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What is a DNA-binding domain?
I am confused about the term DNA-binding domain. Does it mean that there are some parts of the DNA that tend to coil up? Does it happen because some proteins tend to stick around that area? Also it is my understanding that with some proteins DNA (say for bacteria like E. coli) tends to coil up. Do we know what is the approximately the size of these coils? What is a ‘motif’ in this context.

Welcome to Biology.SE!
The term "domain" in biochemistry and molecular biology is usually used to refer to a part of a protein that has a conserved structure and function, is similar between related proteins, and can generally exist or function on its own if it was separated from the rest of the protein. A DNA-binding domain is a protein structure that has a high affinity for DNA, and so binds to it when the two molecules are in the same vicinity. An example is a type of protein called a transcription factor, which binds to DNA in the nucleus of the cell (in Eukaryotes, bacteria and Archaea don't have nuclei - the DNA just floats free) and causes changes in the transcription of genes. The following image from WikiMedia shows how transcription factors work in general.

"DNA coiling" is a very generic term that describes many different things. The basic structure of DNA itself is a coil, with two sugar chains (the deoxyribose in DeoxyriboNucleic Acid or DNA) coiling around each other, and attached by nucleic acid bases. In the eukaryotic cell, individual strands of DNA are associated with structural proteins to create chromatin, which is what makes up chromosomes in the nucleus of each cell. In the first stage, naked DNA is wrapped or coiled around structural proteins called histones into a structure called a nucleosome. These then stack into a "solenoid" or fiber structure, which makes up so-called "relaxed" chromatin - regions of the genome where active transcription is taking place. If a part of a chromosome has been marked as inactive, or during certain steps in the cell cycle when one cell splits into two (mitosis), the fibers further coil into condensed chromatin, forming the typical structure many people associate with chromosomes. This image, from Wikipedia, visualizes each step in the process.

The word "motif" can sometimes mean the same thing as domain - for example, someone might refer to a "DNA-binding motif" in a protein. However, a motif is typically smaller than a domain, can occur in DNA, RNA, and proteins, and has to do with the specific sequence. A "structural motif" in a protein is something like a helix-loop-helix or a beta-hairpin turn that can appear in multiple different kinds of protein domains, and doesn't necessarily have the same exact function in those different domains, but typically has a fairly conserved sequence that is very similar. As an example, the zinc finger motif is found in protein domains that bind DNA, RNA, and other proteins.
All of this terminology can be very confusing at first, but if you stick with it it'll get easier over time. Biochemistry and molecular biology are fascinating fields, so keep up your studies!

Does "binding" mean the protein attaches to the DNA? In the figure the pink protein seems to attach to the DNA.

@anvSnMusater yes, binding means that the protein and the DNA are attached to each other, but they can separate later.

Thanks, finally, I want to ask you, does the binded protein fold the DNA?

It can, especially if it is part of a large complex of proteins, like those involved in replication or DNA damage repair.

This answer is vastly overweight. You should use your discretion in choosing illustrations. The first is especially incomprehensible. Do you really expect the poster to be able to follow it?

@David who cares? The question and answer are 3 1/2 years old, and my answer has apparently been found useful by at least 6 people, so it's not all bad. Remember, the point of Stack Exchange is not to just help the OP - in fact, that's only a side effect. The point is to assemble a compendium of knowledge in Q&A format. I link to all my sources in case the reader is in need of more details or explanation. Additionally, the meat of the answer is really contained in only three paragraphs, which I wouldn't characterize as "vastly overweight."

@MattDMo — didn't notice it was you, but there it is. That's how I see it.

Domain and motif are indeed related, but I would think that domain indicates the region in a protein (or DNA) involved in the function (be it DNA binding, catalytic etc for protein / transcription factor binding etc for nucleic acids), while motif is used to describe the particular sequence of building blocks in that domain / region. Motif is used to indicate the particular amino acids that one typically finds in the protein domain, but also to indicate the particular nucleotides in a DNA/RNA strand.

can you add some references to back up your answer? it would definitely add strength and credibility.


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Book-recommendation: Biochemistry
I need to have a book which covers following topics two may also be fine:
(a) Structure and role of carbohydrates, fats, fatty acids and cholesterol, proteins and amino-acids, nucleic acids. Bioenergetics.
b) Glycolysis and the Krebs cycle, oxidation and reduction, oxidative phosphorylation, energy conservation and release, ATP cycle, cyclic AMP – its structure and role.
(c) Hormone classification (steroid and peptide hormones), biosynthesis and functions.
(d) Enzymes: types and mechanisms of action.
(e) Vitamins and co-enzymes
(f) Immunoglobulin and immunity.

I would say that the "usual suspects" aka Lehninger, Stryer and Voet should all be fine. Go into a bookstore, have a look in all three of them and then decide. They are a bit different in their approach.

http://www.typotex.hu/konyv/sarkadi_livia_biokemia_mernok_szemmel But it is in Hungarian... :D You don't necessary find all of these terms in one book, because hormones, vitamins, immunoglobulins are related to human physiology, immunology, etc...

Sorry but I don't know Hungarian, but thanks for your reply

Lehninger Principles of Biochemistry by Nelson and Cox is quite popular and covers everything you listed in great detail except for immunology.
I don't really have a recommendation for an immunology book; I think pretty well any of them will cover immunoglobulins (they're pretty integral). My university uses Kuby Immunology by Kindt et al. Molecular Biology of the Cell by Alberts et al. has a couple chapters (some 115 pages) on the subject. As a bonus, it's an amazing reference for cell biology (which you'll need, at least someday, if you're pursuing biochemistry).

Does the book Molecular Biology of the Cell also covers topics like:
1-Structure and function of cell and its organelles (nucleus, plasma membrane, mitochondria, Golgi bodies, endoplasmic reticulum, ribosomes, and lysosomes), cell division (mitosis and meiosis), mitotic spindle and mitotic apparatus, chromosome movements, chromosome type polytene and lambrush, organization of chromatin, heterochromatin, Cell cycle regulation.
2-Nucleic acid topology, DNA motif, DNA replication, transcription, RNA processing, translation, protein foldings and transport

@Ankit Yes, it does.

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Correlation between diffusion coefficient and ligand–receptor binding?
A cell may have different types of cellular receptor for different molecules. Furthermore, the same cellular receptor may bind many different molecules (competitive ligand binding). My question is:
a) Is there any kind physical factor shared by ligands that bind to the same receptor?
More specifically, are the diffusion coefficient similar to one another in such cases?
b) Are there cases where different molecules binding to the same or different receptors on the same cell have similar diffusion coefficients?

Why the focus on diffusion coefficient?

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Can Programmable Cell Death (PCD) be engineered in a bacterium like E. coli?
I am reading a paper which says :
Messages not received after a certain time can be considered lost, as bacteria carrying them will suicide.
I even read some paper which says about PCD like this, but it just tells about a mechanism of Toxin and Anti-toxin.
My question: is there a reference which talks about genetically modifying E. coli bacteria (i.e. introducing a plasmid in it) which will cause cell death of the bacterium after a certain time. In short, we decide the life time of a bacterium after which it just commits suicide.


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Why does protein kinase C activated by different means have different effects?
I could be way off base but I think I remember learning that Protein Kinase C has some effects when activated by one pathway and other effects when activated by another. How does this happen? Is it just phosphorylated differently or what?

Can you provide some background? Protein kinase-C would do the same job (in a molecular sense) irrespective of the upstream pathway.

It's good to take a step back sometimes and look at a bigger picture: PKC got activated, but what else is being activated or deactivated by other signals at the same time?

You probably remember correctly — at least in part. The part that is missing is that protein kinase C isn't just one enzyme, but perhaps a dozen different isoforms that fall into three different classes, differing, among other things in their requirements for activation (e.g. whether they require calcium ions as well as diacylglycerol). It would be theoretically possible for protein kinase C activated by one pathway to have different effects from that activated by another if the different isoforms involved had different properties. This has indeed been suggested, although it has been difficult to establish experimentally.
The following two reviews that deal with this are about 20 years old, but may allow easier general access (and are easier to read):
Dekker, L.V. and Parker, P.J. (1994) Trends in Biochemical Sciences vol 19 pp 73–77.
Jaken, S. (1996) Current Opinion in Cell Biology, vol 8, pp 168–173.
The following quotation from the summary of a more recent and more extensive review article (Steinberg, S.F. [2008] Physiol. Review. vol. 88 pp. 1341–1378) may be pertinent:

"There is growing evidence that individual PKC isoforms subserve unique (and in some cases opposing) functions in cells, at least in part as a result of isoform-specific subcellular compartmentalization patterns, protein-protein interactions, and post-translational modifications that influence catalytic function."

One other feature of protein kinase C is relevant to this question. Most other protein kinases (which tend not to have multiple isoforms) have a more or less restricted substrate specificity determined by residues of a particular type at particular positions with respect to the phosphorylation target residue (Ser, Thr or Tyr). This limits the proteins the kinases act on to specific targets. In contrast, protein kinase C can phosphorylate target residues in a wide variety of contexts. The current model (above) allows specificity of protein kinase C for target proteins to be obtained in a different way — by the specific proteins that each activated isoform binds to, i.e. by protein–protein interaction rather than target-site context.

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What determines the physical location of differentiated cells in an organism?
Exposition:
As a little kid, I always thought of DNA as being a description of how to build an organism. For example a human DNA would have "Add two legs and two arms", a dogs DNA would have something like "put a tail here". Now, at school, I have learned that DNA codes for proteins, for structural proteins, enzymes etc. But how does a growing fetus actually know where to put the different parts of the body?

Examples:
For example, why don't I have retinal cells growing on my feet? Why is my cerebral cortex not in my mouth? And where is the information stored that humans do not have tails, or that elephants have trunks?

Summary:
What determines where different cells should be located, and how is that information stored?

I have edited your question to remove the anthropomorphic implications. Cells do not ‘know’ anything — they are not sentinent beings, and it encourages sloppy thinking to use this term, even in quotation marks. Otherwise, the scope of your question is huge — it is not my field but it would seem to cover the whole area of embryology and determination of cell fate, which is only partly understood. Perhaps someone else can point you to the chapter of a basic biology text where this is covered, but I doubt whether this question can be answered here.

Which organisms? There are several very different answer across life. nematodes and houseflies use very very different methods. For humans and houseflies you may want to look into hox genes or just embryology in general.

Cool question. As the other answer mentions, the process is very complex, and we are still learning the relevant mechanisms in organisms other than the fruit fly. But it is considerably well described in the fruit fly which merits a brief summary.
Since a lot of asymmetric (A-P axis, for our purposes) development occurs pretty early in embryonic growth, whatever drives this pole-specific differentiation must act early. As it happens, it begins as early as maternal ovum (Bicoid mRNA). Using cellular machinery (microtubules, motor proteins), these are concentrated towards one end of the egg and subsequently of the early embryo. Once such an asymmetry in the concentration is achieved, further development genes can take advantage of this patterning by being influenced by downstream signalling. Hence there is a cascade of gene activation downstream, which involve Gap genes, Pair-rule genes and several homeotic genes (see Hox genes) which are also differentially expressed along the A-P axis. They directly control patterns of the organs formed from there. Using a gradient of these genes, further patterning of organs can be similarly achieved (the retina gene would be activated only at a concentration of these genes which is found only at the top and so on).

Developmental biology is a huge field, and we are still learning a lot.
But a basic principle would be "The cells in the developing embryo develop differently depending on where they are".
We understand fairly well how fruit fly embryos figure out their head-to-tail axis; it starts with the fly ova having an asymmetrical distribution of maternal mRNAs
https://en.wikipedia.org/wiki/Drosophila_embryogenesis


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Optimum pH of Catalase
I am aware that certain organs in the body have specific pH environments to increase the activity of their enzymes. I'm also aware that enzymes only work at certain pHs due to the configuration of the amino acid in their active site and the way this is altered as the pH is changed. What I want to know, however, is why their amino acids are as they are to begin with - has it got to do with the substrate molecules they react with? Particular reference to catalase would be helpful.

Are you asking about how the amino acids of an enzyme interact with the substrate molecule with particular reference to catalase?

It would be helpful if you could answer this for me but, in particular, I was asking whether there is any reasoning behind why the amino acids of an enzyme's active site are arranged in a specific way.

The optimum pH for catalase can be found be a simple search. According to the Wikipedia entry for catalase it is approximately 7.
With the exception of extreme pHs, which can cause denaturation, the pH optimum of enzymes is often related to the ionization of the amino acid residues that participate in the reaction (and hence their pKa). Often what happens is that the reaction mechanism requires a residue to alternate between an ionized and non-ionized form, so that the optimum pH approximates to the pH of half-ionization. (This may not be the same as the pKa of the amino acid in solution, as the environment at the active site can alter this greatly.)
You need to understand ionization chemistry to appreciate this. If you do not, you could try this section from Berg et al. first. If you do, look at the mechanism of action of well-established enzymes like lysozyme and the serine proteases.
I cannot help you further with catalase. Apparently it is not well understood.

Do you have any recommendations for what to read to understand the mechanisms as how reactants reach the Transition state without a catalyst? I'm finding all sorts of information but all are unrefrenced.

@Tytoalba — Heat. But you could post on SE Chemistry (or check previous questions there) for a more comprehensive answer.

I don't prefer asking there the answers are often not backed with references. (This isn't the right place to ask unrelated questions, I just don't know how we may discuss if you are interested).

@Tytoalba — I make a point of not doing discussions on this list. In any case my chemistry is rusty. However the Wikipedia entry on activation energy — https://en.wikipedia.org/wiki/Activation_energy  seems reasonable to me. In general, if you want some of the reacting molecules to be able to adopt the transition state without a catalyst, you need to put in the energy in the form of heat. (For particular reactions there may be other factors such as pH that would help.)

From your comment:

I was asking whether there is any reasoning behind why the amino acids of an enzyme's active site are arranged in a specific way.

After the binding of a substrate to the active site of an enzyme a series of chemical reactions occur at the active site. These reactions in turn convert the substrate into product. So for these reactions to occur a specific arrangement of amino acids at the active site is necessary.
Here's an example:
In the $6th$ step of Glycolysis Glyceraldehyde-3-phosphate is oxidised and phosphorylated to form 1,3-Bisphosphoglycerate.

This reaction is cataysed by the enzyme Glycealdehyde-3-phosphate dehydrogenase. The active site of this enzyme has two amino acids; Cysteine and Histidine. The side chains of these two amino acids participate in the conversion of Glyceraldehyde-3-phosphate into 1,3-Bisphosphoglycerate.
Mechanism:

The thiol group(-SH) of the Cysteine residue reacts with the aldehyde group of the Glycealdehyde-3-phosphate to form a Hemithioacetal.Its a nucleophilic addition reaction.
Then a H+ (proton) and a H- (hydride) from the Hemithioacetal moves to the imidazole group of His and the benzene ring of NAD+ respectively oxidising the Hemithioacetal to a Thioester.
The reduced NAD+ (NADH) then leaves the active site and is replaced by another NAD+ molecule.
Finally, a molecule of inorganic phosphate attacks the thioester and forms a tetrahedral intermediate, which then collapses to release 1,3-bisphosphoglycerate.

Thus after the completion of 1,3-bisphosphoglycerate formation the active site of the enzyme gets back to its original state. By state I mean that the H+ from the imidazole group returns to the Cys forming the thiol group of Cys.

So you can see that the specific arrangement of amino acids (Cys and His) at the active site was necessary for the conversion of Glyceraldehyde-3-phosphate to 1,3-Bisphosphoglycerate, had there been some other amino acids the reaction wouldn't be possible.Even if the amino acids had a different arrangement than what is present in the diagram, the enzyme would not be able to catalyse the reaction.
References:

Wikipedia
Biochemistry, 5th edition-Jeremy M Berg

Interesting answer, but you leave out catalase completely.

Yeah actually after seeing the question I was overjoyed as I found something on this site for the first time that I could answer and cited the enzyme from which I had understood the concept. I'll add catalase to the answer soon.

@Biology Student
I found two links that explain the chemical reactions taking place at the active site of catalase. I couldn't fully understand the mechanism so could not add it to my answer. Expecting you can comprehend here are the links:
[1]: https://en.wikipedia.org/wiki/Catalase#Molecular_mechanism
[2]: https://www.researchgate.net/figure/232700780_fig1_Figure-1-The-catalytic-reaction-and-HRG-mechanism-Active-site-of-catalase-the-haem


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A new species of small bird?
This picture is take from my village in Gujarat, India. I think it is a small bird which I have never seen before. It is smaller than an Indian hummingbird and even smaller than a neem tree leaf. You can see the leaf and the flowers. That flower's diameter is maybe a half inch so you can see how small the bird is. This bird has a very little trunk like a butterfly. You can't see this in the picture, but I saw it. This bird sucks liquid from flowers by that trunk.

I have shortened your title. A good title expresses the essence of the question for readers who may be interested or able to answer, and to make later indexing easier and more relevant. Try to do this yourself in future.

When I was in Afghanistan, I saw what looked like a large moth but it flew like a hummingbird. Another soldier that was nearby me saw it too. It was the only time I have ever seen anything like it and no one would believe us when we told them what we saw. I had to google it to see if what I saw was real. The funny part is that I described it to people as a hummingbird-moth. And that's what it was called!

Great picture and great find.  But unfortunately I don't think that is a new species of bird...or even a bird at all!
It looks like a hummingbird hawk-moth, Macroglossum stellatarum.

Here you can really see the 'little trunk' (as you described it) known as a proboscis, which it uses to feed on flowers.
Fun fact: It's believed not to be a mimic of the hummingbird, but rather an example of convergent evolution.

@DhirendrasinhSisodiya If this answer addressed your problem, please consider accepting it by clicking on the check mark/tick to the left of the answer, turning it green. This marks the question as resolved to your satisfaction, and awards reputation both to you and the person who answered. If you have >= 15 reputation points, you may also upvote the answer if you wish. There is no obligation to do either.

@DhirendrasinhSisodiya And don't give up on finding new species. They're all over the place.

+1 That was a fun fact indeed! But what benefits would there be in biomimicry of a humming bird?

+1 These are cool little moths. I first saw one in Japan and was completely baffled.

I had one in my garden in the UK once - it caused much confusion for a while util I managed to get a closer look.

Image relevant to this question and answer

There are also moths that mimic bees and are active during the day (cephonodes picus)

Omg, fascinating creature! I had no idea such fat moths existed :)  Wow, what a good picture too.. The eyes make it look like a Pokemon.

@HC_ Pokemon Go has forever changed humanity's view on reality.

The words "I don't think that is " should be replaced with "that is not".

I'd also like to poimt out that I have seen a larger species of this family,Manducca quinqueimaculata,flying around in september. They can generate some heat in ther bodies.


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How many co-expressed genes would be expected in a tissue?
I am working with gene expression microarrays of tumor tissues and I want to use a program to find the clusters of co-expressed genes in order to know if some particular genes are co-expressed with another genes and which genes are those.
As I must do this for many microarray experiments and I have read that there are a lot of genes that have constant expression in a tissue, I ranked the gene by its variability (coefficient of variation) that they had in the experiments and keep the first 3000 genes to search their co-espression. Then I employed a program (a bioconductor package) to find co-expression.
Now, I was expecting to find several clusters of genes (no particular reason for this) in the experiment that I was using as example, but instead of that, I only find one cluster of co-expressed genes of about one hundred, and the others genes didn't were co-expressed.
My question is: this result could have a biological sense, or I'm making a terrible mistake in some place?, Thanks in advance.

You clustered the genes based on what?

It's really not possible to interpret your analysis when we don't know what the data is. How many samples (array hybridizations) are there? What are the conditions, do you expect a good diversity of expression profiles? Is there any indication that the data is good quality, like concordant replicates? Many publicly available data sets are small / poor quality and cannot be used for cluster analysis.

Also, you might want to check out Olga Troyanskaya's lab at Princeton, http://reducio.princeton.edu/cm/ogt  They have worked on large-scale coexpression problems for some time and provide software libraries that solve many of the basic problems.

Check the beautiful publication of Daniel Ramsköld et al. 2009, which holds the numbers for generally anticipated co-expression.
The specific level of co-expression, which applies to your scenario, will depend upon your tissue, your thresholds, and your definition of co-expression.
It you look for a co-change of some genes across different specimen (rather than co-expression), the number of genes that should change will depend upon the underlying biology (and thus prevent a general answer without considering the specifics of your specimen).

There are certain very well defined groups of genes that you would expect to be co-expressed, e.g. ribosomal proteins, proteosome subunits, splicesome components, VHATPase subunits; and each of these groups are co-expressed in different circumstances. It therefore looks to me that either your different tumour tissues (if that is the situation) are in similar conditions so you can’t differentiate these clusters, or that there is some problem with your analysis.


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How did Extracellular electron Transport evolve?
According to an on-line article at Smithosonian.com “Some microbes can eat and breath electricity”. This refers partly to the fact that Shewanella use extracellular electron transfer. Does such a different metabolic process imply a separate origin for this type of life, or, if not, how could it have evolved?

can you provide the link to the article you are referring to?

I find the down-votes of this question very negative. The poster is quoting an article in a publication of The Smithsonian Institute, which I had thought was a prestigious publication. The particular bacteria it describes a unusual, and few of the readers of these pages will be familiar with their mode of respiration. This at least makes it question with the potential to invoke educative answers. No prizes for guessing whose answer I am talking about, but I learned something I didn't know in researching it.

Prestigious publication in the above was unintended. What I meant was establishment. I have edited the question to make the provenance of the report and its specific claims clearer.

Very interesting how journalists can make something catchy out of scientific evidence. Kudos to that!

supposedly "eat" electricity

Bacteria don't eat electricity. Electricity in it's most basic form is the flow of charge (in this case ions) from a higher gradient (concentration) to a lower gradient (concentration).
So these bacteria, they utilise this flow of charge within their biological processes allowing them to survive and propagate.

if these exotic bacteria really originate from a separate genesis or just an example of how diverse life on Earth can get if given the chance?

These bacteria are not the only ones utilising electrochemical gradients to power their biological processes. Eukaryotic cells contain an organelle called mitochondria. I will not go into details, you can read that here, but eukaryotic life arose as a result of an endosymbiosis event where two organisms developed a symbiotic relationship, and the mitochondria was born, when organism A engulfed organism B. Mitochondria, also called the powerhouse of the cell, contains it's own DNA, which is very dissimilar from the nuclear DNA, which leads many people to believe that originally they came from an integration event between two different organisms. Mitochondria functions, by ways of the ETC to provide energy to the cell.
That is the dominant role for mitochondria, and it also processes an electrochemical gradient. So no, the answer is no these exotic bacteria did not originate from a separate genesis, but rather an example of how diverse life on earth can get. Believe me there are more weirder things nature has come up with, that bacteria processing heavy metal ions in their biological processes.
As stated by David, I may have created a correlation where there was none. My apologies for that. To point you the right way though,
Shewanella belongs to a class of bacteria called Dissimilatory metal-reducing bacteria, which are characterized by their ability to couple metal reduction with metabolism, if you take a look at the link you will find that Shewanella also contain a very high concentration of sigma-factors; factors which are associated with providing transcriptional robustness under environmental stress.
Coming to their origin, which is the topic of discussion here. I would point you towards MRSA here, the analogous question here is was Methicillin resistant staphylococcus aureus born out of nowhere? The answer to this question is no, this relates to the overuse of antibiotics. Here is a link from the NIH which will give you a brief history of the origin of MRSA.
Principally, this same concept can be generalized here, if you put a population (in this case Shewanella) under stress (heavy metal ions), a large number of the population will die off, but a smaller subset will develop a resistance towards the stress.
Please note, that this line of thought contains two possibilities, the first being that individuals developed the resistance with the aid of mutations in their DNA allowing them a survival advantage over the population, a popular example is the presence of the Delta32 mutation in the CCR5 gene which makes a subset of humans resistant to HIV(AIDS) infection. Did this happen in response to the HIV outbreak the world faced in the late 20th century? No, this most probably happened much earlier (In humans a mutation must move to the germline to propagate across generations) and only came to light after a significant amount of resources had been invested into HIV research. Meaning, that the mutant was already present during the diagnosis, but the selective advantages came to light after the stress response had been faced.
Therefore MRSA could have developed from an existing subset of Staph since antibiotic treatments began in the 1940s (please take into consideration that bacterial replication is faster than human, therefore time flows faster and there is no concept of germline and somatic mutations in bacterial fission). But also, it is entirely possible that MRSA existed beforehand, and that continued treatment with antibiotics resulted in the emergence of the same subset.
So no, the answer is no these exotic bacteria did not originate from a separate genesis, but rather an example of how diverse life on earth can get. Believe me there are more weirder things nature has come up with, that bacteria processing heavy metal ions in their biological processes.
The presence of the sigma factor already tells you that they share the same genesis as all other existing microorganisms on earth, and as to how they developed to gain a survival advantage in environments containing high concentration of heavy metal ions, that relates to the stress response of a population outlined above.

I find your statement that "Bacteria and for that matter all life on earth are gene machines…" as contentious and completely irrelevant to the question. I suggest that you remove it. Likewise superfluous are statements about mitochondria, as this is a question on bacteria, and even more so that they have their own DNA. You would have done better to explain what precisely the electron transfer to the metal oxides achieves in relation to metabolism. As it is, you seem to be confusing electrochemical gradient and terminal electron acceptor.

Addendum: The shoddy article that provoked this question concerns two completely different bacteria (although you would be forgiven for not knowing)
The article concerns mainly Shewanella, which is one of a number of well-known bacteria that can use metal ions as terminal electron acceptors for the electron transport chain: i.e. they donate electrons to the metal.
However the authors have also done work on completely different — and also well-known — bacteria called chemlithotrophs that obtain electrons, which they can use as a source of reducing power (analogous to electrons from light energy).
Shewanella
The question of whether Shewanella has a separate origin is easily settled by the phylogenetic similarity to other bacteria based on its DNA and its repertoire of proteins, including those involved in energy generation and electron transfer.
So, No, Shewanella oneidensis MR1 is just one of several bacteria that use final electron-acceptors other than oxygen in their respiration.
However, there seems to be a misunderstanding about the role of the extracellular electron transport in the provision of energy for the organism — people seem rather shocked by the electric current — so let me clarify the situation.
The initial source of ‘energy’ is reduction of carbon metabolites
The metabolism of Shewanella has been reviewed by Fredrickson et al. Like other bacteria it can be grown on carbon compounds which give rise to intermediates that are oxidized by NAD+ — e.g. in the tricarboxylic acid cycle — resulting in NADH. (I’m ignoring FAD/FADH2 for simplicity.) This involves the transfer of two electrons (the second is to H+) — as we remember from chemistry, oxidation is the removal of electrons. It is the NADH that can be thought to embody the ‘energy’, in so far as the reaction of its reoxidation by an appropriate electron acceptor can result in a large decrease in Gibbs free energy (see, e.g. Berg et al. 18.2).
The electron transport chain allows the free energy changes to produce ATP
Just as with aerobic bacteria such as Escherichia coli, all the potential free energy of oxidation of NADH is not liberated in one step, but in a series of steps, with smaller free energy changes. Some of these result in the extrusion of hydrogen ions into the intermembrane space, producing an electrochemical gradient which drives the production of ATP via the trans-membrane ATP synthase in oxidative phosphorylation. (It’s still oxidative phosphorylation even though oxygen is not involved.) The components of the electron transport chain differ partially from the standard one presented in text books for bacteria with a different final electron acceptor (see e.g. review by Haddock and Jones). However it is important to realize that this is where the ATP is generated in Shewanella, before the electrons get to the cell surface and have any involvement with the extracellular space.
The role of the extracellular metal oxide is as final electron acceptor
For the sequence events from the reoxidation of NADH to be completed, the two electrons have finally to be transferred to some external oxidizing agent. For E.coli it is molecular oxygen with cytochrome oxidase catalysing its conversion to water. Other bacteria use different electron acceptors, some use sulphate (which becomes reduced to sulphite) for example, although the free energy changes of these reactions will not be the same as with oxygen. In the case of Shewanella the final electron acceptor is usually Mn(IV), which is reduced to Mn(III), or Fe(III), which is reduced to Fe(II), although other metal electron-acceptors are known (see e.g. Hartshorn et al. 2009).
What about the electricity?
What’s clearly different about Shewanella is that the solid metal oxide electron acceptor is extracellular, and therefore not in contact with the multi-cytochrome electron donors in the bacterial outer membrane, unlike the diffusable oxygen or sulphate ions. Furthermore, no enzyme is involved. Hence, rather than the electrons being transfered in a reaction at the active site of an enzyme, they flow through the extracellular milleu as an electric current. The electrochemistry of this may be intriguing, but what is clear is that this is not providing any energy to the bacterium, which is certainly not ‘eating’ — or in any other way utilizing — electricity.
And evolution?
Shewanella is certainly different, and had to evolve new electron-transport components and transporters to take these components to the outer membrane (see diagram, below). But bacteria with other electron acceptors had to evolve similarly new redox components (Alberts et al. discuss this in The Molecular Biology of the Cell). Whenever bacteria have taken over a new (and often unpromising) niche, new enzymes or protein have evolved to allow them to do so. And electricity certainly isn’t foreign to Nature, nor is the interaction of bacteria with their external environment.

Multi-haem cytochromes in the outer membrane of Shewanella and reduction of extracellular Fe(III): from Fredrickson et al. 2008.
Chemlithotrophs: something completely different
The original article actually refers to two types of bacteria. The first is Shewanella, which is well studied and for which the quotation below is entirely in concord with my answer, above

Shewanella consumes electrons from carbohydrates, but it sheds them in
  an unusual way: “It swims up to the metal oxide and respires it.”
  Nealson says.

However, the title of the article is based on the following teaser:

One of Nealson’s graduate students, Annette Rowe, has found six new
  bacterial strains dredged from the ocean floor that don’t need a
  source of carbon at all, reports Powell. They can live off of
  electricity alone.

Now it is clear nonsense that anything can live — in the sense of grow — without a source of carbon (and other elements) to supply the structural components that make up the organism, but it turns out that it has been known for a long time that certain micro-organisms can oxidize metals — i.e. in contrast to Shewanella obtain electrons from metals, rather than donate them to metal ions. These are known as chemlithotrophs and often obtain their carbon from carbon dioxide, and usually use molecular oxygen as the final electron acceptor. The enzymic details of this process obviously differ between chemlithotrophs, and the down-voting of this question makes me reluctant to invest the time into researching and then presenting details of the metabolism.
The latest paper that I can find from Rowe and Nealson, published in Frontiers in Microbiology 2015, makes it clear that they are studying lithotrophs, and what is new is that they are replacing the metals by electrodes as electron donors, partly in order to find new lithotrophs which can utilize different redox potentials. Very different from the smoke and mirrors of the Smithsonian article!

Updated my answer, having finally realized that the articled quoted is about two different types of bacteria, the metabolism of which is well-known (although not previously by me). The answer is rather unbalanced, but, I hope, clarifies the situation.


text:
Do two compatible tRNA codons bond together?
Can two tRNA with complementary anti-codons link together?  For instance UUU with AAA. If not, why not?

@Ashafix has given an answer to your question which is technically correct, although it relates to artificial conditions rather than cellular ones. Perhaps this is what you are interested in. However I wonder whether you were thinking about such interaction competing with the interaction of the tRNA anticodon and mRNA codon in the cell. If so, you should make that clear so that we can provide an answer addressing that point.

Yes, tRNA can form dimers. For example it was shown that E. Coli tRNA GCC forms homodimers, i.e. two identical molecules interact with each other. In this case the dimerization occurs between the anti-codon loops (what was probably meant with UUU and AAA).
References:

Sequence and structure of naturally-occurring tRNA transcripts and site-directed variants are significant barriers to forming oligomers beyond dimers.
(Harold S. Bernhardt, Warren P. Tate, Advances in Bioscience and Biotechnology, 2013, 4, 1-16 ABB)
Anticodon-anticodon interaction induces conformational changes in tRNA: yeast tRNAAsp, a model for tRNA-mRNA recognition.(D Moras, A C Dock, P Dumas, E Westhof, P Romby, J P Ebel, and R Giegé, Proc Natl Acad Sci U S A. 1986 Feb;83(4):932-6)

A naturally occuring mutation, A3243G in human tRNA(Leu(UUR)), causes dimerization via a motif which is not in the anti-codon loop.
Reference:

Wittenhagen LM1, Kelley SO., Nat Struct Biol. 2002 Aug;9(8):586-90.,
Dimerization of a pathogenic human mitochondrial tRNA.

Link-only answers are generally not acceptable on Stack Exchange sites. The link may change or become unreachable in the future, and without a summary of what the link contains this answer would be useless. Please summarize what is in the link (don't just copy and paste) and use the link solely for reference. If you remove the link and the answer cannot stand on its own, it is not a good answer.

Thanks for the info! I will update the answer later. I thought that giving a reference to a published scientific article would be safe even if the link is dead.

The reference is fine, and while I only skimmed the article it looks like it may be useful for the OP. We (as in the Stack Exchange community) don't like link-only answers as the link may change or die, but also because it requires you to go to another site and attempt to interpret the research (in this case), which may not be possible for some readers  given the level of their scientific education. Just summarizing the abstract should be fine. One question though - it seemed like the paper only talked about dimers, and couldn't find multimers. You may want to change your answer.


text:
What determines when twining plants twine?
Some climbing plants, such as clematis and honeysuckle use their leaves like tendrils. Others, like Aristolochia use their stems. The young leaves of these plants are able to twist around slender objects. Twining stems twist around whatever they touch, be it a pole, branch, wire or chair leg. The stems will wind clockwise or counterclockwise, depending on the species of plant.
AFAIK, plants can't see or feel, but the way they climb clearly shows they have some way of knowing when to twine. How does this work?


text:
Statistical genetics: Allele frequencies that follow a Dirichlet distribution
From Foll and Gagiotti (2008) (software BayeScan). They consider a model where several subpopulation are derived from a unique ancestral population.

We consider a set of $I$ loci and let $K_i$ be the number of alleles at the $i^{th}$ locus. The extent of differentiation at locus $i$ between subpopulation $j$ and the ancestral population is measured by $F^{ij}_{ST}$ and is the result of its demographic history. Let $p_i=\{p_{ik}\}$ denote the allele frequencies of the ancestral population at locus $i$, where $p_{ik}$ is the frequency
  of the allele $k$ at locus $i$ $\left(\sum_k p_{ik} = 1\right)$. We use $\mathbf {p} = \{\mathbf {p_i}\}$ to denote the entire set of allele frequencies of the ancestral population and $\mathbf {\tilde p_{ij}} = \{ \tilde p_{ijk}\}$ to denote the current allele frequencies at locus $i$ for subpopulation $j$. Under these assumptions, the allele frequencies at locus $i$ in subpopulation $j$ follow a Dirichlet distribution with parameters $\theta_{ij}\mathbf {p_i}$,
$$\mathbf {\tilde p_{ij}}  \space \tilde \space\space  \text{Dir}(\theta_{ij} p_{i1}, ..., \theta_{ij}p_{iK_i})$$
, where
$$\theta_{ij} = \frac{1}{F^{ij}_{ST}}-1$$

(I don't have much experience with Dirichlet distributions but I understand its definition and its usefulness in bayesian statistics).
Can you please help me to understand why $\mathbf {\tilde p_{ij}}$ follows this Dirichlet distribution?
Calling the $j^{th}$ parameter of the Dirichlet distribution, $\alpha_j$, I typically don't understand why they "chose" $\alpha_j = \left(\frac{1}{F^{ij}_{ST}}-1\right) p_{ij}$ and not, say just $\alpha_j = F^{ij}_{ST} p_{ij}$ or anything else.

It looks like it is a solution to an integral equation as described in Sewall Wright's Evolution in Mendelian Populations, Section Nonrecurrent Mutation https://www.genetics.org/content/genetics/16/2/97.full.pdf.

Largely an informed guess based on properties of distributions rather than specific knowledge of statistical genetics: a beta distribution is useful for modeling the frequencies of two alleles at one locus. A Dirichelet distribution, which is a multivariate generalization of a beta distribution, would thus be useful for modeling a set of loci.
The flip side is to think of beta as just a special case of Dirichelet: if you only have one locus, beta works. If you have multiple loci, then Dirichelet.

Thanks for your answer. Yes, those are things I know about statistics (+1 anyway as a thanks). I fail to understand why typically $\alpha_j = \left(\frac{1}{F^{ij}{ST}}-1\right) p{ij}$ and not, say just $\alpha_j = F^{ij}{ST} p{ij}$ or anything else. (I will add this precision in my question).


text:
Ecological specialization and relative abundance
I am reading Evolution in Changing Environments by R. Levin but have a hard time.
Claim
At page 25, Levin says as a conclusion

The more efficient a caste at meeting the contingency for which it is specialized, the lower its abundance. This is seen in Figure 2.5b

Here is figure 2.5b It is actually a reprodcution I did in R but ressemble closely the original

W1 is the fitness in environment 1 and W2 is the fitness in environment 2. The figures comes with the following legend:

The optimal population consists of two castes in the proportions of the line segments by the Adaptive Function (dotted line). Thus castes C1 and C2 are more or less equally common, but a population of C1 and the more specialized C3 will be mostly C1.

The terms "Adaptive Function" is not really defined in the book but it basically mean the overall fitness given the fitness components W1 and W2. The terms "castes" and "contingencies" aren't accurately defined either. In his model, the population experiences only these two environments, where $p$ is the probability to be found in one specific environment. As I understand little from this book, it is hard to know what kind of a prior information I could/should give you.
Question
Can you help me to understand the above statement and why it makes sense?


text:
Could alcohol be used as an antibiotic?
I was thinking about how alcohol is used to sterilize, and I was wondering if it would be possible to use alcohol as an antibiotic? if it kills bacteria, couldn't (conceivably) alcohol in the bloodstream kill any bacteria there, and the alcohol would be cleaned out by the liver later? Or would the concentration of alcohol necessary be too high and cause poisoning?
Sorry if this has an extremely obvious answer, but all of the results I found in Google were about drinking alcohol while on antibiotics.
Could, in theory, alcohol (delivered in any way) be used as an antibiotic? If so, how? If not, why?

No.  The CDC recommends using a hand sanitizer at at least 60% ethanol.  Most preparations used in the lab are 70% ethanol.  Humans start to risk death somewhere around the 0.3% alcohol level (BAC), especially around 0.5%.  People have gone higher, but even 1% BAC would be completely useless against bacteria.  You'd be dead long before the bacteria died.  Besides, if you've got bacteria in your blood, you've got bigger problems than a simple infection.
In a pinch, though, it can be used as a topical antiseptic, as per this fun article.

Thanks. I didn't think that this would work, but I thought I'd ask some people who actually know.

Out of curiosity, what makes alcohol poisonous to humans? Is there any chemical that can inhibit that?

@Linuxios that deserves a question (well, two actually), it's not really something that can be answered in 600 characters.

Minor quibble: as elaborated in the rest of your answer, the answer is arguably "technically yes, but it would kill you".


text:
what makes our body warm?
I would think that there would so many chemical reactions going inside our body,friction produced by blood in veins, subcutaneous and visceral fat acting as heat insulators.
I was wondering to what extent different factors play a role in protecting our
body against cold.for example say blood circulation might be responsible for
creating 70% of the body heat and also a person with high blood pressure may produce more heat in his body.
also, perhaps fever or any other disease would be an exception to the normal
heat creating process in our body.just like the gonads or testes which are
cooler than the rest of the body.

Pretty much Mitochondria.

I cannot vouch for this source, but it has a basic overview of mitochondrial heating. http://education.seattlepi.com/heat-human-body-generated-mitochondria-6094.html

Specifically, we are burning the carbon-carbon bonds in the sugar molecules we ingest. You could call this oxidation; oxygen is the terminal electron acceptor in the electron transfer chain (as in loss of electrons is oxidation, and gain of electrons is reduction). The process is not 100 % efficient, so while some of the energy is captured as ATP, or reducing power, the portion that is not captured is given off as heat. Phillip Morrison has a great video of cyclists in the Tour de France where he burns a pile of donuts on a barbecue to show how much energy they burn every day.

In summary, cellular respiration and thermogenin.
Most of the energy in our body comes from cellular respiration. Cellular respiration is how ATP, the major source of cellular energy, is made from glucose. Cellular respiration generates heat mo matter what because not all of the energy from glucose is converted to ATP.
In certain cells, a protein known as thermogenin allows the protons in the cellular respiration to flow from the inner membrane to the matrix (the protons are in the inner membrane of the mitochondria as the electrons from glucose were used to pump them). This generates heat. In regular cellular respiration, the proton gradient is used to make ATP, but now, it juet generates heat.
Also, ATP can be hydrolyzed directly in brown fat cells and muscle cells to produce heat along with inorganic phosphate and ADP.

Not only respiration generates heat; pretty much all cellular processes generate heat, including the usage of ATP to drive various things. Muscle contraction is a large contribution.

@Roland yes, but isn't cellular respiration the process in which most of the heat is generated?

Respiration is certainly a large component, but I'm not sure it's the largest. Basically it amounts to how large the free energy of a reaction is and what fraction of that energy is released as heat. I don't have the numbers, but certainly muscle contraction is a large component too.


text:
How many proteins on PDB have unknown function?
I was wondering how many of the files in the Protein Data Bank (PDB) have unknown function. The only paper I can find from an internet search is this one from 2012, which I assume might be outdated. I’d welcome suggestions of how to find this information for myself.

The article cited in the question indicates that the authors searched the PDB with the term “unknown function”. There is nothing special about this — you just type in the standard search field and hit ‘Go’. I conducted a search of this type myself:
http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=91CA3A5F

Which returned 4384 structures out of approx. 149,600 in the data bank.
Of course, it is evident from the first page of the results that the number of unique proteins is smaller than this because a single study may examine different forms of the same protein.
I admit that I was surprised to find that people had spent time and money determining the structure of so many proteins of unknown function, but it appears that there is at least one blanket initiative to determine the structures of bacterial proteins of unknown functions because of their roles as potential pathogens. The idea would seem to be that they even if their mechanism of pathogenicity is unknown they could still be targeted on the basis of their structure.

There are a number of structural genomics projects.


text:
Does sunlight kill rotavirus?
Does sunlight Kill Rotavirus? Maybe freezing? Norwalk or similar. Its a practical question for bedding.

So you have bedding contaminated with rotavirus? These can live more than a week in a variety of conditions. Freezing will not do the job and sunlight won't either. I'd recommend a high temperature wash/dry cycle with bleach. Most other disinfection methods will bleach your fabrics anyways. What you should really do if they're extremely soiled is discard them, however.

According to this study, both a high temperature wash (57C) and full spectrum sunlight will kill rotavirus.
It would appear that a washer with a sanitation cycle (newer models often have a cycle that hits or exceeds 165F) would be your best bet for treating bedding.
See Figure 2.

Oof, that figure though... I presume the y-axis should be labeled "log activation"? And the units aren't FFU/mL they are plotting a dimensionless ratio of FFU(t)/FFU(0). Importantly, though, if log10(FFU(t)/FFU(0)) = -2, that's only a 99% reduction which may not be enough for OP. Still, I have trouble trusting a source that can't label their axes properly.

I think it is correctly labeled.  If you measure at time(t) and find 5 units still alive, and at beginning of experiment (t0) you had 100 units alive.  Then log10(5/100) = log10(.05) = -1.3.    A Y axis value of -2 would mean that 99% of the initial population of rotavirus was inactivated.

Point taken about 99% not being enough though.

The y-axis numbers are correct, the word "inactivation" is not. If "inactivation" is plotted it should be something more like [FFU(0) - FFU(t)]/FFU(0), where inactivation=0 means the FFU is unchanged from baseline. 5 units alive should be greater inactivation than 10 units alive but on the chart it is less. Clearly what they are actually plotting is activity.

My concern is OP's issue has to do with bedding, whereas the paper here is testing inactivation in liquid broth or what have you. I don't think the two media are comparable.

@CMosychuk Also a good point: presumably in a broth there is fairly direct access to the light, whereas with bedding there may be many nooks and crannies not exposed to direct light and therefore the broth test is probably a significant overestimation of the susceptibility to sunlight.

OP asked if sunlight can kill the virus. Apparently full spectrum light can. It is certainly valid to question the ability of sunlight to access the nooks and crannies of bedding. Personally, I found the info about heat particularly useful, as many new washing machines have a heated water sterilization setting that exceeds 57C. The slope of the line for heat indicates it likely be a 99.9 percent reduction in virus particles after 5-10 minutes of this temp (-log10 = 3).


text:
Homework question on chemically defined medium
Why would the following medium not be considered a chemically defined medium:
Glucose, 5 grams (g); NH4Cl, 1g; KH2PO4, 1g; MgSO4, 0.3g; yeast extract, 5g;
distilled water, 1 litre
I am unsure why it is not a chemically-defined medium considering all measurements and grams are given and such is required for it to be one. Therefore I am unsure why it would not be a chemically defined medium.

Welcome to Biology.SE. Your question appears to be a homework question that is considered off-topic on this site, unless you show attempts to answer your question. Please edit accordingly and give information about what you think could be a possible answer and people will be glad to help you. Additionally, please edit your title so that it gives an actual question. Otherwise your question will very likely be closed and left unanswered. Thanks. :)

Please read this before posting homework questions

Agree that this should be closed as homework, but I'll give a hint: Look at all the ingredients. Do you know precisely what each and every one is, chemically? Or is there at least one ingredient that is more ambiguous...

@canadianer And I thought my hint was too obvious :-P

@BryanKrause Haha sorry, I didn't read your comment all the way through.

For what it's worth, I think the subsequent edit by the OP shows sufficient effort for this question to remain open. I think it's clear where their confusion comes from.

I think a good example of, well, what is a chemically defined medium is helpful here (RPMI 1640).

A chemically defined medium is, according to this Wikipedia article:

... a growth medium suitable for the in vitro cell culture of human or
  animal cells in which all of the chemical components are known.

Four of the five components fit this criterion precisely, as they are chemical formulae (and of course a common name for a compound whose formula is well known).
However, even though you know exactly how much yeast extract was added to the medium, you do not know its exact chemical composition. To be sure, assays of the chemical composition of yeast extract have been run, and one could come up with approximations of it's makeup. But the bottom line is that there is no precise chemical formula for yeast extract as there are for the other components of the medium.

it does make a bit of a difference :)

The yeast extract would consume and metabolize some of the medium components and metabolic products will be formed. This new introduction of products by the yeast, whether waste materials or otherwise, is unaccounted for and changes the composition of the medium. Therefore, it would no longer be chemically defined.

This is wrong. Yeast extract is prepared from yeast cells by removing cell walls, see here.


text:
Which position do retro aldol reactions occur in (comparing glucose and fructose)?
Regarding glycolysis, my text states:

What is the biochemical rationale for the isomerization of glucose 6-phosphate to fructose 6-phosphate and its subsequent phosphorylation to form fructose 1,6-bisphosphate? Had the aldol cleavage taken place in the aldose glucose, a two-carbon and a four-carbon fragment would have resulted. Two different metabolic pathways, one to process the two-carbon fragment and one for the four-carbon fragment, would have been required to extract energy.

I am trying to understand this and I found this diagram. It seems that glucose undergoes a [4+2] retro aldol reactions but fructose undergoes [3+3]. Why is this? What determines which position a retro aldol decomposition occurs in? Is there any particular reason glucose could not undergo [3+3] decomposition?

If you have found a diagram, please present it in your question, as questions here should be self-contained. Also give details of your text. I suspect, however, that your question — when properly formulated — may attract more responses on SE Chemistry.


text:
Pyruvate as a final electron acceptor in the electron transport chain
During anaerobic respiration, why are electrons carried by NADH not transferred to the electron transport chain (ETC)? What happens is that lactate dehydrogenase reduces pyruvate to lactate, while removing H+ from NADH to form NAD+.

Why doesn’t pyruvate simply take the place of O2 as the final electron acceptor in the ETC during oxidative phosphorylation? Electrons would still be able to flow through the ETC and allow for the regeneration of NAD+, wouldn't they?

Someone else may come along later with a definitive answer but I found this question intriguing so here are my thoughts:
The standard redox potentials of the mitochondrial ETC carriers are:
NAD⁺/NADH              -0.32 V
complex I (Fe-S)       -0.27 V
complex II (cyt b₅₆₀)  -0.08 V
complex III ((cyt c₁)  +0.23 V
complex IV (cyt a₃)    +0.38 V
O₂/H₂O                 +0.82 V

Note that electron transport is carried out from negative to positive.
Now, for pyruvate/lactate the standard redox potential is -0.19 V so on the basis of this pyruvate could in theory accept electrons from complex I, but not any further down the chain. However, complex I normally transfers electrons to coenzyme Q within the membrane. The standard redox potential of CoQ is +0.04 V which is already too positive to be able to then reduce pyruvate at the membrane surface. Thus there would have to be a novel way of transferring electrons from the final FeS centre of complex I, which is within the membrane, to pyruvate. Pyruvate is, of course, soluble and is generated by cytoplasmic glycolysis, so this transfer would have be at the membrane surface that faces the intermembrane space of the mitochondria.
If such a scheme had evolved then it might be possible to achieve some proton pumping through the novel version of complex I, which would be  energetically advantageous.
Another complication is – assuming that a complex I with pyruvate as electron acceptor had evolved – how would the cell/ mitochondrion regulate electron flow during aerobic respiration? Presumably the pyruvate-accepting version of complex I would have to be kept inactive somehow until needed.
Clearly it is much simpler to have a soluble lactate dehydrogenase to deal with the pyruvate and regenerate NAD⁺.

Summary Answer
In anaerobic respiration the free energy change of the reoxidation of NADH by pyruvate is less than would be required to phosphorylate a molecule of ADP to ATP. The purpose of  the electron transport chain is to harness the much greater free energy change in the oxidation of NADH by molecular oxygen. So pyruvate can neither “take the place of O2 as the final electron acceptor”, nor would there be any point in modifying this complex machinery just so that it could be used by pyruvate to regenerate NAD+ when a single cytoplasmic enzyme (lactate dehydrogenase) will do the job.
More detailed numerical answer
This answer is taken from section 18.2 of Berg et al. and involves calculations of free energy changes from the redox potentials of the different half reactions and their relationship to the free energy of hydrolysis of ATP. It is worth careful reading, but I will summarize the key points.

Both pyruvate and oxygen can oxidize NADH, but the concomitant Standard Gibbs Free Energy change is very different in the two cases. This is the crux of the matter.
The standard redox potential for NADH → NAD+ is +0.32 V
The standard redox potential for Pyruvate → Lactate is –0.19 V
The standard redox potential for O2 →  H2O is +0.82

Combining these half-reaction redox potentials in the two oxidation reactions and then converting to standard free energy change (ΔG˚ʹ):

Oxidation of NADH by Pyruvate: ΔG˚ʹ = –6.0 kcal/mol
Oxidation of NADH by Oxygen: ΔG˚ʹ = –52.6 kcal/mol

But ΔG˚ʹ for ADP → ATP = –7.5 kcal/mol
So it can be seen that the energetics of the oxidation of NADH by pyruvate do not yield enough energy to synthesize even a molecule of ATP, never mind the approx. 3 that are obtained from oxygen. The electron transport chain is a device for breaking up this latter oxidation reaction into stages so that the free energy change can be used for generating the proton gradient that is used to generate ATP. It can only work with a powerful enough oxidizing agent.
The oxidation of NADH by pyruvate is useful, but only to regenerate NAD+ to allow glycolysis to continue and generate a smaller amount of ATP by substrate-level phosphorylation made possible by the glyceraldehyde 3-phosphate dehydrogenase reaction. For this oxidation only a simple enzyme, lactate dehydrogenase is required. There is certainly no reason to transport the pyruvate into the mitochondria (assuming they exist — think erythrocytes), which process, though incompletely understood, may well have an energetic cost.

It would be nice if the person who voted my answer down explained why, especially as it is correct. Can't handle numbers or thermodynamics, perhaps?


text:
How does aminoacyl-tRNA synthetase recognize different tRNAs?
There are about 20 aminoacyl-tRNA synthetases, one for each amino acid. Each aminoacyl-tRNA synthetase has a binding site that recognizes a specific amino acid, and other binding areas that recognize a particular tRNA through unique identity sites at the acceptor stem and/or anticodon loop of the tRNA.
When there are different tRNAs for the same amino acid, the aminoacyl-tRNA synthetase that recognizes a specific amino acid must also recognize the set of tRNAs that can be charged with that amino acid. Given that all tRNAs have different anticodons, how does the enzyme achieve the aforementioned task?

https://www.ncbi.nlm.nih.gov/books/NBK22356/#A4154

like you already said: each aminoacly-tRNA synthetase has 'binding areas that recognize a particular tRNA through unique identity sites at the acceptor stem and/or anticodon loop of the tRNA' - the anticodons only thing that are needed/used for the recognition

You give the answer in your question:

binding areas that recognize a particular tRNA through unique identity sites at the acceptor stem and/or anticodon loop of the tRNA.

The point is that aminoacyl-tRNA synthetases that recognize tRNAs with different anticodons have to supplement any partial codon recognition with recognition of common features elsewhere, in particular the anticodon loop. Unfortunately this has evolved on a case-by-case basis and there is no simple ‘code’ one can refer to.
Thus, Berg et al. (Chapter 29), in discussing  threonyl-tRNA synthetase, write (my emphasis):

As expected, the CCA arm extends into the zinc-containing activation
  site, where it is well positioned to accept threonine from threonyl
  adenylate. The enzyme interacts extensively not only with the acceptor
  stem of the tRNA, but also with the anticodon loop. The interactions
  with the anticodon loop are particularly revealing. The bases within
  the sequence CGU of the anticodon each participate in hydrogen bonds
  with the enzyme; those in which G and U take part appear to be more
  important because the C can be replaced by G or U with no loss of
  acylation efficiency.

The four codons for Thr are ACN, so in this case recognition of two bases of the anticodon will identify all tRNAs.
A diagram from Berg et al. showing the multiple interactions in threonine tRNA-synthatase is shown below.

Hi David, thank you for your answer.     I was wondering, when different codons code for the same amino acid, it is because these codons differ in the 3rd base, not the first. So wouldn't the interactions between the first 2 bases of the tRNA anticodon be more important than the 3rd base? I am operating under the assumption that each enzyme recognizes a specific amino acid, and the set of tRNAs which the amino acid is supposed to be attached to, but the anticodons of this set of tRNAs differ in the 3rd base.

@JonathanSmith — The confusion here is caused by using first and third, rather than 5' and 3'. Thus the codons for threonine are 5'-ACN-3' (with N, the ‘wobble’ base), whereas the tRNA anticodon that Berg et al. refer to is, in my opinion, best written 3'-UGC-5', so that the complementarity to the codon bases is evident. (Strictly they are correct to write CGU, as the direction is assumed to be 5' to 3', but in a text book every effort to make things clearer is appreciated by the reader.)


text:
Beetle with long, slender iridescent green body and orange legs
I recently saw this beetle while on a trip in central Texas, USA (in a rural area just before sundown). The body was about 2-3 inches long (compare to nearby chair leg and floorboards) and had a long body. It was very vivid green, and its upper legs were very bright orange (which made me wonder if this is aposematism). Its antennae had very uniform half-circle arcs (instead of the uneven parabolic shape often seen in cockroaches and similar common insects) and didn't seem to bend besides being rotated ~5 degrees up and down.
It carried itself pretty high off the ground, perhaps half an inch between the belly and ground-level. It seemed to move fairly fast, but not as fast as a cockroach. It didn't fly in the few minutes I observed, and didn't seem like it could fly since the shell appeared solid, but I might have mistaken well-fitting sheaths for fused ones.

What is the most likely species? Is it poisonous?

I can't see the antenna well, but they look long. Could it be some sort of longhorned beetle?

@user137 For anyone wondering, the antenna were quite long - all of the blurry blackish line is antenna. Based on my recollections, if I pulled on them and straightened, they would be between 1.25 and 1.5 times the length of the beetle's body - consistent with your answer as well!

With this image, I've had one bite me, after maybe 6 hours a blister began to form. I believe it's a blister beetle.

I'm going to guess it's an Plinthocoelium suaveolens, based on the image found here, which I show below:

I found this link through a Texas beetle page here and is the best I can do from the image provided.


text:
How to map the Gene name to its Gene Symbol?
I am learning in Gene data lately so I apologize for the silly questions in advance. I read a paper for a cancer on human which found some important genes. For example, the paper listed one of genes in its name as
gene1:    chromosome 12 open reading frame 52

May I know how I can find its corresponding gene symbol as
C12orf52

Is there a mapping table or  tool I can use ?
Thank you very much,

What species are you interested in?

Unfortunately, protein and gene name mapping is one of the most annoying problems in modern computational biology. There is no surefire way of doing this. Especially from hopeless gene names as the one in the paper you cite. Here are a few services you can try though:

General, text search, useful if you have a gene description (as in the case described in your question):

NCBI Entrez,
UniProt search

Mapping servers, useful if you have an actual gene/protein symbol/name (e.g. P53_HUMAN, AF240684, NP_001119585 etc)

UniProt ID Mapping
DAVID Gene ID Conversion Tool

“one of the greatest problems” – uh.

@KonradRudolph, you disagree? Believe me it is. I don't mean problem in the sense of a scientific problem but of a technical one. Each database often uses its own identifiers, the identifiers change over time, as does the sequence as errors are corrected. For the list of ~15000 proteins (UniProt) I am working with, on average 1-2 identifiers change PER WEEK. Correctly mapping the names between the various databases and other sources of information I use has been the great headache of my Post-Doc.

Well, I agree that it’s a nuisance but we have stable identifiers (= don’t change) and services to translate between the different ones. It’s a solved problem (in that it may still require manual work, but not intellectual work).

@Konrad, unfortunately, the stable identifiers are only good if your input data is using them. If you have to combine interaction data from 15 databases, each of which uses a different ID schema (RefSeq, GIs, UniProt, HUGO, Flybase, Wormbase etc) the identifiers become a very real problem. The translation services are often buggy (UniProt, for example, was not creating unique IDs for each job submission, and was returning my queries mixed up with somebody else's!), limited to certain species or ID types. It may indeed not be an intellectual problem, but it is a very real technical one.

Just use a genome database such as Ensembl. Paste your gene name into the search box and hit “Go”. The first hit in the result list is what you’re searching for.

It worked. But I am still configuring out how to input a list of gene names not only one at a time.

If the original source used the official human nomenclature, you can search the HGNC (HUGO Gene Nomenclature Committee) site.


text:
How is deviated nasal septum related to cold
I have a deviated  nasal septum and I always suffer from  common cold I was just wondering how a deviated nasal septum can be the cause for chronic common cold

Question: What makes you think it's the deviated septum instead of different cold strains?

I am not sure but I was told by a doctor that I have deviated nasal septum and he suggested for and operation

Nasal septum deviation is a condition where the cartilage which divides the nasal cavity into two nasal passages isn't centrally aligned, making one of the nostrils smaller and thus obstructed. Now, in our nose we have something called mucociliary clearance and that is the mechanism getting rid of unwanted particles and pathogens that get into contact with the mucous membranes in the nose.
Studies show that in individuals with a deviated septum the nasal mucociliary clearance time is slower than in individuals whose nasal passages are symmetrical. From this information one can conclude that the particles and pathogens that you inhale are getting to spend more time inside your nasal passages, thus giving the pathogens a better chance at striving and giving you sinusitis.
By looking at the information above you could think that the connection between nasal septum deviation and chronic sinusitis is clear. This literary review however states that the correlation between a deviated nasal septum and having chronic sinusitis is still unclear.


text:
Evolutionary explanation to why we have such large memory capacities?
The scientific consensus is that no one ever fills up their memory capacity by learning facts and so on, even in the information age.  My question is therefore, is there an evolutionary reason as to why we have evolved to have such large memory capacities, when we never come close to filling it up?

@Chris didn't you answer your own question in a way? if we did use our entire memory capacity, that might provide evolutionary pressure to select organisms with greater capacity. that's just speculation on my part though.

@JeffZemla, what you say makes sense, but we would evolve to have memory capacities that we would only just not be filling up.  But we evolved our memory capacities thousands of years ago when there was much less to remember than today, and even in the information age of today, we still don't come close to using it up.

See my comment here, increased memory (or at least brain and head size) has a cost. Vaguely, I think that the processes that led to our abnormal intelligence may have led to high memory as a side effect.

"But we evolved our memory capacities thousands of years ago"  RED FLAG

We don't have large memory capacities.
If anything I would have asked the opposite, why is our memory so bad and unreliable considering how large our brains are. Even with this gigantic brain we struggle to remember a few phone numbers. Here's how our short term memory compares to monkeys: https://www.youtube.com/watch?v=zsXP8qeFF6A&ab_channel=BBCEarth . I have no explanation as to why humans are so bad at this, this amount of data should be nothing for a brain of our size.
As for long term memory, I'm not really convinced it is that large really, it seems to me people in general in ten years.. have forgotten pretty much everything. Occational glitch.. occational stuff, and even that is usually vague and full of wrongs.
And when people cram for exams.. take the best students ten years later and see how much they still remember, it will be just a tiny fraction.
What do you mean by "filling up their memory capacity"?
Are you expecting some sort of a state where the persons hard disk is full and nothing.. nothing new can be learned? That state doesn't make any sense, the brain is always deleting from memory plus it would make more sense to have the memory slowly deteriorate, rather than fall off a cliff into no functionality at all.
We don't remember anything. We always feel like we are going to remember the now for so long and all but we don't. And we have this bias because we don't remember what we don't remember, which is nearly everything.

Can you summarize the contents of the youtube link? That video is not accessible (it's a good practice to summarize links even if this were not the case).

that monkey is trained and the people were not. thats the difference

Maybe. Not sure. I have heard humans have a short term memory of 5 to 9 units. And that cannot be trained up. Its just a constant. But maybe there could be some way around that. Would be cool to have a competition where all lifeforms are allowed. And see the best, of humans.. monkeys... computers.. whatnot. and in a bunch of different sports/games. Could learn a lot about who we all are.


text:
Organize sequence database
I recently took up the task of organizing the sequencing database for a research project. I am still quite unsure of which database type I should use for this. Some advices/recommendations would be wonderful.
This research project is more like a class where students are taught how to sequence a piece of plasmid via Sanger sequencing method, with paired end primers. For each plasmid there will be two entries (~1kbp each). Then the students would BLAST the sequence, mostly to see if there is any close match with certain related organisms.
The main purpose of this database I'm creating is to monitor the sequencing progress, as well as to single out the samples that need to be redone. So far, the record-keeping is not exactly accessible, hence the need for re-organization. Additionally, the students would need to be able to view their own results and enter the BLAST results themselves. The last condition seems to necessitate a web-server type of thing that the student can connect to enter their information.
The total number of bacteria clones containing plasmids are ~18k, which means there will be ~36k entries in this database. It would be great if there is anyway to manage the trace files of the entries, or if not, I think I can add a column for the file path.
Is there a database management program that is appropriate for organizing sequence and trace file, with easy access for data entry by multiple users? It would also help if the program don't have a high maintenance need.
Disclaimer: I have very limited knowledge with database structure, having only taken an online intro to database class. About programming language, I am still learning Python. This project is a way to force myself to learn more.

I think this has more to do with the informatics end of it rather than the biological one.

I am afraid this is off topic here. That said, there is nothing special about managing sequence and trace files. They are simply text files like any other. Have a look at phpMyadmin, it should do exactly what you need.

Like it says below, text files should be good enough, but make them in fast format. If you haven't already, look at BioPython - it will provide a way to feed your text files into BLAST searches at NCBI.

Thanks for your suggestion, I will try that out. On the other hand, I was unsure which site to post.

Normally we ask that bio-informatics questions have a strong biological component to the question, this doesn't seem overly apparent here.


text:
Hearing system as in visual system: exists well also - in protecting the inner mechanical parts of both sensing systems - a similarity?
I prefer answers, not just discussing.
In the mechanical part of the human eye the control system to protect for overload of the diaphragm in the iris with a strong coupling to the light intensity that falls on the retina has his place in the visual system as close as possible to the light source in the chain of control devices of the human visual system. The iris is disk-shaped and consists of two muscles. Like a diaphragm for light, the iris regulates how much light comes into our eyes. In bright conditions, the muscles of the iris limit how much light comes in. In lowlit conditions, the muscles of the iris increase the amount of light comming in.
Basic hypotheses is that the protection device in mammalian human hearing system is based on similarity as in the visual system and therefore should well also be using similar protection tools as used in the visual system and should well also be placed in the chain of control devices as close as possible to the signal source, as an experienced system engineer will always place a protection device in the chain of control devices as close as possible to the signal source.
Exists such an continuous functioning simalarity analogue in the protection system for sound signals ?
Both the iris in the eye (two muscles) and eardrum+ossicular chain in the ear (two muscles): in protection.
Exists that similarity ?

I'm not sure what the question is, yes the ossicular chain is believed to have a function as 'overload protection' - but I feel you're aware of that already.  Could you clarify at all?

The cooperative functioning of the eardrum and ossicular chain attenuation can be regarded as in this schematic drawing of the ear as an externally activated spring-mass system. Fig. 2.
Ossicular chain and eardrum function, together operating as a continuous sound reduction mechanism for changes in the strength of the offered signal. The tympanic membrane and the ossicular chain can be seen as a spring-mass system with amplification facilities, like it is shown in this figure.
The combined action of the ossicular chain and the eardrum is hypothesized to provide for both permanent volume control of the input sound and for overload protection. The stapedius reflex, evoked by sudden strong sound signal, cannot be seen as anything else than an extreme manifestation of the very mechanism that the schematic drawing of the ear as an externally activated spring-mass system propose.


text:
Distance between species
Is there an on-line database that will enable one to find the genetic distance between two species?
I'm vaguely aware that there are various metrics used that may give different results, but I'm looking for a database that can be used to derive any of these metrics.

Unless someone has already done the work to determine genetic distance between the two species you're interested in, unfortunately the answer is "no, there is no such database".  If representative members of the two species have had their DNA fully sequenced, any of the relevant metrics (e.g., those described in Wikipedia https://en.wikipedia.org/wiki/Genetic_distance) can be used to calculate a value for the genetic distance.  But it's important to keep in mind that "genetic distance" is a pretty vague notion when talking about different species.  There are all sorts of epigenetic factors and gene rearrangements that can play important roles in determining the developmental and phenotypic differences between species; and those factors won't show up in most methods for calculating genetic distance.


text:
Is there a comprehensive life science techniques/methods database?
There are so many techniques/methodologies in the life sciences that we can use to interrogate interesting questions. The thing is, most of us are completely unaware of the available methods we can employ. Rather, we go with the techniques we are familiar with or that are popular in our subdomains at the time. But that's pretty limiting.
So I'm wondering... we have databases for everything else... is there one for life sciences techniques/methods? Something like this could be immensely helpful in experimental planning. In particular, I think a comprehensive database would help scientists break outside of their spheres of familiarity and to employ less known (but potentially illuminating) methods to their questions.
I know there are journals that publish protocols and methods, but they are fragmented and don't encompass everything.
Does what I'm looking for exist? If not, how might one go about creating such a tool?

There's Benchfly, which is a video-based protocol library:
http://www.benchfly.com/video-protocols.php
There's also JOVE, which is a peer-reviewed video journal that sometimes covers protocols:
http://www.jove.com/

Thanks. I knew about JOVE but not Benchfly. These looks good. By database, I was thinking something a little more 'smart' in that it would help you select experimental techniques based on various parameters that one might set. JOVE and Benchfly are broken down at a very high level (categories like chemistry or biochemistry) but they don't have much more metadata that would facilitate technique selection. Perhaps a future project for me :)

There is also protocol online, but without tags, only sorted by category. It could nevertheless be interesting.

My personal favourite is OpenWetWare. Think wikipedia for scientific protocols and an open access lab notebook.
There's a problem with this things. Despite the common stereotype of scientist being open and good at sharing, my experience is the opposite. Many laboratories are not good at all in sharing their techniques/secrets. They will share the basic stuff that you can find online, no problem, but that's about it.
Seems they're afraid that everyone's else after them, trying to scoop them. I have suggested OpenWetWare to some other labs and they refused for that same reason. Even though some will use it to find protocols, they don't see a reason to share back.

you can use something like https://www.synbiota.com/ where you can store and share your protocols with collaborators. If you make your project open, then anyone in the world can view your protocols.
The nice thing about this is you can reference actual experiments that made use of the protocol (and literature) and this gives better context and understanding about the protocols...

Looks like it's dead now...


text:
PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?
I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors.  I do this by predicting the location of Hydrogens on residues and then calculating how far these Hydrogens are from aromatic rings.  If a certain Hydrogen is <7.0 Angstroms from a certain aromatic ring, then I take it under consideration: I form the N-H vector, which is the vector created by the Hydrogen under question and the Nitrogen in the backbone of the residue that the Hydrogen belongs to.  I test that this N-H vector is pointing toward the plane of the aromatic ring, and I also test that the point of intersection between the plane of the aromatic and the N-H vector is within 6 Angstroms of the center of the aromatic ring.
If all of these conditions are met, then I consider it a Hydrogen bond between the Hydrogen and the aromatic ring.  However, my data must be incorrect, because I am seeing situations where a Hydrogen is < 1.0 Angstrom from the plane of the aromatic.  Atoms should not be getting that close to each other.
I thoroughly tested my method by hand using an example situation where my code identified one of the sidechain Hydrogens on an ASN is 0.3 Angstroms from the plane of the aromatic of a TRP.  Unfortunately, I could not find any bugs.  You can find a PDF of this verification here.
Any suggestions on how my method might be flawed would be greatly appreciated.

Constructive criticism is far more useful than a down vote.

Try looking at the structure in question using a program like Chimera or PyMol, so that you can see how these programs interpret the direction in which the hydrogen should be pointing.

if you are using NMR structures you might be making the mistake of using several superimposed structures - it would be nice to develop with x-ray structures at less than 2.0 A resolution for starters.
Some of the models at low resolution can be sloppy, but submitted after 1994 or so will not have any center to center distances as that's when the x-ray structures used molecular models rather than just electron density rigorously and wierd steric violations in the structure should be rare.
Still, this might not be wrong - the hydrogen might be pointing right into the aromatic ring's center.  This has been observed quite a bit.  In such a case, the atom to ring plane distance might be very small.
You only need to worry if the center to center distance between atoms is less than the vanderWaals radius.   I would filter for atom center to center distance and see if you see violations.

Excellent idea.  Indeed, when I test for the distance from the Hydrogen to the center of the aromatic, I do not find any situations where the Hydrogen is within 1.0 Angstrom.  Indeed, situations where the Hydrogen is within 2.0 Angstroms is rare.  As for the NMR consideration, I did take care of that.  My parser successfully parses all of the NMR's MODEL's, and then it throws out all but the first one for the sake of this project

Now, I am left with only one problem: I expected to see most Hydrogen bonding situations between aromatic rings and sidechain Hydrogen donors.  To the contrary, I am seeing far more Hydrogen bonding situations between mainchain Hydrogens and the aromatic ring.  Can you think of any reason why?  I would expect the large backbone structure to be unable to get near to the small aromatic rings.

Glad you had already worked through a lot of this.  I would tend to think that main chain h-bonds will be selected for more strongly as the sidechains tend to change very easily.  Sidechains also tend to form stronger (i think stronger) aro-aro or pi-aro interactions and so there may be a tendency for important h-bonds to not from as readily.  Selection arguments are hand wavy, but maybe you can think of some clever stat test for this.


text:
Looking for a database of plant features
To perform some private data science experiments I am looking for accessible information on morphological plant features (tabular information would be best). Crawling the web I found many websites with limited more general description and a lot of information on location and population data.
Do you know a website, institute or person in possession of such data and willing to share it? Since I am located in Germany my main interest is in the local flora, but any other would also do the job.

-- Traits --
TRY
TRY is a Plant Trait Database. More formally, it's a network of vegetation scientists headed by DIVERSITAS/IGBP, and the Max Planck Institute for Biogeochemistry, providing a global archive of curated plant traits.
BioTraits
This is an online resource for empirical data on how biological traits respond to environmental drivers such as temperature, light, and salinity.
Nate Swenson
Nate and his collaborators have compiled a ton of traits for species all over the world (though focused on the tropics).
Coyle et al. 2014
Appendix 2 of their 2014 Ecography paper lists primary literature sources and publicly available trait databases they used to examine 3 traits: leaf nitrogen, seed mass, and wood density.
-- Images --
Morphbank
An international Web database that contains thousands of high-resolution photographs and other images of plant and animal specimens.
Botanical Images Databases
This site provides dozens of links to databases containing plant images. There are also regional databases provided (e.g., Pflanzenphotos.de).
Botany.ch
This site contains both text sources (e.g., lectures and essays) as well as links to morphology picture databases (e.g., Botanical Image Database of the University of Basel).

See also FAO Online Catalogues for a number of morphological sources in both English and German.

There is the TRY database of plant traits:
https://www.try-db.org/TryWeb/Home.php


text:
How to detect Single Nucleotide Variants (SNVs)?
This image is obtained from this paper.

The description of this image is as follows:-
DNA-sequence reads from a tumor sample are aligned to a reference genome
(shown in gray). Single-nucleotide differences between reads and the reference genome indicate germline single-nucleotide variants (SNVs; green
circles), somatic SNVs (red circles), or sequencing errors (black diamonds).
(a)
In a pure tumor sample, a location containing mismatches or single
nucleotide substitutions in approximately half of the reads covering the location indicates a heterozygous germline SNV or a heterozygous somatic
SNV - assuming that there is no copy number aberration at the locus. Algorithms for detecting SNVs distinguish true SNVs from sequencing errors by
requiring multiple reads with the same single-letter substitution to be aligned at the position (gray boxes).
(b)
As tumor purity decreases, the fraction
of reads containing somatic mutations decreases: cancerous and normal cells, and the reads originating from each, are shown in blue and orange,
respectively. The number of reads reporting a somatic mutation decrease
s with tumor purity, diminishing the s
ignal to distinguish true somatic
mutations from sequencing errors. In this example, only one heterozy
gous somatic SNV and one hetererozygous germline SNV are detected
(gray boxes) as the mutation in the middle set of aligned r
eads is not distinguishable from sequencing errors.
This is my understanding below. Am I correct?
There are multiple reads that are aligned such that for a given location in the reference genome,(here fourth), if approximately half or more of the reads covering that location has a single nucleotide mismatch with the reference genome,then it is a heterozygous SNV.
Eg:-

Please add the paper you mention as a valid link.

Also, cross posting to other platforms is very poor form.  It's not nice to make someone on biostars take the time to answer you when you already have answers here.

Your link doesn't link to the paper, and you seem to be ignoring half of what the image is trying to get across.
The point is that since tumors are heterogenous, you very well might have only 40% of the cells heterozygous for a particular SNV, which means it would only be observable in 20% of the reads.  But if multiple reads with different start sites show the same SNV, it's likely to be real.  If coverage is so low that you only get one read showing a real SNV, you won't be able to distinguish it from noise.

The existing answer is correct, but I want to expand on this a bit.
In the ideal world, a tissue sample will be completely homogenous (every cell has exactly the same genomic DNA with 0 differences), DNA sequencing machines will make 0 mistakes, and sequencing experiments will sample each portion of the genome (evenly) to a deep level of coverage. In this ideal world, distinguishing heterozygous SNVs from homozygous SNVs is trivial: for homozygous SNVs, 100% of the reads aligning to the position of interest will have the same nucleotide that differs from the reference; for heterozygous SNVs, there will be a perfect 50%/50% split between reads that match the reference and reads that match the alternate nucleotide.
The big problem is that none of these 3 ideals are true in the real world. Sequencing experiments DO NOT sample the genome evenly, so some regions have many reads mapping (we say these regions have "high coverage") while other regions have few reads mapping ("low coverage"). Also, DNA sequencing machines DO make mistakes, on the order of 1% for Illumina machine and 10-30% for long read sequencers like PacBio and Oxford Nanopore. Since sequencing errors are random, they're usually fairly easy to distinguish from real genetic variation, but only in regions of medium
 to high coverage. Finally, we cannot always assume that all of the cells in a sample will have identical DNA--this is ESPECIALLY true with tumor tissue.
For all of these reasons, we cannot distinguish heterozygous SNVs by simply requiring that exactly 50% of the reads mapping match an alternate nucleotide. As swbarnes2 states, it might be much lower than 50%, but with sufficient coverage you can make a confident decision.


text:
Can cancer grow forever if supplied with unlimited resources?
If somehow a human could give a tumor unlimited resources, would the cancer grow forever?  It seems like it would until it gets so large that it physically affects vital organs.  Is what would likely happen?

Yes. The very first cells used to study cancer are still around (HeLa Immortal Cells - Named for the subject Henrietta Lacks) and are basically immortal as long as they're fed.
As for tumors, whether cancerous or not they most definitely can continue to grow until they become a serious medical issue (WARNING: GRAPHIC - 3 Largest Tumors Recorded). One of the largest recorded tumors was 300lbs (~140kg) in a woman's abdomen that sprouted off of an ovary. They had to operate with her laying on her side, otherwise it would have crushed her abdomen and killed her.
Not all forms of cancer are immortal or produce large tumors (the 300lb tumor was benign), but it's definitely within the realm of plausibility.

Well, there's evidence emerging that the bulk of tumors may operate aerobic metabolisms more than normal cell respiration because of the lack of blood. I'd never use the term 'Cancer' on its own because there's about a thousand different types, and while all have regulatory mechanisms gone awry - saying they all grow when fed is also wrong. A thyroid cancer I read about recently also couldn't elongate its telomeres - still potentially fatal, but definitely 'mortal.'

not all cancer cell lines are immortal either.  But in some cases, in a liquid culture they appear to have unlimited growth potential.

@leonardo In my understanding most cancer cell lines are in fact not immortal. When they found that HeLa wasn’t dying they had in fact already been searching for an immortal cell line for quite some time without success, and finding HeLa was a big surprise.