The underlying theme of this chapter is to gain an understanding of how cells regulate the genes encoded by their DNA. If each cell of an organism has identical DNA, then only certain parts of it are transcribed and translated. This is gene expression.

In Chapter 9, we used the term expression to describe phenotype, and that is one way gene expression is observed. A modern approach to understanding gene expression is through DNA technology. Any attempt to understand gene expression really is an attempt to understand how those genes are regulated, allowing transcription and translation to occur only at specified times.

Gene organization/regulation in prokaryotes (bacteria). Frequently, the genes which are related in function are located close together and are also transcribed together. This group of genes is then called an operon. In 1961, Jacob and Monod described the first bacterial operon, the lactose operon. The genes in this operon code for proteins that will break down lactose to a form the bacteria can use. Since lactose isn’t always available to a cell (and glucose would be its first choice anyway), it doesn’t make sense for the cells to continually make the lactose digesting enzymes. As a result the lactose operon is generally in the ‘off’ position. Only when glucose has been depleted, and lactose is present does the cell turn ‘on’ the lac. operon. How? With Lactose....lactose inactivates a repressor, causing it to fall off the operator.

A second bacterial operon is the tryptophan operon, or trp operon. This operon is usually turned ‘on’ because the cell needs to make the amino acid tryptophan. If that amino acid is provided in the growth medium, then the cells don’t have to make their own. They turn the trp operon off by the binding of tryptophan to a repressor (which is normally inactive). Once trp has bound to the repressor, it becomes active and binds to the operator, stopping any transcription.

Eukaryotic Gene Regulation. Eukaryotic processes are more complicated than those which occur in bacteria, and can occur at a variety of stages.

Transcription regulation – involves transcription factors such as activators or repressors. Activators are proteins that bind to enhancers, DNA sequences far away from the gene to be transcribed. Somehow, the activator/ enhancer can cause the DNA to bend in such a way that the RNA polymerase can bind to the operator and transcription is turned ‘on.’

Conversely, repressors bind to silencer DNA sequences and prevent RNA polymerase from initiating transcription.

When genes in a metabolic pathway are on different chromosomes, the same activators bind to each gene, wherever it is located. Then transcription can occur simultaneously.

Transcription regulation also involves modifying RNA transcripts. Modifications including adding a 5’ G cap to a transcript as well as a 3’ poly-A tail. These protect the RNA from attack and help ribosomes recognize the transcript. Eukaryotic RNA also contains large non-coding sequences called introns. Introns must be removed and the remaining coding sequences, exons, are then spliced together. Alternative splicing means that slightly different versions of exons are spliced together. This allows a relatively small number of genes to result in a large variety of resulting proteins.

Translation regulation – The stability of mRNA depends on its specific type – some are very stable, some are highly unstable and degrade after a few minutes. Sometimes there are inhibitors that prevent mRNA from assembling in a ribosome. Hemoglobin is regulated in this way. Until heme binds the inhibitor and removes it from blocking translation, no hemoglobin is translated. Sometimes, post-translational modifications are made, where the translated protein has a segment removed before it becomes functional. This is the case with insulin.

Now that we’ve seen how genes are regulated, we should figure out how all the genes are stored in the chromosomes, because this plays a role in gene regulation as well.

All of the methods above are important in determining which genes are transcribed and translated, and which parts of the chromosomes remain tightly supercoiled, unavailable for transcription. This brings up the question of whether cells which have already become specialized in their function (blood cells, brain cells, liver cells, etc.) can ever have their inactive DNA (supercoiled) reactivated. This is the basis of the early frog cloning experiments and the cloning of Dolly the sheep. These show that inactive segments of chromosomes can be reactivated. This is also how salamanders are to to regenerate a lost limb or tail. Cells surrounding the injury undergo de-differentiation, and undergo a re-specialization to replace the lost body part.

Signal transduction pathways. This is the method by which one cell receives a message from a neighboring cell indicating that it should initiate transcription. The neighboring cell releases a signal molecule which binds to a receptor protein in the cell’s membrane. This initiates a series of relay proteins that results in the activation of a transcription factor. The transcription factor enters the nucleus and initiates transcription of a new gene.

Genetic Basis of Cancer. Several mutations are generally required for the development of cancer. Chromosomes of many animals contain genes that can be mutated to become oncogenes, a gene that results in cancer. These are called proto-oncogenes, and they often code for growth factors. Mutations in proto-oncogenes primarily occur in somatic cells so there is little chance that the mutated cancer cells would be passed to offspring. However, certain versions of proto-oncogenes can predispose an individual to cancer, and those proto-oncogenes are hereditary.

Mutations that lead to cancer may result in a hyperactive protein, multiple copies of a gene or, a gene that has moved to a different location with different regulatory factors. Also, changes in tumor suppressor genes will reduce the cell’s ability to stop uncontrolled cell growth.