The larger the genome, the more information it can, at least in theory, contain. 

The parasitic or obligate symbiotic archea Nanoarchaeum equitans has the smallest known genome (as of March 2005), it is ~ 490,000 base pairs  (490 kilobases or kb pairs) in length. 

The small bright dots are N. equitans cells, the large structures are its host, another archea, Ignicoccus. 

Another small genome organism is the bacterium Mycoplasma genitalium, the cause of non-gonococcal urethritis.  It contains ~580 kb of DNA, which encodes ~500 distinct genes.

Based on comparisons between organisms, and the results of experimentally disrupting specific genes, it appears that ~300 is the minimum number of genes required for cellular survival and reproduction.

Humans have two copies of ~3.2 x 10⁹ base pairs of DNA, which encodes approximately 25,000 genes.  

One interesting point is that even though a human cell contains about 5500 times the amount of DNA as does a M. genitalium cell, humans have only about 50 times as many genes.  

An interesting aspect of the information coded in the genome is that it comes in two particular types.  

Locating information within DNA:  The DNA molecules that contain genes can be thousands to millions of base pairs in length.

More to the point, a single DNA molecule can contain hundreds or thousands of genes. 

To access the information stored in a gene, it is necessary to find the sequence of the gene so that it can be transcribed into RNA.  This sequence has to be recognized and distinguished from all of the other DNA sequences present within the cell. 

This is accomplished by using a two-component system.  The first part of this system are specific sequences of nucleotides within the DNA.

These sequences provide a molecular address that can be used to identify the specific region of a specific strand of the DNA to be transcribed. 

The set of sequences involved in identifying the region of a gene to be transcribed is known as the gene's regulatory region. 

The regulatory region of a gene can be simple or complex.  In some human genes, the gene's regulatory region is spread over thousands of base-pairs of DNA.

Regulatory DNA sequences are recognized by proteins that bind to DNA in a sequence specific manner; these proteins are known as transcription factors because they regulate transcription.  

Specific regulatory sequences are bound by specific transcription factors, and it is common that multiple transcription factors are used together to recognize and regulate the expression of a specific gene.

A specific transcription factor protein can act either positively or negatively.  

Positively-acting transcription factors, known as activators, stimulate transcription.

Negatively-acting transcription factors, known as repressors, suppress transcription.

Sometimes a transcription factor that acts positively at one DNA regulatory site will act negatively at another, depending upon its interactions with other proteins that bind near by, or that associate with the transcription factor.

DNA-binding transcription factors recognize specific DNA sequences by interacting with the surfaces of the base pairs visible in the major and minor grooves of the DNA helix.

A single base pair change in a gene's regulatory region can profoundly alter the efficiency or timing of transcription.

• How could a protein that acts as a transcriptional activator on one gene act as a transcriptional repressor on another?
• Why does binding of combinations of transcription factors increase the selectivity of the regulatory system.

The binding of transcription factors recruits or inhibits the recruitment of an enzyme complex, the DNA-dependent, RNA polymerase, to the DNA.

This RNA polymerase synthesizes RNAs.

Where RNA polymerase starts transcribing RNA is known as the transcription start site.  Where it falls off the DNA, and so stops transcribing RNA, is known as the transcription termination site.

As transcription initiates, the RNA polymerase moves away from the transcription start site. 

Once the RNA polymerase complex moves far enough away (clears the start site), there is room for a new polymerase complex to associate with the DNA, through interactions with transcription factors. 

The efficiency of RNA polymerase binding and activation determines the rate at which RNA molecules are produced. 

• If active RNA polymerase bound to DNA on its own, what predictions would you make about the RNA molecules you would find in the cell?
• What would happen to the rate of transcription of a specific gene if an inactive RNA polymerase bound to a transcription start site