text:
Twist in the DNA double-helix
DNA, has a deoxyribose sugar — phosphate backbone with the purine and pyrimidine bases, adenine, cytosine, thymine, and guanine connected to the deoxyribose sugar. (The base–sugar molecules are nucleosides, and those with phosphate, nucleotides.) In the double helix structure of DNA the two strands are twisted and connected by hydrogen bonds between the bases.
How is this "twist" created in the cell, and why is it necessary?

@heather, you are a middle school student (therefore max 14 years old I guess), you ask a good question about molecular genetics and in the meantime you have on github some Python and $\LaTeX$ code. You also have some notes on calculus, trigonometry, Collatz Conjecture and general relativity. You also have 5.5k reputation on Physics.SE with a number of quite highly upvoted answers. I must say, I am impressed!

@Remi.b, thank you =) I just read about your research on your website, and you said that much of your work falls within the realm of computational biology - what is the sort of "standard" programming language for that? I am aware that R is used a lot for data analysis, but didn't know if that was what you used.

Let's continue this discussion in chat.

@heather I have deleted my comments and converted them to an answer. Let me know if something needs to be explained better. We can talk in chat, though I do have to leave soon.

I have cut your question drastically, replacing your query about the basic structure with a statement of fact which can be found in Wikipedia or any basic biology or biochemistry text. This allows the focus to fall clearly on the single question appropriate to this forum (and we like single questions) — that about twist. Please don’t be offended. It makes your question clearer.

First, your description is accurate. The only pedantic critique I would make is that the technical term for nucleotides in DNA is deoxyribonucleotide.
Second, I don't want to say that non-helical DNA never occurs since the structure of any macromolecule is dynamic, but I am specifically avoiding exceptions to the rule to avoid confusing the issue.
The helical structure of DNA is a low energy form which makes its formation thermodynamically favourable. Chemical bonds in DNA (and every molecule) have conformational flexibility which means that the molecule as a whole can adopt different structures. If you picture two DNA strands joined by hydrogen bonds but in a non-helical, straight form, you can simply twist the strands about their central axis to form a helical structure. This twisting is allowed because of the conformational flexibility of the chemical bonds. The helical structure is more stable than the "straight" form (because of base stacking interactions), and so it forms spontaneously. I struggled in vain to find a good animation of this, but came up short. You can skim through this video to see an example of what I'm talking about. It's subtle, but you may be able to see, or conceptualize, that as the two strands are twisted around each other, the adjacent bases in a strand come closer together. This permits stabilizing interactions between the adjacent bases which favours spontaneous helix formation (I briefly discuss this at the end of another answer).
As for how frequently the "rungs occur", this is dependent on the specific helix geometry. In B-form DNA, the geometry thought to occur predominantly in vivo, the helix completes one full turn approximately every 10.5 bases and the spacing between adjacent bases is ~3.4 Å, as shown below:

One key point for someone coming to structural biology from another disciple is to understand the basic thermodynamics underlying the concept of ‘stable’ structure. This is described in an introductory chapter of  Berg et al. online. Although it is strictly necessary to consider the entropy of the total system, in many cases the most important factor is the (Gibbs) Free Energy of a structure. If one compares two (or more) structures, the most thermodynamically stable is the one with the lowest free energy.
Factors contributing to a low free energy state in a structure (‘stabilizing it’) are presence of chemical bonds and lack of steric or electrostatic repulsion. The double-helical structure is stabilized by hydrogen bonds between the bases of opposite strands, and stacking interactions between the aromatic rings above and below one another in the helix. This is mentioned by @canadiener, although the perspective of his diagram is not optimal for showing the stacking. Frame (a) of my diagram below views the DNA helix from ‘above’ with the purine bases red, the pyrimidine bases blue and the sugar–phosphate backbone white.(Frame (b) shows the hydrogen bonds as broken lines between the bases, although the blue half does not show up well.)

The reason for the ‘twist’ that is the basis of the helix in the DNA is simply that it is part of the structure that allows the strongest hydrogen bonding and base stacking with the lowest amount of steric or electrostatic repulsion. This will be the structure with the lowest free energy.
[See also the description of the double-helix in Berg et al., which includes a diagram of base stacking. I would very much advise refering to the biochemistry and molecular biology texts online at NCBI Bookshelf for standard material rather than Wikipedia. The scholarship, refereeing and consistency of the latter are generally much higher.]

Maybe my diagram isn't optimal because someone changed the question ;). Nevertheless, good answer.

@canadianer — Whoa! I wasn't criticizing your diagram I was describing it. Your diagram isn't optimal to show the base stacking because it is optimal for showing the hydrogen bonding and other features. My diagram does not show the hydrogen bonding at all. In general one needs two diagrams to describe the structure of the DNA double helix: you provided one, I provided the other.

@canadianer — Actually your diagram does not show the hydrogen bonds, so I added a second frame.

I was just kidding. The more information the better and I like your explanation better. I just added that diagram to show the spacing between bases and the number of bp/turn.


text:
Larynx descent in male and female deer
Male red deer (Cervus elaphus) and Male Fallow deer (Dama dama) have a descended larynx, presumably for size exaggeration - to attract mates and intimidate other animals.

Does this descent occur after sexual maturation?
Do females of these species also have descended larynx?
In males, does this occur twice - just as it does with human males?
Do deer use size exaggeration to intimidate other animals, other male deer only or both?
Lastly, are there other typical behaviors associated with size exaggeration (i.e. standing on back legs)?

Thank you in advance. I attempted to search for these online but so far have not found any answers. Of course, any cite-able literature containing the answers would be ideal.

Welcome to SE Biology. This site attempts to build up a repository of questions and answers that can be useful to others as well as the poster. Thus, we discourage multiple questions in one. As your five parts are all about the same topic, this is not a criticism here, but I have edited your title to remove "5 questions about" so that the subject is clear and abides by our guidelines.

I apologize. The most important question is if larynx/hyoid descension occurs in both sexes. If someone could answer or point me to the appropriate literature for that I would appreciate it.

No need to apologize. I can't help you but let's hope someone else can.

Apparently not...

I’ve modified the title slightly and voted the question up to give it some more exposure. It may just be that this list doesn’t include the sort of specialist who could answer your question. Some areas (ornithology, for example) are more highly represented than others.

Thank you. Since posting I have finished reading "The descended larynx is not uniquely human" by Fitch and Reby. They conclude the larynges of male red and fallow deer do descend, although these animals have control, whereas we do not. They (deliberately) avoided does of these species which makes it difficult to contrast with human females (who have one post infancy descension for speech.)

Male mammals who use deeper mating calls are successful because it exaggerates their size. Researchers studied mating calls produced by 72 species of land mammal.

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What sounds deter sharks?
Have any studies been done to find sounds that alienate sharks?

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

If you want to drive away, maybe it would be better with substances that trigger a particular taste.

Have you tried doing any of your own research on the topic??

Sharks hear from 10-800hz.
Sharks jump out of water for fun, which makes  huge noise pressure next to their ears. Sound weapons aren't very renowned in Darpa or defence tech. i'd say, you play any kind of patterns to a shark at any frequency, you'll have a tough time upsetting it.  you may have a very good effect at attracting them from afar and delaying predatory response as they assess/avoid the prey. LF takes huge batteries compared to HF. curiously, dolpins hear up to 100khz, whales as low as 2-3 hz for booming across the ocean. precise answer here : https://scholar.google.fr/scholar?hl=en&q=shark+sonic+deterrent&btnG=&as_sdt=1%2C5&as_sdtp=

Todays best shark deterrents have z range of 5-10 meters and are magnetic and electric: https://prwire.com.au/pr/77309/worlds-first-boat-and-beach-long-range-shark-deterrents

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Relation of conformational entropy and protein folding
I'm trying to figure out the relation between conformational entropy and protein folding.
I read the following in Lehninger, Principles of Biochemistry (6th edition):

Most of the net change in free energy as weak interactions form within a protein is therefore derived from the increased entropy in the surrounding aqueous solution resulting from the burial of hydrophobic surfaces. This more than counterbalances the large loss of conformational entropy as a polypeptide is constrained into its folded conformation.

In this context the meaning of conformational entropy is that the higher the stability of the proteïn is the lower the conformational entropy is (I think).
Why does the surrounding entropy increases because of the burial of hydrophobic residues?
Why does the burial of those hydrophobic residus couterbalances the large loss of conformational entropy?
I think maybe because the unfolded protein has more conformation then the protein when it's folded because of the hydorphobic core, it lowers the possible conformation because the hydrophobic interaction restrict the possiblities. Am I right?

I have tidied up your question. Don't leave unnecessary space that makes people have to scroll to see answers in the context of your question.

This question is an example of an important general problem in chemical biology: “How does an ordered system arise without violating the second law of thermodynamics?” Berg et al., Biochemistry, addresses this in the following manner:

The Second Law of Thermodynamics states that the total entropy of a system and its surroundings always increases for a spontaneous process. At first glance, this law appears to contradict much common experience, particularly about biological systems. Many biological processes, such as the generation of a well-defined structure such as a leaf from carbon dioxide gas and other nutrients, clearly increase the level of order and hence decrease entropy. Entropy may be decreased locally in the formation of such ordered structures only if the entropy of other parts of the universe is increased by an equal or greater amount.

Your question is about the spontaneous folding of proteins. You ask:

In this context the meaning of conformational entropy is that the higher the stability of the proteïn is the lower the conformational entropy is (I think).
Why does the surrounding entropy increases because of the burial of
hydrophobic residues?

Comments on your interpretation: Do not use the term ‘stability’ in this context. It is not a thermodynamic term and its meaning is imprecise. If we think of entropy as the degree of disorder or randomness, then we can see that Conformational entropy is used by the authors to mean the entropy of the protein as a random coil which can adopt many different structures. This has clearly a greater entropy than the folded protein with (to an approximation) a single structure. The adoption of the folded structure is thermodynamically favoured because it represents a state of lower energy (specifically Gibbs Free Energy) compared with the random coil structures, but entails a loss of entropy.
My answer: The surrounding entropy increases for the following reason. The surrounding entropy is that of the water molecules vibrating and interacting with other water molecules by means of the δ+ and δ– charges on H and O, respectively. In a system containing a protein with a random coil, the movement of these molecules is restricted by the hydrophobic side-chains they encounter, hence limiting the entropy, as it were. When the protein folds into a globule with polar residues on its surface, the vibrating water molecules are less restricted in their movement and hence have a higher entropy.
Further you ask:

Why does the burial of those hydrophobic residus couterbalances the large loss of conformational entropy?
I think maybe because the unfolded protein has more conformation then
the protein when it's folded because of the hydorphobic core, it
lowers the possible conformation because the hydrophobic interaction
restrict the possiblities. Am I right?

My Answer: I have explained that in general terms above, in response to your first question. If you want a quantitative, mathematical justification you’ll be pushed to find one. Assuming that there are no other factors involved, we assume that it must be so because of the second law.
Comments on Your Answer: I don’t understand what you mean by “it lowers the possible conformation”. You can decrease the number of possible conformations — you cannot "lower possible conformation”. I assume English is your first language. You must try to use it more precisely if you are going to write about science (as well as checking your spelling, grammar and capitalization). If I were marking this paragraph as an exam answer I would put a line through it as unintelligible. The key thing is that you are comparing a single conformation of the lowest energy involving specific weak interactions and a polar surface, with a number of conformations which expose hydrophobic residues and restrict the free vibrations of the water molecules.
Further Clarification
The diagram below illustrates the problem:

The protein is changing from a disordered to an ordered state so, its entropy is decreasing:

ΔSprotein = x ,  where x < 0

Whereas the water is changing from a more ordered to a less ordered state, so its entropy is increasing:

ΔSwater = y ,   where y > 0

and

ΔStotal = ΔSprotein + ΔSwater = x + y

If ΔSprotein + ΔSwater = 0 (x + y = 0), we would say that the increase in entropy of the water counterbalances the increase in entropy of the protein. For the folding to occur spontaneously, the total entropy must increase (ΔStotal > 0 , i.e. x + y > 0) and we would change the previous statement to  “more than counterbalances”.

Thankyou for your explanation and critic! However I still don't understand what they mean with "counterbalances"? @David

@RickBeeloo — I've added further clarification. (Hope I haven't got any of the > and < the wrong way round.) Glad you took the criticism in the right way. It was direct (some would put it stronger) but it was intended to be constructive.

Everything is clear now, thanks a lot! @David


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Effect of pH on protein solubilty and denaturation
I'm a little bit confused about the influence of pH on proteins.
Increasing or lowering the ph will give the protein a net positive or net negative charge, respectively. However a lower pH or higher pH will cause the protein to denaturate --> more hydrophobic amino acids will become free to interact between different proteins --> less solubilty.

let's clarify my question

take a look at the following figure:

this figure indicates that a lower or higher pH then the Pi will increae the protein solubility. However the Introduction to this article, for example, cites papers to support the following statement:

Changes in pH are shown to trigger formation of amyloid fibers and aggregation

the figure and the article are inconsistent in my opinion, so I'm definitly missing something. The first figure indicates that protein solubilty will increase when the pH becomes higher (then the pI). However the article statement indicates that an increase in pH will cause the proteins to aggregate, so lowering solubilty right?

http://biology.stackexchange.com/questions/43149/why-do-denatured-proteins-tend-to-be-less-soluble-than-the-native-protein

@akaDrHouse — Your reference is to a question to which there are no answers. This shows why people should not ignore the injunction not to use comments to provide answers. If you think the comment to that question is correct, feel free to copy and paste it as an answer. That is how StackExchange works.

My link had a comment that was correct.  A simple search in google reveals that denaturation of proteins often causes exposure of hydophobic regions, thus reducing solubility. @David perhaps that is why no more formal "answer" was needed. StackExchange also "works" to discourage one line answers, despite the fact they are often all that is needed.

@akaDrHouse Yes, denatured proteins are often less soluble because of the exposed hydrophobic inner residues. However, no one has yet made a connection between a pH change and denaturation. If you (or anyone else) can find evidence of that (it may exist, I just haven't searched), please make an answer.

@akaDrHouse — A search of Biology SE would list the previous question as unanswered. If someone chose to look at the question and read the comment they would have had no way of judging whether it was correct, as you assert, because it couldn't be voted up or down. There is a reason for the injunction you see when you open the comment box, and there is no excuse for ignoring it.

Sorry that my question was unclear, I clarified it and hope it's clear now @David

OK. Clarification fine. Have withdrawn my close vote and deleted my comment.

However, having looked at the paper you cite I have corrected your question. You say that the paper concluded the statement you cite. In fact the paper was about the correlation of pH optimum and stability in proteins and the citation is from the introduction and is only one of many examples given on the importance of pH for protein function.


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How does salicylic acid ingestion affect insect metabolism?
It is well known that plants may use salicylic acid as a signalling hormone when under attack by certain phytophagous insects.
Moreover, exogenous salicylic acid admixing with insecticides seems to synergistically potentiate these insecticides.
One would suspect that this effect is caused by salicylic acid ingestion by the herbivore parasites on top of improved hormone signalling within the plant. However, almost all articles I read about this subject focus on crop yield, with one exception.
Hence, my question: How does salicylic acid ingestion affect insect metabolism? I am especially interested in the effects on members of the suborder Sternorrhyncha.
Any links to a good review article would also be well appreciated.


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What determines when plants grow?
I am interested in dryland ecosystems, and I am trying to find material on what determines the time at which plants in dryland ecosystems, either shrubs or grasses, grow and shoot? Is it only related to water availability? Is temperature also a factor?

Plants are not sentient beings and do not know anything. Please phrase your questions in scientific terms.

Metaphoric language that I meet here and there (http://www.whataplantknows.com/)

Best avoided. Making your words reflect and clearly communicate your thoughts is part of being a scientist.


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Is the affinity of an enzyme or transporter for its substrate or solute influenced by the amino acids at the binding site?
The affinity of an enzyme or a protein transporter indicates the strenght of the binding of substrate/solute. An enzyme with higher affinity binds its substrate more strongly than a counterpart with a lower affinity. Is affinity always a function of the protein structure of enzyme? If the same enzyme in two different species had different affinities for substrate, would that indicate that there were differences in amino acids at the binding sites of the enzyme in the two species?

I wouldn't say "can bind with more substrate" I would say "binds substrate more strongly" - the answers to your other two questions are yes - affinity is a function of the structure of the enzyme (as well as the shape/structure of the ligand), and yes a difference in affinities in two species indicates there is a difference in amino acids that affects the binding site. Note that it wouldn't necessarily have to be directly at the binding site, just as long as it affects the shape of the binding site.

Km can most easily be understood as the concentration of ligand that results in half saturation of its target. https://arxiv.org/pdf/1305.5533.pdf

I have edited your question to remove the erroneous description of affinity, corrected in the comment and tightened the wording. I have changed the title to reflect the actual question. I have removed reference to Km because 1) transporters are not enzymes and do not have Kms 2) Km is a parameter that is interpreted in terms of affinity, which may only partially be correct. However as your question is about affinity there is no reason to muddy it with mention of Km. Apologies to @WYSIWYG, but this seems the only way to produce a good question worthy of an answer.

@David It depends on how narrowly you define "enzyme", but transporters can indeed be treated identically to enzymes, where the reaction is converting "substance inside" to "substance outside" (or vice versa) rather than making/breaking chemical bonds. Transporters will show the same saturation kinetics as enzymes, and will have kinetic descriptions which have a term equivalent to Km. (Whether you actually call it "Km" is another question.) -- That said, the mention of Km was unnecessary to the question, and I have no issue with its removal.

@RM — That same point struck me after writing. But transporters was an odd choice. I'd have thought general ligand binding as for membrane receptors and proteins such as heamoglobin should be included, in which case you would be talking about Kd, I imagine.

@David - Thanks for bringing Kd up. I agree with what you and RM have said above. Yes, transporters show the same saturation kinetics as enzymes. e.g. - an organism can be exposed for short term with metal and its influx can be studied at different concentrations and this data can be fitted into MM equation to get Km and Vmax. Important caveat is that these Km and Vmax are blended values from several transporters. I have read that -Log of Km can be called Log Kd (dissociation constant). Higher the log Kd, stronger the binding. Would you be able to shed some light on this relationship? Thanks

In a reaction which follows a saturation kinetics, KM is basically the concentration of substrate/ligand at which the rate of the reaction is half of the maximum rate (or the binding sites are half saturated).
The biophysical meaning of KM would depend on the underlying model. For example, in the equilibrium approximation of Michaelis-Menten model, KM is same as dissociation constant (of enzyme and substrate). In the Briggs-Haldane model (quasi steady state approximation), it is slightly complex: KM = (kr + kcat)/kf.
Overall, the thumb rule is that lower the KM faster will the reaction saturate.

Is affinity always a function of the protein structure of enzyme? If
  someone study same enzyme in two different species and observe that
  the enzyme has different affinities in two species, then does it
  indicate that there might by slight difference in key amino-acid
  component at the binding sites of the enzyme between these two
  species?

Almost every property of the protein (not just affinity towards a ligand) is because of its chemical composition and structure. Although they are directly involved in binding, the amino acids at binding site are not the sole contributors to the affinity. The other amino acids that are critical for the overall structure of the protein are also important in preserving the function.

I will add to the answer by @WYSIWYG by turning your question round: “If you changed the amino acids at the binding site, would this affect the affinity of a protein for a ligand*?”
The answer to this is yes, and for an enzyme you can change the substrate specificity entirely, as one can discover from reading this review by Wilson and Agard.
However one should also be aware that changing residues at parts of a protein outside the ligand-binding site can also affect the affinity of binding — see, for example, this paper by Oue et al.
[*This makes the question more general to include other proteins that bind ligands such as membrane receptors and transport proteins such as heamoglobin.]


text:
Can pheromones be received other than by odor?
I'm trying to understand how deodorants affect pheromones in humans.
Wiki states:
Axilla

In humans, the formation of body odor happens mostly in the axillary
  region. These odorant substances serve as pheromones which play a role
  related to mating.

Deodorant

A deodorant is a substance applied to the body to prevent body odor caused by the bacterial breakdown of perspiration in armpits, feet, and other areas of the body.

Can the opposite sex receive pheromones if a person uses crystal deodorant (doesn't have a fragrance; doesn't block sweating; prevents body odor by creating an invisible, protective barrier against odor-causing bacteria)?

Despite the Wikipedia page you link to, the existence of human pheromones is still a matter of debate. For the most part human body odor comes from the breakdown products of sweat and skin by bacteria. These smells may play a role in sexual attraction, but they aren't strictly pheromones since the odorants aren't actually secreted by humans, but by bacteria that live on our skin.

We have only 5 senses, a 6th sense has been controversial, and some 6th senses are sometimes reported in new research in newspapers, but none have been conclusively been added to the clearly known 5. There is a second olfactory organ that deals with social signals in other animals, that we possess, the vomeronasal organ.
Pheromones are only olfactory molecules, so you can't get them other than by catching molecules and analysing them, i.e. smelling.
Humans react very strongly by attraction to some perfumes other than pheremones, and you arent supposed to block all your smells, only make them containable, a bit is probably a good thing.
Scientists did publish a study claiming that people can tell if they make a good immune response / metabolic genetic combo with a partner from smelling a potential partner's t-shirt.

"We have only 5 senses, a 6th sense has been controversial" - This is meaningless. There are well over 5 senses. The 5 senses thing is a biology myth taught to children.

Are the pheromones in the bad scent after sweating? As I said, take for example, deodorants that don't block sweat but "disable" bacteria. Can opposite sex catch these molecules or deodorants block them?

Meaningless? It's BioPhysics categorization, and current affairs, news headlines, So, No, Actually it is a Bio-Physics subject. And Artmal is not a doctor, no one even understands the question very scientifically, If you know a kinder reply to him, give it. Energy is transmitted in 5 major groups into the human mind: Chemical scent of the air, and chemical scent of taste, Soundwaves, Photons, Kinetic Energy.


text:
What can a human do in a short time (10-20 years) to improve their genome?
I'm wondering what can I do to make my children receive better genes?
For example, can fitness, cold showering, studying etc. change my hereditary material and affect my children?

Reproduce with someone whom you think has "better" genes than you. There is nothing you can do for your own genes.

You could also reproduce a whole lot, and cull the children who end up with worse genes, preserving only those with the best genes. Some species, like certain birds, do this by allowing their offspring to fight for food, only feeding their stronger offspring. Of course this is easier if you have multiple offspring at once. IANAL but you might want to check whether this is legal in your jurisdiction before proceeding.

@BryanKrause: despite the ethics debate over designer humans, well-intentioned genetic engineering sounds much more humane and efficient than your solution.

@kmm Couldn't epigenetics be affected within one's life?

There is evidence that epigenetic marks can be inherited, though last I checked it was still somewhat controversial.
I recall a paper where obese parents were (epi)genetically more likely to have obese children. Therefore, if you spend your life taking care of your health, it's likely that your children may benefit from this.

No amount of lifestyle practice will change your germline (heritable) genome.
However there were 2 recent articles where researchers experimentally fixed dangerous genetic defects in embryos using CRISPR-Cas9 which could form the basis of future tech that corrects all known dangerous genetic diseases.
Bear in mind that the idea of "designer humans" (using gene-editing to make more perfect humans rather than just fixing serious hereditary problems) remains incredibly controversial and bitterly contested/debated (and illegal in most Western nations). Expect it to remain that way over the next 10 years.
If you want perfect offspring and aren't up to waiting, you might consider diving into robotics and AI instead and build a robot. That way, if it has any problems, you can always order new parts or provide tech support.


text:
Queen ant identification
I'm planning to start an artificial ant nest and I'd like to learn something about this specific species of ant that I captured in central Colorado.
Could you tell what kind of queen is that? Is there any image reference that would help me find out? Ideally with some location search possibility.

Where was the ant collected? There are some online resources for different countries that may be useful but unless there is some information to help narrow it down, you must start with the 12,500-22,000 species found across the globe.

It was captured in Colorado. Hopefully someone with more experience than me has a pretty good guess because all the sites I have found have not been to helpful.

The picture is unclear but this ant looks like a Solenopsis queen. Maybe a Solenopsis invicta! Sorry if I'm wrong, I've only ever kept Camponotus and Lasius queens. I hope this is helpful though

This is clearly wrong, there is a post-petiole and a petiole in Solenopsis whereas you can clearly see that there is only one on his picture.

@lucas Adam: I think so you have captured the wrong ant (worker), because the queen's head will always be shorter than its thorax. It's probably a carpenter worker ant. Further , capturing a queen is a big task because queen ants rarely come outside. And if you capture it , the entire colony it have already created will die within 2 days or maximum by a month.

There is clearly only one segment between the thorax and the abdomen, which rules out the possibility that this ant is a Myrmicinae.
It looks like a queen of Formicinae, probably in the genus Camponotus.


text:
Can a regulator genes be more highly expressed when it has more places to bind?
I am doing some research on small cell lung cancer and, from what I have found, many tumors show high levels of ASCL1, which is a regulator for neuroendocrine cell differentiation. However, no papers propose a mechanism for the higher levels of ASCL1. Instead, many of them refer to ASCL1 target genes with "amplified" enhancers and propose that ASCL1 may bind more frequently to these enhancer regions.
In general, if there are more places for the regulator to bind on an enhancer, is it possible that this is sufficient for the regulator to be more highly expressed?


text:
Why bacteria and viruses are so much smaller than animal cells?
Why are bacteria and viruses so much smaller than animal cells? -
I don't have more information about the question, sorry if this is too vague.

I actually think that this is an interesting question. The problem is that the format for this site would make this a difficult question to answer properly. Viruses use the cells they infect to make more copies of themselves, so right there, they would need to be much smaller than the cell itself, otherwise it couldn't reproduce itself. There are also energy efficiency issues, replication times, simpler genomes, fewer organelles, and on and on to explain bacterial smaller size.

Cells/viruses vary in size mainly according to their function, components & requirements imposed by cell division/virus replication.
Bacterial cells are so small because they need a large surface area to cell volume to take in nutrients. Bacteria accumulate nutrients from the environment by diffusion alone, and so adopt certain sizes and shapes so they can import nutrients most efficiently. other evolutionary advantages are also existent in response to the demands of the environment and predators
Viruses function is pretty minimalistic. they pretty much consists of nucleic acid surrounded by a protective coat of protein called a capsid. this is the primitive virus, all it nedds is to infect cells and pass the information stored inside them.
The size of animal cells however depends partially on the type of cell and its function. Red blood cells are pretty small in comparison to other animal cells, they don't need to divide (so do not own a nucleus) and need a large surface area in order to diffuse Oxygen efficiently. Egg cells for example serve to store nutrients and don't need to carry out active metabolism, and so they are much bigger.
I took some of the examples from here, and for more technical information about the upper limits of cell size and plant cells click here.

All cells take nutrients in from their environment, including those of multicellular organisms, even mammals, so your second paragraph is irrelevant. Viruses can be packages with enzymes such as reverse transcriptase and integrase, etc. so your third paragraph is incomplete. Your fourth paragraph is somewhat true, but neurons would be a better example. Also you make no mention of the hypothetical size limit of all cells due to surface area to volume to diffusion rate limits. And your answer lacks references. I know the OP accepted the answer, but it lacks quality and should consider removing,

I agree with you @AMR that this topic is broad. I added reference to some more detailed article for the specifics. I think the answer fits the question. A more specific answer will meet a more specific question.

@AMR 's arguments are valid but you can answer them if you explain a parameter regarding the shape: surface area/volume ratio. While increasing surface area will allow a greater chance of nutrient uptake and synthesis, increase of volume will result in higher energy consuption. The cell has to strike an optimum. Therefore bigger eukaryotic cells are dependent on organelles for energy.


text:
What chemicals/substances exist in green capsicum (peppers) that do not exist in red capsicum?
I have known 3 people in my life that have incredibly adverse reactions (one called it an "allergy" and his symptoms did resemble such) to consuming any form of green pepper (capsicum) but have no problems with red peppers (also capsicum). Besides the obvious chlorophyll -- which I rule out since none of these friends had issues with green vegetables -- what else is unique to the green peppers that could possibly cause such reactions?
My limited understanding is that green and red peppers (at least with bell peppers) are actually the same peppers at different stages of maturity. If that is true what changes within the plant during the maturation process?

You mean chilli peppers, right? Peppers are actually a totally different species.

Thanks for asking, I will clarify the question. Capsicum includes both chilis and bells, as did/do my friends' problems.

@VanceLAlbaugh if you will note, in the question I wrote "red peppers (also capsicum)"

Why all the down votes on this question? What is wrong with it?

There are no down votes.

@WYSIWYG. My alerts are showing a -40 points for this question with no explanation. If there are no downvotes then what caused the -40 points?

There cannot be -40; that would require 20 downvotes!! or reversal of 8 upvotes. Neither of which seems to be the case. You have given a bounty of 50 points. Those 50 points get deducted from your rep. You got 2 upvotes i.e. 10 points. So the net rep change on this question is -40.

@WYSIWYG -- Doh! Of course it was the bounty. Sorry but it just didn't click. Of course you can see why I was so concerned about what I thought was 20 downvotes. :P

Your limited understanding is indeed correct - the different colours indicate different stages of maturation, even though different colour cultivars exist (e.g. some that remain green even if fully ripe).
It is known that the different maturation states have different vitamin and/or mineral concentrations (see here or here). This indicates that different biochemical pathways are active and that therefore the enzymatic set-up is variable during pepper maturation (which could have an effect on tolerability as it might also affect other plant components).
Moreover, you are right that the green colour is - at least partially - caused by chlorophyll but also non-green bell peppers often have chlorophyll (Lancaster et al., 1997) but that probably is not the cause of your friend's responses.
More likely the cause is 3-isobutyl-2-methoxypyrazine (IBMP) which gives the characteristic (green) pepper smell and has highest concentrations in green peppers (that's why it is called green pepper smell). It has one of the most intense odours that can be detected at very low concentrations, even within the complex odours of wine (Pickering et al., 2007), according to Roth, 2014 perhaps even below PPT concentrations.
So how does this fit together? Pickering et al., 2007 also suggest that one should determine 'consumer rejection thresholds' for methoxypyrazines, indicating that it might be repellent to some people even in low concentrations of 1-2 ng per litre. This could explain your friend's aversion but evidence for the allergy component is dubious.
I did find one paper (Jensen-Jarolim et al., 1998)  about allergen expression in peppers (birch allergy like). However, no green-specific allergens are reported, and it even seems like green peppers would be a better choice to avoid these allergens.

Thank you. Very interesting about the odors. I am reluctant/cautious to use the term "allergy" myself, just passing on what one of my friends called it. His reaction to an accidental ingestion of a tiny amount (undisclosed odd ingredient in a potluck dish at a social event) was rapid onset of significant respiratory distress and intense nausea to the point of needing emergency medical intervention. I only observed one such incident but he advised there had been a few prior incidents over approx 50 years.

@O.M.Y: That sounds quite weird, yes. But well, there are rare or unheard/unthought of allergies and now you know that there are green pepper-specific (or at least enriched) substances. So who knows ... Maybe your friend should have that checked.

It actually is 3 friends/aquaintances I've known through the years who have had this problem so it is not unique. All of them have consulted doctors, one has consulted an allergy specialist and had the whole "grid-of-pins-on-the-back" test. They tested positive on a whole range of usual's like shellfish and strawberries but also on odd items like vinegar, nutmeg, olives, and alcohol. Another friend (not one of the 3) has a weird allergy to real gold, makes their skin inflame soon after contact (but no reaction to other metals). Yes, they have been tested by a doctor also.


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What protein(s) bind together the calcium carbonate tiles in abalone shell to give it strength?
The articles that I've been able to find on the structure of abalone shells mention that they consist of calcium carbonate plates connected by proteins, but don't name the proteins. These proteins are key to the shell's strength. What proteins connect the calcium carbonate plates to give the shell its strength? What other proteins are they related to (if any), both structurally and phylogenetically?
I searched via DuckDuckGo using phrases such as "abalone shell protein", "abalone shell structure protein" and "abalone shell structure calcium carbonate protein". The best match I found on proteins was "In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix"; while it names many proteins, it doesn't identify their function.

What did you find when you googled “what is the protein found in abalone shell?” Using this phrase got me a very interesting article.

@anongoodnurse: I used DuckDuckGo. Updated question includes search terms. Looking over "Proteomic analysis of the organic matrix of the abalone Haliotis asinina calcified shell" now.

The article is quite interesting, but seems focused on identifying proteins for their shell growth function rather than tile binding (the proteins may have both functions). This is ambiguous in parts, since "bind" is also used for CO₃ crystal growth.

Pif-80 might be one protein identified as potentially binding plates in that it hypothetically "binds in vitro to calcium carbonate crystals" (rather than binding CO₃ molecules together), according to another study (Suzuki et. al., "An acidic matrix protein, Pif, is a key macromolecule for nacre formation", 2009). The proteomic analysis article also describes some proteins as fibroin-like, which could be involved in the shell strength.

The article also mentions even other species in the same genus have vastly different proteins in their shells, which means the question might be too broad at the given taxonomic rank.

In that paper alone, you have 14 proteins listed. They were identified by tandem MS (fractionated proteins isolated from crushed shell). Does that paper answer your question in part? I also recommend looking at a more recent one where some of the same authors more recently (in 2018 as opposed to 2010) identified 297 proteins from the nacreous shell layer and 350 proteins from the prismatic shell layer, in a different abalone species. A total of 448 proteins were found. Would that satisfy your question?

@SPr: Unfortunately, no. I'm not only interested in the proteins in general, but the proteins with specific function (as described in the question). The more recent one you mention is also the paper I linked in my question. Neither of the two papers identify with certainty the proteins that connect the CO₃ plates for strength.

I see. It is difficult to identify proteins with specific niche functionality ("carbonate plate-connecting") by MS/MS. That method is designed to identify isolated proteins, and in this case, the entire shell was isolated. I hope you will find your answer, but it's possible it doesn't exist. Seemingly, the group interested in this research did a whole shell extraction in 2018, and I can't find anything relevant since. I think the protein motifs and domains discussed in the two papers we link here may provide hints. Plate connecting protein(s) must have domains that can interact with carbonate.

@SPr: Pif-80 and the fibroin-like HasCL10contig2 & P0025F23_658 (mentioned in "Proteomic Analysis ...") are the best candidates at this point.


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Can salt-water frogs survive in normal water (A well)?
I don't know much about frogs, but there seem to be salt water frogs.
1) Are there such things as salt water frogs?
2) Are there frogs that live in the sea? (in reference to Vivekananda's quote)
3) Can salt water frogs survive in well water or fresh water?

Well, one day another frog that lived in the sea came and fell into the well. - Vivekananda

There are no salt water frogs. There is only one species which lives in mangrove swamps and is perhaps the only amphibian that can tolerate salinity.

There's a bit more detail on the crab-eating frog here: http://www.biodiversityscience.com/2011/04/27/saltwater-frogs-water-conservation/

@WYSIWYG So, was Vivekananda's quote "A frog that lived in the sea" scientifically wrong. Also see the updated Q.

@Wally He must have meant it metaphorically.

He also mocked evolution so.. http://www.swamivivekanandaquotes.org/2014/04/swami-vivekanandas-frog-in-well-story.html

"A frog lived in a well. It had lived there for a long time. It was born there and brought up there, and yet was a little, small frog. Of course the evolutionists were not there then to tell us whether the frog lost its eyes or not," - Vivekananda

frogs are a pretty specialized/derived group in amphibians anyway so it is not surprising they are fresh water only, there are saline living salamanders though, well one species anyway, Ambystoma taylori.

According to Wikipedia the Crab-eating frog is the only amphibian that can survive in sea water. However Wikipedia also suggests that it can only survive brief excursions into the sea.
There are no such things as sea frogs.
Even the Crab-eating frog doesn't live in the sea though. Its natural habitat is mangrove swamps.

The crab-eating frog (Fejervarya cancrivora), is a frog native to south-eastern Asia including Taiwan, China, the Philippines and more rarely as far west as Orissa in India. It inhabits mangrove swamps and marshes and is the only known modern amphibian which can tolerate brief excursions into sea water.
This frog can tolerate marine environments (immersion in sea water for brief periods or brackish water for extended periods) by increasing urea production and retention, and by remaining slightly hyperosmotic within urea and sodium flux. Adults can survive in salt water with salinity as high as 2.8%, and tadpoles can survive salinities as high as 3.9%.

https://en.wikipedia.org/wiki/Crab-eating_frog


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Western blot transfer issues
I am having some issues with transfer efficiency to nitrocellulose membranes. To get all the technical info out of the way:
Transfer method: Wet, tank transfer overnight at 30V with normal tris-glycine transfer buffer + 20% methanol. I do this at RT with stirring. Of note: I have not recently been equilibrating my gel in transfer buffer, as this was reported to decrease transfer of basic proteins due to the stripping of SDS (I can furnish this reference if anyone is interested).
Sample: In all cases these are in vitro reconstituted nucleosomes with or without certain enzymes--the main transfer issues are the core histones, which are highly basic (pI 10-11). There should be no more than about 100 ng of each histone being transferred per lane. The salt in the sample is <25 mM. They are boiled prior to loading. There is no noticeable precipitate in the samples before or after boiling, however the volume is quite small (20 ul) so I would not necessarily detect precipitation.
Nitrocellulose is 0.2 um and is pre-equilibrated in transfer buffer prior to transfer.
The gel: I use a 15% gel, 1.0-1.5 mm thick. The acrylamide I use is 37.5:1 acrylamide:bis. Some issues could arise here--the acrylamide solution is about 1 year old and has been stored at RT that entire time (which is what is recommended on the label). In addition, we typically keep a stock of 10% APS at 4C, so I cannot guarantee my APS has not gone bad.
I have been quite careful generally to ensure there are no bubbles between any components of the sandwich and filter paper/foam pads are soaked in transfer buffer.
Now to the issue. Attached are images of the membrane after transfer (and also after processing, thus the relatively high background from the blocking buffer) as well as the gel after transfer. As you can see from lane to lane I seem to have differing transfer efficiencies. This has occurred with my last three blots. My first thought was sample precipitation, but I have not had this issue before despite running essentially the same blot many many times over the past year.
Any thoughts? Quite frustrating, as it has appeared suddenly with identical protocols/reagents as before.

I've never done it, but I remember hearing that histones are very hard to work with in SDS-PAGE and Westerns because of their basic nature -- conventional gels and blots assume that the proteins are acidic because of the SDS bound to them, but that isn't true with histones. I see one protocol for histones here.

The first thing that comes to mind for me is that the transfer seems excessive... isn't histone sub-20 kDa? I have often transferred similar-sized proteins at 4C for 30 min, 30V.
In general, presence of SDS will inhibit transfer efficiency, and increasing alcohol in your TG buffer will counteract the effect of SDS present. Perhaps bring down the methanol to 10%? I would be curious to see that reference regarding the SDS/pre-equilibration, though. That certainly runs contrary to how I understand it working. (Note: I flip-flop between equilibrating or not equilibrated my gels without any observable differences.)
If your acrylamide or ACS had gone bad, your gel wouldn't set.
If you don't already, I'd suggest running a Bradford or BCA on your samples to be sure that you're loading the same amount into each well. Having loaded more into each well could give the appearance of uneven transfer.
To be honest, I don't really see what you mean by uneven transfer, based off the Coomassie and Ponceau. If you're seeing a gradient effect across a large portion of the gel, I would suggest you visually inspect to make sure that the gels you cast are even width all the way across. Having a thicker gel in one place than in another could impact the resistance (heat) in that part of the gel and impact transfer. If you're seeing a lane-by-lane transfer efficiency shift, I would suggest localized pH or temperature changes due to uneven loading of salts, protein concentration, or lipid concentration.
Hope this helps!


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What is the fate of NADH produced in the liver during oxidation of lactic acid?
NADH (‘reduced NAD’) is produced during the oxidation of blood lactate in the liver. Glycolysis requires NAD+ (‘oxidised NAD’), whereas gluconeogensis requires NADH. However the NADH is apparently not always used for gluconeogenesis (How is NAD+ used in lactic acid fermentation after it is oxidized from NADH?), i.e. the Cori Cycle does not always operate — so what becomes of the NADH in this case?
My best guess is that, along with the pyruvate, it may be transferred in the blood somehow to do to the site where it is needed, and it will then be taken into the electron transport chain, while the pyruvate will be taken into the Krebs cycle.

I have condensed your question to make it clearer. If I have altered your meaning please say so.

The “best guess” in this question is incorrect and the question itself indicates a lack of understanding of the roles of NAD+ and NADH in energy metabolism. (To rectifiy this, Chapters 17 and 18 of Berg et al. are suggested.)
The production of NADH in the oxidation of carbohydrates and fats is the energetic rationale for these processes. Under aerobic conditions the re-oxidation of NADH to NAD+ via the electron transport chain in the mitochondria* generates ATP for the energetic processes of the cell.
The fate of NADH produced by the oxidation of lactate reaching the liver from the blood would be similar under conditions where it is not needed for gluconeogenesis (in the reversal of the GAPDH reaction).  In these circumstances it would be reoxidized to NAD+, generating ATP in the mitochondria*.
[Note also that pyruvate is most likely to be oxidized by the liver mitochondria to produce metabolic intermediates and ATP, rather than transferred to the blood. NADH is certainly not transferred to the blood.]
*Advanced Point: Cytoplasmic and Mitochondrial NAD
The statement above, that NADH is “reoxidized to NAD+, generating ATP in the mitochondria”, is correct, but may be taken to imply that the NADH enters the mitochondria. This is not the case becase the NADH and NAD+ cannot pass through the mitochondrial membrane (as @tomd has commented). However the electrons that represent the reduced state of NADH do pass through the membrane. They do this in the guise of other molecules which are reduced in the cytoplasm by NADH in what are known as electron shuttles. The electrons enter the electron transport chain and are finally accepted by molecular oxygen. More detail of shuttles can be found in section 18.5 of Berg et al.

@tomd — Thank you for that elaboration but the question was not about NAD transport (or effective) transport across the mitochondrial membrane. Including it in my answer would have reduced its clarity and obscured the basic principle of what the NADH is used for.

@tomd — I have now modified the question, the first paragraph of my answer, and added a footnote about shuttles. I trust this incorporates the points you raised.


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Can the concentration of a kinase be used to identify its substrate?
I'm currently working on a dataset were I'm trying to identify substrates of an kinase in silico, I have a dataset which contains the concentrations every 0h 2h,4h,6h,8h,10h,24h for a lot of proteins found in the sample when the kinase was active. However some of these aren't targeted by the kinase but other proteins that got activated or were indirect activated by the kinase. So what I did I used R to plot the concentration of the detected proteins only if they fitted the concentration line of the kinase of interest(with a little devition allowed) this gave me the following graph:

the blue line is the kinase and the other lines are proteins found in the dataset. I know there could be postive or negative feedback which has effect on the concentation of these proteins.So my question is could the lines shown here be a possible substrate?

The concentration of a kinase is completely independent of the concentration of the substrate, and vice versa. In a typical kinase cascade (such as the Ras→Raf→MEK→Erk pathway), signal transduction is generally amplified with each successive step. A relative small population of one kinase (like Raf) phosphorylates orders of magnitude more of its substrates (like MEK1/2), which in turn phosphorylate orders of magnitude more p44/42 MAPK (Erk1/2) molecules. These then phosphorylate transcription factors like c-Myc which translocate to the nucleus and affect the expression of target genes. Over time, protein levels inside the cell are changed, including the levels of the various components of the pathway or their inhibitors (such as phosphatases, components of the protein degradation machinery like ubiquitin ligases, etc.), allowing for regulation of the signal.
Therefore, for any given kinase at any given time post-stimulation, such as with a growth factor, the concentration and phosphorylation state of its substrate(s) can vary tremendously. For example, in the classical NK-κB pathway, activated by TNFα, one of the main substrates of the IKKα/IKKβ kinase complex is the inhibitor IκBα, which upon phosphorylation is rapidly ubiquitinated and degraded by the proteasome. However, one of the first target genes of the activated NF-κB p65/p50 transcription factor dimer is Ikba itself, which negatively regulates activation of the pathway.
I don't know exactly what information your data set contains, so I can't comment too much on your results. However, just graphing substrate concentrations that correspond to kinase concentrations at various time points will only give you one piece of information - that some substrates have grossly similar concentrations to the kinase - which means nothing. All that is is confirmation bias - you've decided on your result, then picked the data that confirm it. I bet if you were to graph the concentrations of direct substrates along with your kinase, you would find no relationship whatsoever, because as I've described above, there is none biologically.

Thankyou for your explanation! I have a dataset which contains all proteins downstream of the kinase (so substrates and non substrates), but I found it quite remarkable that the pink line has almost exaclty the same concentration changes as the kinase has, maybe this could be coincidence? @MattDMo

@RickBeeloo most likely it's just a coincidence. It could also be that your protein of interest is some sort of regulator of the kinase, and expression levels may correlate with it. You'll have to dig into the biology to answer that.

The hardest part is that there is nothing to find about the proteins of interest because they aren't identified before, but thankyou anyway! @MattDMo


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Thermodynamics of spontaneous protein folding: role of enthalpy changes
I'm trying to get clear why protein folding occurs spontaneously.
$$\ce\Delta G=\Delta H-T\Delta S$$
According to thermodynamics the ΔG should be negative for a process to occur spontaneously.
When a protein folds the ΔS (Entropy) is decreasing, because the protein gets more ordered. However I think the forming of the bonds (disulfide and other weak interactions) counterbalance this unfavourable rising entropy by forming an enthalpy (ΔH) which thus would result in a negative ΔG.
However I saw some other explanation online which didn't apply the Gibbs free energy formula to the protein but instead to the water. Because the water is more ordered when the protein is unfolded it would be favourable according to the second law of thermodynamics to fold the protein because after folding the water molecules can move more freely --> higher entropy -->negative ΔG --> spontaneous folding.
So my question is which of these two (or maybe both) are the cause of the spontaneous folding of proteins?

I have edited the title to avoid confusion with a related question that focuses solely on the entropy change. Hope that is ok. If not revert it.

Summary

The first explanation is commonly encountered.
The second explanation cannot be correct, as it stands, as it ignores the free energy change in the protein.
A modification of the second explanation (perhaps what was intended) is that it is necessary to consider the protein folding and change in the water as being coupled, in which case the overall free energy change — the sum of the two considered separately — is the determinant of protein folding. The assertion would then be that a negative free-energy change in the water system is the deciding factor. This view has been persuasively advocated on the basis of experimental measurements.

Free energy change in individual transformations
It is standard practice in biochemistry to consider the Gibbs Free Energy of transformation of the sort A → B in isolation in determining whether it will proceed spontaneously. A chemical reaction for which ΔG is negative may generate heat (i.e. have a negative enthalpy change (ΔH) ) which affects its aqueous surroundings, but it seems justified to consider the reaction in isolation as there is no sense that the change in the vibration of the water molecules is driving or coupled to the reaction.
This approach has been applied to the structural change of protein folding with the conclusion (consistent with the first explanation) that the change in enthalpy (ΔH) is sufficient to produce a negative ΔG and hence drive protein folding (Citation 1, below).
Free energy change in coupled transformations
Many biochemical changes involve transformations which individually have a positive free energy change, but are made possible by coupling to another reaction with negative free energy change, of greater magnitude:

A → B , ΔG1 = +x
C → D , ΔG2 = –y

If y>x and these two reactions are coupled (generally through a complex reaction path on an enzyme) , then we have:

A + C → B + D , ΔGoverall = –ve

See also Berg et al.
Although one can reject the second explanation in the question as it stands because it ignores the free energy change in the protein folding, perhaps it was intended to mean that the folding of the protein (A → B) should be considered as coupled to the change in the environment of the water (C → D), and that the negative ΔG for the aqueous environment made a greater contribution to the overall ΔG than that for the protein folding.
Is it valid to consider these two systems as coupled? In the original version of my answer I argued against this point of view, but am no longer convinced by my own arguments. The water environment is clearly essential for the hydrophobic effect — the burying of the hydrophobic residues in the centre of the protein away from the water. This is evident if one considers the same protein in a hydrophobic environment such as a cell membrane — it would not fold. In membrane proteins it is hydrophobic residues that are exposed to the lipid bilayer and it is their interiors that sometimes have hydrophilic channels.
So in this coupled system, what is the determinant of the negative free energy change? Minikel (Citation 2, below) asserts that there is no net enthalpy change for the protein folding, and it is the entropy effect on the ΔG for the aqueous environment that drives the folding. He indicates that this view is supported by differential scanning colorimetry and, although he doesn’t cite references, there is a recent (if rather complex) review of this topic by Christopher M. Johnson.
Citation 1: Assertion of role of ΔH of protein
The following explanation, taken from Essential Biochemistry, treats the protein folding in isolation and asserts that change in enthalpy is sufficient to produce a negative free energy change:

The folding of a protein also provides an example of the "ΔH" and "–TΔS" terms competing with one another to determine the ΔG of the folding process. As described above, the change in entropy of the protein as it folds is negative, so the "–TΔS" term is positive. However, in addition to entropic effects there are enthalpic contributions to protein folding. These include hydrogen bonding, ionic salt bridges, and Van der Waals forces. An input of thermal (heat) energy is required to disrupt these forces, and conversely when these interactions form during protein folding they release heat (the ΔH is negative). When all of these entropic and enthalpic contributions are weighed, the enthalpy term wins out over the entropy term. Therefore the free energy of protein folding is negative, and protein folding is a spontaneous process.

Citation 2: Rebuttal of role of ΔH of protein and assertion of role of water
The following explanation, taken from on-line lecture notes of  of Eric V. Minikel of Harvard University, rebutting the point of view above:

An incorrect and simplistic view of protein folding is as follows. An unfolded protein has high configurational entropy but also high enthalpy because it has few stabilizing interactions. A folded protein has far less entropy, but also far less enthalpy. There is a tradeoff between H and S here. Note that because ΔG = ΔH - TΔS, increased temperature weights the S term more heavily, meaning that higher temperature favors unfolding.
That entire explanation only considers the energy of the protein and
  not that of the solvent. In fact, hydrophobic domains of a protein
  constrain the possible configurations of surrounding water (see
  explanation above), and so their burial upon folding increases the
  water’s entropy. Moreover, it turns out that the hydrogen bonding of
  polar residues and the backbone is satisfied both in an unfolded state
  (by water) and in a folded state (by each other). Therefore enthalpy
  is “zero sum,” and protein folding is driven almost entirely by
  entropy.

thankyou great explanation! I understand your point "it would seem very diffucultto specify how many water molecules were affected".However thermodynamics usually calculates the free energy of the total system, so this confuses me a little bit. @david

I think you are right to be confused and even sceptical about my answer. The warning signal is the personalization in “In my opinion…” and “I find…”. Why should you or anyone else care about my opinion? And the fact that I was writing in that way suggests that I was trying to use my authority in lieu of a convincing argument. I have now modified my answer so that it no longer rejects coupling of the changes. Apologies to anyone who has already up-voted my answer — do feel free to withdraw your vote.

I found an explanation about considering the solvent(water) in protien folding thermodynamics (http://www.cureffi.org/2014/09/05/molecular-biology-02/) it's at the bottom of the page,maybe you are interested @david. It looks like the solvent is important.

@RickBeeloo — Pretty convincing, despite having to take his word for "it turns out". Need to revise my answer again, but it may have to wait until tomorrow.

I have revised my answer once more, including the source cited by @RickBeeloo.

If you change the solvent will a given  protein still fold spontaneously?  One could argue that the only biologically relevant solvent to use is one with the pH, osmolarity, and concentration as intracellular cytoplasm (you could also include the inside of the endoplasmic reticulum).  In ethanol, or olive oil the same protein might night fold spontaneously.  So the solvent is paramount for setting the context of your question. What you call folding, others might call "being pushed into shape by the solvent." The hydrophobic effect is crucial (see Tanford's book of the same name--a classic).


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Regulation of the concentration of precursors of DNA and RNA synthesis
What is the specific cellular process for regulating the amount of the four DNA bases (adenine, thymine, cytosine, and guanine) that are present in the cytoplasm of a cell?
Basically, how do the cell's mechanical processes "know" that there are enough of these present in the cytoplasm for DNA/RNA processes to operate effectively?
From what I understand, DNA/RNA sequence production involves simply grabbing these out of the cytoplasm as they randomly pass near the sequence assembly protein.
As a side topic, but also important here, the cytoplasm is apparently just a random fluid containing all sorts of molecules flowing and diffusing in random directions via Brownian motion. I do not know if there is a specific direction cytoplasm flows around the inside of a cell, and if so, how the cell would manage to coordinate that either.
There does not seem to be a way for cell processes to "read" the proportional molecular contents of the cytoplasm to know if there is sufficient numbers of these present for proper cell function.
If there is a lack of any one of these four base molecules, DNA/RNA processes will slow or stop functioning, leading to systemic failure and potentially cell death.
If there are too many of any one of them, the cell could become so packed that nothing can move around and the cell's function is impaired. Possibly the cell wall could rupture if there are too many.

The specific cellular process that regulates nucleoside synthesis has chapters in books dedicated to it, but I think the question is still good and can be answered with an overview. You're side topic may be better off as an entirely different question. Diffusion is definitely important but, as a start, you can look up cytoplasmic streaming and cytoskeletal transport.

@canadianer, nice mention of cytoplasmic streaming and cytoskeletal support: Brownian motion is only an approximation, and a very over-simplified one. However, keep in mind a whole different question may be needed to discuss the answer in the case of prokaryotes vs. the case of eukaryotes. Also, I believe you meant Your (not You're)

No no, I did mean "you are side topic", my grammatical mistakes came later ;)

There is an area of biological science called Biochemistry that includes the processes by which cellular chemicals are interconverted — metabolism. You are correct in assuming that metabolism, including the pathways for the synthesis of nucleic acid precursors, is regulated, and in general this operates by certain intermediates acting as sensors, modulating the activity of key enzymes. Your question regarding the eight precursors of DNA and RNA synthesis is far too broad, and I have voted to close. I recommend Chapter 10 (Regulatory Strategies) in Berg et. al. (NCBI Bookshelf, online).

You would also benefit from reading the details of nucleic acid synthesis and that of its precursors, which are not free bases, but nucleoside and deoxynucleoside triphosphates. Again, there are chapters on this in the previously mentioned Berg et al. and other biochemistry texts.

I am not a biologist, just someone with a casual interest. Is there a reason why these are being posted as comments and not as answers, if you are suggesting these are answers to the question and reasons to close? Is distillation of the overall mechanisms not easily summarizable within a few paragraphs?

This information does not appear to be accessible online for free in any sort of open format. Is it possible to summarize it here? https://www.ncbi.nlm.nih.gov/books/NBK21158/#NBK21158_dtls   "By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed"

If they are not the originator of the post (question or answer), you need to @'user' for them to be notified of your comment. That being said, I believe that David is saying that this is too broad a question (it would require multiple book chapter to adequately answer). Unfortunately the book @David recommended is no longer available — perhaps he can make an alternative suggestion, but you can also search for resources using the key words he mentioned. I have also found that Khan Academy can be very helpful when starting to learn about a new area.

@tyersome — It was available in 2017, and so the OP had a chance to consult it if he wished. As it is only a comment, my only update is to suggest purchase of a second-hand copy.


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What is the weight percentage of all people as compared to all Natural life?
If we compare the total mass  with the mass of all Naturally living beings with all creatures on Earth, be they bacteria, viruses, fish, insects, plants, etc., then what is the weight percentage of all people?
I ask this because I saw it mentioned that once people and all life they cultivated made up 0.1% of all animals and now 98%. With an exclamation mark. I am not sure if these were percentages of the total number of animals or their weight. I guess it is the number.

Why is the question downvoted? Please give a reason. I dont care about downvotes but I dont like irrational ones. Is it about the word Natural? What is Natural?

This has been studied in this paper, and they came up with:
Total biomass = 550 gigatons of carbon
Human biomass = 0.06 gigatons of carbon
So this would make humans about 0.01% of all biomass.  If this sounds like a little, a couple of points are worth mentioning:

They highlight that the mass of humans is an order of magnitude higher than that of all wild mammals combined.
Global human-made mass exceeds all living biomass.  This is mostly concrete and aggregates.

Graphical representation of the global biomass distribution by taxa. (A) Absolute biomasses of different taxa are represented using a Voronoi diagram, with the area of each cell being proportional to that taxa global biomass.  (B) Absolute biomass of different animal taxa.

Biomass and anthropogenic mass estimates since the beginning of the twentieth century on a dry-mass basis.

Wow! Great answer. Luckily we form a small part. For every person 100 000 kilo!

10,000 Kg actually.

I'm surprised that livestock and humans are so close in mass. I'd thought that livestock would be higher, given the inefficiency of meat.

@jakebeal I'm sure human omnivory helps, but also that the life of livestock is so brief. Chickens are slaughtered around 6 weeks age, pigs at 6 months, beef just over a year. A dairy cow produces about 10X its weight in milk per year (though of course a lot of that is water), a hen >3X its weight in eggs.


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Why do we have two kidneys but one liver?
Both the liver and the kidneys are involved in "cleaning" our blood. But why we have one liver and two kidneys? I can just as well imagine that we have two livers and one kidney. Is this just a coincidence?

Most "why" questions are super vague, they need to be narrowed to some level of analysis to be meaningfully answerable, otherwise you're likely to get answers that don't really approach what you are thinking about at all, and that's frustrating for everyone.

In addition to being unclear and likely to answered with opinions, this is a duplicate of at least these two other questions. As part of the expected prior research you should search on this site for similar questions before posting.

All your organs come in pairs, with one major exception, the digestive tract and the outgrowths from it (liver included) are singular. The real questions is why do you have two lungs. its the only organs that breaks the rules.

@BryanKrause asking why some organs are pair and others are not a fairly straightforward question, I don't see how it being a why question makes it vague, any more than asking why male deer have antlers.

@John Do you mean that lungs break the rule because we have one mouth?

The liver can change in size and adapt based on what you throw at it, the kidney not quite so much. This at least partly explains why you don't need two livers but why it's nice to have redundancy wrt the kidney.

Your organs can be grouped into two categories.
The digestive tract organs, which are singular.
These form from the endoderm.
The liver and pancreases are all direct outgrowths from the digestive tract which is again singular.
Everything else which comes in pairs.
These form from the mesoderm or ectoderm.
Even the brain and heart are paired organs, the heart starts as two organs and fused during embryonic development. The whole circulatory system starts perfectly paired, (embryonically and evolutionarily) but then specific parts close off to create the complex circulatory system of "higher" animals so we can have a high pressure section and low pressure section.
The spine is also sort of singular but is basically the the line splitting the left from right half of the body. Everything that branches off the spine does so in pairs.
The real questions is why you have two lungs and one spleen. They are the only organs that breaks the rules. The lungs are an outgrowth of the digestive tract and the endoderm, but is paired. The spleen is part of the circulatory system, but singular. Now the most primitive lungs are singular, it split later likely as animals got larger and needed more lung capacity and also needed a tight connection with circulatory system (paired). The spleen is the weird one, and likely harkens all the way back to before vertebrates existed, it predates the closed circulatory system, and develops on the midline of the body just like the spine and digestive organs. Just like how the spine is the midline dividing the nervous system into pairs the spleen divides the circulatory system into pairs.
https://www.researchgate.net/figure/Embryology-of-the-gallbladder-A-In-the-early-embryo-liver-specification-occurs-in-the_fig1_303959093
https://embryology.med.unsw.edu.au/embryology/index.php?title=Cardiovascular_System_-_Spleen_Development
https://embryology.med.unsw.edu.au/embryology/index.php/Gastrointestinal_Tract_Development#Germ_Layer_Contributions

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Can all elements be found in our body?
There are many Natural occurring atomic elements.
Can they all be found in the human body?
Is our system capable of letting them all in?
Are they all contained in our food?
Three in one.

On http://www.lenntech.com/periodic-chart-elements/human-body.htmlanguage, you find 118 elements sorted by the percent of appearance in the human body, starting with oxygen (65%) down to "very low traces of lead". There are a lot of elements which can't be found, including Osmium.
You can sort the table by other orders like name, symbol, mass, and others.

Perhaps this is more of a chemistry question than a biology question? Our body doesn't make use of all elements, as far as we know, (somewhere between 20 and 29 elements have been suggested to have some use by mammals) but it probably contains every naturally occurring element in some tiny concentration, if you measure with sufficient sensitivity. Barring obviously those which are extremely rare or unstable.
Proving a negative is very difficult - I don't know how you could say with confidence - "there are zero atoms of osmium in this body".

This question is about biology. It concerns living beings. Bio. -1


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Is it possible to grow a fertilized human egg entirely outside the woman's womb?
Many science-fiction movies (for example, The Island) show the possibility of growing a fertilized human egg cell (from the beginning to the end) outside the womb of the woman.
This means that you have to create the exact circumstances for the fertilized egg cell to develop into a human being. These exact circumstances coincide, obviously, with the womb of a woman.
Doesn't this require a woman, where those circumstances are exact, which means the only place where a fertilized egg cell can grow is the woman itself? So basically I'm saying that you need a woman (the womb is connected to the entire body) to let the single fertilized egg cell into a fully grown 9 months baby.
Well, this isn't exactly true: after development for 5 months or so in the womb, an artificial environment can take over, which is possible with current technology. But to devolop the fertilized egg right from the start is another story? Can it be done, or is it impossible (of which I'm certain, but nevertheless I ask this question)?

I believe what you're describing is referred to as ectogenesis which is essentially developing a fertilized egg inside an artificial womb until it’s able to survive outside the controlled environment. So is this possible outside of science fiction? To answer this we have to compare the stages of human reproduction and how close today's science and technology can come replicating/sustaining them.
We'll begin by dividing these stages into two groups: fertilization and development of embryo to fetus.
When it comes to answering the question of whether fertilization can be replicated in vitro or not, the answer is yes it can be done! In fact in vitro artificial fertilization (IVF) has been possible for several decades. In most cases when IVF is performed the egg is then placed inside the mother's uterus where it goes onto to develop into an embryo and then fetus. In regards to "ectogenesis" the IVF egg would be placed into an artificial womb.
In order to form a zygote (fertilized egg) to develop properly into a fetus it has to be an environment to meet it needs. In a female uterus all these needs are met but replicating them might be difficult. An artificial womb would have to be able to provide nutrients, oxygen, and channels for the development process of a fetus as well as system to expel (birth) the fetus once its development is complete. So can today's technology and science do all this? In theory yes, if resources and time where dedicated (and red tape cut) it would be possible to develop a fertilized egg in an artificial environment within the foreseeable future. There have been multiple experiment where artificial wombs were implanted with fertilized eggs and began to grow but were stopped due to legality.
I encourage you to read the following Wikipedia and motherboard articles regarding artificial wombs and ectogenesis.
https://en.wikipedia.org/wiki/Artificial_uterus
http://motherboard.vice.com/read/artificial-wombs-are-coming-and-the-controversys-already-here
*Note there is a lot of biology I did not mention regarding zygote to fetus development which is the biggest question/obstacle that ectogenesis might face

Thanks for your answer! But to make the fertilized egg grow the right way don´t the egg´s circumstances must be an exact copy of the womb, wich can only develop in the woman (and thus out of a fertilized egg cell). So don´t you need for the development of the fertilized egg something that can only spring from a fertilized egg wich developed in the womb? I can´t see how the development of a human fertilized eggshell, considering the growth from one cell to the fully grown baby, is compatible with an artificial womb made out of the conscious thoughts and hands (-made mechanics) by men. :-)

Okay, getting the egg to grow is not the problem, getting the egg to grow correctly would require trial and error. As far was matching the condition of the uterus, I "feel" would not be impossible, the reason I say this is discussion the uterus its self is very simple, it is composed of smooth muscle lined with glands . You can look at an experiment done at Cornell where a mouse was grown inside an artifical uterus to see its impossible, the cell grew but the mouse was severly deform and ultimately died before being "born".

But it´s not only the uterus that´s involved in the growth of the just fertilized egg. Also, the woman that surrounds the egg, and even more affects the growth, and that´s something we can´t imitate.


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How can my sister have dark brown eyes, while my parents have blue eyes?
Both my father and mother have blue eyes, just like me. But my sister has dark brown eyes, contrary to what I've read about the dominance of brown eye genes and recessive blue eye genes. What happened (apart from the possibility that my mother dated a brown eyed guy from which she was born, which for sure didn't happen because we both look like our father and mother; though you never know with those Italians...) that gave her those dark eyes?

A related 5 year old post.

you can visit this page it's fully explained how blue eyed parents can have brown eyed children by just - carrying the gene -http://genetics.thetech.org/how-blue-eyed-parents-can-have-brown-eyed-children

Another post.

And what would be the answer? I can't infer it from what is written there. Besides the question is about a man with blue eyes and a woman with brown eyes.

@descheleschilder The answer is that the simple "blue eyes are recessive brown eyes are dominant" explanation is wrong, because that infers that there is a single gene involved in eye color. That is not true.


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What is the maximum height of a tree?
I know there exists a huge variation in the height of trees. But what is the maximum height a tree can reach?
It must have something to do with the ability of the capillaries to transport life fluids all the way to the top. What is (are) the theor(y)(ies) about the maximum height, if there are any, and what do(es) it (they) predict?
Does it match reality?

You can refer to this link-http://www.livescience.com/14667-tall-trees-grow.html

The transport of water, and dissolved minerals, from the soil to the tops of trees is a combination of three factors. Root pressure pulls the water in due to factors related to osmosis. Capillary action helps draw it up the hydrophyllic vascular tissue. But the most important factor is due to evaporation in the leaves. This has some rather detailed aspects, search "transpiration" for details.
Although Coastal Redwoods are typically cited as being the tallest, some Douglass Firs are also in the competition. If you re seriously interested, here's a link to a Humbolt State University professor, Steve Sillett, who both studies and climbs these trees in search of the record. His book is a great read, also introducing you to the remarkable ecology near the tops of these trees. http://magazine.humboldt.edu/fall09/tallest-trees-unveiled/


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Why have people much more different cells than rice plants, while they have roughly the same number of genes?
Rice plants have about two times as much of genes in their DNA than humans have. Then how is it possible that people have much more different cells than a rice plant has?

See https://medium.com/.../human-genome-shrinks-to-only-19-000-ge...
The rice plant cell contains 30 000 genes.

Actually, rice has about twice as many genes than humans (you can check yourself on bionumbers). But who cares? It is not because two species have the same number of genes that they would look alike. Human and rice have quite different genes. Numbers in themselves do not matter.
Consider the situation where Paul has twice the number of clothes in his wardrobe than Jack, it does not necessarily mean that Paul and Jack dress up differently. Conversely, when playing poker, Paul always has the same number of cards in his hands than Jack, yet their hands may well be very different.
Generally speaking 'higher plants' tend to have way more genes than 'higher animals'. There are several hypotheses for that. Plants are more often polyploid and therefore have more neofunctionalization. Also, plants don't move. It is not impossible that they would need more genes to cope with a more varying environmental conditions.

@Remib- I know the number doesn't count, but why do half the number of genes can produce so much more different cells in the human body?  Can it be that the proteins in humans, coded for by the genes, are complexer than those in a rice plant? Or can it be that the amount of non-coding DNA is much bigger in humans than in rice plants? Or do more combinations of genes (and genes can be used in many different cells) produce more combinations of proteins which more different cells?

@descheleschilder I would say the determining factor in "number of cell types" has mostly to do with regulation of genes. If you have two regulatory genes, just "on" and "off" could give you up to 4 cell types, but having three levels of each could give you 9. There are certainly way more than 2 regulatory genes, and they can regulate each other, to the point that there is a potential for essentially an infinite number of cell types in a human or a rice plant. The question is whether it is advantageous to develop a new cell type, not the number of available genes, for rice or humans.

@BryanKrause-In that case, why can't rice plants and humans make the different cells they need (which is much bigger in humans) with much fewer, but equal amounts of genes? If the number of regulatory cells is n, then they can give rise to $\ 2^n $ cell types. So if there are 10 of those genes the number of different cells they can give rise to has already grown to 1028 (the same genes can take part in the formation of different cells). And those regulatory genes can give rise to many new advantageous cell types, depending on the varying circumstances, by turning on or of different genes.

The biggest difference though between rice plants (or other plants) and humans is that human cells contain much, much more non-coding DNA, which in my opinion is the cause of the big difference in different kinds of cells.

@BryanKrause-Are regulatory genes bound to specific genes which code for a protein, or can they regulate all genes?

If Paul has twice as many clothes as Jack, Paul can show a bigger variety of clothes. Or put them on all together, which Jack can do too. Insofar the fact that plants are non-moving, don't you think that moving creatures encounter more diversity in their surroundings? Why doe polyploidy implies more neofunctionalization?

It is not because two species have the same number of genes that they would look alike. But how can fewer genes make a living organism more complex?


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Identification of cocoon
Looks like metal and has grown lines around it. Tried to search about it but didn't find results. Hanging on 1 of my plants. Curious to know which insect is inside. Please answe4 if anyone knows

Please answer fast .....want to know

people will answer in their own time, if at all, and requesting that people hurry is not an appropriate use for comments. Improving your question will help to attract an answer. I can think of three things that will help. 1, Correct the spelling errors. 2, include the geographic details of where the cocoon is. 3, add a photo that has the cocoon in focus so that people can identify it.

Are you asking about the thing that is not in focus? Because if you are, then I suggest getting a new photo where it is. Could you add information about where you took the photo, what time of year, and what kind of plant? All of this will be relevant.

In spite of the fuzzy picture, I think it's safe to say the chrysalis is that of the Common Crow Butterfly in its shiny stage.
Here is a sharper picture:

The orientation of the chrysalis is about 180° from yours; however, the various bulges and markings match up, and the host plant looks appropriate (without identification.)

The common crow (Euploea core) is a common butterfly found in South Asia and Australia. In India it is also sometimes referred to as the common Indian crow, and in Australia as the Australian crow. It belongs to the crows and tigers subfamily Danainae (Danaini tribe).

If you want to know how I found it, I used Google Images and searched "gold metallic colored cocoon". it was right on the first page. :)

A nice LMGTFY answer! +1

@James - Teach a man to fish, and all that.


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Bimodal frequency distribution of size of protein loops

The graph of number of amino acid (AA) residues in a loop Vs the frequency of their occurrence in proteins largely follows a tending-to-zero pattern. However, there appear to be some specific number of AAs where the frequency suddenly drops, leading to bi- or multi-modality in the plot. Is there some molecular explanation for this, or is it just an artifact?
I’ve attached the figure from a paper with a different research question but the same graph(Figure 2), albeit more detailed. (The same graph can be found in Brandon and Tooze (fig.2.8).) In the paper from which this is taken “A loop structure was defined as any region between two regular secondary structures that was at least three residues in length.”

Thank you for adding the graph. I have changed the wording to remove "oscillation" which has other connotations, and "probability", as what is plotted is frequency. I have also added a definition of a loop.

A curve of this type, showing a bi- or multi-modal distribution,
  suggests two or more constituent species
  in the population. In this case this is borne out by further analysis
  in the paper of different types of secondary structure components
  anchoring the loop, the peak at low numbers of amino acids reflecting
  the loops connecting β-strands in anti-parallel β-sheets.

The second frame (B) of Figure 2 is shown below (dashed line):

Anti-parallel β-sheets are abundant in proteins, and in many — although not all — cases adjacent strands are connected by short (four- or five-amino acid) loops such as the β-turn, the β-hairpin or the β-bulge loop.
Repeating small loops are especially well illustrated in β-sheets displaying β-meander:

The β-meander motif from the outer surface Protein A
Examples in larger domains of the β-barrel and immunoglobulin type also show some larger loops.

Beta barrel of green fluorescent protein, showing loops at end of strands

Immunoglobulin domain of PDB 5IML showing β-sheet with loops connecting strands


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Plant identification: San Francisco, USA

I am taking a biology lab class and I need to identify all these plants which are from the San Francisco area.
My question is how can I find the right keyword to find their names on internet? Or can you recommend any book that I can find in library?

some pictures with more details would be great. the plants are all quit jung - which make it difficult. also some additional inforamtion about the context: it look a little bit like a peatland?  is it a kind of garden? or what is the type of landuse in your side?

Those are grow under the shade of the pine cone tree which is near by my college. I have no idea how to use the word to find them on google. Yes I can post clearly picture if you would like to help me pick some word to find them. Thanks

I'm going to refrain from giving you the answers because the point of the assignment is to  learn how to do it yourself.
You should likely start  by using a dichotomous key (likely provided by  your instructor).
You could also try  searching the Jepson California eflora or CNPS Identifying Native Plants for online keys.
Check out  the California Native Plant Exchange website if you don't know the name of the plant but know the general area where you saw it.
If you don't know what general type of plant  you have,   you should try keying  the plants to family  first  to get better search terms.  Try here.
If you don't know plant terminology  used  in  these keys,  try  "Plant Identification Terminology: An Illustrated Glossary" (Harris & Harris, 2001)

I am from another country who just move in here and  I already try all those words that you show me but still did not get how those plants look like some kind of group. That's why I try to ask more specific word.

@SiriwanLaoketkit This is not a guide to keywords for google, it was a guide to identification  key websites and books which help you identify plants, usually by a step by step questionnaire. https://en.wikipedia.org/wiki/Identification_key


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How can sequence analysis establish whether a genomic sequence is a functional gene or a pseudogene?
BLASTX of a query gene shows 5 hits in my subject, how can I find out which of these are expressed and which are pseudogenes (using DNA sequence or by sequence analysis)??

Perhaps search the EST or TSA database?

Think for yourself. What types of pseudogene exist? How do they differ from functional genes? If you do not know the answer to this search on the web. When you understand what pseudogenes are some of the answers to your question will be apparent.

There is no good single answer genes which long have been though to be pseudogenes may have function in a very narrow set of cells.
That being said, some of the best indicators are; destruction of the ORF, accumulation of C->T and G->A mutations (methylation/deamination in mammals).
Expression is probably not a good indicator, because once you start including long non-coding RNA, pseudogenes may be transcribed, but may not have a protein-encoding function (if any).
You can also measure loss of introns and a poly-A tail in the DNA sequence which is consistent with a retro-pseudogene, but that doesn't mean that the 'pseudogene' doesn't have it's own function.
Overall, evolutionary conservation is the fastest and most reliable indicator, but ultimately genetic knock-out would be required.
If you have more information about the pseudogene, there may be other useful information which could help distinguish the two.


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Why does BLAST employ local alignments?
Why does BLAST use Local alignment, not Global alignment? And when would a global alignment be useful?

This sounds a little like a homework question. Otherwise, there are too many answers, so it would be good to narrow down the question.

BLAST was devised to compare one sequence (the query sequence) with all the sequences in a database (target sequences), in particular the Genbank database(s). In 2012 Genbank contained over 3x1011 nucleotides in approx 109 sequences. So it is not feasible to do a rigorous comparison of the query sequence with each of the target sequences in the database, e.g. by the dynamic programming method, either local or global. It would just take too long. Instead BLAST uses heuristics to get the most likely best matches in a reasonable time.
The key assumptions of one of the heurists used is that any good overall match between sequences will contain some high-quality short matches, called high-scoring pairs (HSPs). (HSPs would be perfect matches of short runs of nucleotides, or high-score matches of amino acids (tripeptides) when one uses an amino acid comparison scoring matrix.) The program can make an index or library of those HSPs present in the query sequence and then just compare these (i.e. make a local alignment) in turn with target database sequences — a great time saving. So that is the basic answer to the first part of your question.
Just to quickly complete the story, an attempt is then made to use these high scoring pairs as 'seeds' to extend the alignment in either direction, and high scoring target sequences are saved and ranked.
An answer to your second question is you would do a global alignment when you were working with just a couple of sequences and had some scientific reason to believe that they were related, even though there were regions that had diverged appreciably. For example, you might be aware of key rare amino acids or nucleotide sequence motifs that should align in these regions and want to display them. Or you might want to align a protein of unknown three-dimensional structure with a related one of known structure to model it. But you wouldn't use BLAST to do the alignment, you'd probably use an implementation of the Needleman and Wunsch dynamic programming algorithm.