DNA Molecule

DNA (deoxyribonucleic acid) is a complex molecule that expresses, stores, and replicates all of the genetic information that is contained in eukaryotic cells. This genetic information is responsible for all the characteristics expressed in a particular species (e.g., color, size, and gender). In addition to physical characteristics, information pertaining to behavior and intelligence is also stored in the DNA molecule.

The DNA molecule is composed of two long strands (which are sugar-phosphate) and repeating units called nucleotides. Each of these nucleotides has three components: a 5-carbon sugar (which is deoxyribose in DNA vs. ribose in RNA), a phosphate group, and a nitrogenous base. Four nitrogenous bases make up the DNA molecule: two purines, adenine and guanine, which are composed of two nitrogenous rings, and two pyrimidines, thymine and cytosine, which are composed of one nitrogenous ring.

By forming hydrogen bonds, adenine pairs with thymine, and guanine pairs with cytosine. These pairs are known as base pairs and are responsible for the structure of the DNA molecule. The two adjacent polynucleotides are wound into two spiral-shaped strands called a double helix.

These long stands of the DNA molecule are organized by various proteins into individual units called chromosomes. Chromosomes are located in the nucleus of all eukaryotic cells. There are 46 chromosomes in each human cell, except in the sex cells (i.e., the eggs and the sperm), which have 23 chromosomes. On the chromosomes, there are regions of DNA, called genes, which are responsible for individual inheritable characteristics. A gene carries the actual biological information and can be as short as 999 base pairs to as long as several hundred thousand base pairs. It was estimated in 1996 that 30,000 to 40,000 genes exist in the genetic make up of Homo sapiens. However, upon the completion of the Human Genome Project in 2003, it is now postulated that only 20,000 to 25,000 genes exist.

The history of the discovery of the DNA molecule is an interesting one. It first began with the idea that physical traits of species are actually inherited in a predictable pattern from the parents to offspring. However, it was not until the middle of the 20th century that scientists began to actually identify the mechanism of inheritance and its molecular basis.

Gregor Mendel, a mathematician, known as “the father of genetics,” conducted many scientific experiments involving pea plants, which he began in 1857. The results of his experiments illustrated that pea plants distributed characteristics to their offspring in a mathematically predictable pattern. Mendel postulated that these characteristics (e.g., height of the plant) were inherited by the parent plant. However, at this time, the term character was used to define a heritable feature, such as the color of a flower. These characters vary among individuals. Each variant of a character is called a trait, such as purple or white. Even though he could not physically prove the biological foundation of this phenomenon, his work dramatically increased interest in the study of genetics.

In 1928, Frederick Griffith hypothesized that a molecule responsible for inheritance must exist. His work involved experiments using mice and the bacteria Streptococcus pneumonia. First, a virulent strain of S. pneumonia was injected into a mouse, and the mouse died. Second, a nonvirulent strain of S. pneumonia was injected into a mouse, and the mouse did not die. The next phase of his experiments involved heating up the virulent strain to denature and kill it; then, this killed strain was injected into a mouse, and the mouse lived. Finally, he injected a mouse with nonvirulent S. pneumonia that had not been heated up together with a virulent S. pneumonia that had been heated up, and the mouse died. Griffith postulated the killed virulent bacteria had passed on the virulent characteristics to the nonvirulent strand to make it virulent. He called the passing on of the inheritance molecule “transformation.”

A scientist named Oswald Avery revisited Griffith’s experiment 14 years later. Avery attempted to identify the inheritance molecule. In Avery’s experiments, he selectively destroyed different molecules in the virulent S. pneumonia (e.g., carbohydrates, proteins, lipids, and ribonucleic acids). After the destruction of these molecules, transformation still occurred—until he destroyed deoxyribonucleic acid, and transformation did not occur. Avery had at last isolated the inheritance molecule, DNA.

In the 1940s, a scientist named Erwin Chargaff discovered that the DNA molecule is composed of four bases: adenine (A), guanine (G), cytosine (C), and thymine (T). In addition, he found that the amount of adenine is almost equal to thymine and that the amount of guanine is almost equal to the amount of cytosine. Therefore, Chargaff postulated that A = T and G = C. This became known as “Chargaff’s rule.”

Two scientists named Rosalind Franklin and Maurice Wilkins attempted to crystallize and make an X-ray pattern of the DNA molecule, in order to understand its structure. Their results showed a pattern that appeared to have ladder-like rungs in-between two strands that were arranged side by side. In addition, the X-ray results showed an “X” shape and that the DNA molecule had a helical shape.

In 1953, two scientists, James Watson and Francis Crick, were working together and tried to put together a model of the DNA molecule. By examining the X-ray results of Franklin and Wilkins’s picture, they produced a model of a double helix that had rungs connecting the two strands. The rungs were actually the bases of the nucleotides that were paired together using Chargaff’s rule, so that all the adenine bases were paired with all of the thymine bases and all of the guanine bases were paired with all of the cytosine bases. These pairs are held together by a sugar-phosphate backbone, which makes up the double helix of the DNA molecule.

Watson and Crick also discovered that thymine and adenine each had two hydrogen bonds available and this is why they readily pair together. In addition, they discovered that guanine and cytosine each had three hydrogen bonds and this is why they pair together. Therefore, thymine can pair together only with adenine, and guanine can pair only with cytosine. Thus, one side (or strand) of DNA is a complement to the other side, which is made up of the corresponding base pairs.

The DNA molecule performs two functions: replication, where the DNA molecule “unzips” and makes an identical copy of itself (described below), and transcription, which is a process in which the DNA unzips and produces an mRNA molecule that ultimately produces a protein molecule (a process called translation).

These nucleotides are grouped side by side in threes (triplets), called codons (e.g., ATT or CGA); this is also known as “the triplet code.” Each codon codes for a particular amino acid, and usually 2 to 4 codons will code for the same amino acid. Amino acids are the organic molecules that serve as the building blocks for proteins. Some codons initiate a start or stop point on a particular segment of DNA.

How exactly is protein produced from DNA (i.e., how do we go from gene to protein)? During the process of transcription, a molecule called RNA polymerase helps to unzip the two strands of DNA by breaking the hydrogen bonds between the base pairs. The RNA polymerase knows where to begin by locating the start codon (called “the promoter”); it does this with the help of other proteins called transcription factors. Once it attaches and separates the two strands of DNA, the exposed bases attach with newly available complementary bases, forming a complementary strand of “mRNA.” This mRNA will continue to grow until the stop codon (and terminator sequence) is reached. Transcription ends after the RNA polymerase releases the newly made strand of mRNA and then detaches itself from the DNA after it has zipped it back up.

After transcription is complete, the mRNA molecule leaves the nucleus of the cell and makes its way to a ribosome, which uses the mRNA to synthesize protein. This process is called translation. During translation, mRNA slides through the ribosome, while a molecule called “tRNA” serves as an interpreter and brings the appropriate amino acid to the corresponding codon on the mRNA molecule. Each tRNA contains what is called an anticodon, which attaches to the codon on the mRNA; on the other end of the tRNA is an amino acid. The mRNA transcript is secured on the ribosome and will temporarily bond with the appropriate tRNA. Once this bond takes place, the tRNA transfers its attached amino acid to the chain of amino acids, which is growing as the mRNA is being read. This continues until the stop codon is reached, at which time termination of translation occurs, and a free polypeptide is released into the cytoplasm of the cell.

In addition to protein synthesis, it is important to note that the structure of the DNA molecule provides a reliable mechanism of heredity. This is based on the fact that genes carry important biological information. They must be copied accurately each time the cell divides, to form two identical daughter cells in order for successful transmission of inheritable characteristics to take place. This is done during replication, which is the process by which the DNA molecule replicates itself.

Replication begins when the DNA molecule is unwound and prepared for synthesis by the action of several types of molecules. Some of these are DNA gyrase, DNA helicase, RNA primers, and single-stranded DNA-binding proteins. These molecules work together to separate the two strands of the double helix, forming a “replication fork.” Single-stranded DNA-binding proteins work to stabilize the unwound DNA. The replication fork moves in one direction, and only one strand, called the parental DNA, is replicated; the newly replicated stand is called the leading strand. This leading strand is synthesized in a continuous direction known as the 5 prime to 3 prime direction, which is directed by DNA polymerase. The other strand called the lagging strand (travels in a 3 prime to 5 prime direction), which is not replicated continuously and produces short discontinuous replication products called Okazaki fragments (named after the Japanese scientist who discovered them). These fragments, which are formed by DNA polymerase, are usually 100 to 200 nucleotides long and are joined together by a molecule called DNA ligase.

During the replication of DNA, enzymes “proofread” the DNA and repair damage to existing DNA. This is done in two ways: Proteins proofread replicating DNA and correct errors in base pairing; this is called mismatch repair. The other way DNA is repaired is called excision repair; this is where repair enzymes actually fix DNA that is damaged by physical and chemical agents (including ultraviolet light).

The DNA molecule contains segments that are “noncoding.” These sequences are called introns (short for intervening sequences). The regions that do code for the translation of protein synthesis are “coding regions” and are called exons (because they are expressed). The exons are separated from one another by introns (i.e., the sequence of nucleotides that codes for proteins does not exist as an unbroken continuum).

The DNA molecule differs from the RNA molecule in several ways. First, the DNA molecule is composed of two strands, or is “double stranded,” whereas the RNA molecule is composed of only one strand or is “single stranded.” Second, the actual molecular compositions in their structure are different. The nucleotides that compose the RNA molecule are adenine, guanine, cytosine, and uracil, while in DNA, uracil is replaced by thymine. Like thymine, uracil is also a pyrimidine and pairs together with adenine during the processes of transcription and translation. Another structural difference between DNA and RNA is the type of sugar (a pentose sugar) found in the sugar-phosphate backbone. The DNA molecule contains deoxyribose, whereas the RNA molecule contains ribose. The final and most important difference between DNA and RNA is in their function. The DNA molecule makes RNA, and the RNA molecule synthesizes proteins.

Up to now, the DNA molecule has been presented as a highly organized unit that can replicate itself without error. However, a phenomenon called mutation can take place. A mutation is a change in the DNA of a gene; that is, the actual nucleotide sequence of the DNA is altered. An example of this would be if ATG changed to AAG. This change, no matter how small or drastic, will do one of three things: First, it could serve as a benefit by enhancing that specie’s physical or biological attributes. This could increase a specie’s ability to propagate and flourish, eventually becoming a permanent trait in that species. Second, it could cause an adverse effect in that specie’s physical or biological attributes. This could hinder and decrease the specie’s ability to survive or propagate an inferior version of the species, eventually leading to its extinction. Third, it could have no effect at all. Regardless of what effect a mutation has, it ultimately creates genetic diversity. All gene pools have a large reservoir of genetic mutations.

Because the DNA molecule is responsible for our genetic makeup and influences our physical totality all the way down to our cells, it in effect links all Homo sapiens together. The species Homo sapiens has a wide variety of genetic diversity, from height to skin and eye color. However, the common denominator of our species remains the similarity of our DNA molecules. DNA also in this effect links all biological life on this planet.

Due to the DNA molecule’s many activities, which appear to be influenced by biochemical feedback, it appears to take on a life of its own. This new notion is becoming known as “molecular consciousness,” or more specifically, “DNA consciousness.”

It is also worth mentioning that even though we now know a great deal about DNA, there is still much that we do not understand. In addition, we also have to reserve anticipation for the possibility of life forms in other regions of the universe. What type of molecules will be at the root of their existence? Will they have a molecule similar to DNA or RNA, or will these other life forms possess an entirely different molecule?

Recent advances in bioengineering will have many fascinating implications in regard to the DNA molecule. For example, many genetic diseases can be detected with screening tests that can identify a very specific gene that is responsible for that disease. DNA testing can also be used to determine if an individual is or is not the father of a child with up to 99.9% accuracy in forensic anthropology. In the future, an individual’s DNA will determine what type of medication will yield the maximum therapeutic results, increasing the quality of health in the population at large.

Finally, recombinant DNA technology, which involves techniques that can allow for the isolation, copying, and insertion of a new DNA sequence into a cell, could potentially give rise to new species or modified versions of existing species in the future. This is becoming more of a reality with the completion of the Human Genome Project.

References:

1. Alberts, B., Johnson, A., Lewis, J., Raff, K., Roberts, K., & Walter, P. (2002). Molecular biology of the cell (4th ed.). New York: Garland.
2. Butler, J. (2005). Forensic DNA typing: Biology, technology, and genetics behind STR markers (2nd ed.). New York: Academic Press.
3. Micklos, D., & Freyer, G. A. (2003). DNA science: A first course (2nd ed.). New York: Cold Spring Harbor Laboratory Press.
4. Watson, J. (2001). The double helix: A personal account of the discovery of the structure of DNA. New York: Touchstone.
5. Watson, J., & Berry, A. (2003). DNA: The secret of life. New York: Knopf.