Molecular Biology survival guide for Chemists – II: What DNA is transcribed into

We have 3 RNA polymerases which transcribe DNA into RNA.  Transcription starts at the 3′  end of one of the members of the DNA helix and proceeds toward the 5′ end.  However the RNA produced starts at the 5′ end and proceeds toward the 3′ end.  Why transcribe you might ask?  Because the chemical language is the same — DNA and RNA are both polynucleotides.  The Guanine in DNA codes for Cytosine in RNA, etc. etc.

RNA polymerase I (Pol I to you) transcribes the genes for the RNA found in the ribosome (ribosomal RNA also known as rRNA), RNA polymerase II (Pol II) transcribes the genes for proteins into messenger RNA (mRNA), while RNA polymerase III (Pol III) transcribes the genes for transfer RNA (tRNA) and a lot more. Med students love mnemonics, so here’s one — I makes rRNA, II makes mRNA, III makes tRNA — so the polymerases and the products are in (semi) alphabetical order.

The ribosome is an incredible molecular machine — it contains several RNAs (called rRNAs) containing in total about 4,500 nucleotides and about 50 proteins.  The molecular mass is about 2,500,000 Daltons.  Its job, and its only job as far as we know is to translate the mRNA into protein.  Why translate? Because polynucleotides and proteins are chemically quite different. So information is being translated from one language to another.  Transfer RNAs (tRNAs) are involved. Each different tRNA brings a just one specific amino acid to the ribosome, which then stitches the amino acid to the growing protein.  Since we have 64 possible codons for amino acids (that’s 4^3), we have an abundance of tRNA genes in our DNA, well over 400.

Now it’s time to speak of mRNA or, actually, pre-mRNA.  The previous post noted that most genes come in pieces, parts coding for amino acids (called exons) and parts between the exons, called the introns.  Pol II knows nothing of them, just as the CPU knows nothing of the series of bits it is fed in a program.  It just starts transcribing DNA at a certain point, making mRNA willy nilly, intron and exon and finally quiting.

As mentioned in the previous post, dystrophin has over 2 million nucleotides in its DNA, all of which are transcribed into RNA.  The parts of the RNA actually coding for amino acids is under 15,000 nucleotides long, so all the introns must be spliced out.  This is the function of the spliceosome — another huge molecular machine. It contains 5 RNAs (called small nuclear RNAs, aka snRNAs), along with 50 or so proteins with a total molecular mass again of around 2,500,000 kiloDaltons.   Splicing out introns is a tricky process which is still being worked on.  Mistakes are easy to make, and different tissues will splice the same pre-mRNA in different ways.  All this happens in the nucleus before the mRNA is shipped outside where the ribosome can get at it.

There are some incredible fail safe mechanisms here.  The spliceosome associates a few proteins with the spliced together exon/exon junction, so that if and when the mRNA is read (translated) by the ribosome, if a termination codon occurs too early in the gene, truncating the protein prematurely, a process called nonsense mediated decay destroys the defective mRNA.

The mature mRNA just before it is ready to leave the nucleus has several parts.  From the 5′ end it has a bunch of nucleotides prior to the first codon for the protein (always an AUG which codes for methionine). This is called the 5′ UnTranslated Region (5′ UTR).   U, by the way, stands for Uridine which is the nucleotide in RNA corresponding to thymine in DNA.  Then there is the protein coding part, then there is the 3′ part which is not translated into protein (called the 3′ UnTranslated Region, 3′ UTR).  When Pol II is finished translating the gene, a long stretch of adenines (polyAdenine aka polyA) is added somewhere in the 3′ UTR.   It is added about 30 nucleotides downstream (3′ to) an AAUAAA sequence found in the 3′ UTRs of most protein coding genes.   There are some 20 – 260 adenines in a row in the polyA tract.  Addition is important, as polyA protects the mRNA from degradation — very few things in the cell hang around forever.   Each time the ribosome translates the mRNA into protein some adenines are lost, so for those of you familiar with computer programming, you can regard the polyA as a loop counter.

The 3′ UTR also contains sites where yet another type of RNA (called microRNA) binds.  Genes for microRNA  are also transcribed by Pol II.  Their precursor (pre-microRNA) is then extensively processed (I’ll spare you the gory details)  to form mature microRNAs, which, as the name implies, are rather short — only 20 – 22 nucleotides.  MicroRNAs represent one of the many forms of control on the amount of a given protein that a cell contains. They basepair with complementary sequences in the 3′ UTR of mRNAs and either (1) inhibit protein synthesis of the mRNA by the ribosome or (2) cause degradation of the mRNA.  It’s important to note that a given microRNA can control the levels of many different proteins, if the complementary region is present in their 3′ UTRs.  Also the 3′ UTR of a given mRNA can have regions complementary to many different microRNAs.

That’s quite a bit to throw at you.  I’ve omitted a lot of the complexity, to make the goings on as simple and clear as possible.  Hopefully, I haven’t violated Einstein’s dictum “Everything should be made as simple as possible, but not simpler”.  I think what I’ve said is quite accurate, but comments and corrections are always welcome.

The more I know about the goings on inside our cells, the more impressed I become, and the greater the leap of faith I must make to accept that this all arose by chance.

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  • Wavefunction  On July 12, 2010 at 10:26 pm

    -The more I know about the goings on inside our cells, the more impressed I become, and the greater the leap of faith I must make to accept that this all arose by chance.

    Not chance alone. Chance followed by energetic optimization and self-assembly, which makes things a lot easier. Consider the simple peptide KLVFFAA which self-assembles into structures of great complexity through simple pH changes.

  • luysii  On July 14, 2010 at 11:41 am

    Well KLVFFAA is a 7 amino acid peptide, and one of 20^7 = 1.28 billion possibilities. How was it found? I don’t know. My guess is that it was found in some naturally occurring protein, or a fragment of same.

    How many more like it are in the cohort? They certainly don’t all do this. I’d be happy if one in every thousand randomly made 7mers (by solid phase synthesis a la Merrifield) showed structured behavior.

  • Wavefunction  On July 14, 2010 at 10:41 pm

    -They certainly don’t all do this

    Interesting you say this. KLVFFAE is the central part of the amyloid Abeta (1-42) peptide and structured self-assembly is not unique to its sequence. The beta sheet is one of the most ubiquitous elements of protein structure in nature (more than alpha helices). Virtually any protein can form beta sheets and amyloid under the right conditions.

  • luysii  On July 15, 2010 at 6:45 pm

    Wavefunction: Thanks — didn’t recognize it. Yes, small fragments like this can form beta sheets and alpha helices on their own, but it is a very, very long way to the multiMegaDalton ribosome, spliceosome, mediator complex or even RNA polymerase with all its hangers on which modify the holoenzyme as it marches down DNA.

    [ Nature vol. 385 pp. 774 - 775 '97] The same sequence of amino acids can adopt different secondary structures (alpha helix, beta sheet) depending on the context they find themselves in. An example is given of an 11 amino acid sequence which adopts an alpha helical sequence when inserted one place in a protein and a beta sheet when inserted in another [ Nature vol. 3981 pp. 660 - 664 '98 ] The protein is MATalpha2, a DNA binding protein.

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