Trp Operon - and example of a repressible operon

• five genes (trpA, trpB, trpC, trpD, and trpE) involved in the production of the amino acid tryptophan

• another gene (trpR) produces an inactive repressor protein

• accumulation of the end product (tryptophan) represses synthesis of the enzymes

  • tryptophan binds to the inactive repressor protein at an allosteric site

  • the conformation changes and the repressor + tryptophan complex binds to the operator, repressing the operon

• tryptophan can accumulate due to internal production or from external sorces

  • remember, E. coli is found in the intestines of humans so if you eat a tryptophan-rich meal, this will accumulate in the bacteria and turn off the operon

  • why waste resources when a supply of this amino acid is readily available?

Gene Control in Eukaryotes

Much more complex - take humans for example

• Every cell (except gametes) have the same DNA, with the same information

• This is known as genetic totipotency

  • Almost all eukaryotic genes must be shut off in order to allow for cell normal function (a liver cell cannot have genes for lung cells running, not can it?)

• Usually, every gene has more than one gene regulator (all of which must be on for the gene to function)

Gene Regulation in Eukaryotes

The latest estimates are that a human cell, a eukaryotic cell, contains approximately 35,000 genes.

• Some of these are expressed in all cells all the time. These so-called housekeeping genes are responsible for the routine metabolic functions (e.g. respiration) common to all cells.

• Some are expressed as a cell enters a particular pathway of differentiation.

• Some are expressed all the time in only those cells that have differentiated in a particular way. For example, a plasma cell expresses continuously the gene for the antibody it synthesizes.

• Some are expressed only as conditions around and in the cell change. For example, the arrival of a hormone may turn on (or off) certain genes in that cell.

How is gene expression regulated?

There are several methods used by eukaryotes.

• Transcription Control 

  • The most common type of genetic regulation

  • Turning on and off of mRNA formation

• Post-Transcriptional Control

  • Regulation of the processing of a pre-mRNA into a mature mRNA

• Translational Control

  • Regulation of the rate of Initiation

• Post-Tranlational Control

  • Regulation of the modification of an immature or inactive protein to form an active protein

Transcriptional Control 

 

T ranscription start site

This is where a molecule of RNA polymerase II (pol II) binds. Pol II is a complex of some 10 different proteins (shown in the figure in yellow with small colored circles superimposed on it). The start site is where transcription of the gene into mRNA begins.

The basal promoter

The basal promoter contains a sequence of 7 bases (TATAAAA) called the TATA box (this is very similar to the -10 box or Pribnow box found in prokaryotes) . It can be bound by Transcription Factor IID (TFIID read T F 2 D) which is a complex of some 10 different proteins including

• TATA-binding protein (TBP), which recognizes and binds to the TATA box

• other protein factors which bind to TBP - and each other - but not to the DNA.

The basal or core promoter is found in all protein-encoding genes. This is in sharp contrast to the upstream promoter whose structure and associated binding factors differ from gene to gene (i.e. they are unique to each specific gene).

Although the figure is drawn as a straight line, the binding of transcription factors to each other probably draws the DNA of the promoter into a loop.

Many different genes and many different types of cells share the same transcription factors - not only those that bind at the basal promoter but even some of those that bind upstream. What turns on a particular gene in a particular cell is probably the unique combination of promoter sites and the transcription factors that are chosen.  To see how this all comes together, click here.

An Analogy

The rows of lock boxes in a bank provide a useful analogy.

To open any particular box in the room requires two keys:

• your key, whose pattern of notches fits only the lock of the box assigned to you (= the upstream promoter), but which cannot unlock the box without

• a key carried by a bank employee that can activate the unlocking mechanism of any box (= the basal promoter) but cannot by itself open any box.

• Check out the movie "Matchstick Men" to see this in action

Hormones exert many of their effects by forming transcription factors.

The complexes of hormones with their receptor represent one class of transcription factor. Hormone "response elements", to which the complex binds, are promoter sites. Link to a discussion of these.

Just how do proteins bind to DNA?

DNA:Protein and Protein:Protein interactions are important for transcription factor function. Note modular structure of transcription factors: one part of the protein is responsible for DNA binding, another for dimer formation, another for transcriptional activation (i.e. interaction with basal transcription machinery). 

Dimer formation adds an extra element of complexity and versatility. Mixing and matching of proteins into different heterodimers and homodimers means that three distinct complexes can be formed from two proteins. 

Diverse in nature, but several common structures are found:

• Helix-turn-helix (homeodomain) - three different planes of the helix are established and bind to the grooves of the DNA

• Zinc fingers - cystine and histidine residues bind to a Zn²⁺ ion, looping the amion acid into a finger-like chain that will rest in the grooves of DNA

• Leucine zipper - dimers result from leucine residues at every other turn of the a-helix.  When the a-helical regions form a leucine zipper, the regions beyond the zipper form a Y-shaped region that grips the DNA in a scissors-like configuration