8

The geometry of DNA: a structural revision

This proposed structure for DNA is wholly founded upon mathematical
principles. Although the geometrical modification to the base pairings is
relatively minor, the resulting double helix manifests a clarity altogether
distinct from that offered by Crick and Watson and it would appear to
shed light upon a number of areas of continuing uncertainty.

• Geometric equations predict the dimensions of DNA’s structure. Not
only does the pentagonal geometry predict the helical dimensions but
it would also demonstrate ‘principle causation’.
• The pentagonal geometry provides the dynamics required to build a
consistent, stable and uniform helical structure and also establishes
why there should be consistently ten bases contained within a single
turn of the helix. Incidentally, when converted to the molecular
dimension I would certainly predict degrees of variation, certainly
between 9.5 and 10.5 bases per turn, but perhaps even more.
• Both the hollow centre and side-by-side structural formation ensure
instant access at any point within the helix. This would permit the
DNA (even circular) to open and close during its replication functions
without entangling itself.
• The modification to the base pairing would appear to be able to exist
in either the enol or keto formations.
• While the sugar-phosphate backbones will undoubtedly prove integral
to the stability of the helical structure, it is the geometry of the basepair
molecules themselves

© Mark E. Curtis

Translation

In the process of transcription, an enzyme called RNA polymerase painstakingly copies a strand of DNA, and sends the freshly copied messenger out into the world, ready to tell ribosomes how to synthesise proteins.

Before we get onto how this is done, let’s take a look at what ribosomes are. The ribosome is a protein-making machine that’s actually made of RNA. It has two parts or subunits that bind on either side of the incoming mRNA: the small subunit reads the RNA, and the large subunit joins amino acids together to form a polypeptide chain.

But there’s a catch. Ribosomes don’t speak the same language as DNA does. If they were given the raw blueprints, it’d be like you opening up a box from IKEA and finding an instruction booklet written entirely in Swedish, without any pictures to stop you from attaching table legs upside down. Of course, if you were in that situation, you’d go to Google Translate to help get the information across—and ribosomes actually do the same thing. Well, almost.

The cell has to somehow interpret the genetic message from the sequences of nucleotides from the mRNA, and translate them into the amino acid sequence of a polypeptide. Our interpreter—the cell’s equivalent of Google Translate—is another handy RNA molecule called Transfer RNA (tRNA), which floats around in the cytoplasm. In basic terms, its function is to read the message on the mRNA molecule, then goes and fetches the right amino acids and gives them to the ribosome to attach into a polypeptide chain. It does this with the help of an enzyme called amino acetyl tRNA synthase, which helps match up the amino acid to the tRNA. There are twenty different types of synthase, one for each amino acid.

Basically, it turns the language of nucleic acids into the language of proteins.

But how does the tRNA know how to read the mRNA molecule?

Well, the sequence of bases on an mRNA molecule are arranged in a specific way—in a series of non-overlapping codons. A codon is a group of three nitrogenous bases that code for a specific amino acid. The code CUU (cytosine-uracil-uracil), for example, codes for the amino acid leucine.

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There are different kinds of tRNA that bind to a specific amino acid. Each one has a specific three-nucleotide sequence called an anti-codon that matches up with the complementary mRNA codon.

Some codons don’t code for an amino acid but rather act as a stop or go signal. See, if you’ve got a bunch of bases that have to be read in particular groups, you want to make sure that your tRNA starts at the right spot. Otherwise, the reading frame gets shifted one or two bases over, and suddenly your tRNA is fetching the wrong amino acids and your protein is a complete disaster. There are three different “stop” codons (UAA, UAG, and UGA) and one “start” codon (AUG). These tell the tRNA where to start reading and where to stop reading.

However, as you may have noticed from the table above, there isn’t just one codon for each amino acid. There are 61 different ways you can arrange four nucleotides into groups of three, so there are 61 codons. This means that some codons code for more than one amino acid. As you may also have noticed, the codons that code for the same amino acid all have the same first two nucleotides—it’s only the third nucleotide that changes.

This is a really important point. It means that the third nucleotide in a codon isn’t really that important. Most of the time, you could change that nucleotide and the same amino acid will still be produced. If any of the other nucleotides were changed, this could fundamentally alter what the codon codes for—another, incorrect amino acid would then be added to the polypeptide chain, and it could have a huge effect on the function of the chain. This is a mutation. But if the mutation occurs in the third nucleotide, chances are, everything will be fine.

On that note, another important thing—there isn’t one tRNA molecule for each codon. There are only 45 different tRNAs, and some can bind to more than one codon. Again, this is because the third nucleotide is the most flexible, and less important.

Next: a look at the steps of protein synthesis.

Body images sourced from Wikimedia Commons

Further resources: Translation

The Other Neanderthal

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We don’t know what the Denisovan looked like. We don’t know how it lived, what tools it used, how tall it was, what it ate, or if it buried its dead.

But from only two teeth and a piece of finger bone smaller than a penny, we’ve been able to extract the rich history of a species that split off from Homo sapiens approximately 600,000 years ago. We know they’re more closely related to Neanderthals than humans—though still distantly. We know they made their way to Southeast Asian islands, interbreeding with indigenous modern human groups in New Guinea and Australia. We know their interspecies mingling with modern humans in mainland Asia was brief, but enough to impart a few genes. And we know Denisovan genes reveal evidence of interbreeding with Neanderthals and an even more archaic hominid species.

It’s the first human cousin species identified with more than fossil records. Instead, scientists used the DNA it left behind. There’s now a mystery on our hands: Who were the Denisovans, and where did they go? Read more.

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