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Molecular Biology

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Molecular Biology

Deoxyribonucleic acid, better known as DNA, is located in the nucleus of all living cells. DNA dictates which creatures walk, fly, or bore through the soil. Each DNA strand is made up of four nucleotides or "building blocks": adenine, cytosine, guanine, and thymine. These nucleotides, in turn, are made up of a variety of proteins, called amino acids. The strands of DNA, made up of bonded nucleotide pairs, are very long. Molecular biologists have worked toward breaking the genetic code by identifying the nucleotides in order and searching for patterns.

Nature gave scientists one big hint: adenine always bonds with thymine, and guanine always bonds with cytosine. In the past, researchers found fluorescent molecules that mimic the natural nucleotides. When the known fluorescent molecule bonded with an unknown nucleotide, scientists could identify that particular bonded pair of the DNA strand. The process took a decade or more. Researchers hope to speed up this painstaking work with help from computers, so they can accomplish such tasks in hours instead of years.

The challenges are formidable. Scientists must find a way to isolate and copy genes. Sensitive equipment must be developed to allow DNA sequences to be "read" as they are drawn through some kind of microscopic portal. The monitoring equipment must be fast enough, or the process slowed enough, to allow for an accurate identification of these bonded molecules. Finally, researchers must have algorithms to help them process the multitude of data they would receive from even one single strand of DNA, which could have 70,000 nucleotides. Computers are then needed to transmit and compare the sequence of the genes being studied with known gene sequence databases, a monumental task for which computers are particularly well suited.

The benefits of such research are profound. The study of human genetics is the first most obvious benefit, since these findings will aid research in fields as diverse as inherited diseases and anthropology. Since DNA holds the key to every aspect of the human body, genetic studies could potentially be used to mimic the way different cells work. This would allow researchers to develop and experiment with the effect of medications on the body without using living subjects. Disease processes, such as various forms of cancer, could potentially be duplicated in an electronic model and studied. This kind of understanding would aid in the development of successful treatments. Scientists also hope to use DNA sequences to identify and classify organisms, from the discovery of new bacteria to tracing the evolution of animals. Models of bacterial DNA could help in the study of the spread of diseases.

Gene therapy is a field in which the genes of living things are manipulated and even exchanged with one another to provide a beneficial result. For instance, spider silk, one of the strongest materials on Earth, has been produced by potatoes. Frogs and earthworms have been made to glow in the dark. A type of corn has been modified to fight tooth decay effectively. Vitamin A has been added to rice, making the grain more nutritious. Many of these applications of gene therapy have met controversy, since the long-term effects of gene manipulation in food are unknown.

Bioinformatics is the field in which software is developed to aid in the study of molecular biology. Many of the studies currently being done in molecular biology would be impossible without the help of computers and computer software. This software comes from various places. One researcher developed a basic bioinformatics software application and posted it on the web for others to download and improve upon, as did the creators of the Linux operating system , resulting in a versatile software application. Other firms have hired professionals to develop and copyright applications, which are then sold to researchers and private firms.

The U.S. government has played a pivotal role in the quest for information by establishing the National Center for Biotechnology Information, or NCBI. The NCBI is a division of the National Library of Medicine (NLM), which stores biomedical (such as gene sequence) databases. The NLM itself is a division of the National Institutes of Health (NIH). With all of the resources of the NIH, it is considered the largest biomedical research facility in the world. The NCBI is the result of a cooperative effort. Researchers, academic institutions, and similar agencies from other countries around the world access and contribute to the databases available at the NCBI.

Molecular biology and computers are also finding uses within the medical field. For example, scientists have developed a device that electronically smells the presence of bacterial infections in the lungs. Breath samples are taken from patients and put into an aroma-detection device. The machine measures the electrical resistance of the molecules in the sample of air. The results are then displayed in a two-dimensional "map." Different bacteria produce distinct characteristics on this map. This is a potentially life-saving tool because it allows physicians to treat patients immediately with the correct antibiotic for pneumonia instead of waiting two or three days for sample cultures of the bacteria to be grown and identified.

Although the use of computers is rapidly advancing the field of molecular biology, there is growing evidence that molecular biology is also important to computer science. Researchers at Syracuse University in New York are working with a purple protein called bacteriorhodopsin, produced by a type of bacteria native to salt marshes. This protein is quite stable, readily produced, and easily processed. Many believe it will eventually replace silicon microchips. Bacteriorhodopsin changes shape upon exposure to light. One shape is designated as binary 0, and the other shape is designated as binary 1. Bacteriorhodopsin is suspended in organized layers within a polymer gel. Because an individual protein changes shape upon reacting to different colors of lasers, the shape of an individual protein within the cube can be manipulated.

Floppy drives, CD-ROMs (compact disc-read only memory), and hard drives are different forms of memory that operate on a two-dimensional basis. The bacteriorhodopsin gel would be a type of three-dimensional memory. Researchers believe that one cubic centimeter of this bacteriorhodopsin protein/gel will be able to store between eight and ten gigabytes of information.

Experts agree that future molecular biology studies would be unthinkable without computers. Perhaps in the future, computers will be equally dependent upon molecular biology.

see also Binary Number System; Biology; Image Analysis; Molecular Computing; Pattern Recognition.

Mary McIver Puthawala

Bibliography

Cimino, Daniela. "Modeling a Drug." Software Magazine 18, no.1 (1998): 12(1).

Cooke, Robert. "Brave New Bacterial World." MIT Technology Review 100, no. 3 (1997): 14(2).

Levin, Carol. "High Protein Computers." PC Magazine 14, no. 10 (1995): 29(1).

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