# Yggdrasil

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222

1. ## Glowing Plants

To be able to make the appropriate plasmid in order to transform a plant would require a molecular biology lab as well.
2. ## "Experiments"?

Here's a pretty cool experiment to extract DNA using household items: http://gslc.genetics.utah.edu/units/activities/extraction/ A link to a page discussing the extraction of caffeine from tea: http://www.chemicalforums.com/index.php?topic=7094.0 A page discussion esterification experiments: http://www.scienceforums.net/forums/showthread.php?t=14996 And of couse, the classic diet pepsi + mentos: http://video.google.com/videoplay?docid=-3108487944219284889&q=diet+pepsi+and+mentos
3. ## Sturm Lioville System Problem

for © you shoud find that the p(x) obtained in (b) is zero at the boundaries (x=a and x=b). Therefore, at the boundaries: q(a)y = (lambda)r(a)y q(b)y = (lambda)r(b)y which has solutions only for certain values of lambda. These lambda are your eigenvalues. Also, if you want to look up more resources on this topic a Strum Liouville system is another name for the self-adjoint form of a differential equation.
4. ## Question about selection of college courses(O. Chem related)

If these are both introductory courses, I'd say that they'd be of similar difficulties. If I were to choose which one may be harder, I would have to say it depends on whether you're better at reasoning out answers (ochem is easier) or whether you're better at just memorizing (biochem is easier). However, I think that it's better to take ochem before taking biochem since ochem will help you somewhat with understanding the logic behind some biosynthetic schemes.
5. ## interesting result of laplace transforms...

That's an incorrect usage of the convolution. Here are the correct forms of the convolution: $(xe^x * x) = \int_0^xte^t(x-t)dt = \int_0^xt(x-t)e^{x-t}dt$ What you wrote is a completely different convolution: $\int_0^xt^2e^{x-t}dt = (e^x * x^2)$
6. ## interesting result of laplace transforms...

Are you sure you're evaluating the last inverse laplace transform correctly? I get that the inverse laplace transform gives: $f(x) = 2 (xe^x * 1) - (xe^x * x)$ where * represents convolution. In other words: $f(x) = 2\int_0^xte^tdt - \int_0^xte^t(x-t)dt$ Which gives: $f(x) = 2\int_0^xte^tdt - x\int_0^xte^tdt + \int_0^xt^2e^tdt$ $f(x) = (2-x)\int_0^xte^tdt + \int_0^xt^2e^tdt$ Apply differentiation by parts to the second term: $f(x) = (2-x)\int_0^xte^tdt + \int_0^xt^2d(e^t)$ $f(x) = (2-x)\int_0^xte^tdt + (t^2e^t|_0^x - \int_0^xe^td(t^2))$ $f(x) = (2-x)\int_0^xte^tdt + (t^2e^t|_0^x - 2\int_0^xte^tdt)$ $f(x) = -x\int_0^xte^tdt + x^2e^x$ Apply differentiation by parts again: $f(x) = -x\int_0^xtd(e^t) + x^2e^x$ $f(x) = -x(te^t|_0^x - \int_0^xe^tdt) + x^2e^x$ $f(x) = -x(xe^x- e^t|_0^x) + x^2e^x$ $f(x) = -x(xe^x- (e^x - 1) + x^2e^x$ $f(x) = -x^2e^x + xe^x - x + x^2e^x$ $f(x) = xe^x - x$ So, I see no contradiction.
7. ## electrone

When two atoms (A and B) share electrons in a covalent bond, the electrons are neither in A's atomic orbitals nor are they in B's atomic orbitals. The atomic orbitals of A and B merge to form molecular orbitals which are combinations of the atomic orbitals of A and B. The shared electrons reside in these molecular orbitals. For example, when you look at the molecular orbitals of water you can see that they do not resemble the atomic orbitals of hydrogen or oxygen.
8. ## DNA strands.. why are there 2?

Different genes can be on different strands of DNA. So you are correct when you say that promoters and genes can be on the "other" strand of DNA. For example, when you look at the Homo sapiens X chromosome you can see arrows pointing up and down in the column marked O. The arrows pointing up represent genes on one strand and the arrows pointing down represent arrows on the other strand.
9. ## Sp'cefic Sp'cificity!

The proximate origin of stereospecificity in protein amino acids is not that protein structure causes all of the amino acids in the protein to take on the L-configuration. Amino acids are incapable of converting between the L- and D- forms in solution at physiological conditions. Only D-amino acids are present because the body produces only D-amino acids. The enzymes which catalyze the synthesis of protein amino acids in the human body do not produce a mixture of D- and L- amino acids, they produce only D-amino acids. The percent stereospecificity is 100%. It has nothing to do with protein structures inducing stereospecificity of their amino acids. A protein containing an L-amino acid would not be able to convert this amino acid into a D-amino acid. The stereospecificity is not self-induced but induced by the biosynthetic pathways. Similarly, all other biological molecules have stereospecificity because the enzymes which produce these biological molecules catalyze reactions which are 100% stereospecific. The pathway for production of glucose creates 100% pure D-glucose and does not produce any L-glucose. The pathway for the production of fucose produces 100% pure L-fuccose and does not produce any D-fucose.
10. ## Sp'cefic Sp'cificity!

Whenever a biological enzyme recognizes or acts upon glucose, it will almost always be selective for D-glucose and not interact with L-glucose. Similarly, an enzyme acting on fucose will almost always be selective for L-fucose and inactive toward D-fucose. So, yes, some enzymes act on D carbohydrates and some act on L carbohydrates, but in essentially all cases, enzymes are specific for one enantiomer of each species of monosaccharide. Now, you may ask, why are all amino acids (except for glycine) D while some monosaccharides are D and others L? Amino acids gain their stereochemistry from essentially the same reactions (transaminations) while carbohydrates are synthesized from a variety of different reactions, generating a greater diversity of carbohydrate monomers. Why is it significant that all amino acids are D while some monosaccharides are D and others are L? It is not. The D/L nomenclature system is completely artificial, and by themselves, the D and L designations carry no biological or chemical relevance. It would be very interesting if all biological molecules were (+) or (-) since these stereochemical designations carry physical signficance (the dirrection the molecules rotate plane polarized light), but the D/L designations carry no such physical meaning.
11. ## Finding up to date scholary articles, but not paying for them.

The Public Library of Science is a scholarly journal with completely open access content. The Proceedings of the National Academy of Sciences, USA also publishes a few open access articles on their website. And, to answer your question, I will pose another question. Why do people these days expect everthing to be free? I applaud those who offer high quality products for free, but I also recognize that many products take a lot of time and money to produce, so it's unreasonable to expect people to just hand them away freely.
12. ## what is the difference

A sex-linked disesase is a specific class of genetic diseases. The alleles for sex-linked diseases are located on the X-chromosome so recessive sex-linked diseases (such as hemophilia or color-blindness) occur more commonly in males (who must possess only one copy of the disease allele) than in females (who must possess two copies of the disease allele).
13. ## diff. eq. how to solve this?

When you solve a differential equation, it is not guaranteed that your soultion will exist for all time. Note that dy/dx is undefined when y > sqrt(a). Therefore, when your trajectory passes y = sqrt(a), your solution ceases to exist. In the example you provided in the opening post, the solution you plot is valid from 0<t<pi/2. When you apply this restiction to the domain, the soultion is not periodic (as any soultion to a 1st order ODE should be).

15. ## Photosynthesis

The light reaction of photosynthesis produces ATP which is used to make the biosynthestic reactions of the Calvin-Benson cycle (Dark Reaction)thermodynamically favorable. So, one may ask, why do plants use the ATP to produce sugars, when the energy from sugars is just going to be used to make ATP anyway? Well, the answer is that 1) sugars are a more stable form of stored energy and plants can build up larger stores of sugars than of ATP, since ATP/ADP ratios are strictly regulated within the cell. Furthermore 2) sugars play roles other than in energy metabolism. For example, the main structural component of plants, cellulose, is a polymer of glucose molecules. Sugars play other roles including acting as signaling molecules on the cell surface (in the form of glycoproteins and glycolipids) and they also aid in the reproduction of many angiosperms since the sugars in the fruit attract animals which then help disperse the seed in the fruit.
16. ## Biofuels

It's still questionable whether biofuels are an efficient use of resources. Some have made claims that biofuels require a net input of energy greater than the energy obtained from the biofuels (e.g. Pimentel and Patzek, Natural Resources Research 14 (2005), 65-76). However, others say that biofuels do have positive energy return (e.g. Farrell et al. Science 311 (2006), 506-508). However, Farrell et al. do say that, using the current methods of producing ethanol from corn, only 21% of the energy from the ethanol is renewable and that these methods decrease net greenhouse gas emissions by only 13% compared to the equivalent amount of gasoline. However, based on hypothetical technologies which will allow the production of ethanol from cellulose, Farrell et al. estimate that such cellulosic ethanol would have a positive energy return of 90% and would decrease net greenhouse gas emissions by 88% compared to the equivalent amount of gasoline. Such technology could be implemented without creating more farmland as it would use agricultural waste as the feedstock for biofuel production. However, the concerns about the water pollution and other environmental damages from farms and biorefineries are valid points which need to be counterbalance against any potential benefits of utilizing biofuels. I haven't read anything comparing the efficiency of the conversion of solar energy between biofuels and solar pannels, but biofuels offer one big advantage over solar panels: biofuels allow easier storage and transportation of energy (since ethanol is a stable liquid which can be transported and dispensed to cars using current technologies) wheras solar energy goes into the electric grid and therefore cannot really be stored and dispensed to cars efficiently. Whereas there are commercially available cars capable of running on E85, electric cars (which would be needed to use solar energy for transportation) are less attractive to consumers because of the short range and high cost.
17. ## Retroviruses - can this be real?

Some estimate that about 10% of the human genome consists of endogenous retroviruses. However unlike the retroviral DNA from active viruses, these endogenous retroviruses are mostly inactive and have lost many of their functional elements such as the reverse transcriptase needed to make copies of itself. While there are some active endogenous retroviruses in mice, no human endogenous retroviruses capable of retrotransposition have been identified yet. So essentially, they are just junk DNA and are neither harmful nor helpful (though the fact that organisms conserve endogenous retroviral sequences in their DNA may suggest that they may be, in fact, beneficial to the organism). But, you certainly won't have to worry about an endogenous retrovirus from your ancestors making you ill.
18. ## Help!

What patterns does it follow?
19. ## 50+50=100

When liquids disolve in eachother, their molar volumes can increase or decrease depending on how they interact.
20. ## Questions on chemistry

All of the carbons in C60 are sp2 hybridized and therefore form 3 sigma bonds and have an electron in a p-orbital which gets delocalized into a conjugated pi-orbital which extends throughout the structure. All carbon atoms in C60 are equivalent, each acting as the vertex of two hexagons and a pentagon. Furthermore, all bond lenghts are the same (wikipedia's statement to the contrary is wrong). In fact, buckminsterfullerene is the simplest molecule with icosahedral symmetry, the point group with the highest symmetry. Such a fact can be seen by examining the IR spectrum which has only 4 absorption lines as predicted by symmetry.
21. ## sugar

Powedered sugar is also sucrose, $C_{12}H_{22}O_{11}$ or more accurately beta-D-fructofuranosyl (2-->1) alpha-D-glucopyranoside.
22. ## Somatic cell engineering?

The first somatic cell gene therapy treatment was performed in 1990s in the National Institutes of Health. The procedure was used to correct adenosine deaminase deficiency which is a cause of the so-called "bubble boy" syndrome. The treatments did work, however, because the treatment combined conventional methods of treatment with gene therapy, it was inconclusive whether the gene therapy treatments were the primarily responsible for the patients' improvement. Unfortunately, efforts to continue gene therapy experiments in the US have been stymied by the death of Jessee Gelsinger in a gene therapy trial in 1999 (investigation showed that the death resulted from the negligence of the doctors performing the procedure, not from any inherent flaw in the procedure itself). Despite the setbacks in the US, researchers in France have succcessfully treated SCID (another genetically-cause of bubble-boy syndrome) using somatic cell gene therapy. However, the treatment may have the unfortunate side effect of causing leukemia. So, currently somatic cell gene therapy remains an experimental technology which still has many safety issues which need to be resolved. However, it is definitely closer to clinical usage than germline cell gene therapy, and despite its limitations, will still have important usage in the treatment of genetic disease. Somatic cell gene therapy, however, probably wouldn't be used for cosmetic or purposes other than correcting genetic defects.
23. ## DNA Types A, B & Z

Wikipedia has some basic information on A and Z DNA (http://en.wikipedia.org/wiki/DNA#A_and_Z_helices_formation), while you can find the crystal structures of A & Z DNA on the PDB (http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb23_3.html)
24. ## the principles of breathing

Basically, the transfer of electrons from organic molecules (such as fats and sugars) to oxygen is an exergonic reaction. The transfer electrons from carbon to carbon dioxide will not produce a net release of energy.
25. ## how do you figure this out??

Have you learned about power serries (I think they teach this in Calc BC)? You can express cos(t3) and sin(t2) as power serries then integrate those.
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