All organisms and viruses also use RNA as "messengers" to carry parts of the full code out to other parts of their cell(s) (or host cells) in order to carry out the encoded function, usually the construction of a specific protein meant for a specific purpose.

We'll begin with a review of those polymers, RNA and DNA, then talk about the code itself, how it is copied to progeny, and the mistakes that can be made along the way that can lead to functional differences between a cell or organism and its progeny.

Many thousands of these can be linked through that phosphate group via phospho-diester bonds.

The "busines end" of a nucleotide phosphate is the base. In the figure below that's called adenine — the two-ringed thing — but there are actually four nuclotide bases, which we'll discuss below. In RNA the bases are the same except that the one called thymine is replaced by another, closely-related base called uracil. Uracil is not present in DNA chains.

That's it. It's really simpler than it looks at first glance. There's a phosphate + sugar backbone that displays a base. There are four bases, and the sequence of those as displayed on the phosphate-sugar chain is what carries the code.

All of the bases hook to their respective ribose or deoxyribose sugar by losing the hydrogen atom highlighted in green and forming a bond there.

All contain one or two double-bonded oxygen atoms, which will provide the kind of weak bonding from base to base that we need to form helical shapes and other kinds of structures that protect the code by burying it inside a larger molecule.

Hydrogen bonds are much weaker than the chemical bonds, formed by the sharing of electrons, but they are of just the right strength to form structures between DNA and RNA strands that can be taken apart and put back together as needed.

The hydrogen bonding (H-bonding) between G and C is stronger because three H-bonds can form. Notice the complementary shapes between the bases. They fit together in "lock-and-key" fashion.

You can learn more about H-bonding and intermolecular forces here.

1. separate and copy the sense strand into an RNA as a "message" that can carry the code to the appropriate cellular machinery in order to translate that code into a needed protein.


2. Separate and copy each strand just before a cell splits into two "daughter" cells.

These DNA duplexes coil into the familiar double-helix structure with which you are probably familiar. DNA helices are capable of further coiling into relatively thick structures called chromatin. These are so thick they're visible under a microscope. Chromatin forms into chromosomes, among other reasons, to keep the 23 long DNA strands separate and tangle-free during cell division.

Here are the three strands we're considering now just for review. The sequence is the same as in the figures above.

Review

• The DNA double helix comprises a +strand of DNA and a —strand. The + or sense strand contains the genetic code for the organism.


• DNA is unwound and the strands are un-paired in preparation for reading.


• The —strand is read by RNA Polymerase II (RNA Pol II) and an RNA copy (U instead of T) of the +strand is made. This is the mRNA, ready to be translated.

Three-letter codons are "read" by the ribosome one at a time, matched up – through base complementarity – with the proper tRNA, which carries its amino acid. The ribosome forms a bond between that amino acid and the last one in the chain, ratchets forward and moves on until it reaches a stop signal.

Here's the second amino acid. Notice that the codon AUG means methionine (Met) and GCU calls for an alanine (Ala).

In humans, about 20 amino acids per second are added to the chain in this way. That's fast! Now we need to consider the genetic code itself.

Review

• An mRNA finds (by random diffusion) a ribosome outside of the cell nucleus (bacteria have no nuclei). The mRNA is loaded 5' end (beginning) first.


• The ribosome reads a three letter codon and matches it up with its complementary tRNA.


• Positioning of the tRNA also positions its attached amino acid in the right position for ...


• the ribosome to catalyze its chemical attachment to the growing chain.


• This process continues until one of three STOP codons (UAA, UAG, UGA) is reached.

Notice, for example, that there are four possible codons for the amino acid alanine (Ala): GCU, GCC, GCA and GCG. In fact, any codon beginning with GC encodes an alanine in the protein sequence.

Why the redundancy? Well, one consequence of it is that the genome is somewhat resistant to changes in the protein sequence (which might affect its function) just because of a random mutation in the DNA sequence. Errors do occur all the time, and many organisms have special enzymes to do error checking and repair, but some slip through. In the case of an alanine codon, one-third of all such random errors (that is, errors in the last position of the codon) will have no effect at all on the protein that is build from the template.

Notice further that there are some special codons. We mentioned the three STOP codons above. These signal the ribosome that its work is done in building a protein. The codon for the amino acid methionine (Met) serves as the start codon for proteins. All proteins begin with a Met, though it could be cleaved off later in a set of processes know as post-translational modifications.

All in all, these redundancies in the genetic code give organisms a little cushion from the effects of DNA mutations that can an do occur in every organism on Earth.

One more thing: Notice that at the beginning of this section, we said that the codon table applied to every living organism on Earth, and viruses, too. That's strong evidence for the idea that everything alive on Earth today shares a common ancestor.

So there are 64 possible DNA or RNA trimers, and that's a very short chain. Let's consider a longer chain, say 20 bases. The number of possible 20-nucleotide polymers is

$$4^{20} \approx 1.1 \times 10^{12} \: \text{combinations}$$

That's 1.1 billion possible 20-base oligonucleotides. Now if we consider that most genes contain thousands of base-pairs, then you can see that the number of possible combinations is an astronomical number. The mathematics here have huge consequences and implications in the fields of genetics and forensics, among others.

Protein sequences

Now let's do the same kind of math with protein sequences. The number of naturally-occuring amino acids used by organisms on Earth to make proteins is 20, so for a 20-amino acid protein (a very, very short protein), there are

$$20^{20} = 10^{26} \; \text{combinations}$$

It's an even bigger number, of course. That's 1 followed by 26 zeros. If there's a name for that number, I don't know it. Typical proteins consist of several hundred amino acids.

Viruses, unlike living cells, don't carry around the machinery (ribosomes and other enzymes) to make the proteins that form them. Instead they co-opt their host cells to do that for them. In the cases of RNA-based viral genomes, the viruses do have to supply their host cells with enzymes not generally found in cells, such as reverse-transcriptases, enzymes designed to construct DNA strands from RNA templates.