Teach me about DNA/RNA

Discussion in 'Biology & Genetics' started by BenTheMan, Oct 13, 2008.

  1. Roman Banned Banned

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  3. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

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    BillyT:

    Welcome to 1970! Everything presented above [about DNA, to mRNA and tRNA, to proteins manufactured on ribosomes] had been learned and understood by that year, and is what we were teaching at UC back then. Things progressed rapidly after Watson and Crick deciphered the manner by which DNA reproduced in the 1950s. Until then, we could see the mitosis in action under a microscope in which the chromosomes split and separated into two new sets, but it was not understood how the chromosomes duplicated. It was not even certain by some biologists that the chromosomes carried the genetic material, until Watson and Crick showed how they could both duplicate, as well as code for proteins.
     
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  5. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    OK I made my short string of RNA and earned by "good job" reward.

    But I am not sure what that big colorful "Universal Gene Code" table was all about. On top, right and left sides are the the four code letters and circles fill the interior - are they the amino acids (with abreviated names I do not recognize)?

    Is it like a chinese menu - take one letter from left, top and right to get the codon for the corresponding amino acid?
     
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  7. S.A.M. uniquely dreadful Valued Senior Member

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    Billy T:

    Those are nucleotides, the building blocks of DNA/RNA

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  8. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Reason I guessed 20 to 25, instead of the much larger number of base pairs needed for mRNA was I have tried to follow the conflicting patten claims of companies working in the iRNA field (RNA intererence - these iRNA do seem to be these shorter pieces, as I underatand them.)

    Thanks to both Roman and CharonZ I am getting the impresion that tRNA is sort of like a well organized "just in time" stock room of an assembly factory. I.e. it has collected the "amino acid parts" that will be needed in just the order needed by the ribosome factory working under the control of the mRNA. (rather than have these amino acids just floating around in the (cyctome?) soup. - that would greately slow production if only difusion chance delivered "amino acid parts" - HUNDREDS OF "WRONG DELIVERIES" before chance got the needed amino acid to the exposed site of the mRNA building the polypetide.

    but I have no idea where the tRNA comes form (except vaguely it must come from the DNA at least indeirectly. Also is it somehow "moved thru" the ribosome along with the mRNA? I.e. The ribosome is really just stripping parts off of the tRNA and sticking the on the growing protein as "told" by the mRNA.

    this is surely not correct as then there is really no need for the mRNA - the tRNA could do the entire job as it is a well organized string of the needed parts.

    Any one of you three able to tell me where I have gone astray?

    I think I am getting a reasonably clear idea about histones. They are the proteins than hide most of the information of the DNA and probably only expose the sections needed for the particular cell on the outside as they wrap the DNA around them for the mRNA to copy the infromation that cell (Say a bone or kindney cell) needs. Thus I presume that some how each different type of cells has relatively unique histones proteins. I.e. when a liver cell divides (or make a another- whatever it does to get one more liver cell) it has "liver cell histones" that expose only those parts of the universal DNA with coding for liver cell proteins to be transcribed into mRNA. - I hope that is roughly correct.
     
  9. CharonZ Registered Senior Member

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    Just a quick answer:

    tRNA is synthesized basically the same as other RNA (it gets modified on its way, but that is detail for now), but a difference is that it gets loaded with a specific amino acid on its way.
    They are indeed floating around and to the ribosome (protein factory, if you want call it). And only if the tRNA arrives by chance with the right anticodon the amino acid will get hooked up. It is really that inefficient (if you want to call it that way). The tRNA are not ordered in a sequence specific way. Only if their anticodon triplet (one per tRNA species) corresponds to the codon just being read from the mRNA the it will get unloaded. Without mRNA there would be no template that would direct the the type of tRNA-AA being unloaded.

    Maybe you want to take a quick peek on tRNA structures (e.g. in wikipedia or someplace else). They are very distinct and it is immediately clear that they are not used in a somewhat linear way as mRNA.
     
  10. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Thanks
    Ok, it seems like in my analogy to the whole parts stock room of the factory as the role of the tRNA was wrong. The tRNA is more like the individual storage boxes of the stock room. Thus, the tRNA must be much smaller than the mRNA and the stock room clerk is really stupid, not well orded. He just keeps throwing tRNA boxes at the ribosome factory until the amino acid in one of the tRNA boxes happens to be the one currently needed to build a little more of the polypetide or protein. (Is "polypetide" just a more chemically descriptive term for "protein"?)
     
  11. Roman Banned Banned

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    Here's an image of tRNA:

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    The anticodon loop briefly base pairs with the codon on the mRNA when the mRNA is in the ribosome. If the pairs match, then the tRNA releases the amino acid attached to the acceptor arm, which is added to the growing chain of amino acids.

    Your analogy of the inefficient clerk is accurate.

    A peptide is simply two or more amino acids connected together. It describes the type of bond. A polypeptide are many amino acids linked together. Proteins can be polypeptides (very long chains) or oligopeptides (short chains), as well as containing non-peptide bonds with molecules other than amino acids. Some common molecules or chemicals that can be found in proteins are calcium ions, adenosine triphosphate (ATP), sulfur, or methyl groups. Calcium is often used to activate or deactivate a protein by changing its shape when it binds, ATP is often used as an energy source* , sulfur is frequently used to cross link proteins for strength, such as in the keratin in our hair and fingernails (as well as in vulcanizing rubber). Methylation of the afformentioned histones change their charge, and thus their affinity for DNA.





    *Motor proteins actin & myosin need ATP to work as a sort of ratchet system, where the myosin heads bind and unbind actin to contract muscles. The binding of the myosin causes it to flex and shorten, contracting the sarcomere (the stuff that makes up our striated muscles). ATP is required for the myosin to release the actin. This is why dead people get stiff- no new ATP production means the myosin binds the actin and won't release it.
     
  12. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Thanks again to all three.
    Here is start of a summary of my current understanding. (about 10 questions at end before I can continue summary):

    Double stranded DNA carries ALL the information needed by most organisms to be constructed (but a few simple organisms can function without it – sort of use RNA like coded information)

    The two DNA stands are sugar molecules linked together by a phosphate bond and each sugar molecule has a binding site which can accept one of four other molecules. Their names begin with letter A, G, C, & T (and I will not bother with the full names). The "not bound to the sugar" end of each of these four can also bind to another's “not sugar” end but only to one of the other three “letter molecules.” I.e. A-T bond and G-C can join their “not-bound-to-sugar” ends.

    The length of these A-T and G-C molecules, here after just AT = TA & GC = CG, are approximately the same, so they can and do cross link the two DNA strands, like steps on a spiraling ladder. A short section of the “ladder steps”, flatten out to fit on 2D display, follows partially to illustrate why there is an equality sign in prior sentence.

    AT
    CG
    GC
    TA
    GC
    AT
    CG

    Now while joined, the two strands are only storing the information. The bonds at mid ladder steps must be broken to allow the encoded information to make RNA, which is single stranded and has U replacing the T as the molecule that binds the non-sugar-bound end of A. This splitting of the DNA starts at one end and as the RNA forms on the exposed bonds. Using lower case letters c, g, u & a for the RNA forming on the splitting above segment of DNA we have:

    ..…AT ….Ignore dots (They are here to prevent SF’s computer from reducing all adjacent spaces to one space).
    .…C-G
    ...Gc.gC
    ..Ta…uA
    .Gc….gC
    Au……aT
    Cg……cG

    So the DNA section above has made TWO strips of RNA, but not yet shown as separated from the DNA single strands. I.e. when the top two also have helped make RNA we will have:

    ugcacug & acgugac segments of RNA , but RNA also has a "backbone" of linked sugar molecules. Thus there is much missing in this description of the formation of RNA. Somehow from somewhere these sugar molecules must attach to the newly formed sequences that are given at start of this paragraph. Perhaps what joins to the exposed base of the DNA is not just one of the 4 letters (a,c, g or u) but the entire nucleotide illustrated in SAM's post 64? Probably, if it is really nucleotides that are attaching to the exposed bonding sites of the separated DNA, then as these nucleotides attach they also make the phosphate bonds between each other to make the "RNA's "backbone." Possibly as they form they also separate the fully assembled RNA from the DNA that helped it form; but this is my first question below.

    Now stopping my summary to ask questions:
    (1a) How is the nascent RNA freed for the single strands of DNA?
    (1b) As the RNA is freed from the DNA, there are many open bond sites. For example, in the left of the two RNAs made, the g at the bottom of my illustration could bind with the c of the third from top as cg is an allowed binding. Thus, one would expect the RNA to rapidly become 3D structures. Does 3D structure formation occur while separating* from the DNA, or later?
    (2) Once that RNA is freed, do the two strands of DNA rejoin together or do they break up to resupply unbound A, C, T & G back to the “soup.” I guess they rejoin as the T can only be reused if more DNA is to be made. (RNA needs u, not t.)
    (3) Where do the 5 letter molecules A,C,G,T & U come from? I.e. how are they made? Are they really the four Nucleotides, Na,Nc,Ng & Nu that join up on the exposed binding sites of the splitting DNA, not just the "letter molecules"?
    (4) As the RNA production process makes two closely related, but entirely different RNA sequences are both of use or is one broken up to “recycle” the “letter molecules”
    (5) What starts the double strand DNA splitting (at only one of the two ends?)?
    (6a) As both T and U can bind to the “non-sugar-bound” end of A, is it not a common RNA error to occasionally have tA instead of the correct uA?
    (6b) If answer to (6a) is “Yes, that is common error.” Is there a known correction process?
    (7) I assume that certain sequences of the RNA are “weak points” (or vulnerable to enzymes breaking or *) so that mRNA and tRNA (and probably more I do not know of) form.
    --------------
    *A speculation:
    As noted in (1b) during the separation of the nascent RNA from the DNA, assuming it is also some "un-zipping” process, there should be 3D self-binding structures formed. (As speculated in question 1b.) Thus, as the RNA “unzips” from the DNA, one could imagine that a “chain of balls” forms. I.e. various size complex 3D structures with relatively short linear links of RNA letter molecules joining them are made. These “linear links" would often “snap” due to the independent Brownian motion of two adjacent 3D balls. Perhaps this is part reason why the long RNA copy of the information in the DNA breaks into useful smaller pieces like mRNA, tRNA, and others I do not yet know of. Perhaps some of the "junk DNA" is used to make the "weak linear links" in the first formed long RNA so it snaps apart the longer RNA into useful 3D "balls"?

    I plan to continue my summary when some of the above have been answered, but just to not forget to ask later:
    The tRNA has the anticodon loop at one end, quite remote from where the amino acid would be held on the tRNA molecule. When the anticodon loop briefly binds to the “now being read” part of the mRNA, is its amino acid is released (inside the ribosome?) at the now forming protein? I.e. is the mRNA passing thur the ribosome roughtly the length of the tRNA away from the site where the protein is being assembled? (I guess “Yes.”) Thus, the ribosome must have a “slot” thur it that is orienting the tRNA with the protein being built near one end of the “slot” and the mRNA passing thru the other end of the slot. As the currently being read codon of the mRNA and the matching anticodon of the tRNA separate, does this create some force that moves the mRNA one codon step more thur the ribosome?

    Also does the amino acid release by the tRNA require BOTH the mating with the mRNA codon AND the molecular “pulling” from the already partially built protein site it should occupy? I would guess answer to that is “Yes” because if only the mating of the anticodon and codon is required for release, then that mating should occur often in the soup; However, perhaps loss of the amino acid is not important as the tRNA can just get another form the soup. Comments?

    PS - One thing I learned from my college level teaching as a graduate student is how much one can be stimulated to think about what they assumed they already knew well before an intelligent, but very ignorant, student asked some simple question. One that only one very ignorant of the subject would think to ask. I hope I am doing that for at least some who are helping me.

    This is also why I do not simply search wiki, etc. and get "brain washed" with the answers as facts. I always prefer to try to figure out for myself what must be going on while still very ignorant and innocent of the "facts." That way when I do know the facts, they will be meaningful to me, not just facts.
     
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  13. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

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    BillyT:

    Good questions, and a quick grasp of the concepts. I'll let Roman or others answer your questions in detail, as I don't work directly in that field. However, it is my understanding that when the tRNA briefly adheres to the mRNA as the mRNA is being passed through the ribosome, that a sort of 'flag' of protein develops as the amino-acid is attached to the growing polypeptide chain. The ribosome is composed of two sub-units, and I believe the 'slot' you reference, where the mRNA is read, is where those two sub-units are connected. I don't have a nice diagram to show you, but perhaps Roman does. Also, the proteins need to take specific shapes [not just a long stream of amino-acids], and they fold upon themselves into highly specific and complex shapes, often via Sulfur bonding, and as to how that is guided I'm not certain. Protein functions can be activated/deactivated by shaping/unshaping of the protein depending upon the cellular chemistry at the moment. Again, Roman would likely know more about that than I.

    My interest in biology is more along the lines of the evolutionary morphology of the archegoniates [which of course all require the same biochemistry, as above].
     
  14. Roman Banned Banned

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    As far as I know, this is the case. Every protein that is produced by an organism is, at some point, blueprinted in the DNA. There are levels of epigenetic control though, which function independently of DNA, though much of this is actually silencing (turning off) genes. Women, for instance, have two X chromosomes, and their bodies have to turn one of them to the "off" position. Calico cats are calico due to epigenetics. The genes that code for color are on the X chromosome, and cats randomly turn off X chromosomes in every cell (males don't turn an X chromosome off, since we've only got one), which leads to the patchy coloration. This also means that all calico cats are female (of course there are exceptions, there always are). No need to check for a vagina*

    Correct.

    Yep.



    I'd like to point out here that DNA strands are reported in horizontal fashion, from 5' to 3' end. So in the literature, that would be reported as ACGTGAC. This is because the enzymes that make mRNA read in the 3' to 5' direction (reading TGCACTG), so that the resultant mRNA is ACGUGAC.

    The sugar molecules that make up part of the DNA are cyclical, and at the 5' end you have a phosphate group, and the 3' end you have a hydroxy group. Enzymes that make DNA & RNA can only synthesize by adding new nucleotides to the reactive 3' hydroxyl end. DNA & RNA are synthesized from from a 5' end to a 3' end.

    Transcription factors, enzymes that are responsible for turning DNA into mRNA, form a transcription complex that melts the DNA and exposes it to RNA polymerase II (the RNA polymerase responsible for making mRNA in eukaryotes).


    Let me stop you here. DNA has directionality, so only one strand can be formed, due to the restriction that polymerases can only go in the 5' to 3' direction. One strand acts as the template strand, the other doesn't have anything happen to it since the polymerase would have to run in the OPPOSITE direction, and, presumably, there is not a downstream promoter site (short sequence in the DNA that says "start here!"). Downstream here means at the end of the sequence being transcribed by the polymerase. So in your example, GAC is downstream of CGT, while, on the opposite strand, GTC is UPSTREAM of ACG. I hope this makes sense. It's very hard to picture without a picture.


    You asking about how an mRNA molecule is generally synthesized, yes? A bunch of enzymes work along the DNA, and the current model is that the enzyme facilitates base pairing between nucleotides (which is sugar+letter [the base] already connected) which are just hanging out where the the synthesis is occurring. Whether this acts by simple diffusion and collision, or some sort of mediated process, I don't know, and I don't think anyone does. Most likely, it's facilitated somehow, as the in vivo process with such low concentrations is a gazillion times faster than ex vivo. Anyway, when the right base matches (so U with A, G with C, etc), a conformation occurs in the polymerase which catalyzes the phosphodiester bond, taking a hydroxyl group at the 3' carbon and attaching it to a 5' phospho group.

    Hope that didn't confuse you, as you have the right idea.

    Now stopping my summary to ask questions:
    Depends if you are looking at bacteria or not.

    In both us & bacteria, a hairpin loop is sometimes formed in the RNA from a G-C rich tract of around 10 to 30 base pairs. These bonds are stronger than the AT bonds in DNA, and stronger still than the AU bonds in RNA, as they have 3 hydrogens bonding, as opposed to 2. This stem-loop structure then binds to a protein on the RNA polymerase, which then goes on to code a series of uracils (A on the DNA), which form a particularly weak bond. This causes the whole apparatus to stop, the A-U bonds to unwind, and everything just falls apart.

    In bacteria, another method involves a special protein called Rho that gets recruited to the transcription complex, binds the nascent mRNA, destabilizes the apparatus, and everything falls apart.

    In both cases, termination is caused by a terminator sequence- a series of bases on the DNA that says: mRNA synthesis stops here. In the case of Rho dependent synthesis, the nascent mRNA strand will help recruit Rho by binding it.

    As for what else eukaryotes use to terminate transcription, I'm afraid I don't know. I imagine we use Rho-like termination proteins, as well.


    The short answer is: both.
    A slightly longer answer would be: depends.

    Terminators are due to formation of 3D mRNA-protein structures, for instance. I can't think of any other specific examples of this happening, unfortunately. I'm sure there are quite a few.

    DNA rejoins almost spontaneously, I believe. There may be chaperon proteins (though I am unaware of any), and mis-pairing can always occur. And recall that only one strand has any nucleotides added to it in the formation of mRNA. The other just sort of chills. Though I guess what you are asking is: why, if this is all occurring by collision & chance, doesn't the non-template strand (DNA that's not being transcribed) become covered in nucleotides just floating around? It very well may, it's just that the attraction isn't that strong, and they inevitably fall off. The reason why it will rejoin the DNA is that it can simultaneously form more H-bonds, and helical twist hides the DNA hydrophobic nucleoside core from the aqueous environment. So short answer: passive rejoining occurs because it is more energetically favorable. Though this is just conjecture, I believe it is the case, since it occurs in vitro with a simple PCR.

    They're synthesized by the organism. I feel that they're largely recycled from organism to organism, being considerably nitrogenous, though some stuff out there must synthesize it de novo (my guess is largely producers). And yes, it's the nucleoTIDE that pairs up- that is, both the sugar and the "letter". Just the letter bit, sans sugar, is called a nucleoSIDE.

    Only one strand of mRNA is ever made in a given sequence (as far as I know!), due to the nature of how DNA&RNA is formed and the directionality of their sugar backbones because of phospohdiester linkage. I feel like my explanation of it has thus far been inadequate, so please ask more questions. You are doing a very good job of both conceptualizing and explaining your concepts. It's very helpful for me when you propose what you think is going on.

    However, it is POSSIBLE that two different mRNAs could be made, at the same time, from the same sequence. They would, most likely, code for different proteins, thus be considered different genes. Though it is possible that they could code for the same thing, due to the degenerate code, at least, I think they could be.

    But in general, when transcription begins, only one strand of mRNA is started. The other strand of DNA doesn't do anything during that transcription event, though that does not mean there aren't different genes on that strand. If you read the other strand, which runs backwards to the current strand, there very well could be a promoter on there and a gene that is the reverse complement of the one you were currently transcribing!

    Enzymes. DNA can, and most of is, split in the middle. Split here meaning seperating the two strands- only H-bonds are broking, there is no covalent breakage. There are universal sequences of DNA called promoter regions that are very similar in organisms from diverse phyla that basically say "STAR mRNA HERE". There are also sequences of DNA that are specific to certain proteins. These sequences may never actually be "turned into" mRNA- they are entirely non-coding. However, they are recognized by proteins which then bind them, and change the shape of the DNA. This shape change leads to certain genes becoming active or turning off. And these ENHANCERS or SILENCERS can act from very far away- they can be hundreds of thousands of base pairs away from the actual gene that is turned on or off!


    As far as I know, no, since T is on DNA and U is on RNA. They're sugar backbones are quite different . RNA's extra OH on the sugar bit is recognized by RNA polymerase (DNA gets its own polymerase, DNA polymerase), so there isn't confusion. Since RNA polymerase is specific to RNA, it won't be accidentally grabbing the pieces for RNA (if the transcription process is not mediated), or if it did (in the case of a mediated transcription process), the polymerase won't recognized the sugar part the T is attached to, and so won't catalyze the phosphodiester bond.

    As far as I know, RNA cutting itself is rare. It may be common, and we just don't know it yet, but so far, most modification to mRNA and tRNA after synthesis is mediated by proteins.

    Here's a picture on the wikipedia page:
    http://en.wikipedia.org/wiki/Translation_(genetics)

    As you can see, there are two sites on the large subunit. The first, the A site, is where the exposed mRNA gets base-paired with the anti codon loop of the tRNA. If it matches, the tRNA gets pushed into the P site where it covalently adds the amino acid to the growing chain. Then after it loses the amino acid, it is dispensed with, sans amino acid. In being moved along, the mRNA is also "dragged" through, due to the base pairing. Note that at any given time, two tRNAs are attached to the mRNA, so the motive force is stronger than if a single tRNA was going through.

    I'm not quite sure what you are asking. As far as I know, translation is stepwise. First basepairing occurs, then, if the pairing is correct, conformational change moves the tRNA into a position where it loses the amino acid. This loss of the amino acid causes another conformational change that pushes it into the 3rd and final position where it is released back into the soup to pick up another amino acid. If the ribosome didn't notice that the tRNA was wrongly matched, it could then move the tRNA into the next slot and covalently bond the wrong amino acids. I can't remember if the ribosome has can tell if the wrong amino acid is in the P site and get rid of, though I feel like it can. I'll look into this.


    Ohhh, I know what you are asking, and the answer is "no". Base paring doesn't catalyze the loss of the amino acid, it catalyzes a conformational change in the ribosome to shift it into a new position that enzymatically removes the amino acid and attaches it to another.





    *There's a picture of an exam question floating around on the web that asks something like "You have a calico cat. How do you know if it's female?" And the answer (marked wrong) is "I check for a vagina."
     
  15. Roman Banned Banned

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    Like a chain coming out of the end, you mean, for the amino acids bonded together?

    There are two slots (three in prokaryotes? will have to look that up) in the large subunit of the ribosome-one that facilitates the anticodon pairing with the mRNA- where the mRNA is read, as you said. If it matches, the tRNA is passed along into the slot where the amino acid is removed, then passed on out (or into the third slot, then out, if the wiki is to be believed, for prokaryotes).

    There's a fairly good one on the wikipedia page for translation. I think it's pretty easy to understand.

    Folding can occur both spontaneously due to the specific structure, or due the presence (or absence) of chaperon molecules. They don't necessarily have to be proteins- changes in charge will facilitate proteins to change shape, sometimes irreversibly.

    Right now, predicting how proteins will fold is the hardest question, and hottest, in biology, and probably all of science, at the moment. If we can figure out how, and why, proteins fold the way they do, by investigating the intermolecular forces that make them do so, we will have figured out the building blocks of life. It would do for biology what Newton did for physics.

    The computing power required to do so, unfortunately, are vast. Right now, there's a reclusive billionaire (forgot his name) who has funded the construction of the world's largest supercomputer for the purpose of unlocking the secrets of life.
     
  16. Roman Banned Banned

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    Excuse the triple post, but I would like to excuse myself from any errors I may have made in saying that I am but a lowly undergrad with little talent for organic chemistry and onl a handful of classes on genetics.

    Also, to make sure my ass is well covered: there's probably an exception.

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  17. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    I don't think so.

    CLINK, CLINK (That is two dollar coins dropping in appreciation of the obvious effort expended.) I will read it again more than once, but already about half my questions have been answered. Also some of my prior unknown ignorance has been converted into "known ignorance" so I will have new questions, but today I am pressed for time so will delay asking them.

    What is your major? I hope you continue in this field and go to graduate school. Physics is certainly where man's understanding of nature most advanced in the last century in ways that affected the common man; but this century belongs to the biologist understanding the cellular / chemical processes that both make organisms (and also make them sick). You seem to be driven to seek understanding - stick at it and with luck you may leave your mark on this important field.

    For me, the dawn of this new biological age came while I was sitting in the physics library after work, thumbing thru Nature (I think) as I usually did to let the traffic on the one lane road die down. I turned the page and saw two pages filled with horizontal rows of A,C,G,& Ts and several pages that followed (but I made my DNA vertical to show it separating). What I saw was the DNA coding for the tobacco mosaic virus. At that, never to be forgotten instant I knew, as Dorothy in Wizard of OZ said:

    Mankind was not in Kansas anymore. - Perhaps you can help explore this new found land.

    Anyone who put forth the effort you did to help me learn, certainly has “The right stuff.” Although there are many exceptions, for most of us, earning a Ph.D. is 95% perspiration and only 5% inspiration. – You have what it takes.

    I will get better understanding of what you have explained and revise my running summary of what I have learned after getting some clarifications.
     
    Last edited by a moderator: Nov 6, 2008
  18. fedr808 1100101 Valued Senior Member

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    Here's an analogy, imagine that you want to build a protein, lets pretend for the sake of this analogy that the protein is a nice car. The DNA is the blueprints for the car. The RNA are the managers and builders. The first type of RNA reads over the blueprints writes it down and then heads off to the third kind which will be descirbed last.

    The second kind of RNA is the equipment person, his job is to move the parts of the car to the construction floor. He does not pick them in any sort of order, just randomly picks them up.

    The third kind of RNA is the factory floor, or builder person. The first kind of RNA goes to him and tells him what he needs to build, and what parts to use. Than the third RNA signals the equipment RNA the second kind (this signal is still unknown as to how it works) and the equipment RNA drops the equipment off and goes off to get another random part. The third RNA than gets another piece of info from a new messenger RNA and does the same thing with another equipment RNA.

    Than when he gets the second piece he puts the two pieces together and repeats the process over and over until you get your car, or protein.

    The DNA is basically the database from which the first RNA gets the info from.
     
  19. CharonZ Registered Senior Member

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    Undergrad? I take my words back. Nice work.
    I did not read the newest post, though.

    Just something caught my eye while scrolling:

    Actually self-splicing and self cleaving by RNA is well known (especially in genetic mobile elements).
    There are indeed specific cleavage sites present in these case.
     
    Last edited: Nov 6, 2008
  20. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

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    Yes, like a chain, waving like a flag unless/until it folds. As you mention, the mechanism by which the foldings take place is not well understood as of yet. I would presume that some/all of the folding takes place as the chain grows longer even as it's being formed, but that's not clear.

    I find it interesting that prokaryotes have a somewhat different 'mechanism' for passing through the ribosomes. The evolution of the eukaryote ribosome mechanism from a simpler prokaryote ribosome mechanism is a fascinating history which we do not presently understand, either. Does anyone have good information on the relationships between prokaryote [and mitochondrial] ribosomes, and their more-advanced counterparts of eukaryote ribosomes? What are the differences, both in sequencing of RNA, as well as in size? Fascinating biochemistry work for the future, no doubt.
     
  21. Hercules Rockefeller Beatings will continue until morale improves. Moderator

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    So, Ben, did all this info actually help you?

    I was just ordering some reagents from Promega and came cross their Protocols & Applications Guide. It's not too bad at describing some of the basic techniques routinely employed in molecular biology research. Now that you know all about DNA/RNA, I’m sure you’ll want to know how to actually use it.

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  22. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    23,198
    Thanks. Here is direct link to the 13 chapters (I think):
    http://www.promega.com/paguide/Default.htm
    of discussion. I have been very busy but do plan to return here. When I get time, but I will read many of them first.
     

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