymine [T] on the complementary strand, and visa versa; likewise cytosine [C] always binds to guanine [G], and vice versa i.e. Charagaff's rule).2

Source

What is the difference between DNA and RNA?

A complete table of differences can be found here (sadly I can't create a table in markdown) along with this image:

How are roles of DNA and RNA different?

RNA has several different functions that, though all interconnected, vary slightly depending on the type. There are three main types of RNA:

Messenger RNA (mRNA) transcribes genetic information from the DNA found in a cell's nucleus, and then carries this information to the cell's cytoplasm and ribosome.
Transfer RNA (tRNA) is found in a cell's cytoplasm and is closely related to mRNA as its helper. tRNA literally transfers amino acids, the core components of proteins, to the mRNA in a ribosome.
Ribosomal RNA (rRNA) is found in a cell's cytoplasm. In the ribosome, it takes mRNA and tRNA and translates the information they provide. From this information, it "learns" whether it should create, or synthesize, a polypeptide or protein.

DNA's genes are expressed, or manifested, through the proteins that its nucleotides produce with the help of RNA. Traits (phenotypes) come from which proteins are made and which are switched on or off. The information found in DNA determines which traits are to be created, activated, or deactivated, while the various forms of RNA do the work.3
EDIT- As you've asked another question in comments, I will add it here:

Why is DNA preferred over RNA as genetic material?

DNA offered several advantages over RNA so was chosen by natural selection to represent higher beings:

DNA was chemically more stable than RNA so it was possible to maintain greater length of DNA in comparison to RNA. RNA has hydroxyl group (OH) present on the 2’ carbon. This hydroxyl group invites hydrolysis reaction and so it was not possible to maintain long length RNA molecule. This hydroxyl group was absent in DNA leading to stability of DNA molecule.
DNA was more capable in handling self-repair during replication process due to the presence of Thymine instead of Uracil. It was due to the fact that often cytosine was changed into uracil due to the deamination. Now in case of RNA it was impossible for cell to know if uracil should be present there or not but in DNA since Uracil is not all present so it was quite easy to identify the error and rectify that.
DNA also offers more information security because of the double helical structure.4

A comparison of molecular structure of DNA and RNA from here

References:

https://www.quora.com/Why-is-RNA-single-stranded-in-general-and-not-double-stranded-like-DNA
http://medicguide.blogspot.in/2008/07/why-is-dna-double-stranded-but-rna.html
http://www.diffen.com/difference/DNA_vs_RNA
https://www.quora.com/Why-was-DNA-chosen-to-be-the-genetic-material-instead-of-RNA
http://www.atdbio.com/content/2/Molecular-weight-and-mass

Thank you and But I'm wondering Wallis There is a big role for the Commission in the DNA of synthetic significant role in storing information more than the RNA

yes it help me.  I want the exact image, Does DNA structure advantage in the information stored than the RNA?

I'm sorry about my language

dsRNA is less stable than dsDNA..Not really true.. in fact, dsRNA hybridizes more strongly. RNA, in general is chemically unstable. Nothing specific to dsRNA.

@wysiwyg oh I actually meant dsRNA being recognized by RNases. Seems like I mixed two points up. I'll edit it when I get some time :)


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How do infants get their very first gut bacteria?
First of all, I'm a complete layman in Biology. Recently I read "The evidence for evolution" by Richard Dawkins. Pondering about this matter, I wondered about the origin of human gut bacteria (could be more generalized to mammal gut bacteria).
Generally, I see two possibilities:
These bacteria are

acquired later on through the environment (probably after birth) or
they are produced by the organism itself

The former option seems to me a little bit too vulnerable to be true (different food, different bacteria due to geographical location, etc.)
The latter option seems baffling to me. Bacteria are, as far as I know, independent lifeforms. Is it possible, that our DNA contains the information for other lifeforms as well?

30 percent of the beneficial bacteria in a baby's intestinal tract come directly from mother's milk, and an additional 10 percent comes from skin on the mother's breast.... google search breastfeeding and gut bacteria, it's a fascinating topic. that's the temporal origin. the evolution origin, well, ants have gut bacteria too.

Humans do not "generate" bacteria. Spontaneous generation was disproved by Louis Pasteur in the 1800s.

Well, the former is exclusively the answer. Humans (or other mammals, or any species in general) cannot give birth to new species (of bacteria, here); they have to be acquired from the environment at all costs. However, the environment does vary, leading to variance in gut microbiome, as will be discussed later.
First of all, gut microbiome is only a part of the total microbiome of humans (Sherwood et al, 2013). Now, usually, gut bacteria are acquired by a person within one to two years of birth (Sommer et al, 2013), while the gut of a fetus is considered as sterile. However, microbial colonization in a fetus is possible (Matamoros et al, 2013). For example, species of Lactobacillus and Bifidobacterium were found in biopsies of placenta in one study (Mueller et al, 2017).
During birth and rapidly thereafter, bacteria from the mother and the surrounding environment colonize the infant's gut. Infants born by caesarean section may also be exposed to their mothers' microflora, but the initial exposure is most likely to be from the surrounding environment such as the air, other infants, and the nursing staff, which serve as vectors for transfer. During the first year of life, the composition of the gut flora is generally simple and it changes a great deal with time and is not the same across individuals (Sommer et al, 2013).
Now lets talk about variation in gut microbiome among individuals. The gut microbiome of an individual may vary depend mainly due to:

Age:  the diversity of microbiota composition of fecal samples is significantly higher in adults than in children, although interpersonal differences are higher in children than in adults. Much of the maturation of microbiota into an adult-like configuration happens during the three first years of life.
As the microbiome composition changes, so does the composition of bacterial proteins produced in the gut. In adult microbiomes, a high prevalence of enzymes involved in fermentation, methanogenesis and the metabolism of arginine, glutamate, aspartate and lysine have been found. In contrast, in infant microbiomes the dominant enzymes are involved in cysteine metabolism and fermentation pathways (Yatsunenko et al, 2012).

Diet: Gut microflora is mainly composed of Prevotella, Bacteroides, and Ruminococcus. There is an association between the concentration of each microbial community and diet. Prevotella is related to carbohydrates and simple sugars, while Bacteroides is associated with proteins, amino acids, and saturated fats. Specialist microbes that break down mucin, survive on their host's carbohydrate excretions. One enterotype will dominate depending on the diet. Altering the diet will result in a corresponding change in the numbers of species (Wu et al, 2011).

Geography: In simple terms, gut microbiome composition depends on the geographic origin of populations. For example, the US population has a high representation of enzymes encoding the degradation of glutamine and enzymes involved in vitamin and lipoic acid biosynthesis; whereas Malawi and Amerindian populations have a high representation of enzymes encoding glutamate synthase and they also have an overrepresentation of $\alpha$-amylase in their microbiomes. As the US population has a diet richer in fats than Amerindian or Malawian populations which have a corn-rich diet, the diet is probably a main determinant of gut bacterial composition (Yatsunenko et al, 2012).
Further studies have indicated a large difference in the composition of microbiota between European and rural African children. The fecal bacteria of children from Florence were compared to that of children from the small rural village of Boulpon in Burkina Faso. The diet of a typical child living in this village is largely lacking in fats and animal proteins and rich in polysaccharides and plant proteins. The fecal bacteria of European children was dominated by Firmicutes and showed a marked reduction in biodiversity, while the fecal bacteria of the Boulpon children was dominated by Bacteroidetes. The increased biodiversity and different composition of gut flora in African populations may aid in the digestion of normally indigestible plant polysaccharides and also may result in a reduced incidence of non-infectious colonic diseases (de Filippo et al, 2010).

Also, as @com.prehens.ible says in comments, there are various other modes through which an infant may acquire bacteria to give rise to their gut microbiome. For more information, you can also read the Wikipedia page on Gut Flora.
References:

Sherwood, Linda; Willey, Joanne; Woolverton, Christopher (2013). Prescott's Microbiology (9th ed.). New York: McGraw Hill. pp. 713–721. ISBN 9780073402406.

Sommer F, Bäckhed F (2013). "The gut microbiota—masters of host development and physiology". Nat Rev Microbiol. 11 (4): 227–38. PMID 23435359.

Matamoros S; et al. (2013). "Development of intestinal microbiota in infants and its impact on health.". Trends Microbiol. 21 (4): 167–73. PMID 23332725. doi:10.1016/j.tim.2012.12.001.

Mueller, Noel T.; Bakacs, Elizabeth; Combellick, Joan; Grigoryan, Zoya; Dominguez-Bello, Maria G. (2017-04-08). "The infant microbiome development: mom matters". Trends in molecular medicine. 21 (2): 109–117. ISSN 1471-4914. PMC 4464665 . PMID 25578246. doi:10.1016/j.molmed.2014.12.002.

Yatsunenko, T.; Rey, F. E.; Manary, M. J.; Trehan, I.; Dominguez-Bello, M. G.; Contreras, M.; Magris, M.; Hidalgo, G.; Baldassano, R. N.; Anokhin, A. P.; Heath, A. C.; Warner, B.; Reeder, J.; Kuczynski, J.; Caporaso, J. G.; Lozupone, C. A.; Lauber, C.; Clemente, J. C.; Knights, D.; Knight, R.; Gordon, J. I. (2012). "Human gut microbiome viewed across age and geography". Nature. 486 (7402): 222–227. Bibcode:2012Natur.486..222Y. PMC 3376388 . PMID 22699611. doi:10.1038/nature11053.

Wu, G. D.; Chen, J.; Hoffmann, C.; Bittinger, K.; Chen, Y.-Y.; Keilbaugh, S. A.; Bewtra, M.; Knights, D.; Walters, W. A.; Knight, R.; Sinha, R.; Gilroy, E.; Gupta, K.; Baldassano, R.; Nessel, L.; Li, H.; Bushman, F. D.; Lewis, J. D. (2011). "Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes". Science. 334 (6052): 105–8. Bibcode:2011Sci...334..105W. PMC 3368382 . PMID 21885731. doi:10.1126/science.1208344.

De Filippo, C.; Cavalieri, D.; Di Paola, M.; Ramazzotti, M.; Poullet, J. B.; Massart, S.; Collini, S.; Pieraccini, G.; Lionetti, P. (2010). "Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa". Proc. Natl. Acad. Sci. U.S.A. 107 (33): 14691–14696. Bibcode:2010PNAS..10714691D. PMC 2930426 . PMID 20679230. doi:10.1073/pnas.1005963107.

There is also evidence that exposure of the newborn to the vaginal microbiota of the mother during delivery might be important for the establishment of its own gut, oral and skin microbiota (Dominguez-Bello et al. 2016):

Exposure of newborns to the maternal vaginal microbiota is interrupted with cesarean birthing. Babies delivered by Cesarean section (C-section) acquire a microbiota that differs from that of vaginally delivered infants, and C-section delivery has been associated with increased risk for immune and metabolic disorders


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Cellular demand for antioxidants
Antioxidants such as ascorbate and glutathione serve to inactivate radicals and counteract spontaneous oxidation reactions, such as unwanted disulfide bonds in proteins. These systems are cycles, where a "spent" antioxidant (say, oxidized glutathione) is convert back to its reduced form by another reducing agent, usally NADPH.
My question is, how much NADPH (or reducing equivalents) does a cell devote to this antioxidant defense? What is the flux, in molar amounts per unit time, through these systems? Does it represent a large portion of the energy metabolism of cells?
I am guessing that the flux is quite large, but I have never seen any data on this. Most likely it varies a lot between cell types, but I would be happy to see any numbers. I think this is important for understanding antioxidant chemistry in cells, yet it is rarely discussed in the literature.

Most experiments to try to get at this type of question use stable isotope tracers to measure NADPH production from the various pathways that can make it, and then subtract away the amount that's predicted to be needed for growth/anabolism (based on the observed growth rate and biomass composition). I think this paper is by far the best example:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104482/.
Quote:

The overall demand for NADPH for biosynthesis is > 80% of total cytosolic NADPH production (Figure 4b), with a majority of this NADPH consumed by fatty acid synthesis. At least in transformed cells growing under aerobic conditions, most cytosolic NADPH is devoted to biosynthesis, not redox defense.

Note that these are fast growing cells without additional oxidative stress. Interestingly, what the authors find is that imposing additional oxidative stress doesn't actually change NADPH production that much, but it slows down growth as more NADPH is used for anti-oxidant defense (Extended figure 9).
For skin cells, the situation might be a bit different, at least in terms of the increase in NADPH production upon oxidative stress. You might look at this paper: http://www.cell.com/molecular-cell/fulltext/S1097-2765(15)00456-6

Yes, I am aware of Rabonowitz 's paper. It doesn't contain any direct data on antioxidant fluxes afaik --- the values you refer to are rather model-based predictions.  Zamboni's paper does not really address the question I believe ; it is about pentose phosphate fluxes. But perhaps this is the only data available.

So the major error in the model would come if there was a source or a sink of cytosolic NADPH that was not being considered. Probably you can judge for yourself how likely that is to be, but I for one am reasonably satisfied with the set of reactions taken into account. If anything, I would guess that an unidentified sink (with a net NADPH->NADH result, such as a lipid synthesis and degradation cycle) is more likely than an unidentified source, which would even further lower the estimate of NADPH used for antioxidant defense.

Also I can reemphasize that to me, the major caveat is really the cell type and environment being considered -- doing this type of exercise in a real in vivo context as opposed to a cell line would be really fascinating.


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Why is the brain dependent on glucose?
The strict dependence of the (human) brain on glucose has always been puzzling to me. While ketones can substitute for a portion of the brain's energy needs, it cannot substitute completely: blood glucose levels below 2--3mM somewhere causes serious neurological problems and can lead to unconsciousness.
Other body tissues are not strictly dependent on glucose, but can oxidize amino acids as well, which is a good backup solution since there is always lots of protein around. But not the brain.
In terms of evolution, this strict glucose dependence must be a major drawback --- falling unconscious just because you don't get enough sugar is probably a bad thing out in the wilderness, when the lions are after you ... So there must be a very important reason.
So why is the brain so dependent on glucose?

Everything is bad when the lions are after you ;)

Actually you can get sugar everywhere where there are plants.

I don't have a clue, but just plausible ideas: (1) amino acid or lipid processing is more dangerous or hinders function. Neurons need to survive for a life time. (2) the rate at which neurons need to regulate their energy level requires fast modulation, and only glucose can do it.

@Memming, those sound like good starting points! For (1), amino acid oxidation does yield ammonia, which perhaps could cause a problems; I'm not aware of toxicity / risks with fatty acid oxidation. (2) sounds like an interesting angle. The brain oxidizes glucose completely though, so it's not related to rapid glycolysis I think.

This is a great question. Most answers one can find are shallow, along the lines neurons rely on glucose because they don't use protein/fat. The equivalent superficial answer for red blood cells is because they don't have mitochondria to do oxidative phosphorylation. But neither explains why neurons specialized in this way. This might well be an unexplored question!

@SeanJ — I don't see why the explanation for red cells is superficial. They are very specialized cells of limited lifespan. Their dependence on glucose is not a problem as the pyruvate is all converted to lactate and recycled via the liver. This situation with neurons is quite different.

Very interesting discussion. i studied biochem and eventually got an MS, but it was over 30 years ago and i don't remember all the metabolic paths and whatnot. And of course the field has advanced a lot in 30+ years. CRISPR, for God's sake! what i have actually been looking for is answer to one question: can the brain get by w/o glucose? Because cancer cells usually can't. They almost always rely on fermention of glucose to pyruvic acid. And they can ferment a heck of lot of glucose, sometimes 200X what a normal cell would use. Which can lead to metabolic drain and acidemia. i was thinking tha

My opinion on this matter is that this is actually quite simply to free up fats for the rest of the body to burn for energy. If I recall correctly in certain research it has been noted that neurons are not strongly dependent on insulin levels for glucose uptake -- i.e., in other words they have "vip/preferential access" to almost however much blood sugar they'd want to uptake regardless of where the blood insulin level is at. As a result they (1) don't have a strong need for fat energy, and (2) it would probably be useful to in fact save that energy for the rest (comment continued ahead...)

(comment continued from before) ... of the body's cells that, unlike neurons, are not simpy blithely free to just go ahead and ignore whatever blood insulin levels the organism has decided to set for itself.

I agree very much with ManRow's idea as it is the one I always thought I was the only one to have. Good hint at insuline, as vice versa, just as the brain gets all the sugar when it's rare, muscles are allowed to store it away only when it is plentiful. Specializing to run a very frugal barn yard. Fast and slow, muscles and brain. If there is a metabolic block that forbids fatty acids being turned into glucose, and considering the blood-brain barrier to fatty acids, that seem the opposite to insuline to me, saving  fatty acids for the muscles that are not dumb at all.

I want to present another (possibly more practical) approach towards this phenomenon. Lets begin with amino acids as alternatives.

Amino acids, apart from being a source of toxic ammonia, are also harmful to the brain in another way. The two (concerned) types of amino acids, aromatic and acidic ones, are a lot more than just energy sources for the brain. Aromatic amino acids: tyrosine, phenylalanine and tryptophan, are precursors for the biosynthesis of neurotransmitters like serotonin, melatonin, norepinephrine, dopamine, etc. The greater the amount of precursors, more the product formed. Talking about acidic amino acids, glutamate and aspartate are themselves neurotransmitters. So, same case could apply to them too. So, it might have been that neurons, in evolution, decided to just get rid of such sensitive and powerful energy sources which can disrupt their basic function. You can see Fernstrom, 1994 for a study on this.
Fatty acids are definitely a nice candidate. But they have some side effects too. For a long time, it was thought that since fatty acids (or lipids in general) are attached to albumin while in blood, they cannot cross the blood-brain barrier (see Stryer for example). But, this is not the case, as now proven. Then why are fatty acids not a preferred energy source for brain? There might be quite a few reasons for this.

First, $\beta$-oxidation of fatty acids demands more oxygen as compared to glucose, making neurons more vulnerable to hypoxia. For example, the reaction for complete oxidation of glucose is (from Molecular Cell Biology):

$\ce{C_6H_{12}O_6 + 6 O_2 + 36 ADP^{3-} + 36 P_i^{2-} + 36 H^+ \rightarrow 6 CO_2 + 36 ATP^{4-} + 42 H_2O}$
On the other hand, the reaction for $\beta$-oxidation of palmitic acid is (from pharmaxchange):
$\ce{C_{37}H_{66}N_7O_{17}P_3S (Palmitoyl-coA) + 23 O_2 + 108 P_i^{2-} + 108 ADP^{3-} \rightarrow C_{21}H_{36}N_7O_{16}P_3S (coenzyme-A) + 108 ATP^{4-} + 16 CO_2 + 23 H_2O}$
where palmitic acid is $\ce{C_{16}H_{32}O_2}$. This clearly shows that glucose oxidation requires less oxygen (1 molecule per carbon) as compared to fatty acids (almost 3 molecules per 2 carbon).

Second, nonesterified fatty acids (NEFA) decrease membrane potential at inner mitochondrial membrane, causing collapse of electrochemical proton gradient.
NEFA also interfere with electron transport chain, stimulating generation of reactive oxygen species like superoxide ions (see Zhang et al, 2006 for example).
Apart from this, the rate of ATP generation from fatty acids is slower as compared to glucose, which makes glucose a better option for neurons (see Stryer).

All these factors might have a played a role in making neurons choosy for glucose. This is also supported by the fact that one of the enzymes of $\beta$-oxidation, 3-ketoacyl coenzyme-A thiolase, has significantly lower activity in neurons as compared to other tissues (Yang et al, 1987). You can see Reiser et al, 2013 for a study on this.

PS: It has been shown that the brain can also use lactate along with ketone bodies as an energy source. See Wyss et al, 2011 to know more about this.

Very good points Homo Sapiens.

Thanks, if you really like it, you can give an upvote :P BTW if you want to reply to somebody, you need to put @ sign and then that person's name, without spaces (if there are spaces in name). For example, @another'Homosapien' to reply to me :)

Thanks for the suggestions. (1) is interesting. Amino acids are already present in brain tissue though, and oxidizing amino acids might not increase their levels. Also, compartments are probably important here. (2) "beta-oxidation demands more oxygen" -- this is true per carbon atom (respiratory quotient), but the relevant parameter is the P/O ratio, which is very similar between the glucose and fat. I'm not sure NEFAs are relevant here since beta-oxidation handles fatty acids coupled to carnitine, but will think about it. Re: glucose oxidation is slower, see comment to @SeanJ

@roland (1) yeah amino acids are already present in brain "tissue" for their usual purpose (not oxidation), using them for oxidation might also create problems (2) I agree with you about P/O ratio. However, I don't understand your point about free fatty acids. That's why I put Reiser et al paper, they talk solely about NEFA. I'll see for glucose oxidation very soon :)

@roland Just to add here, I think you're missing something crucial here: comparison. Glucose oxidation to $\ce{CO_2}$ is slower than glycolysis, fatty acid $\beta$-oxidation is slower than glucose oxidation to $\ce{CO_2}$. Correct me if I'm wrong :)

They are two entirely different comparisons. The chapter in Stryer you cited concerns glucose oxidation vs glycolysis, which is not relevant here; beta-oxidation vs glucose oxidation is the question. If you know of some evidence that beta oxidation is slower (in terms of generated ATP per unit time) than glucose oxidation, I would be very interested to see that.

@roland the only article I found regarding it is this (which also relies on simple logic). I must say that there hasn't been much research on this topic

Also, I don't think the Stryer page is talking about glycolysis vs beta oxidation (it does say glucose oxidation). Also, even if glycolysis is faster than beta oxidation, then since the later steps (krebs cycle) are same, we can still conclude that glucose oxidation is faster than fatty acid oxidation (both need to form acetyl coA first, glycolysis does it faster than beta oxidation).

Glucose is the only fuel normally used by brain cells. Because neurons cannot store glucose, they depend on the bloodstream to deliver a constant supply of this fuel.
Fatty acids do not serve as fuel for the brain, because they are bound to albumin in plasma and so do not traverse the blood-brain barrier. In starvation, ketone bodies generated by the liver partly replace glucose as fuel for the brain. (Biochemistry. 5th edition.Berg JM, Tymoczko JL, Stryer L.)
Also, amino acid catabolism is the process of using amino acids as an energy source. Turning amino acids into molecules that can be used in the Krebs cycle takes energy, which means that burning protein for fuel is not as efficient as burning carbohydrates. In addition, your body needs amino acids to make new proteins. When amino acids are used as an energy source, it reduces the reserves of amino acids that are available for protein synthesis.

Yes, the fact that glucose is the main fuel of the brain is well established -- the question is why. There seems to be plenty of evidence that the brain takes up albumin-bound fatty acids (but not lipoproteins), see for example http://www.ncbi.nlm.nih.gov/pubmed/17901540 . There is also evidence for fatty acid oxidation by the brain, for example http://www.ncbi.nlm.nih.gov/pubmed/3368026 . But still glucose is required.

Regarding amino acids, during fasting the glucose supplied to the brain from the liver derived from amino acids anyway, so I don't think the efficiency argument works. It rather seems like the amino acid metabolism is not possible in brain tissue, for some reason, and is "outsourced" to the liver. Maybe the brain has difficulties disposing of ammonia?

I think protein breakdown is the important factor in using amino acids. It seems more logical to use i.e. muscle mass than brain mass, as to not lose structures with a memory function.

@Sleepses, that sounds reasonable. There are plenty of amino acids in blood though (largely derived from muscle) that other tissues can take up and oxidize.

Well considering how import fats are in the construction of the brain, breaking down fats for energy probably would be counter productive. Our course it could all just be an evolutionary hold over, the blood brain barrier probably prevented the use of anything but sugars in the early origins of the central nervous system and we might just be stuck with the results.

This is something I have been researching on and off for many years. I studied nutrition back in the early 1980s and our lecturer always said that "fats burn in the flame of CHOs". He said that the citric acid cycle was dependent on oxaloacetic acid - the predominant source was from glucose (pyruvic acid).
https://www.sciencedirect.com/topics/medicine-and-dentistry/oxaloacetic-acid
In nutrition, for patients with epilepsy, they are given a ketogenic diet as this is known to suppress brain signals. Clearly the brain functions sub-optimally when deprived of glucose. One of my concerns with the rise in dementia is the high protein/low carb diet proposed, and the claims that the body (and brain) can do without CHOs.
The other piece of research was from Professor Robert Horn (retired, Oslo) in his work for students. He compiled a wonderful PDF on glucose metabolism and here I quote:
"The blood-brain-barrier is comprised of glia cells, primarily astrocytes. A small fraction of the glucose
released from capillaries wanders directly to nerves and synapses. However, most is "trapped" in
astrocytes and oxidized to lactate by these cells. Lactate goes further into the brain and nourishes
the brain's neurons. This seems to be especially important for glutamatergic neurons which
comprise much of the brain. The astrocytes also efficiently pick up released glutamate, convert
this to glutamine, and send the product back to glutamatergic neurons where it continues to cycle
as a neurotransmitter. The axons do not contain glycogen and are, therefore, completely
dependent upon the lactate sent from astrocytes to maintain ATP levels. Astrocytes and other glia
cells appear to have some glycogen which can serve as a very short-term source of lactate.So the answer to the preceding question is that much of the brain is dependent upon lactate from
glia cells to provide substrate for aerobic energy production; ketone bodies cannot cover their
substrate requirements. One can reduce glucose consumption and use ketone bodies during
starvation. However, some neurons must have lactate and the brain must continue to use blood
sugar."

The body uses 2 dedicated groups of fuel molecules (fats and sugars) and can break down its own structure molecules in case of emergency (proteins). The brain uses sugars, mostly glucose, and ketone bodies, a soluble form of acetyl derived from fat breakdown. I love this question, Roland, since you've probably hit on an open, poorly investigated question that goes to the fundamentals of why neurons evolved to be this specialized. So why does the neuron rely much less on fats and proteins than more flexible cells like those of the liver?
Protein digestion could indeed be dangerous for neurons because it produces ammonium (NH4+). Neither fats nor sugars contain significant amounts of nitrogen. Their final breakdown products, H2O and CO2, are harmless. Ammonium, on the other hand, is very similar to potassium (K+), an ion central to the neuronal membrane potential and thus its function. It has a similar size and charge (see image below) and is hypothesized to mess with potassium signaling in the brain. It might do this by interfering with K+ transporters (see this schematic by Eid).

This leaves us with fats. I have 2 hypotheses here. The final steps of fat breakdown in the mitochondrion involve the transfer of electrons onto oxygen to produce water. An unavoidable side reaction here is the creation of a small amounts of reactive oxygen species that have the potential to damage close-by molecules via radical reactions. Since neurons are so long lived, this is very dangerous for them as they accumulate damage little by little. Not so for liver cells which are readily replaced if damaged beyond recovery. Second, fat breakdown is a much slower way to energy/ATP than glucose breakdown, since it involves the sequential shortening of the fatty acid chain (beta oxidation), the generation of reduced intermediates (mostly NADH in the citrate cycle), and finally oxidative phosphorylation - several dozen steps in total. Glucose metabolism yields ATP quickly in just a few steps (glycolysis). Ketone bodies also fit, since they are already very short and thus much more quickly metabolized than long chain fatty acids. A combination of these 2 reasons might be why neurons prefer glucose to fats, but I believe this is a poorly investigated question that merits more research. PhD anybody?

So if you are offering a PhD, what is your proposal to test your hypotheses and solve a problem that people have been aware of for at least 50 years? It's one thing in science identifying a problem, the trick is to realize when either new concepts or new methods appear to make it possible to solve it.

Thanks for the suggestions. Some comments: (1) toxicity ammonia production is an interesting hypothesis (and it has been suggested before) but I haven't seen any evidence that the brain would be particularly sensitive to ammonia. (2) Regarding reactive oxygen species, consider that neurons already oxidize glucose carbon in mitochondria. (3) I don't think it's true that fat oxidation necessarily is slower (in terms of ATP synthesis rate) than glucose oxidation; and generally, the number of enzymatic steps has little to do with flux through a pathway.  Just some critical feedback!

Hey David, one could try to slow or block flow through glycolysis and see how the shifted energy metabolism affects neurons. I don't find that it's a well identified problem. Most people (but not Roland), textbooks, and articles are perfectly happy with the shallow explanation that neurons have downregulated some enzymes and are thus more glucose dependent than other cells.

Hi Roland, 1) have you had a look at the paper by Eid. They present evidence as to why neurons might be more sensitive. 2) Correct. They might also derive some energy from glycolysis to pyruvate/lactate without oxygen. Does anybody know of data quantifying which energy pathway is used the most in neurons? 3) If it were as fast, why do we use glycolysis almost exclusively for bursts of muscle energy and not oxidative phosphorylation? I'd love to read more about steps versus flux if you could recommend a paper or a book. All the best

(1) Sorry, I missed the Eid et al paper link-- it's quite interesting, thanks!  (3) Fast-twitch muscle relies on glycolysis to lactate, that's quite different; here the choice is between glucose oxidation or fat oxidation. Re: flux through pathways, this depends on a number of factors, such as metabolite concentrations, enzyme amounts and turnover rates, Gibb's energies of reactions, compartmentalization, and what not. Suffice it to say that there is no easy relation between the number of steps in a pathway and flux :)  We might want to move this discussion to chat.


text:
Why do epithelial cells arrest in response to serum?
Primary epithelial cells, for example human mammary epithelium, fail to proliferate (arrest) in serum-containing medium. Therefore, a common growth medium for epithelium contains pituitary extract instead of serum (Hammond et al, 1984). This may be related to the fact that epithelium is normally not in contact with serum in the body.
On the other hand, many epithelium-like cell lines grow well in serum, and most tumor-derived cell lines are cultured this way. But it can be difficult to establish such lines from epithelial cancers: often, only fibroblasts grow out of tumor explants in serum-containing medium, while the (epithelial) cancer cells do not. In contrast to epithelium, fibroblasts increase their proliferation when exposed to serum, and this process is well studied (Iyer et al, 1999).

Why does epithelium arrest in response to serum? Are any mechanisms known? Is there any study of epithelium gene expression response to serum? Why is the behavior of epithelium so different from that of fibroblasts --- is there a physiological explanation, perhaps related to wound healing?
Is this true for all types of (human) epithelium?
Should we consider epithelial-like cells growing in serum to be adapted / selected? Have such cell lines then lost some part of the epithelial phenotype? Is this a serious artefact?

Any pointers to literature would be appreciated!

TGF-beta would be a good candidate. To cite:
"TGF-β inhibits G1/S progression in a variety of eukaryotic cell types. Among these, untransformed epithelial cells are particularly sensitive to the growth inhibition by TGF-β."
http://genesdev.cshlp.org/content/14/24/3093.full
Fetal bovine serum (FBS) contains a high level of latent TGF-β. Human serum as well has high level of TGF-beta (20-50ng/ml)
It is also possible that growth arrest is part of the induction of terminal differentiation by serum factor(s) such as TGFb.
"Type beta transforming growth factor is the primary differentiation-inducing serum factor for normal human bronchial epithelial cells."
http://www.ncbi.nlm.nih.gov/pubmed/2871553
Edit: got more reputation, so now I can post more than two links. Here is a review on TGFb signalling: http://genesdev.cshlp.org/content/14/6/627.full
Also a link to serum levels of TGFb:
http://www.ncbi.nlm.nih.gov/pubmed/16845225

Thanks, this is useful! Will continue to look in this direction.

I don't think that there is a one-size-fits-all answer to this question. There are different types of arrest and there might be different triggers depending on the epithelial cell type.
Even in the cited Hammond et al paper, note that the effect of serum is not an immediate arrest. Human mammary epithelial cells (HMEC) could already go through 3 to 4 passages in serum (at 1:10 splits), according to the Introduction to the paper; the improvement with the serum-free medium was to allow 10-20 passages. And even in that paper, near the end of the Results you will see a difference between HMEC and human keratinocytes in terms of response to calcium; calcium makes keratinocytes differentiate and lose proliferative capacity, while HMEC do best at high calcium.
Recent work has developed ways that can allow many types of epithelial cells (both normal and tumor cells) to proliferate indefinitely in culture, in the presence of 5% serum. Inhibition of the Rho-associated kinase ROCK is critical, as is the production of some yet-undefined factor by feeder fibroblasts. So even if some component of serum tends to lead to differentiation or senescence and growth arrest, that effect can be avoided.
Note, however, that the authors of this newer work do call the cells treated this way "reprogrammed," recognizing that they are not the same as the original epithelial cells in some important ways. What that "reprogramming" entails is under active investigation, and your concerns about selection, adaptation, and potential artifacts of culture are very important. But even if this is considered an artifact, understanding the mechanisms at work should produce some important advances in understanding epithelial biology.


text:
Cattail seeds spring revitalization
There's a genus of plants known as Typha, or cattail.
They have seeds like of dandelion, that form thick heads. Such a head may be cut off from the plant and be used for, say, decorative purpose, but when the spring comes, seeds will spread out their 'hairs' and fly away. It looks like an absolutely dry piece of plant - no life in it - suddenly gets alive.
I suggest that it may be a daytime prolongation of a  that causes it to spread seeds, but I wonder if anyone knows what sort of cellular/biochemical mechanics is at work here.

According to LeRoy G. Holm's World Weeds: Natural Histories and Distribution:

Seeds are protected from germinating in the stalk by the swelling of the pistillodes that are distributed throughout the inflorescence. In humid conditions, they swell and keep the spike intact. They can swell 15 to 20% in 15 min in 100% relative humidity. Upon drying, the pistillodes shrivel, air again reaches the seed, and the perianth hairs spread. Their collective pressure causes the inflorescence to burst, releasing the fruits to the air. If they fall on water, the hairs close and the pericarp releases the seed which then sinks.

So it's all about the humidity!

So the plant should get completely dry to let its seeds free. Wow.


text:
Is it a common behaviour in insects to mate with a dead partner
I have a few specimens of Orgyia antiqua of both sexes, and I've been able to observe a mating behaviour where male and female sit close to each other, their rear ends connected.
Today though I've seen the same, but the female was day-long dead - and that didn't stop the male from the mating attempt.
I do understand that it can be explained with the male just reacting to some pheromones, still present on the female body, but that is a bit weird anyway.
Thus the question. Is it a common or well-known behaviour for an insect male to mate with a dead female?

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


text:
Is it possible to identify the wasp species/family by the nest?
I've seen a weird looking wasp nest recently.
Here's the picture:

I'm saying weird because it's the first time I see a nest that isn't a ball made of grey paper. Although this one is also made of paper, I don't understand where does the colour come from.
Is it possible to say, what species or family does it belong to?
(location is the North-West of Russia, close to Saint-Petersburg)

Ok, my bad. Should've googled better.
It seems that it might be a common wasp aka Vespula vulgaris. It's said that the colour of the nest is caused by material being collected from the rotten tree trunks.
See the identified sample:

It's said that they don't make nests in houses too often that's why I'm not accustomed to the look of the nest.


text:
Who and when was the first human diagnosed with hemophilia, or considered a carrier?
The earliest case I can find is Queen Victoria of England, who ruled from 1837-1901. Is this the first hemophilia case on record?

The disease hemophilia has been known for much longer than that. At the time the Talmud was written, for example, it was known that if some boys in a family died from circumcision, the next were also at risk. This might have been because physicians recognized an inherited blood disorder.
Abulcasis, an Arab physicians of the 10th century, wrote about families in which male members died from bleeding out after injury.
In 1803, John Conrad Otto wrote about

a hemorrhagic disposition existing in certain familie

Tracing the condition back three generations in that family named Smith, who lived in  Plymouth, New Hampshire. So there were definitely earlier cases where we even know the names of the patients, eben before the disease was named.
The word haemorrhaphilia, later shortened to hemophilia was first used in 1828 by Friedrich Hopff, before the birth of Queen Victoria.
Queen Victoria herself did not have the disease, though, she was a carrier. At least one of her sons had the disease and at least one of her daughters was also a carrier.
The history of hemophilia
History of Bleeding Disorders


text:
Why do eggs lack an endoplasmic reticulum?
Trueman's Elementary Biology book I found says that the endoplasmic reticulum is absent in eggs, but no reason is given. Why is it absent?

I did not know there was no endoplasmic reticulum in the eggs. Can you please add a reference we could easily check up?

I just found in my book. It might had initially but i thing it is reduced later .But I will try to add a reference

I think there is some mistake, check [this] (http://www.sciencedirect.com/science/article/pii/S0012160699994459). It shows eggs (at least mammalian) have ER

In addition, these Calcium waves produces by ER stores are way to block another sperm entry into egg.

I THINK THE BOOK SAID ABOUT CHICKEN EGGS ..

I could find no indication that eggs are lacking an endoplasmic reticulum. On the contrary, I could find papers written on the ER in eggs of several species.
Mouse: The onset of activation responsiveness during maturation coincides with the formation of the cortical endoplasmic reticulum in oocytes of Xenopus laevis
Sea urchin: Structural changes of the endoplasmic reticulum of sea urchin eggs during fertilization
Human: The relationship between pregnancy outcome and smooth endoplasmic reticulum clusters in MII human oocytes
Frogs: The onset of activation responsiveness during maturation coincides with the formation of the cortical endoplasmic reticulum in oocytes of Xenopus laevis
However, as can be read in the sea urchin paper, the ER changes after fertilization:

We interpret these observations to indicate that in the first few minutes after fertilization, the egg's ER is fragmented

For other species, I could only find evidence that the ER reorganizes after fertilization because of changed calcium signaling needs


text:
Why does immunity from the flu vaccine appear only after two weeks?
It is said that immunity from a flu vaccine appears after about two weeks. However, from experience, the flu usually lasts only a few days.
If sufficient antibodies appear only after two weeks shouldn't the flu also last that long? Or is there a difference between how the body reacts to the actual flu virus as opposed to the dead one in the flu vaccine (like maybe there being more viral particles in an actual infection or something)?

Most information here can be found broadly in Cellular and Molecular Immunology, 8th Ed.
Here's how the flu vaccine works: Scientists forecast months in advance which strains they think stand to cause the most problems. The vaccine is often trivalent, protecting against three different strains on flu: Two influenza A and one influenza B. You can read about the process directly from the CDC.
The two major viral receptors are neuraminidase and hemeagglutinin. They determine the serotype of the virus, such as H1N1. They serve as peptide antigens for immune recognition. Where influenza infects a cell, it starts to produce proteins essential to it's replication in the host cytoplasm.
The innate immunue system, upon realizing there's an infection, does quite a bit to try and mitigate things but it's a messy job. Looking at the link, lots of inflammation, damage and dead tissue. At that, there will be no memory of the same infection, and the same process happens over and over unless there's a better way to take care of things.
This is really where your adaptive immune system comes in, T/B cell, antibodies, etc. A wild type influenza virus stimulates the same adaptive response as the strains in a flu vaccine: Proteins such as the neuraminidase are picked up by macrophages or dendritic cells, and they enter transport to the closest lymph node. On the way, they chop up the viral protein into peptide antigens and load them onto MHC-II molecules, and export the complex to the cell surface, becoming antigen-presenting cells or APCs. T cells expressing CD4 coreceptor can interact with the MHC-II on APCs in a cascade of events that lead to effector T-helper (Th) cells. Th cells, in concert with follicular dendritic cells and recognition of cognate antigen by naive B cell can result in proliferation and differentiation of B cells to plasma cells that secrete antibodies specific to the viral antigen that was initially recognized.
The problem, is that this process takes time to ramp up plasma cells numbers and antibody production. The average time often denoted by literature is about 2 weeks.

Furthermore, with adaptive immunity you get memory cells that will remember a given infection and quickly resolve it with antibodies should you ever catch the same bug.
The difference between our wild type influenza and the ones in the vaccine is attenuation. The point of the wild type influenza people often catch is it's really good at infecting humans, and upon infection it causes a lot of damage. We can attenuate influenza's pathogenicity by growing the flu strains in tissue that is not human. Over a few generations, the virus adapts: it becomes more pathogenic/virulent in non-human tissue, but harmless to humans. You then remove the harmful parts of the hemeagglutinin and neuraminidase genes from a wild type strain to get inert HA and NA (so that you get the wild type immunogenicity), combine them with structural proteins from the attenuated strain, and combine them to form a new, live-attenuated vaccine strain that can be grown in the non-human tissue (see image below).
So also keep in mind that just because your infection resolved in under 2 weeks that the antibodies you produced wont help you from getting the same bug again. During flu season it tends to come at your from all sides and the antibodies that evetually get produced help a lot.

Thank you for such a detailed response. I'm afraid it's a bit difficult for me to follow all of the acronyms and biochemistry. In layman's terms, are you saying that basically there is no difference between a vaccine and an actual infection in terms of how fast an immunity forms? In other words, if you recover from infection in, say, three days you probably still don't have immunity which will only appear after about two weeks on average and so you can still get reinfected during that period?

Right the way they develop the vaccine you should get just about as strong a reaction as the natural infection. The chart in there is basically saying you start developing antibodies after a few days. You can always get reinfected but your immunity will determine whether the pathogen is cleared before a symptomatic stage or not.

Take a look at this figure. You can see that for a given infection there in an incubation/prodromal stage before you experience symptoms in full. Once your adaptive immunity is up to speed, it takes care of the infection at these stages.

So basically most of the fight against the infection, at least in terms of making you feel better, is waged by the shoot-now-ask-questions-later kind of cells and the smart guys appear pretty much after the symptoms subside? That is helpful, thank you.

For an average case sure, we can boil it down to that, but we want those antibodies because first-line defenses beat you up quite a bit, and they don't always succeed.

Did I read that right that you are saying that the vaccine does not allow you to build adaptive immunity e.g. memory cells that will remember the infection?

I was going to point out that it's actually "1-2 weeks", not "roughly two weeks" as you can clearly see in that chart on proliferation up there. The reason flu seems a few days long, frequently: a body usually already has at least related defenses, and flu has to ramp up, itself. Immunity response time and virus growth overlap. Sure, flu gets first move in the chess match, but it's not like your body idles as flu goes nuts. Game clock starts before you feel terrible.

And yes, vaccines provide for memory. Not as good for that as a full raging infection, (which would lead to more memory t cells) but it's pretty obvious which scenario is preferable.

Here's a short and simplified explanation.

The antibodies that arise in a flu infection are more "intended" to prevent future infections than to clear the present infection.
Infections drive T cell responses as well as antibody responses, and the T cells appear a little earlier (peaking at maybe a week) and are probably very useful for clearing the present infection.
Remember that just because we can't measure the antibodies (or T cells) doesn't mean that they're not functional.  We measure responses in blood, not local tissues, whereas a very low general response can be very useful in the local site.  T cells are probably doing something locally within 3 days; antibodies, perhaps within a week.