With respect to Roman's previous comments, there is a general flow of information within each cell. The DNA in your nucleus has a copy of every single gene in our genome (two, actually, going back to the haploid/diploid discussion), but not all of them are being used at once. Once a cell specializes (e.g. bone marrow cells, brain cells, liver cells, etc), it will only need the genes that are specific to it's function. The DNA is
transcribed into RNA, which is a complementary strand to the gene that is being transcribed. The transcribed copy of the gene is an mRNA molecule, which then travels outside the nucleus to the ribosomes, where it is
translated to the protein end result. This is the general flow of information from what is stored in the DNA to a functional end product.
Reactive with respect to what?
1.) How does it "coil"? It seems that if it's, say, laying out on my table, it would need some impetus to "coil".
2.) Given that there are only a finite number of base pairs, it seems to me that large chunks of the strand (I'm assuming it's a strand) look more or less like other large chunks of the strand. Given that the base pairs bind with some strength (van der Waals forces?), and that the strand of RNA itself has some tension, I can imagine a situation where one large chunk of base pairs could be out of place, and the interaction between conjugate bases would be too strong for the tension of the RNA to overcome. Does this happen?
3.) Given the above, does it coil up the same way every time? What if it coils up wrong?
RNA is generally single stranded, but nucleic acids are more comfortable in a double-stranded conformation. So we notice that the strand will twist and contort so that it is able to form hydrogen bonds between bases elsewhere in the strand.
Each nucleoside, which is the nucleotide base attached to either ribose (in RNA) or deoxyribose (in DNA), is covalently bound at the 5th Carbon atom of the sugar molecule to a Phosphate ion. The phosphate is then covalently bound to the 3rd Carbon of the sugar in the next nucleoside (forming the sugar-phosphate backbone). The nucleotides are covalently bound to the 1st carbon of the sugar. This covalent binding of the nucleotide to the sugar backbone prevents mismatching in the way you are describing in part #2 above, because the strands of nucleic acids are fed through the transcription or translation machinery like ticker tape.
RNA will fold the same way each time under normal conditions, since the conformation they land in is the most thermodynamically stable. Under pH changes, temperature changes, etc, a more stable conformation may be found that looks different.
So the mRNA is just somehow a copy of the DNA, I guess? What is the mechanism for "copying", and does it happen at regular intervals? If so, how does the "copier" know when to do its job? Behind all of this is some chemical reaction, like some intricate swiss watch made out of carbon, nitrogen and oxygen---is this correct? What makes the whole process go?
mRNA is a transcription product, and is an intermediate in the flow of information. Transcription is handled through a multi-protein complex that binds to the DNA strand takes free nucleosides to create a complimentary strand. This complementary strand is the mRNA. The copier has many signals that it needs to do it's job, and a lot of them are not well understood. Ion concentrations in the cell's cytoplasm, hormone messengers that bind to protein receptors, the presence of a toxin -- chemical signalling, in other words.
Why would you want to modify it? And what does this even mean?
mRNA can be processed before it is translated into protein. This is useful because it allows a single gene in the DNA to be used for several similar proteins. Regions can be conserved between different proteins -- even ones whose function is very different. Sections of the mRNA will be excised, so the strand will be shortened and some of the information transcribed from the DNA will not be used.
I don't understand this at all. Why does it need to be translated? Isn't RNA/DNA a protein anyway? And what does "translated" mean? And how does this "translation" take place? Again, there is a chemical reaction taking place, which means that it is energetically favorable to store information in the protein, right? And if this is the case, why doesn't the protein just copy the DNA directly?
RNA/DNA are nucleic acids, not proteins. "Translated" means that the information stored in the mRNA (which was copied from the DNA) is taken and turned into a protein strand. The sequence is read in groups of three bases, called
codons (see RNA Codon table), which correspond with a particular amino acid. Energy in the form of
ATP is used to drive a lot of these reactions, so they are not necessarily energetically favourable.
This tells me that genetic information of less than three base pairs long is irrelevant. That is, if there are three sequences that all give the same amino acid, why do we need three sequences? Given that nature typically doesn't do irrelevant things, why should this be the case?
Mathematics -- there are more possible three base combinations of the four available bases than there are amino acids (at least the ones that are used in proteins, which is approximately 20). If some amino acids didn't have multiple codons that coded for it, we would have codons that did nothing which isn't an efficient use of energy. This will also affect the amino acid make-up, since amino acids with more codons will generally have a higher probablilty of making it into the protein -- this is chemically significant since this is largely what determines protein shape. Shape confers functionality.
This seems unlikely. How do all of these different molecules come in to play? And how does this happen in a finite time---naively there are 100! different ways for these different molecules to float by. So what gives?
It seems highly unlikely, yes. They interact the way they do based on chemistry. The details on some of the interactions may be less well known than others, but each individual reaction would happen on its own if we removed other substituents.
