Genes to RNA to Proteins

Regulation of Gene Expression

Several factors regulate which genes are expressed at any given time.
DNA provides the original code for protein synthesis. This code is converted into RNA and then into a sequence of amino acids. The order of the amino acids in the polypeptide chain determines which protein is produced. After synthesis, each new protein has a particular function. However, the gene that codes for a protein might not become active until a later time in the organism's life. For example, consider that a butterfly begins life as a caterpillar. Genes that encode the size, shape, and colors of the adult butterfly's wings are not active during this stage of its life cycle. As the butterfly grows, genes are activated that stimulate it to build a cocoon. This triggers the activation of the genes for wing size, shape, and color, among many others, that are expressed in the adult butterfly. A tissue sample from the caterpillar and the butterfly would show the exact same genetic code, just with different genes being active. Gene expression is regulated by various mechanisms, such as cellular signals or environmental cues, that control this process.

Prokaryotic Gene Expression

Prokaryotes regulate gene expression and protein production primarily at the mRNA level.
Prokaryotes are single-celled organisms that lack a nucleus. Prokaryotic gene expression is different from that of eukaryotes in several ways. Prokaryotes make proteins only when they are needed instead of all the time. This helps them conserve much-needed energy. Prokaryotes can also turn off their protein factories when conditions call for it. They can do this in the following ways:
  • Preventing translation of mRNA
  • Keeping the protein from functioning
  • Hydrolyzing the mRNA to keep translation from happening

If the prokaryote recognizes that conditions are not favorable early enough, it can prevent the protein from being formed, thereby conserving the energy needed to make it, referred to as transcriptional regulation. While all of the listed methods are used, prokaryotes use transcriptional regulation most frequently. There are two types of transcriptional regulation: negative regulation uses a repressor (which inhibits RNA synthesis) to prevent transcription, and positive regulation uses a promoter (which begins RNA synthesis) to induce transcription.

In prokaryotes, a collection of genes that are transcribed together and contains at least two regions of control called a promoter and an operator is called an operon. Prokaryotes often use these clusters of genes to regulate transcription. They usually consist of a promoter, an operator, and two or more structural genes, which are genes that code for anything other than a regulatory factor. The operator is a segment of DNA that sits between the promoter and structural genes and tightly binds with other proteins that can turn transcription on or off.
Operons regulate transcription in prokaryotes. For example, when presented with a diet high in lactose, prokaryotes will activate the lac operons to synthesize the enzymes needed to digest it. When lactose is absent, the repressor (red) is bound to the operator (yellow), preventing transcription. When lactose is present, it binds to the repressor, releasing it from the operator and allowing RNA polymerase (gray) to bind to the promoter (green) and begin transcription.
To start the transcription process, prokaryotic cells turn on a special protein that binds to RNA polymerase called a sigma factor. Sigma factors direct RNA polymerase toward the specific areas to be transcribed and must be attached before the process can begin. The number of sigma factors varies based on the species of prokaryote.

Eukaryotic Gene Expression

Eukaryotes regulate gene expression through a wide variety of mechanisms including regulation of transcription and post-transcriptional modification of mRNA.
Eukaryotes are organisms that have a nucleus, and many of them are multicellular. Development of eukaryotes requires the precise timing of different genes being activated or turned off. As in the butterfly example, proteins must be made in order for characteristics to be present when needed. Another example would be the production of milk in mammals after childbirth. Milk does not need to be produced at other times in the female's life— only when she is nursing her young. This gene expression is monitored and regulated at several different places during protein synthesis. These efforts are very similar to those in prokaryotic cells, but there are differences because of the presence of a nucleus in many of the cells in which proteins are made.

The first main difference between prokaryotic and eukaryotic protein synthesis is that eukaryotes use a promoter called a TATA box to initiate transcription (writing RNA from DNA). The TATA box is the part of a eukaryotic promoter that binds a transcription factor (molecule that helps make RNA) and helps to initiate the process of transcription. It has many AT base pairs in it and is the place where the DNA starts to unwind. There are several other types of promoters used, each of which can enhance or silence part or all of the transcription process. Most genes have their own individual promoters and can be found far apart on the chromosomes (bundles of DNA). To compensate for this, there is a coordinated effort by the transcription factors to activate the genes at the same time. For example, when plants experience drought conditions, several responses must take place in many different parts of the plant. Roots must extend down further in search of water, stomata must close to reduce water loss, and cells must shrink in size, causing the leaves to wilt. If the efforts by transcription factors to produce the proteins needed to perform these tasks were not coordinated, then the plant would not be able to survive.

It is also possible for genes to be modified after transcription has taken place. There are several mechanisms used to accomplish this. The first is called alternative splicing. The mRNA transcript usually contains introns (which do not code for proteins) and exons (which do). The introns are normally removed during mRNA processing. In alternative splicing, some exons are also removed along with the introns. This creates new proteins that would not otherwise be present. Alternative splicing occurs quite often in the human genome. An estimated 50% of human genes are formed in this manner. Another post-transcription method of regulating genes is through the use of microRNA (miRNA). These are pieces of RNA produced from the non-coding regions of the gene. Scientists have discovered about 1,000 miRNA areas in the human genome. Each one can alter the normal process of translation and cause it to skip the addition of certain amino acids. This results in different proteins being made. A third method of post-transcription regulation is by regulating translation. MicroRNA can prevent translation of the mRNA. Another way is by altering the cap on the 5′ end of the mRNA molecule, preventing the normal attachment of the tRNA to the mRNA strand.
Repressors, activators, and coactivators are used to bind with select genes to turn on or off certain traits in an organism. Repressors bind segments of DNA to prevent transcription. Activators bind near promoters to enhance DNA transcription. Coactivators bind to activators and transcription enzymes to help RNA polymerase begin transcription.