text:
Why are certain animals much much bigger than other ones?
If you look at the following image:

The Argentinosaurus was the largest dinosaur that ever existed. If dinosaurs came through the process of evolution, and evolution is small changes in DNA and/or mutations, how can certain species by immensely bigger then others?
Even consider the blue whale. Why is it so much bigger then other  whales. None of the others even come close to it, and same as the Argentinosaurus.
I understand if some are "a bit" bigger, but this dinosaur was the length of 3, and really the question that I want to ask is that, can evolution really make someone/something that much bigger then it's kind?

can evolution really make someone/something that much bigger then it's kind? Downvoted and tempted to flag for closing as "Unclear what you're asking".  Obviously evolution can make bigger animals, because it has made bigger animals. What is the question here? Are you asking if titanosaurs were created rather than evolved? Are you asking how dinosaurs could be so large?

Could anyone please correct the typo in the last sentence: then should be than

Why there are so many big dinosaurs
In evolution there is something called preadaptation or exaptation that is adaptations that have benefit in one way that happen to have another benefit after another adaptation occurs. Consider the avian breathing system which evolved in small ground running animals turns out to also make their breathing work at high altitude, this was not part of the conditions the adaptation evolved in/for but is a side benefit that is exploited later. Because there are multiple solutions to an adaptive problem and evolution has no foresight, some groups will just happen start in a better position anatomically to evolve large size.
Compared to mammals dinosaurs start out with better preadaptations to large size. mammals have a lumbar region in which all the weight is supported only by the spine while dinosaurs have ribs from the neck all the way to the pelvis, this means the torso is far more rigid, if you grow very large this helps distribute weight more efficiently. The avian breathing system (in theropods and sauropods) scales better and doesn't loose efficiency as fast as the mammalian system, air sacs allow them to better compensate for the large dead air spaces caused by large size. Air sacs also allow bones to be larger for the same weight, sauropod bones are mostly hollow where as mammal bones are either solid (or filled with something just as heavy) so if they were the same size the mammal bones will be significantly heavier. Now this is not to say dinosaurs are completely superior, live births is a big advantage for large size, but the simple anatomical advantage dinosaurs start with just make achieving large size far easier.
Why size and fossilization vary
As for why animals vary in size it is the same reason they vary in so many other respects, different solutions to the same problem, how to get your genes into the next generation, the same factors that favor different diets or anatomies can favor different sizes. A rat and an elephant are drastically diffrent is size but both are successful body plans. You are mistaken that nothing comes cclose to these animals it is just that the ones that do are dead (in the case of whales) or didn't leave fossils, keep in mind only the tiniest sliver of a fraction of organisms ever fossilize. Only one Argentinosaurus fossil is known to exist, that does not mean that 95 million years ago only one Argentinosaurus existed. Fossilization is so rare that in a population of literally billions you might only leave one or even no fossil remains. The fossil record is like taking one random photograph in paris and trying to reconstruct france we know we are missing massive amounts of what was there but it is still incredibly informative compared to not having it.
Why does size vary.
This one is simple, because selective pressures vary, different pressures favor different things, and different condition create different costs. In whales for instance the fact Blue whales have to fast for part of the year encourages large stores and thus large size, that is just one factor favoring large size.  the largest whales and dinosaurs are not significantly bigger than their ancestors, the changes in each generation is minor and usually due to changes in different developmental triggers/regulators. Argentinosaurus is big nut it is comparable to other large sauropods.

WRT fossils, it's also much easier to recognize that you've stumbled across the fossil bone of an Argentinosaurus than of its rat-sized cousin.

There is much more size variation than you seem to acknowledge!
The blue whale is actually much heavier than the Argentinosaurus was (180 tons against 90 tons).
If you are impressed by size different between humans and some dinosaurs, then you will really be amazed to appreciate of how much size variation exist.
You currently spend one orders of magnitude (2 meters for humans and 30 meters for the Argentinosaurus). If you include all of life, including bacteria, you will spend 9 orders of magnitude from ~$10^{-7}$ meters for the smallest bacteria (I excluded viruses, viroids and prions) to ~$10^2$ meters for the blue whale and the sequoia trees.
Of course, size does not mean much. Do you mean, the longest, the heaviest, the tallest, etc... A fungi might actually well deserved to be recognized as the biggest living thing on earth (see The biggest underground living animal)
You might also want to have a look at How did the huge dinosaurs cope with gravity and loads on bones?.
Evolution misrepresentation
You said

evolution is small changes in DNA and/or mutations

Evolution has brought different lineages to have DNA sequences that differ drastically. Compare an angiosperm (say a dandelion) and a bacteria (say and E. coli), you will hardly be able to align any of their DNA sequence. They are genetically completely different.
The standard saying from layman people is to say that evolution occurs through small gradual changes. Over a long period of time, such small and gradual changes end up making organism that differ a lot. The most recent common ancestor between the dandelion and the E. coli lived about 3 billions years ago (maybe more).
Now, even the saying that evolution is necessarily very slow and go through small gradual changes is quite wrong. Specific mutational event can be extremely drastic and there are period of extremely high speciation rate in a given lineage. But all of this is a story for another time!
Coming back to size, you might want to have a look at the post Do large animals often evolve into smaller animals?.

Also, changing size really doesn't seem like it should require that much of a DNA change.  Very simplistically, looking at it as a software program, there would be instructions that basically tell cells "double N times then stop" during the growth process.  So a mutation that replaces N with N+1 doubles the size of the organism.

Why has this answer bin downvoted???

@cezar I think it is being downvoted (not me!) because it appears not to answer to the question. I think Remi.b tries to say that the size range is normal.

@jamesqf except just doubling the size on an animal will not work, the square cube law forcins parts to chang in size at diffrent rates to still remain functional.


text:
Feffects of frequent & sudden variation in room/surrounding tempratues
If out door temprature is like 40°c with 100% humidity and indoors temperature is around 35°c. Whereas an air conditioned room in the house has  a temperature maintained at 20°c with very less humidity.
A person doing household chores moves in & out of all three temperature zones very frequently, like 3 to 5 times every ten minutes, for a total duration of say half hour.
In such a situation, what could be the physical effects on ones body?
Can it cause dizziness, sleep onset, fatigue, headache & muscular cramps, palpitations, breathing problems etc?

We cannot give medical advice or diagnoses on stack exchange. There are legal repercussions for such advice.

Rehan, you might ask this (after depersonalizing it) on Health.SE. Personal health is exactly that: personal. I'm an old lady. My dogs thrive on activity, so I go outside and chuck balls in awful heat for a few minutes, then come in to cool off, then go out again, etc., and I feel nothing untoward. That doesn't mean someone who has, say, an autonomic nervous system problem wouldn't suffer from doing that.

@John - Medical advice on Stack Exchange does not constitute a professional (doctor-patient) relationship, therefore does not constitute a legal problem. It is not technically different than the advice given on Law.se or a cooking site (if a bad answer ruins your dinner party, can you sue? I doubt it.) The problem is ethical.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
How is a portion of DNA selected and unwound from nucleosome?
If I understand this correctly during interphase most of the DNA strand is tightly wound around histones in the form of nucleosomes, to conserve space in the nucleus. Yet RNA polymerase in order to work needs a part of DNA to be temporarily unwound. How does the polymerase find the particular part of the DNA (and especially the promoter for a gene coding the protein needed to be synthesised) in this mass of tightly wound DNA?

I was told that during interphase the DNA is actually looser and more accessible to RNA polymerase, and that it is wound up in chromosomes only during mitosis?

This answer will be a very broad overview and is based largely on information from the textbook "Molecular Biology of the Gene" by Watson et al. (which I highly recommend).
Nucleosomes are dynamic structures.
The interactions between DNA and histones are non-specific and dynamic. Regions of DNA can be transiently unwrapped from the nucleosome and thus recognized by DNA binding proteins. In fact, because of the non-specific nature of the interaction, DNA can slide relative to the histone core and expose different sections of DNA. This can be facilitated by nucleosome remodelling complexes which can also catalyze complete ejection of histone octamers to expose even more DNA.
Nucleosomes can be positioned specifically.
The association of DNA binding proteins with specific sequences can prevent or control nucleosome formation at specific loci and leave tracts of exposed DNA accessible to the transcription machinery. Additionally, certain DNA sequences that form bent helices are preferentially bound by nucleosomes.
Chromatin compaction is highly regulated.
Two broad classes of chromatin are present in the interphase nucleus: highly condensed, transcriptionally inactive heterochromatin and less condensed, transcriptionally active euchromatin. Chromatin compaction is regulated by post-translational modification of histone tails, and modifications such as acetylation and phosphorylation, especially of the N-terminal tails, can prevent higher order, repressive chromatin compaction. The specific pattern of histone modification is referred to as the histone code and certain modifications are associated with gene expression. These modifications can be recognized by remodelling complexes and even transcription factors.
Further Reading:
Becker PB, Workman JL. 2013. Nucleosome Remodeling and Epigenetics. Cold Spring Harb Perspect Biol 5(9):a017905.

There are a number of different ways. The histone may be marked through some histone modification (a form of epigenetic modification) that relaxes the DNA and makes it more accessible.
For example certain forms of acetylation "remove the positive charge on the histones and decreases the interaction of the N termini of histones with the negatively charged phosphate groups of DNA. As a consequence, the condensed chromatin is transformed into a more relaxed structure" this then makes it easier for RNA polymerase to access it and find the promoter for example

Nucleosome is a structure formed when negatively charged DNA is wrapped around positively charged histone octamer.
Now, for transcription only one strand of  DNA is copied to RNA having polarity 3'-->5' known as Template strand, the other strand known as Coding strand (5'-->3') has same sequence as RNA (except thymine at place of uracil)
Promoter is located towards 5' end(all references are made with coding strand) while terminator end is at 3' end.
The presence of PROMOTER in transcription unit defines the template and coding strand. In transcription only a segment of DNA is copied.
For unwrapping of DNA there are special enzymes like helicases(for unwinding helix), DNA Gyrase(for relaxing strain and supercoiling), Telomerase and holoenzyme.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Why do fully grown organisms need protein intake?
If proteins are building blocks of an organism then it makes sense why a growing organism would need an intake of them, but why would a fully grown organism need proteins (aside from those lost by shedding skin, growing hair etc.) and not recycle other proteins back into amino acids.
I understand that protein can be broken down to generate energy when needed or when there's too much of it in the body, but given enough energy from other sources (like glucose), it seems that proteins wouldn't need to be used for these processes.
Is there perhaps a net loss of amino acids during protein biosynthesis?
My question was inspired after reading this study of a man who was fasting for 382 days and was given only water and mineral supplements:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2495396/pdf/postmedj00315-0056.pdf

I've checked both of these and they still don't answer my question. Protein degradation explains that proteins can be broken down into amino acids, which I am aware of, hence the question: If the body can do this, then why the need for external amino acids? Just supply energy for analysis and new synthesis.

Please note that the man was using/losing protein as well as using fat as evidenced by the continual excretion of creatinine (which comes from muscle protein breakdown.) This is not ideal and were he not morbidly obese and on a medically supervised fast, he most likely would have died.

I see you have edited your question to clarify that the question is one of why not all the amino acids used for breakdown are not available for reuse. I'll remove my close vote and delete my comment.

@David The question hasn't been edited (unless it was deleted and reposted and I missed that) - it was always about why recycling doesn't provide enough amino acids.

@David I have not edited the question.

Ok. Can't have read it properly.

One reason is hair, skin, and certain excretions also contain protein which is lost. Hair contains little else in fact.

@anongoodnurse: And for an opposite extreme, consider the stereotypical 98 pound weakling who takes up bodybuilding :-)  Or even me, as I shift from my winter skiing muscles to summer hiking/biking/horse riding ones and back again.

If we can trust medlineplus, urine accounts for only around 80mg of the required 40-65g daily protein intake: https://medlineplus.gov/ency/article/003580.htm

Take it from the man: "This process of recapture is not completely efficient, and some amino acids are lost by oxidative catabolism. Metabolic products of amino acids (urea, creatinine, uric acid, and other nitrogenous products) are excreted in the urine; nitrogen is also lost in feces, sweat, and other body secretions and in sloughed skin, hair, and nails." https://www.ncbi.nlm.nih.gov/books/NBK234922/ ("Recommended dietary allowances 10th ed.")

Protein is polymerized amino acids.
Humans do not require protein intake, but certain essential amino acids are required.  These essential amino acids are usually obtained through protein intake, but intake of the free amino acids themselves would suffice.
Amino acids, in free or protein form, are lost from the body due to urination (see Diverse characteristics of the urinary excretion of amino acids in humans and the use of amino acid supplementation to reduce fatigue and sub-health in adults), perspiration, menstruation, ejaculation, tear drops (see Amino Acid profiles in human tear fluids ), skin exfoliation, hair and nail growth, nasal mucus (see Identification of human nasal mucous proteins using proteomics), and vaginal mucus (see Proteins of Cervical Mucus).  Additional loses can occur due to additional bleeding, lactation, child birth, spitting (and other activities causing loss of saliva), and coughing up mucus.
Synthesis of new proteins from amino acids is constantly required by the body (see NUTRITION AND PROTEIN TURNOVER IN MAN). Though there are chemical pathways to reuse amino acids, it is necessary for the concentration of each amino acid to be non-zero, and therefore some fraction is necessarily lost through excretion.
Beyond just direct excretion of amino acids and proteins, there is excretion of nitrogen-containing metabolites such as urea, uric acid, creatinine, ammonium salts and bilirubin.

Just as a note, the first study you cited reports an average excretion of 5.1 mmol amino acids per L of urine. The average weight of an amino acid is somewhere around 110 g/mol (Histidine is at 155 and Glycine at 75, so the two most prevalent amino acids nicely balance each other out to the average of 115 as well). That makes 0.0051 * 110 = 0.56 g of amino acid per L of urine. Daily urine excretion is between 800mL and 2L, so that's perfectly in line with medline's 80mg excreted per day. (Healthy) urination is therefore unable to account for any significant fraction of amino acid loss.

Which basically leaves us with losing about 50g of protein through the other things you mentioned. If you consider how much we sweat (10-14 L PER DAY), lose skin and hair, and how much enzyme juice we secrete into our food to digest it...

@Armatus 50 grams lost per day is only if you eat more than you need.  24 grams per day is enough to supply all the needed nitrogen for the body.  https://books.google.com/books?id=bUEfAwAAQBAJ&pg=PA129&dq=minimum+protein+per+day&hl=en&sa=X&ved=0ahUKEwiI_cKNq6rVAhUFOD4KHWP1DiEQ6AEIUDAI#v=onepage&q=minimum%20protein%20per%20day&f=false Only 6.3 grams per day of essential amino acids are required according to table 12.7 of that reference.

@Armatus if protein is the only nitrogen source, some will go to  porphyrin synthesis https://en.wikipedia.org/wiki/Porphyrin#Synthesis which is excreted as bilirubin in feces and urine https://en.wikipedia.org/wiki/Bilirubin and related molecules.  So there are indirect ways of excreting protein, beyond just directly excreting amino acids or protein.

@Armatus I don't think an average human sweats 10-14 L per day (possibly excluding extreme heat and such), because that means you would need to drink probably well over 16 L of water to account for this loss plus urine and water loss due to breathing. From what I understand most of the excess proteins end up as an additional fuel for the body.

@Armatus Urea excretion through urine is something like ~25 grams per day. That would be the primary method of excretion of amino acid metabolites.

@BryanKrause only when protein/nitrogen consumption is high is urea the main route of nitrogen excretion.  When nitrogen intake is 1.6 grams/day, only 20% of nitrogen in urine is in the form of urea.  https://books.google.com/books?id=nUMrAAAAYAAJ&pg=PA93&dq=12+g+of+urea+each+day&hl=en&sa=X&ved=0ahUKEwj9keHvvazVAhVHjz4KHTIXBLQQ6AEIPDAE#v=onepage&q=12%20g%20of%20urea%20each%20day&f=false For the OP situation with no food intake, the urea fraction would be very low.

@DavePhD Yes indeed, I was trying to reconcile with Armatus' statement that 50 grams of protein are being lost (if that much is eaten) and implying that has to be lost in things like sweat, skin, and hair. It doesn't: when 50 grams of protein are lost per day, a large fraction of that would be excreted as urea.

Makes perfect sense. Imo you should modify your answer to reflect that the primary reason for protein intake is then to supply nitrogen or to save the body some work converting other metabolites into amino acids. (Yeah the sweat thing was a bit ridiculous... I've never felt like needing a bucket to collect my sweat)

Some amino acids are also consumed by metabolic activities that transform them into other molecules, like hormones, that can't be turned back into amino acids.

@John yes, like tryptophan in the serotonin and kynureinine pathways

A fully grown organism is subject to senescence and on a narrow perspective one of the signs of aging is the accumulation of large amount of lipofuschin.

In unstressed situations protein homeostasis is balanced by folding and stabilization of proteins by chaperones of the Hsp family [1] and the controlled degradation of proteins by the proteasomal system.[source1]
[see also]

However,

One of the highlights of postmitotic aging is the intracellular accumulation of highly oxidized and cross-linked proteins, known as lipofuscin. Lipofuscin is insoluble and not degradable by lysosomal enzymes or the proteasomal system, which is responsible for the recognition and degradation of misfolded and oxidatively damaged proteins. These aggregates have been found in various cell types, including heart, liver, kidney, neuronal tissue, and dermal tissue, and are associated with the life span of a single postmitotic cell and, consequently, of the whole organism. Lipofuscin formation appears to depend on the rate of oxidative damage to proteins, the functionality of mitochondrial repair systems, the proteasomal system, and the functionality and effectiveness of the lysosomes. This review highlights the current knowledge of the formation, distribution, and effects of lipofuscin in mammalian cells.[source]

Lipofuschin is known to contain oxidised proteins,lipids and glycosides as follows:

This accumulation of aggregates is the final fate of protein damage under stress conditions. Under such circumstances oxidized proteins may not undergo appropriate proteolytic digestion but instead, cross-link with one another or form extensive hydrophobic bonds. It is believed that the cross-linked proteins react further with other cellular components, forming a fluorescent material referred to as lipofuscin (Fig. 1F). Lipofuscin is accepted to consist of oxidized proteins (30–70%) as well as lipids (20–50%) [23] and from the fifth decade of life, bound sugar residues were also detected in human lipofuscin. [source]

The lipofuschins are present in residual bodies of lysosomes ,the centre of protein recycling.
Lipofuschins render the non digestibility of the oxidised proteins as follows:

According to this model, an intralysosomal accumulation of lipofuscin can be considered as the long-term result of a decreased degradation of oxidized proteins and an increase in intracellular free radical formation. Metals, including Fe, Cu, Zn, Al, Mn, and Ca, comprise up to 2% of lipofuscin [26] and especially catalytic iron seems to be an important factor in further oxidation reactions of the initial protein aggregate. In mammalian cells iron is the most abundant cellular transition metal and a fundamental player in the above mentioned mitochondrial–lysosomal axis theory of aging [source]
Another major characteristic of lipofuscin is its ability to inhibit the degradation of oxidized proteins by competitively binding to proteolytic enzymes including the 20S proteasome as mentioned above as well as lysosomal proteases. How exactly the proteasomal substrate recognition functions is still under investigation, but one of the recognition motifs might be exposed hydrophobic patches from oxidatively damaged and partially unfolded proteins [5,28]. It seems likely that the proteasome also binds to such exposed hydrophobic oligopeptides on the lipofuscin surface but is then unable to completely degrade or to release these peptides, resulting in proteasomal inhibition [source]

The lipofuschins being the undigested remains,it can be said that the lysosome fails to recycle the entire endosomal protein specifically with aging (when it becomes very prominent).
Thus, some of the loss of amino acid may be attributed to its lack of recycling.

Can you try to add some scale of reference to how much waste protein really ends up as lipofuschin? Given how long it takes such material to build up, and given that it seems like most sources focus on the lipid, rather than protein content, I am doubtful that it consists of any substantial fraction of the day-to-day amino acid needs. A different answer here says that about 6 grams are needed daily; if this was all accumulated as irrecoverable wastes in cells, we'd be growing over 2kg of body weight annually just in those granules - that makes no sense.

@Bryan Krause senescence takes years! OP asked:" but why would a fully grown organism need proteins (aside from those lost by shedding skin, growing hair etc.) and not recycle other proteins back into amino acids."aside from these phenomenon ( already discussed in the 1st answer)the only one i could find was senescence...i think i stated there will be some loss of amino acid during recycling not all...and speaking of accumulation...gaining weight? i think there will be age related degeneration of the cells rather than weight gain...apoptosis too.

@Bryan Krause as for "scale of reference"try the aging link already in the answer

What I mean by scale is: of the daily requirement for protein (that is, the inherent waste or use in the system), what percentage belongs to the mechanisms you are describing? I think that percentage is very low; I don't see in your references where that information is given, just a note that it accumulates with age.

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


text:
transitional mutation, repair mechanism
I have read an answer to a question about dna repair during and after replication.
But how is dna repaired if a deamination of of 5-methylcytosine happens? How does a repair mechanism identify which base was mutated (on '3 or on '5 strand, a C to T, or on the complementary strand an A to G)?

I don't have time for an answer right now, but you can look up very short patch repair for bacteria. For higher organisms where methyl-C occurs in CpG sites, repair enzymes can recognize the mutated strand by the presence of methylated CpG on the complementary strand.

DNA Glycosylases, like UDG, and hSMUG1 contribute to specifically sniffing out instances of Uracil that occur in the DNA. Havent time for a full answer myself, but these are just a few resources.

Deamination of 5mC gives T, not U.

Yikes, that's embarrassing! Disregard my above comment unless you're curious!


text:
What are the differences between isozymes, allozymes and isoforms?
As far as I have understood

Isozymes are derived from different genes but perform similar functions
Allozymes are derived from the same gene but different loci, functionally conserved
Isoforms are a result of post transcriptional modification of the same gene, I am not sure for its functional conservation.

Are there anyother things to know about them?
Thanks

You have the basic idea:
Isozymes come from different genes but carry out the same enzymatic reaction.
Allozymes come from the same gene - i.e., the gene at a particular point on the chromosome; but chromosomes come in pairs, and the allozymes come from the 2 different chromosomes in the pair.
Isoform proteins ["protein variants"] are from the same gene, but they can have the same or different functions, depending on how they are spliced = which exons are included, and in what order. There's a nice picture in the Wikipedia article "protein isoform."
Here are Wikipedia links:
Isozyme - Wikipedia
https://en.wikipedia.org/wiki/Isozyme
Isozymes (also known as isoenzymes or more generally as multiple forms of enzymes) are enzymes that differ in amino acid sequence but catalyze the same chemical reaction.
Alloenzyme - Wikipedia
https://en.wikipedia.org/wiki/Alloenzyme
Alloenzymes (or also called allozymes) are variant forms of an enzyme which differ structurally but not functionally from other allozymes coded for by different alleles at the same locus.  ...These are opposed to isozymes, which are enzymes that perform the same function, but which are coded by genes located at different loci.
Protein isoform - Wikipedia
https://en.wikipedia.org/wiki/Protein_isoform
A protein isoform, or "protein variant" is a member of a set of highly similar proteins that originate from a single gene or gene family and are the result of genetic differences. While many perform the same or similar biological roles, some isoforms have unique functions.

Complementing Helen's answer, I can give one example of isoforms. The main production of nitric oxide in brain is driven by three enzime isoforms of the same gene: neuronal, endothelial and induced Nitric Oxide Synthase (nNOS, eNOS and iNOS). Despite de fact they have their origins from the same gene, they are quite different in terms of regulation and activity. The different isoforms are regulated by different genes and pathways, they are found in different tissues in brain, induced isoform can produce much more NO than the others and, of course, they promote different effects in body physiology, from regulating vital pathways in brain cells to regulation of blood flow.
You could not tell if we're looking at isoforms or allozymes just by analysing their effects in organisms since they both are different forms from same type of enzime, but it's important to know their origins if we want understand how they work.

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


text:
Why can we use mouse-produced antibodies on mice tissues?
I have seen biologists use mouse grown primary antibodies in mouse tissue, and they've told me that if the blood is perfused well then there is no problem with this method. How does the secondary antibody (anti mouse) not stick everywhere on all the mouse antigens in the tissue?
Clarification: I  understand that the secondary antibody is very specific to all mouse "class" primary antibodies. Can I ask then why using a secondary mouse antibody does not recognize background antibodies in the tissue, the ones that the mouse produced for itself naturally before I added any of my primary antibody? Are the existing primary antibody levels already present in the mouse much lower than the levels of the primary antibody I am adding?

The reason why the secondary antibody only recognizes the primary antibody is relatively simple: It is directed against the Fc-part of the primary antibody. As this part is species specific (but constant between all antibodies from one species, hence the name constant) a secondary anti-mouse antibody is directed against all mouse antibodies.
The general principle can be seen in the figure (although this is from immunolabelling, the principle stays the same, Image from the Wikipedia):

The anti-mouse secondary does recognize the antibodies which are present in the tissue. These are usually present at low levels (unless you work with immune tissues as spleens) and only cause a relatively low background. If it causes a problem, you can treat your sample before you add the primary with an Fc block which blocks the antibodies present in the tissue so that the secondary antibody will not recognize anymore later.

I think we essentially said the same.

Antibodies are very specific on what they recognize (this is called epitope that is the small part of the antigen that is recognized by a specific antibody), and secondary antibodies are made to attach to a specific part of the primary antibody - you can achieve this with monoclonal ABs. Antigens can be recognized by many antibodies (because they can have many epitopes for different antibodies), but usually a single antibody recognizes only a few or more likely a single antigen at max (since the specific epitope it attaches to is only present on a few or a single antigen(s)).
The wiki page for antibodies has plenty of detail on how ABs work.


text:
What is the justification of Chargaff's second parity rule?

First parity rule
The first rule holds that a double-stranded DNA molecule globally has percentage base pair equality: %A = %T and %G = %C. The rigorous validation of the rule constitutes the basis of Watson-Crick pairs in the DNA double helix model.
Second parity rule
The second rule holds that both %A ~ %T and %G ~ %C are valid for each of the two DNA strands. This describes only a global feature of the base composition in a single DNA strand.

[source]
It makes sense that in the context of dsDNA, that A = T and C = G, but I don't see an obvious reason why in a single strand of DNA, A ~ T and C ~ G.

Please avoid uploading text in images. They are not searchable, they are often hard to read (it is the case here) and they pose problem to visually impaired people. Also, please add a link when you cite from a source.

This is an excellent question, which was the cause of some confusion in the field over the years:
"The validity of the second Chargaff rule was unexpected. Obviously it should be regarded as a global rule, i.e. applicable to large sections of chromosomes. Nonetheless, not being derived from a compelling principle, such as the one underlying the first rule, it remains a mystery. This is even more so, when one studies extended versions of Chargaff’s second rule." (paper)
There are a few things to note here:

Chargaff's rules were purely observational; they pre-existed the double helix (see your same Wikipedia ref), and thus pre-existed the double helix model (which was in fact famously a rendering of the first rule in a 3-D model, as Watson wrote about in his book "The Double Helix"). There is thus no logical or mechanistic justification for the rules; they were simply what Chargaff et al. observed for dsDNA and ssDNA. Perhaps I have misinterpreted, but I felt the question implied a belief that there must be some logical requirement for this.
Note that the first rule uses "=" and the second rule uses "~" ("approximately"). That is, if we believe that all bases in a genome are paired, then it follows as a mechanistic/logical requirement that Watson strand and Crick strand must match up compositionally. This is obviously not the case with ssDNA, as I think you indicate in the Q. However, it is nonetheless true that genomes have overall compositional biases; they tend to have consistent (G+C)/(A+T) ratios across the molecule (on average). More recently, it has become clear that this is true not only for single nucleotides, but also for $k$-mers, or short DNA sequences of length $k$ (paper). Indeed, these patterns have been used to match up different pieces from the same genomes (paper). These biases exist on both strands, therefore each strand of a genome is subject to these biases. (The reasons why these biases exist are often argued over, but may have something to do with mutational biases). Therefore, both ssDNA strands of a dsDNA genome have the same compositional biases, and they must complement each other's similar biases, so even within a strand the statistical expectation is Chargaff's second rule. Chargaff, again, probably didn't know many of these things when he came up with the rules. This explanation for Chargaff's second rule has been explicitly discussed in the literature, in the first paper cited.

Notably, the second rule only holds reliably for long sequences, because in short sequences sampling error may lead to a failure to match the biases of forward and reverse strands. This is more or less what everyone means when they call it a "global" rule.

In addition to the answer by Maximilian Press, the papers

[1] Intrastrand Parity Rules of DNA Base Composition and Usage Biases of
Synonymous Codons
[2] Properties of a General Model of DNA Evolution Under
No-Strand-Bias Conditions

show that under a no-strand-bias assumption, the base frequencies of a single strand at equilibrium, denoted as $A^*,T^*,G^*,C^*$, are such that $A^*=T^*$ and $G^*=C^*$.
I would try to explain it briefly here, but please refer to the original papers for a complete and better explanation, as some of my explanation is simplified.

First, we denote the base frequencies (in time $t$) of a single strand $A(t),T(t),G(t),C(t)$.
(each frequency is in $[0,1]$, and $A(t)+T(t)+G(t)+C(t)=1$)
Next, we denote the substitution rates in a single strand $r_1, ..., r_{12}$, as follows:

(diagram copied from [1])
E.g.:
$$\frac{dA}{dt} = -\left(r_{1}+r_{4}+r_{6}\right)\cdot A\left(t\right)+r_{2}\cdot T\left(t\right)+r_{3}\cdot G\left(t\right)+r_{5}\cdot C\left(t\right)$$
Similarly, we denote the substitution rates in the other strand (in the double helix) $r'_1, ..., r'_{12}$.
If we assume no-strand-biases$^{(*)}$ (i.e., the substitution rates are independent of the strand: $r_1=r'_1, ..., r_{12}=r'_{12}$), then using Chargaff's first parity rule we can deduce:
$$r_1=r_2,r_3=r_9,r_4=r_{10},r_5=r_7,r_6=r_8,r_{11}=r_{12}$$
(because $r_7=r'_5$, etc.)

$(*)$ If I understand correctly, there is another implicit assumption here - each substitution rate in time $t$ is independent of the base frequencies. E.g., regardless of whether the frequency of $A$ bases in one strand is different from the frequency of $A$ bases in the other strand, we assume that $r_1=r'_1$.

So we can (under a no-strand-bias assumption) denote the substitution rates in a single strand $a, ..., f$, as follows:

(diagram copied from [1])
I.e.:
$$
\left(\begin{matrix}\frac{dA}{dt}\\
\frac{dT}{dt}\\
\frac{dG}{dt}\\
\frac{dC}{dt}
\end{matrix}\right)=\left(\begin{matrix}\left(-a-e-c\right)\cdot A\left(t\right)+a\cdot T\left(t\right)+b\cdot G\left(t\right)+d\cdot C\left(t\right)\\
a\cdot A\left(t\right)+\left(-a-e-c\right)\cdot T\left(t\right)+d\cdot G\left(t\right)+b\cdot C\left(t\right)\\
c\cdot A\left(t\right)+e\cdot T\left(t\right)+\left(-b-d-f\right)\cdot G\left(t\right)+f\cdot C\left(t\right)\\
e\cdot A\left(t\right)+c\cdot T\left(t\right)+f\cdot G\left(t\right)+\left(-b-d-f\right)\cdot C\left(t\right)
\end{matrix}\right)
$$
Or equivalently:
$$
\left(\begin{matrix}-a-e-c & a & b & d\\
a & -a-e-c & d & b\\
c & e & -b-d-f & f\\
e & c & f & -b-d-f
\end{matrix}\right)\left(\begin{matrix}A\left(t\right)\\
T\left(t\right)\\
G\left(t\right)\\
C\left(t\right)
\end{matrix}\right)=\left(\begin{matrix}\frac{dA}{dt}\\
\frac{dT}{dt}\\
\frac{dG}{dt}\\
\frac{dC}{dt}
\end{matrix}\right)
$$
At equilibrium:
$$
\left(\begin{matrix}\frac{dA}{dt}\\
\frac{dT}{dt}\\
\frac{dG}{dt}\\
\frac{dC}{dt}
\end{matrix}\right)=\left(\begin{matrix}0\\
0\\
0\\
0
\end{matrix}\right)
$$
So we have to solve:
$$
\left(\begin{matrix}-a-e-c & a & b & d\\
a & -a-e-c & d & b\\
c & e & -b-d-f & f\\
e & c & f & -b-d-f
\end{matrix}\right)\left(\begin{matrix}A\left(t\right)\\
T\left(t\right)\\
G\left(t\right)\\
C\left(t\right)
\end{matrix}\right)=\left(\begin{matrix}0\\
0\\
0\\
0
\end{matrix}\right)
$$
It turns out that every vector proportional to the following solves the equation:
$$
\left(\begin{matrix}d+b\\
d+b\\
e+c\\
e+c
\end{matrix}\right)
$$
The relevant solution to us is a solution such that each frequency is in $[0,1]$ and $A(t)+T(t)+G(t)+C(t)=1$:
$$
\left(\begin{matrix}\frac{d+b}{2\left(d+b+e+c\right)}\\
\frac{d+b}{2\left(d+b+e+c\right)}\\
\frac{e+c}{2\left(d+b+e+c\right)}\\
\frac{e+c}{2\left(d+b+e+c\right)}
\end{matrix}\right)
$$
I.e., $A^*=T^*$ and $G^*=C^*$.

I’m too old to follow your maths (it was different when I was a school boy), but if I understand you correctly, Chargaff’s second “rule” is a mathematical consequence of his first. Pity he didn’t devote himself instead to understanding the basis of the first — he would have died a less embittered man.


text:
How can histidine be classified both as positively charged and hydrophobic?
I saw the chart in this post Histidine aromaticity. Since I'm not allowed to comment and post a question instead of an answer, I have to ask my question in a separate thread.
How can histidine be classified both as positively charged and hydrophobic?

Histidine is not hydrophobic

BTW: You are going the right way here - asking new questions in the answer (or comment) section under other questions is not well liked.

Charged or not, histidine is aromatic because it fulfills all of the aromaticity criteria:
1.The molecule is cyclic.

2. The molecule is planar.

3. The molecule is fully conjugated (p orbitals at every atom in the ring).

4. The molecule has 4n+2 π electrons, where n is a positive integer.

As a matter of fact, the chart above is not wrong; it is quite correct. Indeed, histidine can carry a net positive charge, but when unprotonated, i.e. in a charge-neutral state, its aromatic π-system (belonging to the imidazole moiety) can behave like a hydrophobic group, e.g. it can become involved in π-stacking (aka CH-π) interactions. In the 2RS2 NMR structure, for example, HIS83 is δ-protonated and appears to be behaving like a typical hydrophobic residue: it is buried below the protein surface, stacked against several aromatic residues and packed along with several aliphatic ones; it is shielded from solvent by polar and charged residues.

2H95 is a very interesting structure where we see four ε-protonated histidines stack against tryptophans, as well as pack against aliphatic side chains, forming a transmembrane proton channel. The histidines appear to be involved in hydrohobic interactions, and, notably, at the same time form the inner surface of the channel.

Conversely, in the 2NBJ NMR structure, we see HIS56 behaving like a polar amino acid - its (doubly protonated) side chain is involved in hydrogen bonding to the backbone oxygen of a DNA fragment, as well as to a backbone oxygen atom from the protein. Moreover, in the same structure, HIS16 is doubly protonated and solvent exposed, likely interacting with water and contributing to solvation, in stark contrast to HIS83 in the 2RS2 structure, which is monoprotonated and buried in the hydrophobic interior of the protein.

Histidine's pKa can easily be perturbed by its surroundings, e.g. by the surrounding residues in an enzyme active site, which makes it highly functionally versatile, one of the manifestations of its functional and chemical versatility being its ability to behave both as a polar/charged amino acid, as well as a hydrophobic residue; this is the reason histidine is often found in functional sites in proteins, e.g. enzyme active centers.

You make assertions which may or may not be right, but you provide no third-party support for your answer. Although it has been accepted, the poster has no basis on which to judge it correct. What you need to do is to edit your answer to provide examples of proteins (with links) in which histidine is clearly uncharged and involved in π-stacking interactions. Then I and others can go to the links and decide whether to vote your answer up or down.

I look forward to seeing that. It will enhance the standards of this site. Take your time.

I've already added the reference to the answer.

I've read the paper and it seems to me to relate only to theoretical calculation of π-π interactions, assuming they exist, with the conclusion that they are relatively weak compared with other His interactions. What is lacking in the paper is a single example of a π-π interaction in a protein. I am familiar with PDB, but do not see how to perform a search for π-π interactions involving His to quickly return examples. (A slow search by eyeballing, I understand.) I am not saying you are wrong, but I do not think you have proven your case. At the moment it seems just hand waving.

I have added several illustrative images and examples; I would love to expand this topic in more depth and will gladly do so, provided I find the time.

Thanks. Very good. The proton channel seems intriguing, although I'm not actually a protein chemist. Must ask a colleague about it. (If you add any more pics, I'd scale them down a little for ease of reading your whole answer.)

As @Chris says, the charge depends on the pH: when the pH is different from the pH(I) of the molecule, this one is charged.(Take a look at this).
Anyway, talking about Hys, its pH(I) is 7.47 (here), so at a pH below its pI, the Histidine carry a net positive charge, otherwise it can be also in a netrual form. Obviously it's all a matter of equilibrium!

Yeah, I think so...

As @wysiwig stated, Histidine is not hydrophobic. Depending on the pH different parts of the molecule can carry charges, see the image below (from here):

The nitrogen atoms can be protonated in an acidic environment, the carboxylgroup will loose it proton in a basic environment. All these forms are transferred into each other, when the pH changes.


text:
Does osmosis take place in prokaryotic cells?
As far as I know, osmosis occurs in Eukaryotic cells, and I'm wondering if it could take place in prokaryotic cells too.

Since osmosis is a physical-chemical phenomenon, it happens along all concentration gradients.

So that means, it could happen in prokaryotic cells too ?

yes, even happens across non living membranes if they let water across, that's how dialysis works.

Osmosis works across every cell membrane along a concentration gradient as its a physico-chemical principle. Water can cross the membrane (or cell wall), while the substance dissolved in it (for example salts) can not. Because eukaryotic cells only have a cell membrane, they will burst eventually, while bacteria (and also plant cells) have a more rigid cell wall, which will mostly prevent bursting. However the influx (or outflux) of water creates a pressure which is called turgor pressure. How this works is shown below (figure from here), bacterial cells and plant cells work pretty much the same way:

That's a good explanation of osmosis, but most bacteria have a cell wall to prevent too much swelling.

You are right - I took the wrong turn here. I corrected the answer.

The force driving osmosis exists in any system with an imbalance of solute molecules across a semipermeable membrane.
Think of a concentration gradient as an electrical potential, where high concentration is negative charge and low concentration is positive charge. In the case of electricity, its the magnetic force which causes the interactions leading to charge equilibrium.
In osmosis, there is no communication between solute molecules by an 'osmotic force'. Osmosis is a result of entropy. In chemistry, a separation of solute concentrations is called a chemical potential. As entropy increases in the system, this chemical potential is decreased, either endo or exothermically.
Here's a chart showing the change in heat for the dissolution of substances. Negative numbers mean a system loses heat (enthalpy) and is exothermic. Cold packs use ammonium nitrate, which absorb heat as they are dissolved in water.
The processes of osmosis, entropy are fundamental to our universe, not to a specific domain of life.
Enthalpy change of solution for some selected compounds
hydrochloric acid   -74.84
ammonium nitrate    +25.69
ammonia             -30.50
potassium hydroxide -57.61
caesium hydroxide   -71.55
sodium chloride     +3.87
potassium chlorate  +41.38
acetic acid         -1.51
sodium hydroxide    -44.51
Change in enthalpy ΔHo in kJ/mol in water at 25°C[1]


text:
Do pharmacodynamics and pharmacokinetics of the drug in animals are the same as in human?
I'm trying to understand the purpose of different clinical trial phases, and the following question comes into my mind :

Do pharmacodynamics and pharmacokinetics of the drug in animals are the same as in human?

The reason I asked this question is that our professor said that pharmacodynamic and pharmacokinetic studies are performed during pre-clinical studies (in animals), as well as during clinical trial's phase 1. The answer I was thinking about is that animal's physiology cannot be the same as human's physiology, thus, pharmacological profils should be different.
I just want to know more about this and feed my curiosity.

Drug metabolism in humans is different than animal models.
Here is one example: http://www.ncbi.nlm.nih.gov/pubmed/17125407
The link is a review where they compare different animal models to humans with a focus on CYP enzymes commonly involved in drug metabolism.  While they describe similarities, they note:

CYP2C, -2D and -3A show appreciable interspecies differences in terms of catalytic activity and some caution should be applied when extrapolating metabolism data from animal models to humans

Essentially your instincts that different species have different pharmacology is accurate and based on the many genetically-based differences in the drug processing machinery.
Similarly, there are differences in drug metabolism between humans with different genetic backgrounds, which is the basis for pharmacogenetics (https://en.wikipedia.org/wiki/Pharmacogenetics).
More recently, differences in gut microbes have also been raised as contributory factors (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529681/).  In this case, identical twins with different diets could conceivably have different pharmacokinetics.

Tying this all back, the reason human drug trials are needed is because animal and tissue culture models are necessary, but insufficient to predict drug efficacy or safety.

So, what is the purpose of pharmacodynamics and pharmacokinetics studies on animal if the drug metabolism is not the same as in humans? can't we just wait until the study is performed during clinical trials?

Is the same article on CYP enzymes, the authors also describe similarities, so the animal models do provide some insight into how drugs might behave in humans.  More simply, would you volunteer for a phase 1 drug trial for a drug that has never been tested on any living creature?

You are correct.  The pharmacokinetics are different, but also quite similar.  The good thing is that we know what most of those differences are and can account for them when we scale models from animal species to humans.
Conducting pharmacokinetic studies in animals before conducting studies in humans is necessary and useful for a few reasons.

The Dose-Toxicity relationship can be assessed.  We will also get a better idea of what specific toxic effects to look for.
Scaled physiologically-based pharmacokinetic models appropriately predict pharmacokinetics in humans from animal data.
Variability can be assessed (i.e. if I administer a certain dose, how much variation can I expect in concentration profiles for a group of individuals?)

Physiologically-based pharmacokinetic models use a bottom-up rather than a top-down approach to modelling.  This approach allows accurate interspecies scaling simply by changing the system parameters according to the species of interest.  To begin, a virtual animal or person is created with organ volumes, blood flow rates, enzyme activities, etc. as defined in literature.  These are the system parameters.  Next, drug-specific parameters (solubility, charge, partition coefficients) are determined from literature or experimentally where possible.  Finally, all processes which are theorized to affect the drug's absorption, distribution, metabolism and excretion are described with a system of ordinary differential equations, using the system and drug-specific parameters. Any unknown drug-specific parameters can be fitted to animal data at this time.  It is useful to be able to determine estimates for drug-specific parameters with animal models that can be later applied to human models.
The model is validated by comparing the model simulations with actual experimental data from animals (Animal PK Trials!).  If the model makes accurate predictions, all we have to do is change the system parameters (organ volumes, blood flow rates, enzyme activites, etc.) from animal values to human values, while keeping the drug-specific parameters constant, and the system of ODEs will make a good prediction of the pharmacokinetics in humans.  Of course, this is a simplified methodology.  Occasionally the model equations or drug-specific parameters must be changed between species to account for some physiologic differences.  This process is called interspecies scaling and considerable research efforts have been put forward to standardize it.
These conclusions can be used to find an ideal First-in-Human dose.  PBPK modelling gives great insights into more than just First-in-Human trials.  Pediatric and Geriatric simulations are also very useful.  By changing the system parameters from adult to pediatric or geriatric (recognizing that humans change a lot with age), we can make guesses about the doses that are safe for children or the elderly.  The FDA now requires PBPK modelling to be done for its submissions.  All of this starts with animal PK trials.

great answer - if you could add some links to some of the terms, etc it would greatly strengthen it - thanks for your efforts!

Sorry I'm new, what audience should I be writing for w.r.t the terms that I define

that's a great question Poly... I usually err on the side of too many links to terms, helpful pages, etc - even if the links are just to a wikipedia type page with a very basic definition. The community is broad - with undergraduates all the way up to biomedical and other scientific faculty at academic universities throughout the world. I think most of the time you can tell the level of detail necessary based on how much detail or level of sophistication that the individual asking the question uses - hope that helps! Welcome to the Community!


text:
Size constraints on CRISPR guide RNA
I had a quick questions on the size limitations of a CRISPR guide. More specifically on the shorter end. Can I make a guide that is say 7-10bp and still have an active complex? I transfect using an RNP system.
Just curious.
Thanks in advance.

You can definitely make such gRNA, but chances of off-targeting increases as you decrease the size of gRNA. It is always better to have 17-20 bp gRNA. However, you can check off-targets of a gRNA through several online tools.


text:
Why is Hydra classified under Hydrozoa when it has neither a planula larva, nor a medusoid form?
If the general basis of classification of cnidarians is with respect to the body form - medusoid or polypoid, or in the incidence of metagenesis (as is common in hydrozoa), both, then, on what basis is Hydra placed in class Hydrozoa?

I'd say modern taxonomy doesn't (or at least tries not to?) classify things based on how they appear, but based on how related they are.

Probably relevant: Nawrocki et al. 2013. Phylogenetic placement of Hydra and relationships within Aplanulata (Cnidaria: Hydrozoa)


text:
Why does decreasing intake of protein prolongs the lifespan of a fly?
A book I read about aging suggests that it is established that a fly lives much longer when it is fed less protein. What does protein intake has to do with the lifespan of an organism? Why not carbohydrates?

In which book did you read this?

It is a Korean book of which author is a professor at New York University. I can search for the exact title, but I doubt it will help you.

Hmm. Do they have references to scientific articles in that? Korean would indeed not help me :-)


text:
Are changes in flexibility from stretching due to changes in the nerves or the muscles?
For many people, stretching repeatedly over a period of time improves their flexibility. I want to know whether this improvement commonly seen is due to a change in the nerves or the muscle’s material properties.
Are the changes in flexibility seen on the order of minutes/hours to weeks/months due to changes in the nervous system's reaction (e.g. reflex habituation) or changes in the viscoelasticy properties of the muscles (e.g. muscle length via serial sarcomere number)?

Excerpts:
To help answerers, I want to provide a few excerpts from two sources. The first source is from 1998.

"This article reviews recent findings regarding passive properties of
the hamstring muscle group during stretch based on a model that was
developed which could synchronously and continuously measure passive
hamstring resistance and electromyographic activity, while the
velocity and angle of a stretch was controlled. Resistance to stretch
was defined as passive torque (Nm) offered by the hamstring muscle
group during passive knee extension using an isokinetic dynamometer
with a modified thigh pad. To simulate a clinical static stretch, the
knee was passively extended to a pre-determined final position (0.0875
rad/s, dynamic phase) where it remained stationary for 90s (static
phase)."
“A significant decrease was observed for energy (30%) and
stiffness (13%) in the dynamic phase, and passive torque in the static
phase. However, the observed decline in the variables measured was
transient and they returned to baseline within 1h.”
“Long-term stretching (3 weeks) increased joint range of motion as a result of a
change in stretch tolerance rather than in passive properties.”

Source: Magnusson, Stig Peter. "Passive properties of human skeletal muscle during stretch maneuvers." Scandinavian journal of medicine & science in sports 8.2 (1998): 65-77.
The second source I want to cite is The Complete Guide to Stretching by Christopher Norris. Paraphrasing pages 56-58, he says stretching can affect the following:

Habituation – when the stretch reflex becomes desensitized and the
reflex doesn’t activate as easily when stretched
Muscle stiffness – a muscle has an elastic recoil when stretched. The degree of this
recoil is the “muscle stiffness”
Stretch tolerance – the amount of discomfort induced by a stretch that a person can endure
Serial Sarcomere Number (SSN) – a muscle can lengthen or shorten in length
when the number of sarcomeres change

Norris also notes that the first 3 criteria usually change on the order of months (called “acute” or short-term) while the SSN tends to change on the order of years (called “chronic” or long-term).


text:
Is it possible to get (an estimation of) reaction rates from the Michaelis constant?
I want to apply the Gillespie Algorithm to a biological system so I need to know the reaction rates for the relevant reactions. However, for all those reactions, I only know the Michaelis constant $K_M$ and the maximum rate $V_{max}$ (see Wikipedia). Is it possible to derive (an estimation of) the reaction rates $k_f$, $k_r$ and $k_{cat}$ (see image below) given $K_M$ and $V_{max}$? If so, how can it be done?

$K_M$ is a ratio and for QSSA it is $\dfrac{k_{cat}+k_r}{k_f}$ and for equilibrium approximation it is $\dfrac{k_r}{k_f}$.
It is clear from the formula that you cannot obtain all the constants simulataneously. If you know two (in case of QSSA) you can get the third.


text:
What is a PCR test?
I know that PCR is used to amplify DNA, but what do people mean when they mention 'PCR tests' for diagnosis of disease? And what does a positive/negative PCR test mean?

Whether or not the amplified DNA fragment is present

So we add in known sequences (primers), and if the initial DNA is amplified, that's how we know that the original sample contains the sequence of interest?

PCR tests would involve amplification of DNA before actual tests happen. PCR tests actually refer to tests that occur after PCR has been done. Most of the time when you look at PCR tests you see images like this

This is the result of gel electrophorosis, and not specifically PCR, as PCR only increases the content of DNA so that it is sufficient for gel e. to take place (if not you won't be able to visualize the bands, etc).
Diagnosis of genetic diseases are made available through similar processes (gel e., RFLP analysis). They are just categorically termed under PCR. They detect the presense of mutant or healthy alleles and subsequently whether the subject is tested positive or negative for the disease.


text:
oversecretion of the thyroid gland
What are the reasons for the oversecretion  of thyroxin in the thyroid glands?
Its name was mentioned in my book but there was no explanation.
What are its symptoms,can it be fatal?

what book? where else have you looked? this is a relatively straightforward question/answer if you search the internet...

Elevated levels of thyroid hormone in the blood is called thyrotoxicosis. If this is due to a hyperfunction of the thyroid gland, it is known as hyperthyroidism. In common parlance, these terms are often interchanged.
Although a simple google search would tell you more, I add some detail here.
Hyperthyroid can have various causes. There can be a functional cancerous/ non-cancerous mass in the thyroid gland producing the hormone. Or as in graves disease which is an autoimmune condition where antibodies mimic to stimulate the thyroid gland to hyperfunction.
Non hyperthyroid causes of thyrotoxicosis include inflammation of thyroid or thyroiditis, where preformed hormone is released. It can also occur sometimes in a condition called struma ovarii where the tumor in the ovary turns into a thyroid like mass producing the hormone. Another possible case is an iatrogenic one where the the problem is due to the patient taking exogenous thyroid hormone.
Thyrotoxicosis is not fatal and can be controlled by drugs. Symptoms include cardiac problems, high BMR, ocular changes (bulging eyes), diarrhea and many more.
A special case of Graves disease called thyroid storm is a medical emergency and can be fatal.
Heres the medscape link for further reference. http://emedicine.medscape.com/article/121865-overview

what is a thyroid thaw?

There can be a functional cancerous/ non-cancerous mass in the thyroid thaws producing the hormone.

Typo there! Corrected :)

Your answers are usually of much better quality than this one, which has a lot of errors. It makes me wonder if you actually read the medscape article. -1 (Sorry)

@anongoodnurse I actually wrote this up from Robbins pathology. I gave the Medscape one as an online reference. Frankly speaking I dint read i dint read it. Anyway, could you please point out the errors?


text:
How to measure surface area of plated bacteria?
For my project, I'm growing Baker's yeast and probiotics in two liquid cultures before mixing them together and plating them.
I'm trying to measure the impact of the probiotics on the yeast.
How could I measure the amount of fungi on the plate, whether by cell counting or surface area?

You can count the individual colonies on the plate, with this number being the number of "Colony Forming Units" (CFU), as theoretically, only a single cell is needed to spawn a colony.
To do this though, you will need to do a serial dilution of your liquid cultures before plating, so you would have one plate of 10$^0$ dilution, then 10$^1$, 10$^2$, and so on, generally a ten-fold dilution is performed.
Hopefully this will yield at least one plate with a countable number of colonies, that is - not too many, and not too few - usually 30-300.
cfu/ml = (no. of colonies x dilution factor) / volume of culture plated
This usually yields a very large number, so it is common to then take the log of this number, and report that as your result.
And then you will be able to compare your results between probiotics. It's a very good idea to do replicates of each dilution!

As explained by user GrumpyMammoth, you can do serial dilutions until the colonies are few enough to be counted and then calculate the CFUs using the dilution factor.
If you do not want to count the colonies yourself, you can use ImageJ's "Analyze particles" function. This will give you the number of colonies.
ImageJ's "Analyze particles" function will also give you the colony size (surface area) in pixels. This can be converted into millimeters in ImageJ by opening the Image>Properties tab and changing the pixel width parameter.


text:
Carrying out a BlastP on ORF and achieving hits but 2 have the exact same score, evalue and query cover?
I'm working on a project in my university and we were all given different sequences to work off of. I am meant to compare my blastN to my blastP result. However, when I carried out my blasP I got many hits but the top 2 hits had 100 percent cover, 100 percent identity and 0.0 evalue. I am meant to work off of one of the species I achieved from blastp to compare to blastN. How do I know which one to compare to see what's most significant to my blastn species? I have to continue on and use clustalw and phylogeny after so I need to be sure.

We can't help really help unless we know the sequences you are working with. Please [edit] your question and show us i) your query protein and nucleotide sequences and ideally ii) the HSPs (the matching sequences) you found. That said, you could always just compare both. Running a blastN is not very hard or time consuming.

If I understand it correctly, you have two subject protein sequences that are exactly the same as your query. You say they are different species, so I guess you made sure they are not the same species and different strains, or subspecies.
I would suggest to now query your nucleotide sequence using blastn against both results (since a priori it could be either species, or neither), and focus on the one that gets a higher score using blastn in your phylogenetic analysis. Due to codon degeneracy, it could be that your blastn results differ between the two.


text:
Effects of lactic acid ingestion
What would happen if I drink lactic acid?
I use lactic acid to clean an espresso coffee machine and I wonder what injuries could occour drinking it.

Welcome to Biology S.E.! If you need additional assistance or have questions regarding policies, please visit The Help Center.

You should not ask personal health questions on this site; however, I do not believe this is a personal health question. I am going to try and find you some authoritative information on the subject and get back with you.

I voted to close this as a personal medical question, although it could be easily changed so that it's not. The question is also kind of hard to answer without knowing the specific parameters. It is an acid, so drinking a concentrated sample probably wouldn't be too pleasant. However, it is produced naturally by the body and is often present in milk, hence the name. You could drink rat poison if sufficiently dilute.

I'm OBVIOUSLY not asking for personal medial advice and I OBVIOUSLY not going to drink lactic acid. If I were into it, I would, at least, be nice enough to auto-answer my question :P This is hypothetical of course, since LA is endogenous I wonder if it can be drunk up to some amount and what effects this will have. After all Caffeine is a poison but we drink it anyway.

@knm241 We do ingest some - every time we ingest some type of milk product.

@L.B. I didn't realize that milk contains LA thought it sounds obvious. My question however is more on the line of: What if I drink a small glass of LA? What about a glass? a cup? a bottle?

@knm241 I had a really difficult time finding information on that subject. I thought at least I could cover the basics of what happens.

No, don't drink it... And here's why.
Ingesting lactic acid or for some reason having too much of it in your body can cause a variety of health problems ranging from mild to deadly. There are two types of lactic acidosis; the first is called metabolic acidosis and the second is known as respiratory.
Metabolic acidosis - which is what would be caused by ingestion - occurs when the fluids in your body build up too much of the acid and your kidneys can no longer keep up with the demand placed on them. Or they over respond and remove too much base from your body, leaving you acidic.
Respiratory acidosis is caused when your lungs cannot effectively remove CO2 from the blood. A buildup of CO2 leads to a more acidic body chemistry.
Regardless of what the cause of the acidosis was, you can expect some of the following.
Symptoms of metabolic acidosis:
~Rapid and shallow breathing
~Confusion
~Fatigue
~Headache
~Sleeplessness
~Lack of appetite
~Severe acidosis can cause shock, organ failure and even death
Diagnosis of acidosis:
A series of blood tests will check calcium, sugar and electrolyte concentrations in your blood.
My sources for this information:
Healthline
WikiPedia on Lactic Acidosis

Whoever did the down vote, please do tell me why. I would be very happy to edit my question if necessary.

Pardon moi, I'm not an expert in biology: So LA will pass intact in the stomach and adsorbed by intestine and make to the bloodstream. Since then it is analogous to the naturally produced LA and I will experience the same symptoms? Assuming the concentration is not high enough to sore my throat

@L.B. I did not downvote but whoever did probably did so because your answer sounds rather facetious -- i.e, practically speaking, normal/healthy humans would probably have no more trouble tolerating an acid load from some lactic acid solution than they would by simply eating a lemon, for example. So, your answer is simply quite the exaggeration for normal/healthy folks, to say the least!


text:
Using a Sphygmomanometer
If you were to use an older sphygmomanometer and a stethoscope to record blood pressure, why would you hear no sound when the cuff was inflated to 160mmHg

Welcome to Biology SE. Here at Biology we expect people to show at least some effort in answering the question when it comes to home work assignments. What did you try to solve this question? Any thoughts?

This happens with a new sphygmomanometer too.

The measured blood pressure is the radial pressure exerted by the blood column againt the arterial wall.
In a normal patient, this pressure varies between 120 mm of Hg and 80 mm of Hg.

click on the image to go to the source
When a cuff is inflated to 160 mm of Hg, the arteries collapse and circulation is temporarily suspended. As blood flow does not occur, no sound is audible.

The korotkoff sounds that are heard while measuring BP are due to disturbance in the streamlined flow of blood. When auscultating an artery without applying pressure no sounds should be heard in a normal person. Generally they are heard when blood flow occurs in spurts. This occurs when the cuff pressure is lesser than the systolic pressure but more than the diastolic pressure.


text:
What's the best wat to combine biological replicates in qPCR gene expression analysis? (2^(-∆∆Ct) method; one-way anova, turkey's test)
I am measuring the levels of gene x after transfection of cells with a plasmid and I want to compare them to the levels in mock-transfected cells. I did three different transfection experiments, in different days (three biological replicates). I then quantify expression through RT-qPCR.
How can I combine the data from the three biological replicates?
I was applying the ∆∆Ct method to each biological replicate separately, and then combining and analyzing the final fold change of the three replicates in a one-way anova, with turkey's test for significance calculation.
My supervisor suggested a different strategy: calculate the ∆Ct values (Ct mutant - Ct housekeeping) of the three biological replicates, then calculate the difference (∆∆Ct) of each ∆Ct with the average ∆Ct of the mock-transfected cells (∆Ct(transfected cells; replicate nr. x) - ∆Ct(mock; average of replicates)). Then, calculate the 2^(-∆∆Ct) of each ∆∆Ct obtained.
In both ways, at the end three fold change values are obtained (one for each biological replicate). However, the variance is much greater in the second method and, for example, there's no significative difference (one-way anova, turkey's test), while the significance is reached with the first method.
My question is: which method is the best? And, possibly, why?
p.s. I really hope I made myself clear, it's not easy to explain with words what I mean. Please tell me if you cannot understend some parts of the question.


text:
Feet size correlated with testosterone in women?
Do females with bigger feet have more testosterone? Examples:
1.Regular-sized women with larger than average shoe size
2.Taller women who tend to wear larger shoe sizes more often than not
I ask because some people say that when women feet get bigger they resemble men's feet more. I ask if this such resemblance is indicative of testosterone higher naturally in these women vs. women with smaller feets. I hope someone can understand and apply these methods to an answer.
For example my sister have bigger feet (size 10 in women's Canada) and people have always told her, especially family, that her feet look like a guy's feet/structure more because they are bigger.
Like the genes that mold the bone structure and design of the foot could having higher test. impact the feet and give the women with larger types feet that people say are more masculine more natural test?

can you add any scholarly publication to support asking this question? this sounds unfounded... also, how does testosterone affect bone growth? you suggest that bone length is somehow increased by increasing concentrations of testosterone in the blood - is there any evidence for that at all?


text:
Hedgehog AP Bio question
Could someone please explain this AP Biology question? I know the answer is C but I do not understand why. Doesn't Smo prevent gene transcription? If you "block its activity" then wouldn't it cause gene transcription, whereas the goal of treating cancer is to prevent transcription? Please help!

Reread the line: "When Hedgehog is absent, Ptc inhibits another protein known as Smo"; Hedgehog is present in the cancer cells, so what you want to do is to mimic Hedgehog's absence. The question is hard because there is a lot of inhibitory and disinhibitory activity in this pathway, so that's what you have to do, try to follow all those +s and -s; it might be helpful to draw the whole thing out as a block diagram, and to take that approach with similar questions in the future.

Thank you! This was actually helpful, I think the information was worded a little weirdly - "When Hedgehog is absent, Ptc inhibits another protein known as Smo, which, in turn, blocks the activation of a group of proteins..." I think I was thrown off by the end of this sentence, because the way the sentence is constructed makes it seem like when Smo is inhibited it blocks the activation of a group of proteins, when it was actually the opposite idea!

I'm just going to outline the alternatives, I'll leave validating why choice C to you.
Choice A. If the new molecule acts in the same fashion as Hh, the results will be identical. If the new molecule bound to Pct but did not effect a response, that might work.
Choice D. Addition of Ci into the nucleus initiates transcription which seems to be the issue here.
Choice B. Best wrong answer! Can you inject enough stem cells to make a difference? Will the cells have some adverse effect? More importantly, the binding of messengers to receptors is a reversible process. The Hh will be able to detach from Ptc on the stem cells and eventually interact with Ptc on the native cells.
So, what effect will Hh have if the Smo in unable to respond?

Thank you! This was great! Especially your justification for B and explanation that binding to receptors is a reversible process. Now I why that choice was incorrect! :)


text:
How does genetical variability works on bacteria?
I'm very Lay in biology, but I was studying the subject and the following problem emerged:
It's known that all bacteria are unicellular beings, and their reproduction it's asexual. Besides of that the indiscriminate use of antibiotics leads to the development of more severe infections, because of a process of natural selection and survival of the most resistant. How do we explain this process considering that asexual reproduction doesn't generate genetic variability, besides mutation? Why do we have this differences, if asexual reproduction generates clones?

Have you heard about plasmid

The question is based on the false assumption that sexual reproduction creates genetic variance. If we neglect epistasis, then on average segregation and recombination do not increase genetic variance within the population.
All 3 of the following processes present in some bacteria lineages do increase the amount of genetic variance:

conjugation
transduction
transformation

You should have a look at the wikipedia articles.


text:
How conscious are mammals that mating leads to pregnancy and offspring?
Does a pregnant female mammal know that its pregnancy is the consequence of a previous mating? Or are humans the only mammals which are conscious of it?

Some animals present potential mates with nesting sites; the female chooses the mate based of the suitability of the site. Many females are attracted to mates by specific characteristics before they mate (a present of food to demonstrate hunting prowess, etc.) Some females protect their litters from non-paternal males, but allow the patenal male access. Does this mean anything in terms of consciousness of the result of mating or is it all sub-cortical? We'd have to have some method of communicating with animals to know. Otherwise we risk projecting our beliefs onto the animals.

Within mammals there is a huge diversity in any trait, including cognition. A dolphin can make concepts connections that a shrew certainly can't. Are you interested to any mammal?

I have trouble citing the exact source now as it's in one of my books at home, has 'sex' in the title (Sex in History), and I'm at work and can't Google that. But needless to say, the book made mention of studies of isolated, modern human tribes where it was evident that the people of the tribe had not made the connection between pro-creation and child-birth. Rather, intercourse was often tied to specific rituals that had a side effect of birth.
So there are a few things that one can extrapolate from this:

Pre-historic humans may have often not been aware that sex led to procreation
From that one can extrapolate further that no animals have this awareness either, as we are the most intellectual species on the planet

Further, the evolutionary development of sex points to this too. The ultimate cause of child-bearing is propagation, but the proximate cause of child-bearing is pleasure. Before life could be aware of the connection, there needed to be a reason to have sex, and so we would have developed in a way that encouraged pro-creation for no other reason than we liked doing it. Eventually we were bound to connect the dots, but we're oriented for this behavior regardless.

This really cast doubts on (or is casted doubt on by) the concept of paternity. In species where the father expends significant effort for the offspring, I am wondering how this can be motivated without a sense of ownership of the offspring. If such a sense exists, I wonder how it can come about without knowing that the offspring it is born of the father as much as of the mother

It is completely feasible for paternalistic behavior to exist without being 'conscious' of the connection between mating and pregnancy, but without going further into that in a comment, I'll just say that parental behavior across the animal kingdom is incredibly diverse.

Wow, I've asked a question about this on another stack exchange. Please if you find the book, I would be very grateful if you gave an answer. See my question here.

For that an animal would have to know the concept of mating and pregnancy. It’s not called the sex “drive” because it requires consciousness in order to mate or become pregnant. It’s pretty automatic and subconscious. As any couple that actually tries to become pregnant but can’t can probably attest to.
So unless you need to communicate a concept to somebody else you may as well not have a concept. Like those human cultures that only have three numbers. One two and many.


text:
Is this a counter-example to Darwin's theory of evolution?
Somewhere I read following paragraphs giving one counter-example to Darwin's theory of evolution.
(By the way, I am a physicist and not a biologist, but I am interested in this field.)
Do these paragraphs point to the reality? What is the current status of "theory of evolution of species" ?

"Darwin cited the giraffe as an outstanding example of natural
  selection.  Supposedly, as a result of extended droughts, the supply
  of green leaves could be obtained only at the top of the trees, and
  therefore the shorter necked giraffe died off.  The giraffes which
  grew longer necks survived.  However, there is no evidence whatever in
  the fossil record or elsewhere that giraffes with short necks have
  ever existed.  And what would have happened to young giraffes with
  relatively short necks?
Darwin failed to realize that body characteristics in offsprings are
  determined and programmed by DNA factors of the Genes or the Genetic
  material of the parents, and not by the stretching of the neck or any
  other bodily exercise."

Where is that quotation from?

@James: I got an email from someone whom I do not recognize/know; this is similar to a spam email.

Ignore it. There is a lot of painfully wrong/uninformed statements in there. Berkeley is a good place to get an overview of the modern understanding of evolution.

As a matter of fact, there is fossil evidence of shorter-necked giraffe ancestors: http://www.livescience.com/52903-transitional-giraffe-fossils.html  Also remember that fossilization is a very rare happenstance (otherwise we'd be up to our necks in them), so not every intermediate form will have left fossil evidence.

Wow...Are some creationists spamming people to spread their believes now?!

That missing links are not found doesn't mean they are not there. Further, why on earth bother about spam?

"and not by the stretching of the neck or any other bodily exercise." was never put forward by Darwin, instead, it was Lamarck's theory of Acquired characteristics.

the three evolution videos from Stated Clearly are the best video explanations of evolution I have ever seen. I recommend watching them it will help you a lot. https://www.youtube.com/watch?v=0SCjhI86grU

Giraffe necks being long because of 'reaching' is false. The neck size is due sexual selection.
The writer of the paragraph fundamentally misunderstood Darwin, he never argued that the act of stretching of necks would make them longer in subsequent generations, that is Lamarkism, which is what Darwin argued against.
Darwin postulated that there exists some sort of information carrier which can be transmitted from parent to offspring. At the time there was no understanding of DNA or of any type of 'genetic material', all of early genetics actually was done statistically on abstract 'lines' of genes with no conception of DNA. Genetics as a field of study doesn't require a DNA model for genes.
Likewise, knowing what DNA is or isn't doesn't matter to the theory of evolution. Evolution is an intrinsic process of change in any system where there is heritable variation and selection. If you have self-assembling robots competing for a limited amount of scrap metal and which can make errors (and those errors are copied to future generations) they can be thought of as evolving.
Now given the restrictions on any system of heritability, variation and selection the result is evolution. Now the question is can evolution explain speciation that we see in the natural world.
I've studied genetics for just over 10 years and so far the answer has always been yes, it explains it amazingly well. There is no alternative theory or idea which can explain the observed variation in DNA between species, in cancer cells etc... as well as Darwinian evolution does.

In one of the posts here, some one wrote about the famous paper "Gould and Lewontin, the Spandrels of San Marco". Does that paper support Darwin's theory ? I have not read that paper; I came to know about it just few minutes ago. But looking all around, my view is that Darwin's theory is not accepted by ALL biologists. Is this my view correct ? Pardon me for my lack of biology knowledge.

That paper is about another, what I think is more of a semantic argument in genetics. Does evolution act at the level of the entire holistic organism or does it act at the nucleotide. Regardless, there is no doubt that both sides are discussing the action of Darwanian evolution.

Also to clarify, my professional experience is that all geneticist I have met accept and apply Darwin's theory. I would make the analogy that evolutionary theory is as much a consequence of our universe as is the relation of force to mass * acceleration.

A few comments. While it might be true that neck size is under sexual selection, it is not quite the point that the post is trying to make. Also, you would need a reference to backup the claim that mate choice is based on neck size in giraffes. You slightly misrepresent evolution as being the result of natural selection only while several processes affect evolution (such as genetic drift typically). I am not sure I understand the point of highlighting that early evolutionary biologist knew nothing about the structure of DNA (it is true but arguably off-topic for the post IMO).

A few comments (suite). The sentence  knowing what DNA is or isn't doesn't matter to the theory of evolution is quite misleading IMO. I am not sure either why you say "Now the question is can evolution explain speciation that we see in the natural world.". Also "Lamarckism", not "Lemarckism".

@remi.b I understand one can take a DNA-centric view of evolution and for all practical purposes that is correct. The point I'm trying to make is that evolution is a consequence of the properties of DNA based life, namely heredity, variation and competition. In that way one can know nothing about DNA but still understand the theory of evolution. Evolution is the process.

@Artem: And as a matter of simple fact, Darwin knew nothing about DNA (it wasn't discovered until a century later), or even Mendelian genetics.  His theory was based on observation.  Indeed, we could have evolution that's not based on DNA, as for instance self-reproducing machines.

@atom yes, the theory of evolution (whose modern version has, well, evolved enormously since Darwin's days) is absolutely accepted by the scientific community. There are some people (AFAIK exclusively in North America) who reject it but they are essentially considered crackpots by the broader community since they simply don't have any leg to stand on scientifically.

Darwin cited the giraffe as an outstanding example of natural selection. Supposedly, as a result of extended droughts, the supply of green leaves could be obtained only at the top of the trees, and therefore the shorter necked giraffe died off.

The term outstanding is funny in its usage here but otherwise this text is quite right so far.

However, there is no evidence whatever in the fossil record or elsewhere that giraffes with short necks have ever existed.

Actually there is. See this popular science article suggested by @James.

And what would have happened to young giraffes with relatively short necks?

The answer in the text above. It rightly says the shorter necked giraffe died off.

Darwin failed to realize that body characteristics in offsprings are determined and programmed by DNA factors of the Genes or the Genetic material of the parents [..]

This is an awfully phrased sentence making it very clear that the author has no idea about genetics.

not by the stretching of the neck or any other bodily exercise

Sure. The concept that individuals stretch their necks, necks become longer and this characteristic is passed on to the offspring is wrong indeed. This is known as Lamarckism. It is funny because the above text describe natural selection and it then says that it is wrong by making a straw man, misrepresenting natural selection as a Lamarckist process.

What is the current status of "theory of evolution of species" ?

You should have a look at the post Is evolution a fact?.
You should also have a look at an intro course to evolution. There are several online and free introductory ressource of information on evolutionary biology. Understanding Evolutionby UC Berkeley is probably one of the best. It is very short, very introductory and will already teach you a lot.

The theory of evolution of species is about as solid as the theory of general relativity.. may even better considering that there are no known situations in nature that invalidate it unlike say... when general relativity meets the very small and encounters the theory quantum of mechanics.
The  giraffid animal which had short neck... would not have been recognized as giraffe. it would have been the ancestral species to the giraffe. The closest living relative to a giraffe is the okapi. https://en.wikipedia.org/wiki/Giraffid


text:
What is gene,alleles and traits?
Gene is present on chromosomes so the alleles should be same as gene but what is difference between them and what is traits?

The "traits" part of your question (which is really a separate question) is probably answered here: https://biology.stackexchange.com/questions/48692/how-to-define-a-trait-objectively

An allele is a variant of a gene. To understand what that means, the easiest is to consider a simplified example...
Simplified example
There is a gene for eye color. Eye color is a trait (aka. phenotypic trait). In the human population, there are different variants at the gene for eye color. These variants are called alleles. There is the allele 'blue eyes', the allele 'green eyes', the allele 'brown eyes', etc...
Locus
Above I wrote An allele is a variant of a gene. It would actually be more correct to say An allele is a variant at a locus but I did not want to introduce one extra word too early. A locus is a region of arbitrary size on a chromosome.
Genetic variation and phenotypic variation
If there are more than one allele at a given locus, then there is genetic variation in the population at this locus. This genetic variation can cause variation in various phenotypic traits.
Considering again the example of the gene for eye color, the fact that there are different alleles at the gene for eye color causes that there is variation in eye color in the population.
Although it may be too advanced for you, you can learn more about these concepts and how it related to heritability in this post.
Source of information
You can also have a look at the wikipedia articles

Allele
Gene
locus
Phenotypic trait

Or have a look at an intro course such as these ones at Khan Academy.


text:
During acid reflux and vomiting, is the burning sensation from pepsin or acid?
When one's stomach contents enter one's esophagus, a burning sensation usually ensues. Is this from the enzyme pepsin breaking apart your cells or just from the acid?

It is the acid that causes the burn
Medicines like proton pump inhibitors (e.g. Prilosec), or H2 receptor antagonists (like Zantac) that reduce acid secretion reduce the burning sensation.  Medicines that neutralize the acid like calcium carbonate (e.g. Tums) also reduce the burn.  These medicines do nothing to the secretion of enzymes.
ADDENDUM. @anongoodnurse wants references.  Maybe in exchange she will remove that pesky down vote.
Cimetidine won the team that developed it the Nobel prize - the first rationally (as opposed to empirically) designed drug.  It was designed to very specifically reduce stomach acid.
https://www.acs.org/content/acs/en/education/whatischemistry/landmarks/cimetidinetagamet.html

Smith Kline & French's multidisciplinary research team first looked at
  the physiological cause of acid secretion. They confirmed that a
  molecule found in the body called histamine triggers the release of
  acid when it binds to a specific receptor (now called the H2-receptor)
  in the stomach lining. Their aim was to find a molecule that
  successfully competed with histamine in combining with the receptor,
  but then blocked, rather than stimulated, acid release. Such a
  molecule was called a histamine H2-receptor antagonist and represented
  a new class of drugs.

This and the successor class of drugs (proton pump inhibitors) are very specifically designed to decrease acid secretion and do little else.
The fact that billions of dollars worth of these drugs are sold means that persons suffering from reflux pain / stomach ulcer perceive that their pain is reduced by a decrease in acid secretion, and so are willing to pay.

Tagamet® was greeted with great enthusiasm by doctors and patients
  alike. Ten years after its introduction, it had achieved sales of one
  billion dollars and had become the world's number one prescription
  drug.

You need a source for this answer, and truthfully, the pathophysiology of reflux pain is incompletely understood.

@anongoodnurse - adequate references?

I didn't DV! Thought about it but didn't; commented instead. That's the problem with commenting when there's a down vote. :( People make assumptions. (I did DV the other posted answer, however.) But good job adding sources!

Actually, I also just decided to upvote because of the improvement of the answer. (I still maintain that the pathophysiology of reflux pain is incompletely understood.) But still, did not DV. Therefore my UV only counters one DV.

@sorry anongoodnurse.  Actions of any kind are sparse on these bio stack questions and I jumped to conclusion.  BTW: I appreciate the double entendre in your moniker.

Pepsin is a protein breaking enzyme which is most active in acidic pH. Stomach is protected from its effect by mucus, but oesophagus and larynx don't have much mucus so pepsin reflux will cause injury. So burning sensation is from both acid and pepsin.
{In contrast, if pepsin refluxes into the oesophagus and above it is damaging as there is no protective mucus layer and also the squamous tissue (the cells that line the oesophagus) is more sensitive. Research has shown that the surface cells of the larynx and airways are even more sensitive than the oesophagus to injury by reflux and pepsin specifically.} ( an excerpt from  https://www.peptest.co.uk/reflux-the-role-of-pepsin-explained/ )

Your source is a for-profit advert for a diagnostic test that measures pepsin. For profit sites are not a reliable source of information. It's true that pepsin most likely damages the larynx, but it's role in the pathophysiology of "heartburn" (typical reflux pain) has not been proven.

Read this https://www.hindawi.com/journals/ijoto/2012/646901/ Don't say that this is also for profit. Do you have any proof for your claim?

Yes, I do, but commenters don't need to prove they are correct. I actually read that paper you linked to in the comment before you commented; did you? It discusses the role of pepsin in damage of various kinds but not in symptomatology.

Its damaging along with acid so the burning sensation is cumulative. DO you have any proof for your claim?

Again, yes, I do. Your comment is only your opinion; your link doesn't support it. Did you know that a lot of GERD is painless? Sometimes the only symptom is a cough. I suspect pepsin may have something to do with that. Other non-pain symptoms also occur. Yet the acid (and pepsin) is there. Hmm.


text:
Do all human cells have all the same organelles?
I know that not all human cells have nuclei (erythrocytes eject theirs before they are fully matured), but do all human cells have all the other organelles? The two I'm particularly concerned with are the Golgi apparatus and lysosomes.

sperm often lack certain organelles, so are you including germ cells.

The presence of an organelle in a cell is strongly connected with its main function. For example in red blood cells, to have maximum space for haemoglobin and hence oxygen storage, many of the organelles are not present such as nucleus, golgi complex, lysosomes, etc. Another example can be of liver cells or muscle cells having a very high amount of mitochondria and ribosomes for high ATP production and protein synthesis. Similarly, each cell is designed in the most efficient way that aligns with its main function.
The answer to your question is no. Not all cells have golgi complex or lysosomes.
One thing that is important here is that the presence of golgi complex is linked with the presence of lysosomes. If there are no golgi complexes, lysosomes are also not present there.
Hope it helps.

Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers in the help center.

I believe that yes.
Here is more to read about:
https://bscb.org/learning-resources/softcell-e-learning/golgi-apparatus/
"is found in all plant and animal cells"
and explanation why so
https://sciencing.com/would-did-not-golgi-bodies-8657737.html
I am no expert in this but I was looking for it as well, I believe it is right.

This is wrong. Erythrocytes and thrombocytes do not have golgi complexes. OP asked if all human cells have all the other organelles, so he is including those blood cells that lack nuclei. Anyway even then, I would not be surprised if some cells don't have a golgi complex some of the time.


text:
Study on Introns?
I am curious whether there has been a study done on the effects of removing introns. Specifically, what happens if you genetically edit a eukaryote genome to no longer contain introns? Or maybe just a specific gene where the introns don't overlap with exons depending on splicing. Has any such study been conducted?

Have you read up on the roles that introns play in eukaryotes?  To start you could look at a related question on this site and then follow "Related" links from there. What can you conclude from that information?  In general, we encourage you to do some research on your own and then ask questions informed by what you have learned (ideally with references to reliable sources).  ——— You may also wish to consult the help pages starting with [Ask] questions effectively on this site and then edit your question accordingly. Thanks!

The answer is yes of course, and you can find papers on the topic by a simple internet search.