Gene

Genes are functional units of DNA that contain the instructions for making proteins or RNA. Genes also act as units of heredity, transferring the same instructions from parent to offspring. The nature, structure, and regulation of genes has been a central topic of scientific research for more than 100 years.

History of the Gene and Structure of DNA

Genes were first defined as units of hereditary transmission. The name "gene" was coined by Wilhelm Johannsen in 1909, although the concept of a discrete unit governing inherited characteristics goes back at least to Gregor Mendel in 1861. The work of Thomas Hunt Morgan and his colleagues established that genes were located on chromosomes, and in the mid-1940s Oswald Avery demonstrated that genes were composed of DNA (deoxyribonucleic acid). Since that time, some types of viruses have been discovered that use ribonucleic acid (RNA) instead of DNA, but here we shall concentrate on DNA genes. The discovery of the structure of DNA in 1953 by James Watson and Francis Crick set the stage for the next fifty years of research into gene structure, function, and regulation.

DNA is a linear molecule composed of subunits called nucleotides. Each nucleotide is made of a sugar and phosphate group, plus a chemical base, of which there are four types: adenine, thymine, guanine, and cytosine (A, T, G, C). Nucleotides are typically referred to by the name of their base. DNA exists as a pair of strands, wound around one another into a double helix, with the bases directed into the center. The structure and charges of the bases dictate that A on one strand can match only up with T on the other, and C only with G. This complementarity provides the basis for faithful replication of the entire DNA molecule.

Genes Code for Protein and RNA

While all genes are made of DNA, not all stretches of DNA act as genes. Indeed, in eukaryotic organisms, most of the DNA does not function as genes, meaning it is not the code for making proteins or RNA. Some DNA outside of genes has a structural role, some are remnants of old genes that now are functionless, and much of it appears to be "junk," inserted and copied by viruslike sequences. Within a gene, usually only one side of the double helix actually codes for product; the other side is silent. Which side of the helix acts as code varies from gene to gene.

Almost all genes code for proteins. Proteins are strings of amino acids, and the sequence of nucleotides in the gene dictates the sequence of amino acids in the protein. Proteins perform almost all the functions in cells, and can be grouped into four major classes: they act as enzymes that control the rate of chemical reactions in the cell; they form structural components of organelles, membranes, and other cell components; they receive and transmit signals between and within cells; or they act as regulators of genes by latching onto DNA, thereby increasing or decreasing the rate at which the gene is used, or "expressed."

Genes vary in length. The largest human gene is 2.5 million base pairs in length, and codes for the muscle protein named dystrophin, which is more than 3,500 amino acids long. Eukaryotic genes generally produce proteins of about 150 to 3,000 amino acids in length. Some genes are relatively small, as in prokaryotes, which produce proteins of 50 to 300 amino acids. Most eukaryotic protein-coding genes are present in only two copies per genome, occurring in the same position on homologous chromosomes, one of which is received from each parent. If the two copies differ slightly they are called alleles. Changes in nucleotide sequences are termed mutations or polymorphisms, depending on their effect.

Some genes code not for protein but for RNA molecules that have their own functions within the cell. These include the transfer RNAs, ribosomal RNAs, and a variety of other smaller RNAs with roles in the nucleus. RNA-coding genes are usually present in multiple copies per eukaryotic genome.

Gene Expression

Expression of protein-coding genes begins with the process of transcription. During transcription, the helix is unwound, and an enzyme (RNA polymerase) binds to the DNA. It then moves along the DNA, and beginning slightly "downstream" at the so-called initiation site, it copies one of the strands to form a molecule of RNA. Transcription ceases when the polymerase reaches a special DNA sequence called the termination site, usually a region high in G-Cs followed by A-Ts.

In prokaryotes, this RNA product is ready to use for protein synthesis, and is called messenger RNA (mRNA). After the mRNA of a gene is formed, it is used by the cell in protein synthesis (translation) at the ribosomes.

Thus, the prokaryotic gene consists of an RNA binding site (called the "promoter"), a transcription initiation site, the coding region, and a termination signal. The initiation site should not be confused with the start signal for protein synthesis, nor the termination site with the stop signal in protein synthesis. Each of the translation signals is within the coding region, or "open reading frame," of the gene.

Eukaryotic Genes

In eukaryotic cells, genes are more complex. It was discovered in 1977 that eukaryotic genes are functionally separated into coding segments called exons, which are interrupted by noncoding sequences of DNA called introns. The entire region between the initiation and termination sites is transcribed, including the introns, to form the primary transcript. This must then be processed by special enzymes that cut out the introns and splice together the exons to form an mRNA. The mRNA is then exported from the nucleus for translation.

The existence of introns allows for the creation of multiple proteins from one gene, by the use or exclusion of different exons. Such alternative splicing gives rise to protein "isoforms," highly similar but slightly different proteins, with functions that vary as well. Isoforms are typically tissue-specific. For example, the muscle enzyme creatine kinase exists in one form in the heart, and another form in the skeletal muscles (such as the biceps), which have different ends formed through use of different exons. Even though it codes for two or more proteins, most scientists call such a DNA sequence a single gene.

Eukaryotic genes also contain a sequence close to the termination site called the polyadenylation signal. After transcription, this sequence prompts a special enzyme, called poly-A polymerase, to cut the RNA chain and begin adding multiple adenine nucleotides, as many as 250, to the primary transcript. This poly-A tail helps transport the RNA out of the nucleus, stabilizes it in the cytoplasm, and promotes efficient transcription at the ribosome.

Thus, the eukaryotic gene consists of an RNA binding site (promoter), a transcription initiation site, the coding region including exons and introns, the polyadenylation signal, and a termination site.

Genes for RNAs are transcribed in the same way, but the RNA formed is not translated into protein. Details vary among different types, but most RNA-coding genes do not contain introns. Transcripts of the ribosomal RNA genes must be cut apart to form a number of smaller functional RNA molecules.

Controlling Gene Expression

The complexity of any living cell is due to the well-orchestrated interactions of its proteins. Just as an orchestra cannot have every instrument play at once, a cell cannot have all its proteins function at once. One method of regulating protein function is to control when the protein is made, which is to say when the gene is expressed. Prokaryotic genes are usually controlled by operon systems, relatively simple systems that tie expression directly to metabolic activity in the cell. Eukaryotic genes are controlled by more complex regulatory systems that respond to hormones, growth factors, internal conditions, and many other influences.

To ensure that each gene is expressed when, and only when, it is needed, each eukaryotic gene has several control regions, termed the promoter and enhancer regions. These do not code for amino acids but are critical for proper gene expression. Mutations in these regions often change the rate at which a gene is expressed, or the factors in the cell or the environment to which it responds.

The promoter region is a sequence of 20 to 200 nucleotides "upstream" of the coding region to which the RNA polymerase enzyme binds, permitting it to begin transcribing the DNA. Promoters differ in size and sequence in prokaryotic and eukaryotic genes. Promoters attract RNA polymerase by first binding a variety of other proteins, called transcription factors. In some eukaryotic genes, promoter sites also occur within the coding region, allowing alternative transcripts with fewer exons.

Enhancers, also called activation sites, are located either nearby or far away from the promoter. Because DNA is looped and coiled, however, these sites are actually physically close to the gene's promoter even when distant on the DNA strand. Enhancers are gene-specific, and attract a variety of transcription factors. All of these work together to increase the rate of transcription by increasing the likelihood of RNA polymerase binding. Controlling the availability of these proteins is an important factor in regulating expression of the gene.

Elof Carlson

Bibliography

Alberts, Bruce, et al. Molecular Biology of the Cell, 4th ed. New York: Garland Science,2002.

Carlson, Elof. The Gene: A Critical History. Philadelphia, PA: Saunders Publishing,1966.

Muller, H. J. "The Development of the Gene Theory." In Genetics in the Twentieth Century, L. C. Dunn, ed. New York: Macmillan, 1951.

Olby, Robert. The Path to the Double Helix. Seattle, WA: University of Washington Press, 1974.