General Genetics/Gene Expression in Prokaryotes
Gene Expression in Prokaryotes 
A hallmark difference between prokaryotes and eukaryotes is chromosomal arrangement. Eukaryotes, owing to their complexity, have multiple chromosomes containing a variety of mechanisms that regulate gene expression. Prokaryotes, by contrast, possess a very simple chromosomal arrangement. Most of the DNA within prokaryotic organisms is housed within a single, circular chromosome. In some instances, a secondary chromosome, known as a plasmid, may exist. Prokaryotes act as if by default all the genes are on. The DNA is interpreted word by word and it tells the ribosomes to make everything it says. So to control genes the cell selectively turns off parts it doesn't need at certain times.
The mechanism for doing this, as briefly described in the introduction, is preformed by an operon. An operon is a gene regulatory feature unique to prokaryotes. It consists of a group of related genes that must be transcribed in sequence. A "promoter" region lay at the front of the operon, which, when a transcription enzyme binds to it, bends the DNA in a way that makes it easier for transcription factors to access the genes within the operon. Although there are many kinds of operons in prokaryotes, the lac operon is the best understood and most widely used to teach bacterial gene regulation. We will use it as a model for presenting the general features of an operon.
As mentioned, the initial component of an operon is the inhibitor gene. In the case of the lac operon, immediately downfield of the inhibitor gene (lacI), we find the promoter, followed by what is referred to as a "controller," or sometimes "operator" region. The inhibitor lacI gene is called "constitutive." That means that it is constantly encoded by the prokaryotic cell, no matter what the conditions of its environment may be. This inhibitor protein, when translated, binds to the controller region of the lac operon. Once it binds to the controller region, the inhibitor blocks all transcription factors (RNA polymerase) from from progressing down the gene sequence, thus preventing the transcription of genes within the rest of the operon.
This process is known as a "negative feedback mechanism." So long as nothing interferes with the inhibitor enzyme that is bound to the operator region, the genes within the lac operon will never be encoded. There is. however, a way for the cell to break this negative feedback mechanism. In the event that the environmental conditions the cell finds itself in change and lactose becomes available, the lactose will be transported across the membrane of the prokaryote, diffuse through the cytoplasm, and bind to a spot on the inhibitor enzyme called the allosteric site. When the lactose binds, it causes a change in the 3-dimensional structure of the inhibitor enzyme, causing it to let go of the controller region of the lac operon. When it lets go, RNA polymerase is allowed to complete the process of transcription and the rest of the genes in the operon are thus transcribed.
The above is a simplified view of the lac operon system. This complex is known as a cistron. That is, it is a system physically on the DNA strand that controls and produces a genetic product.
Genetic Recombination in Prokaryotes 
Previously, the presence of a secondary "plasmid" chromosome in many prokaryotes, which is much smaller than the primary circular chromosome, was discussed. In terms of evolution, the plasmid serves a very important purpose for the prokaryotic genome. Due to their simplicity, prokaryotes cannot engage in sexual reproduction. You might imagine the inherent genetic dilemma in a population of organisms that are only capable of dividing asexually, through binary fission, as bacteria do. Because every individual within a population of bacterial cells is so closely related genetically, they are put at great risk in the event that an environmental stressor emerges that exploits a weakness in the bacterial genome. One example are molds and fungi that are able to produce molecules that have an antibiotic effect on nearby bacteria -- such as the betalactam molecules that we produce into penicillins. In the event that such a fungi emerges in an environment cohabited by the prokaryote E. coli, for example, the E. coli population is immediately put under great selection pressures. They must evolve, or die. But when its mechanisms for genetic recombination are incredibly simple, how is a population expected to produce enough genetic diversity to survive such an environmental stressor?
In the case of some prokaryotes, such as E. coli, there exists a mechanism for genetic recombination known as the sex pillus, which provides a solution for this dilemma. The sex pilus allows bacteria that are equipped with it to transfer their secondary chromosome, the plasmid, to a neighbouring bacterial cell. This process is known as conjugation. It is the bacterial equivalent of sexual reproduction, or more accurately, a strategy for sharing DNA between individuals in a bacterial population. An F+ bacterium (Reproductive Factor Positive) contains a plasmid that codes for the sex pillus, which allows a tube used for conjugation to hang off and articulate with a neighboring bacterium (the neighbor being F-, or lacking the gene to encode a sex pilus itself), which it binds to and swaps its plasmid with. The actual act of copying the plasmid occurs in a similar fashion to DNA replication
In addition to the F+/F- system of conjugation, there exists the possibility for "Hfr" (High frequency recombinant) cells to exist. Hfr cells contain a fertility factor directly within their primary circular DNA region, as opposed to storing the fertility factor on their secondary plasmid. When an Hfr cell conjugates with an F- cell, the host F- cell remains F-. This occurrence is random, as is the location within the bacterial chromosome that the factor incorporates.
The ability of an Hfr cell to recombine with an F- neighbor comes with some risk. In the event of attempting recombination, extra genetic information can mistakenly be carried out of the Hfr cell. When the F factor leaves that cell, the cell is said to be "F Prime" (F'). The exiting plasmid retains the ability to code for its reproduction factor, and brings this baggage along with it into the F- cell. The end result is the original Hfr cell losing its ability to recombine, while the recombined F- cell becomes an Hfr, because it assimilated the sex factor gene within its own genome.
Conjugation is a haphazard process. Forming a complete F' bacterial cell is a little more difficult than recombination under other scenarios, because the sex pillus is a weak structure and usually breaks before the full F factor is transferred. Regardless, it still solves the problem of genetic diversity in bacterial cells. Cells from whole other species -- for instance, a population of E. coli cells and S. aureus cells -- can swap DNA via this mechanism. It both accounts for the ability of populations to rapidly evolve, and challenges the usefulness of the biological species concept in identifying and categorizing bacterial "species."