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A small lesson in genome stuff

How does Natasha, our golden silk spider (Nephila clavipes) know how to make spider silk? Does she just mix up a bunch of chemicals and out pops silk or does something inside her direct the building process? Each cell

in our (and her) body contains the instructions inside the nucleus (cell shown on left, nucleus shown here on the right). Inside the nucleus are chromosomes and each chromosome contains a number of genes that tell a cell how to manufacture different proteins needed by the body. One of those proteins is the stuff that makes super strong spider silk.

Each gene contains a sequence of nucleic acids from an alphabet of 4 nucleic acids and consists of two long strings of DNA

The strings of DNA are complementary such that the As connect to Ts and the Cs connect to Gs. The resulting structure is a double helix that was discovered by Watson and Crick in 1953. The existance of 2 strings makes reproduction easy: you break the helix into the two strings, and form another string that is complementary (i.e. each A is paired with a T and each C is paired with a G, and of course, each T is paired with an A and each G is paired with a C.

Now the really elegant feature of DNA is that each group of 3 nucleotides (A,T,C,G) tells the spider's chemical factory to add one of 20 amino acids to a chain of amino acids. Its like a small language where the triples specify a word from a vocabulary of 20 words and the resulting string of words is a sentence - and the sentence, we call a protein. The vocabulary is shown in this figure, G for Glycine, A for alanine etc. (see the figure at the bottom).

Each cell in Natasha knows how to make spider silk, but only very special cells make silk. This is because something controls the translation of the silk gene DNA to RNA (expression).

In many (maybe all?) genes exists a promoter region and a repressor region and they control whether the DNA will be translated into RNA and eventually into a protein. If the promoter region is activated, then the DNA is copied to a messenger RNA, mRNA. This string of RNA is then translated to a protein as shown here:

Each amino acid is specified by a sequence of 3 nucleotides, a word in the vocabulary of the genome:

The link between nucleotide words ( composed of the letters A,C,T,G) and their message (a sentence)forms a language. Is there a syntax to this language? Do certain sentences make certain structures like loops or hairpin turn? Are their semantic constructs within this language? Josh has pulled together the ideas and organized them in an understandable way.

Summarizing, DNA provides the roadmap for making the proteins that are used to build spider silk. The DNA is translated to messenger RNA (mRNA) which is turn directs the building of the protein, one amino acid at a time. The entire process appears as:

Now you have all the main ideas to start a new journey down the path of understanding how Natasha makes spider silk.

Many scientists are working on the problem - and you can work on this problem also. These links will help you get started.

Footnote: Here is the table of amino acids and their alphabet codes

Now take your understanding and try a project --->

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