cherry@husc4.UUCP (03/31/87)
In article <3310@udenva.UUCP> agranok@udenva.UUCP (Alexander Granok) writes: >In article <978@aecom.UUCP> werner@aecom.UUCP (Craig Werner) writes: >>In article <11189@teknowledge-vaxc.ARPA>, rburns@teknowledge-vaxc.ARPA (Randy Burns) writes: >>> I was wondering roughly how many 'bytes' of information are contained >>> within human chromosomes? >> >> Hence, if a byte is a base pair, that's your answer, although >>only two bits are required to specify a base, ergo a 'byte' could >>actually be a tetranucleotide, but most sequences are stored as >>letters (ATCG). > >The whole arguement gets caught up in definitions, here. I would consider a >bit to be a base pair, and a byte to be the set of three that encodes for one >amino acid. >.... I guess it all depends on what you mean by "information." >.... I think a better question might be something like: >"How many amino acids (words in the language of proteins) are encoded for >on the human chromosomes?" or "How many books could these words fill? >.... Anyway, I think that would >give a much more easily palpable idea for the enormity of information involved. The unit of information stored in the chromosomes is the nucleotide. Not all of that information ever makes it to proteins. Much of the information in DNA never even makes it to RNA. Also there are many RNAs which either have a structural or catalytic function encoded in the DNA. Thus the information is at the DNA level. Ciliates are single celled animals that have cilia for locomotion and two types of nuclei. One called the micronucleus is where all the genetic information is stored. The other nucleus called the macronucleus is where all RNA synthesis occurs. The interesting fact is that in Oxytricha the macronucleus is made of only 15% of the micronuclear DNA complexity. Therefore 85% of this organism's inherited DNA sequences are not required to make the somatic nucleus where all RNA synthesis occurs, a neccesary precursor to protein synthesis. Mike Cherry Dept. of Molecular Biology, Mass. General Hospital, Boston cherry%frodo.decnet@mghccc.harvard.edu
diaz@aecom.UUCP (04/03/87)
In article <1534@husc6.UUCP>, cherry@husc4.HARVARD.EDU (michael cherry) writes: > > The unit of information stored in the chromosomes is the nucleotide. Not > all of that information ever makes it to proteins. Much of the information > in DNA never even makes it to RNA. Also there are many RNAs which either > have a structural or catalytic function encoded in the DNA. Thus the > information is at the DNA level. Although I hate to pick at others' articles, I have seen the increasing use of the term "catalytic RNAs" to describe those RNA molecules (e.g. the Tetrahymena rRNA) which mediate their own splicing in vitro. This bastardization of the term catalysis has unfortunately infiltrated many of our scientific journals. Let's make it clear that self-splicing RNAs mediate their splicing via intramolecular reactions. Once exons are spliced together, the reaction is over. By definition, a catalyst accelerates the rate of a chemical reaction without itself being consumed in the net reaction. Self-splicing RNAs are NOT catalytic. The only examples I know of genuinely catalytic RNAs are: M1 RNA from E.coli, which has been elegantly shown by Sidney Altman & coworkers to accurately process the 5' termini of tRNAs in the absence of its physiological protein cofactor in vitro; M1 RNA-like molecules from Bacillus subtilis and other organisms; the Tetrahymena rRNA intron left over from the self-splicing of this transcript, which has been shown by T. Cech, et al, to possess RNA polymerase- and RNA restriction endonuclease-like activities in vitro. There may be other examples of which I may not be aware (if so, let me know). Let's be careful in our description of the members of the RNA world. -- dn/dx = Dan Diaz (philabs!aecom!diaz) Department of Molecular Biology & Pizza Chemistry AECOM "Hold the E.coli"
cherry@husc4.UUCP (04/05/87)
>Let's make it clear that self-splicing RNAs mediate their splicing via >intramolecular reactions. Once exons are spliced together, the reaction >is over. By definition, a catalyst accelerates the rate of a chemical >reaction without itself being consumed in the net reaction. >Self-splicing RNAs are NOT catalytic. > >The only examples I know of genuinely catalytic RNAs are: M1 RNA from >E.coli, which has been elegantly shown by Sidney Altman & coworkers to >accurately process the 5' termini of tRNAs in the absence of its >physiological protein cofactor in vitro; M1 RNA-like molecules from >Bacillus subtilis and other organisms; the Tetrahymena rRNA intron left >over from the self-splicing of this transcript, which has been shown by >T. Cech, et al, to possess RNA polymerase- and RNA restriction >endonuclease-like activities in vitro. The group I and II self-slicing RNAs, as well as the viroid RNAs, act on part of themselves. However the work of Cech's group in Boulder and Szostak's group in Boston have shown that the "enzyme" part of the group I self-splicing introns (specifically the Tetrahymena rRNA sequence) is not destroyed by the three reactions taking place in vivo but rather the "substrate" part of the molecule is destroyed. Cech coined the term ribozyme to designate these RNAs which perform the specific reactions involved in the RNA splicing reaction. Generally they are considered not to be catalysts by protein chemist because they only act once not because they happen to cut themselves. In vitro these RNA molecules have been modified by both Cech and Szostak to be true enzymes, acting on multiple substrate molecules, not being changed by the reaction they catalyze, etc. Thus while it is true that in vivo the self-splicing RNAs are not catalytic in the complete sense of the word they do carry out a reaction which would not have happened without them. The change which occurs in one of these RNAs is not the result of the ribozyme becoming involved as an intermediate to the reaction but because the ribozyme cuts itself in a subsequent reaction, it removes the recognition part of the enzyme. If these molecules can be enzymes in vitro, perhaps its just a matter of time before more truely catalytic RNA molecules are discovered which act as enzymes in vivo. Mike Cherry
michael@m-net.UUCP (04/06/87)
In article <11189@teknowledge-vaxc.ARPA>, rburns@teknowledge-vaxc.ARPA (Randy Burns) writes: > I was wondering roughly how many 'bytes' of information are contained > within human chromosomes? and gets large number of replies (some with novel definitions of bits and bytes). Some of the replies made the assumption that only the information that was eventually transcribed into protein was significant, and that repeated sequences, introns, the third base pair of some three-letter codes, and so on, could be ignored. I must take issue with that. Introns may yet prove to have functions beyond their own excision. (Negative feedback on protein production is an obvious candidate.) Some of the regions near protein-coding sections regulate expression. The third codon for the hypervariable part of antibodies is significant (affecting the potential antibodies after DNA editing), and may have other effects in other genes (i.e. affecting the likelyhood of cancer by changing the probability that a growth-regulator will mutate into an "always-grow" form). Repeating sequences may function in DNA repair mechanisms. Because of these and other possible functions of DNA, I would not exclude any information from consideration, and would answer with the number of 8-bit bytes required to specify the reconstruction of the actual DNA found in an individual. At 3*10^9 codons, and two bits per codon, that's 3/4 * 10^9 bytes, or about 750 Megabytes. (Specifying cutting points to separate the chromosomes, and other artifacts like the arbitrary choice of direction of the chromosomes and their order in the representation, gain or lose so few extra bits they're lost in the one-significant-digit estimate of the number of codons). We're starting to see disk drives about that big. But this number really represents the maximum data that the genome could hold. Some of the redundancies could be absorbed in data compressing codings, squeezing down (but not quite eliminating) the data representing repeating regions, but not affecting third-codon redundancies. Sorry, I can't put a number on that. "I've got code in my node." | UUCP: ...!ihnp4!itivax!node!michael | AUDIO: (313) 973-8787 Michael McClary | SNAIL: 2091 Chalmers, Ann Arbor MI 48104 (If you want to be sure I see it, MAIL to the address in my SIGNATURE!)