C_Sagan_Returns

Oh wow, kewl!! I never knew that, thanks so much for the ideas. This was the kind of reply I was looking for. Please, keep em' comin' guys and gals. Also, I understand that most of these species are found almost everywhere but, any suggestions as to how I should isolate these beasts would be much appreciated. CSR

The most obvious example of current conduction in biological systems is that propagated by the "action potential(s)" of nerve cells (as previously stated). A more specific and fascinating mechanism of electricity production in biology is that of ATPsynthase. ATPsynthase is a membrane-bound protein-complex comprised of dozens of species which together function as a molecular turbine. This "proton pump" funnels the residual hydrogen ions (protons, +), left over from the various metabolic processes constituting life, outside the cell. This continuous dumping action inevitably creates a "membrane potential" or gradient because of the accumulation of positive charge outside the cell (or organelle) which results in a charge deficient (due the intrinsic ionization of water), or negative charge, inside the cell (or organelle). The larger the difference, or gradient, the more energy is required to push protons out. Eventually the "flood gates" of the ATPsynthase protein-complex allow protons to flow back, down their concentration gradient, activating the turbine, and manufacturing ATP. Although technically not a flow of electrons, this current of protons is created by the incessant tug of both gradient and charge (opposites attract). Interesting, isn't it? Let's not forget about the Electron Transport System which includes anything involving: NAD+, NADH, FAD, FADH2, and others which participate in oxidation-reduction (redox) reactions transferring electrons from substrate to substrate. CSR

Currently enrolled in Applied Microbiology, I'm responsible for developing a culture collection of > 10 different species. Having only a simple general microbiology background, I don't know many microbes by name. It's been suggested that we bring in samples from outside the classroom and try to isolate and culture several specimens. Fungi can be included, but bacteria should be the focus of this collection. I'm looking for any ideas so feel free to namedrop. Here are some ideas I've got so far: Fungi: Geotrichum fici -- While looking up various genera for an assignment, I discovered G. fici produces a pungent odor reminiscent of pineapple. How would I select an organism ubiquitous to the environment like this fungus (It's found everywhere right??)? Bacteria: Other than the model organisms one is first introduced to (e.g., M. luteus, S. marcescen, B. subtilis, E. coli, etc.) I don’t have many ideas. Characteristics of interest include (!! = Required): --○ The ability to be cultured!! --○ GRAS status (No Y. pestis)!! --○ Possessing unique metabolic processes --○ Having a pleasant scent or beautiful colour --○ Holding historical significance --○ Being interesting in some other fashion Ecological Niches: Aside from hunting specific beasts, one can investigate a plethora of microenvironments. One niche of interest that peaks my interest is the flora inhabiting the human navel and produce that nasty (some have referred to it as "cheese"-like) smell. What are your favorite microbes? Any thoughts? Thanks, CSR

I didn't see anything about exact measurements and different percentages of vinegar. The video only mentions 1L of vinegar and 84g of NaHCO3 (to my knowledge). Was this extra information located in the "sidebar"? If so, I couldn't figure out how to access it!! Where is this "sidebar"? The video also mentions that the final product may develop a yellow tinge as one removes 9/10ths of the water by way of boiling the solution. If one's "Hot Ice" preparation came out dark yellow in colour, would activated charcoal clear up the solution? (I'm not really sure how that stuff works, I just know it does, sometimes...) Thanks, CSR

I saw on wikiHow a pictorial on making "hot ice," and it says, "If you don't have sodium acetate, you can make your own from baking soda and vinegar, but it's time-consuming. Keep adding baking soda to vinegar until it stops fizzing; this reaction yields a diluted solution of sodium acetate and water. Then boil off all of the water to make sodium acetate crystals, which you can treat like the powder as described in the instructions above." What would be the cleanest, most efficient way to make Sodium Acetate? Once it stops bubbling, any extra baking soda might contaminate the desired sodium acetate product. It says to keep adding baking soda, but when the water is boiled off, won't the remaining salt be a homogeneous mixture of sodium bicarbonate and sodium acetate? How do you avoid this and produce a pure product? Thanks, CSR

Is there a CRC or Bible for biochemists? Basically, a reference book which one could use to look up the intra/extracellular concentrations of various metabolites, proteins, lipids, membranes, plasmids and or other macromolecules possibly organized by organism. Maybe containing lists of good buffers to use when working with particular cells or lists of the compositions of certain cells. You name it, it would be found in this tome. Does such a thing exist? What is it? Thanks, CSR

What is the name of this fungi, the article does not specify? Also, let's not forget about Deinococcus radiodurans... http://en.wikipedia.org/wiki/Deinococcus_radiodurans CSR

Whether plants, animals or bacteria, life requires Phosphorous (P) in order to carry out cellular work and provide the hook or glue which links the nucleosides of DNA and RNA. Hypothetically speaking, if one were to prepare media will phosphate buffer, it’s not improbable that Phosphate ions might inadvertently be used as a nutrient. Such processes would eventually destroy the buffer's capacity to stabilize pH. Even under conditions of lower pH (acidic), small amounts of PO4 will be present and their absorption/disappearance should be compensated for according to Le Chat's principle. How is this avoided? Are other P sources used? Or are P buffers used in combination with others for when P is entirely depleted? Thanks, CSR

I wasn't sure where else to post this so forgive me. I've noticed many students with digital recorders in my classes this semester. There are so many different models and brands; I'm not sure where to start. I want something that works well, but at a resonable price. Good battery life and excellent sound quality are my primary concerns. I'm sure many of you own DSRs and I want to know what to check out and what to avoid. Treat this as a poll and share your experience. Thanks, CSR

I’ll start off by saying I’m not an expert (as you might have guessed). So, the big question is, "what would cause something like this to reoccur?" A. Toxin – If the insect injected you with a toxin than that would be the likely culprit for the initial symptoms. Eventually though, this should be expelled from the body. B. Infection – If the insect mediated the transfer of bacteria into you system (i.e. Lyme disease), they could produce toxins, except, like in the first situation, the bacteria would likely die after treatment with antibiotics or just die out over time. C. Virus – This was the first thing I thought of when I read your post. Viruses enter our systems through a wide variety of means including insects and bacteria. Lysogenic viruses like herpes integrate into the chromosome of the cells they infect (skin cells) and rather than just hijacking cells, replicating, and killing the cell (lytic viruses), they lie dormant until awakened. Virulent viral genes will sit there in the chromosome for years, never translated. Then, something (like cellular stress) causes the expression of these genes which leads to symptoms. My Dad suggested it might be Lyme disease which is especially difficult to diagnose. Maybe if you found a specialist, they could help you. Even if it isn’t Lyme disease, there’s a good chance they can help you better than your standard physician. http://en.wikipedia.org/wiki/Lyme_disease Check out the picture. That’s a black and red insect. Hope we helped, CSR P.S.: Where were you bitten (i.e. Country, State, County, Forest/Wet Lands, etc.)?

You can go much lower in what sense?? My point was that bond lengths are measured in Angstroms and biological processes don't exist (to my knowledge) on a smaller level than making and breaking bonds. I suppose an exception would be electron transfer/redox which operates on a smaller level (depending on the distance upon which the reaction is taking place). I think what you're taking about is either a part of quantum mechanics or biophysics not a combination. If you could give me an example I might be more inclined to agree with you. CSR

Beta-N-Acetylglucosaminidase will dissolve Chitin if you can get ahold of some. Good luck with that, CSR

I've noticed you've been using Histidine as an example quite often, is there a particular reason...or just cause it looks kewl? It's okay if you pick the later. So, where is histidine made? Well, you might have already learned that many organisms, including us, are incapable of synthesizing the 20 essential amino acids (including Histidine). We must acquire them from plants or other animals. Plants possess the ability to make ANY of the biological compounds they need from glucose, it's how they were designed (unintelligently mind you), so plants can make histidine if I'm not mistaken. Another huge source of histidine comes from bacteria. Organic synthesis is a given, but it is by far the most expensive mode of production. Reagents in general are not cheap, and you have to pay someone trained to carry out the reactions. The cheapest way to produce Histidine (and other AAs) is by good old natural biosynthesis, which only costs a few dozen ATP (or whatever it is). Almost ALL amino acid supplements found in health food stores were produced by bacteria like E. coli that were bred or genetically manipulated to pump it out continuously at high yields. What I think you're interested in is the chemical origin of histidine or how it's physically made. This can be done in several ways which I've never actually looked into, but you can (Google is your friend)! Once you take an organic chemistry class, it'll be easier to see how the different functional groups might have originated. I would guess that the COOH (carboxyl group) came from CO2, but not every functional group just neatly snaps on like that. For example, you mentioned once the “C-H” between the amino and carboxyl group. This is not a functional group and didn’t just snap into place as is. Any compound made of C-C and C-H alone is called an Alkane. Alkanes, which make up the saturated part of fats and gasoline, are chemically inert and won’t bond to anything without intense heat or UV radiation. The most basic alkane is methane gas or CH4. When histidine is made, methane is not the source for that carbon atom (unless we’re talking about methanotrophic bacteria which are the ONLY organisms that actually use methane as a carbon source). Most carbon involved in biosynthesis comes from either CO2 or sugars and is attached to something reactive like Oxygen or Nitrogen. Note that all amino acids have the same backbone, so I think the more interesting question would be "Where does the imidazole ring come from / how is it made?" This group (sometimes called the R group) makes histidine unique and is responsible for giving histidine its enzymatic properties. Mind you, if it weren't for histidine you won't be able to breathe. To be more precise, you could still suck in air, but because Histidine is required for Hemoglobin (Oxygen Transporter) to work properly, its absence would not allow Oxygen to bind and you would suffocate and die. Does this somewhat answer your questions? I hope this is enough for you to “work with.” If you're looking for something more specific you can look up a step-by-step organic synthesis or the specific biosynthesis/metabolic pathway. CSR

Doesn't quantum imply that we're dealing from within the atom (or at that level)? I don't think there's such a thing as quantum biomechanics, because biochemistry covers all that. The smallest unit of measurement used in biology is the Angstrom. 1 Angstrom = 0.1 Nanometers....that's right, 10X smaller than a nanometer!! To give you an idea, a hydrogen bond is approx. 3 Angstroms (0.3nm). What exactly did you have in mind? Are you talking about something on a smaller level than this? I don't think you can go much lower. CSR

For those of you trying to help me out, I finally figured out how to set everything up (thanks to my prof). Starting with: Moles Acf = moles Aci + moles OH Moles HAcf = moles HAci – moles OH Substitute: “(0.1M)Vol OH” for “moles of OH” in both equations above. Then, substitute: “(Aci)Vol Acid” and “(HAci)Vol Acid” for “moles of Aci/HAci” respectively. This will leave you with: Moles Acf = (Aci)Vol Acid + (0.1M)Vol OH Moles HAcf = (HAci)Vol Acid - (0.1M)Vol OH These two equations can be plugged into the Henderson-Hasselbach Equation yielding: pH = pK + log[ ( (Aci)Vol Acid + (0.1M)Vol OH ) / ( (HAci)Vol Acid - (0.1M)Vol OH ) ] Once you plug in all the numbers and do some math you get: (.4295M)Vol Acid = (.5365M)Vol OH Then, substitute: “(0.05L – Vol Acid)” for Vol OH This leaves you with one unknown…Vol Acid = 0.028L or 28ml That took entirely too long! I guess it was just my algebra. Thanks anyways guys, CSR