1.0 Intro Deweirdifier
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[edit] Physics of cells
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Reasearch/experimental/Original reasearch. Uploaded by --Deweirdifier 14:42, 7 November 2009 (UTC)
Multimedia from here http://www.torrentz.com/96f62b834cac1bbc3abb5eb8555dcc49b7346e23
index The Deweirdifier
[edit] 1.0 Intro
Normaly, the introductory sections, should not be needed, but since a majority of you suckers, came out of skool, believing that the mass of a tree, comes from the ground, i have to plug some of the holes my self.
In theory when you want to study something you just go thru the data. However in real life, raw data are rarely of the quality that we would like. In these cases, a statistical aproach on the observations is obligatory, to make some sense of whats going on, despite that we normaly don't have data of good enough precision. A litle example will demonstrate the trick: Say in a car, we put a sensor, we could put a precise and most importantly, expensive sensor, but the clients would not be very pleased, a more inteligent aproach, is to put an inexpensive and less acurate, sensor. We make the sensor, redo the measurement a great number of times, then we simply take the average of the results, and then we can display a result with more acuracy then what the sensor can realy give. Of course this litle trick works, only if the noise in the data is realy random, this stay true up to a point, no way, to do an experiment with a ruler a quadrilion times, and then do the average, you'll add everything from you systematicaly puting the 0 at the wrong place, to the gravitational pull of the moon. You need to know what you are doing, or it's not going to work. This will be done here all the time. If you doubt this aproach, then you should also doubt the safety of cars, airplanes, trains and whatever.
The power of randomness is so great, that it can even be harnessed to estimate something as esoteric as the value of number π. The nice thing about it is that you can try it out your self. We draw tightly a circle inside a square that touches all 4 sides of the square without spiling out. We through randomly, grains of some kind(seeds, sand...) on the drawing. The number of grains, is proportional to there weight, there numbers are also proportional to the surface of the shapes. So the ratio of there weights is also the ratio of the surfaces, that is π/4 (circle/square). Just weight them. A variation can be done with H2O and corectly shaped colectors.
[edit] Some physics
Heights of meeting waves simply add up, but keep track of their own direction of movement. When superposition is over, they go on with their initial individual shapes. When put in a space where they bonce of the edges, they come back and interfear with them selves. Generaly this will show a patern that varies with time, but for certain particular sizes of the waves, at particular points, the heights will add up to 0 at all time, forming standing waves. Of course the reverse is true too, a fixed frequencie, will have an infinite number of shapes inside of witch it can produce standing waves.
http://www.youtube.com/watch?v=GtiSCBXbHAg
The video shows, a regular board, on top of a regular speaker, with regular salt poured on it. When the speaker is turned on, the board vibrates, so waves travel inside the board and bounce on the edges. Wherever the board vibrates, the grains of salt will bounce off, so we actualy see the negative image of the vibration. When the frequency is just right, some points have at all times 0 vibration and the grains of salt will acumulate there, revealing the stationary patern to us(chladni plate). As the frequencies vary, the sizes of the waves vary too, usualy having a board that vibrates everywhere, but at some frequencies, static paterns emerge. As you can observe, the paterns are not trivial to guess, and depend, both on the shape of the board and the frequencies of the waves.
[edit] 1.2 Some chemistry
Electrons are realy waves, the nuclei too are waves, but at our level we can ignore that, and assume that they are points. The wave behavior of electrons is a litle bit more peculiar then say sound waves, but we can simplify this here. Lets say, that the charge of the electron is distributed in proportion to the amplitude of the wave("electronic wave"). The frequency is proporsional to the energy of the electronic wave. The electronic wave will be traped inside a space around the nucleus, because of the atraction(electric field) from the nucleus, and deflecting at the edges. If 2 or more nuclei get close enough, traping regions overlap, electronic waves can flow inside of the comon traping space, forming a molecule. As a further complication, the electrons tend to deflect from places that alredy have high amplitudes(negative charge). http://www.gwyndafevans.co.uk/thesis-html/node79.html (image only) complicated cross section
In the molecules however, electronic waves, are alowed only as standing waves, at the lowest energy level available(they iradiate energy untill they do). In final analysis, the lowest energy standing wave patern, depends on the positions and natures of the nucleis. The nucleis on there part, try to minimise there energies too, they try to position them selves where the amplitudes are highest (more negative charge) in the 3D standing wave patern, and on the same time, try to avoid each other as much as possible. All the parts, of the molecule are forced in compromise positions, so that the molecule as a whole, minimises it's energy, as much as possible. In this way molecules get there specific shapes and properties.
[edit] Some biochemistry
Molecules aren't frozen solid, they colide with other molecules, and electromagnetic radiations, thermaly vibrating vigorously, around a "base" conformation determined by the standing wave patern. Like a mass on a spring, it's "base" conformation, is to be imobile and as low as it possible, but with extra energy, it oscilates randomly around that position. The equivalent with the board, is that the shape of the board would vibrate around its rectangular "base" shape.
A protein is typicaly a long molecule folded on itself, like a vibrating ball of entangled threads; various parts of the protein interact with eachother and influence the electrons standing wave patern, while thermaly vibrating.
Proteins do everything , in the cell, as nanomachines or as part of structure. A protein is suposed to achieve a specific task, typicaly, when the protein interacts (a electromagnetic field of some sort: colision with an other molecule, charges, temperature, ...) its base-patern conformation can't sustain the standing wave anymore, the electron waves start to exchange net energy with the environment, thus changing there frequencies, frequencies and shape shift until a new base-patern comformation is found. Like when the board change its patern when the sound frequency changes, in the video. This new conformation is not at all random, in the process something useful hapens, the thermal vibration isn't an annoyance, it's taken in to acount in the functioning of the protein.
http://www.3dotstudio.com/zz.html (image only) muscle contraction, red: thin filaments, blue: thick filaments
A litle example, with how muscle work. The elementary moving part of a muscle, is a litle cylinder, thin filaments are anchored on the bases of the cylinder, like 2 flat hairbrushes facing each other, thick filaments are held(but not atached) in between the thin filaments, in paralel with the thin filaments. From the thick filaments, protrudes the active molecules, that actualy produce the movement, basicaly they do this by "walking" on the thin filaments, so that the 2 "hairbrushes" come closer together. The "walking" is done in a series of signaling events and conformation changes, including: a small and very polar molecule(3 very negative parts, forced close together, thus containing a lot of energy), that ataches on the active molecules, a part of the small molecule brakes off, and net energy is transferred to the active molecule(through the comon electron waves), producing a conformation change(the most important) in which the active molecule is croaked. The power stroke of the "walking", on the thin filaments hapens when the croaked molecules shift back in to shape. 5 "steps" are done in a second(1 second is 5 ticks in a mechanical clock) and eficiency is around 14%. Muscle can only contract, they need an outside force(muscle,tissue elasticity) to reset them, they usualy come in compeating pares for performing full movements. Consequence of this, a crocodile's jaw, can reap of, a human arm, but a human hand is strong enough, to hold it closed.
The proteins are carefuly balanced, so at each interaction the apropriate conformation change hapens, in the standing wave paterns. It's extremely hard to engineer by hand a working protein(the universe wouldn't be enough). A real life protein can have thousands of aminoacids, they are way to many variables. Its a type of complexity similar to a rubick cube, but far worse. The more practical way to design artificialy a protein, is stohasticaly. In a test tube we produce trilions and trilions of diferent proteins, more or less inteligently, and we aply some sort of tests, until we run in to the 1 with the properties that we want. You can check this out your self, [DATA/some biochemistry/foldit 19/09/2009 files] or up to date files(ooooohhh, thats reeeeaaly osome shit 8D).
Proteins in a cell, interact, by floating around, and bouncing on each other, when by a hapy coincidence they run in to what they are suposed to react with and in the correct direction. They do this, while restricted in specific areas of the cell, blocked inside certain vesicles, amfifilic proteins floating in side membrane, atached on lipids of membranes, atached on the cellular skeleton...
[edit] Some cell biology
http://www.youtube.com/watch?v=BVvvx5HGpLg
Events, inside and out side of a cell,trigger a cascade of interacting molecules(not only proteins), if certain conditions are met, the reacting chain of molecules will finaly activate a protein that does something useful. The whole cascade, is realy a program, and each of its elements, is an elementary instruction, "if X then Y". DNA is not a programe, is just a cookbook with recipes for proteins, the proteins are doing all the cool stuf. This molecular program is very extensive and complex, a cell is a control freak, it controls whats going on inside it, to a very high degree.
A simplified example, certain proteins translate DNA to RNA, but they can only start at a specific start sequence and end at a specific end sequence. Bacteria are gourmet, they prefer eating glucose, by default the gene that codes for glucose degradation has its start sequence free, and get translated all the time. Don't worry, the cell doesn't get overwelmed with new proteins, proteins actualy don't last long. An other type of sugar is galactose, a protein is atached on the start sequence of "galactose degradation protein" gene. That protein has 2 sites, acepting glucose and galactose, from the out side glucose and galactoze difuse and are free to interact with the protein. If there is glucose, the protein bounds with it, and holds tight on the DNA, no mater what the concentrations of galactoze are. If however there is galactoze and no glucose, the site for glucose will be free, and that of galactoze ocupied, under those circumstances only, the protein will release the DNA brand permiting for the translating proteins to do there thing. Similarly the "glucose degradation" gene will get blocked. For completeness, RNA brands, have a none coding sequence at there end that repeats, a number of time, every time, a protein is finished being synthesised, a peace is cut off, acting like a counter, when the sequence is completely degraded, the whole brand is degraded.
