Structure and Functions Each human being is a biologically unique individual. That uniqueness has its basis in one’s cellular makeup. Appearance derives from the arrangement of cells during fetal development, size depends on the cells’ ability to grow and divide, and the function of organs depends on the biochemical function of the individual cells that constitute each organ. The functions of cells depend on the types and amounts of the different proteins that they synthesize. The substance that holds the information that determines the structure of proteins, when they should be produced, and in what amounts is deoxyribonucleic acid (DNA).
DNA is the molecule of heredity, and as a child receives half of his or her DNA from each biological parent, each individual is the product of a mixture of information. Therefore, while children resemble their parents, they are unique. Each cell in an individual’s body (except for the sex cells) has a complete set of genetic information contained in the chromosomes of the cell’s nucleus. Human cells have forty-six chromosomes (twenty-three pairs). Each chromosome is a single piece of DNA associated with many types of proteins. The major function of DNA is to store, in a stable manner, the information that is the “blueprint” for all physiological aspects of an individual. Stability is one of the key attributes of DNA. An information storage molecule is of little use if it can be altered or damaged easily. Another key characteristic of DNA is its ability to be replicated. When a cell divides, the information in the DNA must be replicated so that each of the two new cells can have a
complete set.
Stability, the ability to be replicated, and the ability to store vast amounts of coded information have their basis in the structure of DNA. DNA is a long, incredibly thin fiber. The chromosomes in some cells would be as long as a foot or more if they were fully extended. The shape of the DNA molecule can be imagined as a long ladder whose rails are chains of two alternating molecules: deoxyribose (a sugar) and phosphate (an acid containing phosphorus and oxygen). The steps of the ladder are made of pairs of organic bases, of which there are four types: adenine (A), guanine (G), thymine (T), and cytosine (C). Adenine always pairs up with thymine to form a step in the ladder (A-T), and guanine always pairs with cytosine (C-G). This complementarity of base-pairing is the basis for DNA replication and for transferring information from DNA out of the nucleus and into the cytoplasm. Finally, the whole DNA molecule is twisted into a stable right-handed spiral, or helix. Because there is no restriction on the sequence in which the base pairs appear along the molecule, the bases have the potential to be used as a four-letter alphabet that can
encode information into “words” of varying lengths, called genes. Each information sequence, or gene, holds the information needed to synthesize a linear chain of amino acids, which are the building blocks of proteins. The information encoded in the base sequences of DNA determines the quantities and composition of all proteins made in the cell.
Under certain conditions, DNA can be separated lengthwise into two halves, or denatured, by breaking the base pairs so that one of each pair remains attached to one sugar-phosphate chain and the other base remains attached to the other sugar-phosphate chain. Because this forms two strands of DNA, whole DNA is usually referred to as being double-stranded. Such separation rarely happens by accident because of the extreme length of DNA. If any area becomes denatured, the rest of the base pairs hold the molecule together. In addition, an area of denaturation will automatically try to renature, since complementary bases have a natural attraction for each other. As stable as these traits make it, DNA must be capable of being duplicated so that each newly divided cell has a complete copy of the stored information. DNA is replicated by breaking the base pairs, separating the DNA into two halves, and building a new half onto each of the old halves. This is possible because the complementarity rule (A pairs with T, and C pairs with G) allows each half of a denatured DNA molecule to hold the information needed to construct a new second half. This is accomplished by special sets of proteins that separate the old DNA as they move along the molecule and build new DNA in their wake.
All the information needed to produce proteins is located in the DNA within the nucleus of the cell, but all protein synthesis occurs outside the nucleus in the cytoplasm. An information transfer molecule is required to copy or transcribe information from the genes of the DNA and carry it to the cytoplasm, where large globular protein complexes called ribosomes take the information and translate it into the amino acid structure of specific proteins. This information transfer molecule is ribonucleic acid (RNA). Many RNA copies can be made for any single piece of information on the DNA and used as a template to synthesize many proteins. In this way, the information in DNA is also amplified by RNA. RNA also participates in the synthesis of proteins from the genetic information. RNA resembles one half of a DNA molecule and is usually referred to as being single stranded. It consists of a single chain of alternating sugars and phosphates with a single organic base attached to each sugar. The sugar in this case is ribose, similar to deoxyribose, and the bases are identical to those in DNA with the exception of thymine, which is
replaced by a very similar base called uracil (U).
There are four major types of RNA. Messenger RNA (mRNA) is responsible for the transfer of information from the DNA sequences in the nucleus to the ribosomes in the cytoplasm. Ribosomal RNA (rRNA) interacts with dozens of proteins to form the ribosome. It aids in the interaction between mRNA and the ribosome. Transfer RNA (tRNA) is a group of small RNAs that helps translate the information coded in the mRNA into the structure of specific proteins. They carry the amino acids to the ribosome and match the correct amino acid to its corresponding sequence of bases in the mRNA.
The first step in producing a specific protein is the accurate copying or transcription of information in a gene into information on a piece of mRNA. There are specific sets of proteins that separate the double-stranded DNA in the immediate vicinity of a gene into two single-stranded portions and then, using the DNA as a template, build a piece of mRNA that is a complementary copy of the information in the gene. This is possible because RNA also uses organic bases in its structure. The A, C, G, and T of the single-stranded portion of DNA form base pairs with the U, G, C, and A of the mRNA, respectively. The complementary copy of mRNA, when complete, falls away from the DNA and moves to the cytoplasm of the cell.
In the cytoplasm, the mRNA binds to a ribosome. As the ribosome moves down the length of the mRNA, the tRNAs interact with both the ribosome and the mRNA in order to match the proper amino acid (carried by the tRNAs) to the proper sequence of bases in the mRNA. The order of amino acids in the protein is thus determined by the order of bases in the DNA. Achieving the correct order of amino acids is critical for the correct functioning of the protein. The order of amino acids in the chain determines the way in which it interacts with itself and folds into a three-dimensional structure. The function of all proteins depends on their assuming the correct shape for interaction with other molecules. Therefore, the sequence of bases in the DNA ultimately determines the shape and function of proteins.
Another class of RNA is involved in translation regulation, by a process called RNA interference, or RNAi. The two types of RNA in this class are short interfering RNA (siRNA) and micro RNA (miRNA). SiRNA is a double-stranded molecule of twenty to twenty-five base-pairs in length, whereas miRNA is single stranded and consists of nineteen to twenty-three nucleotides. SiRNA and miRNA become incorporated in a protein complex known as the RNA-induced silencing complex (RISC). The RISC-associated siRNA targets a specific sequence in its target mRNA, and when bound to the mRNA causes destruction. MiRNA bound RISC binds to the mRNA and inhibits translation of that mRNA; in this case, however, the mRNA is not destroyed. RNAi plays a role in diverse cellular functions such as cell differentiation, fetal development, cell proliferation, and cell death. It is also involved in pathogenic events such as viral infection and certain cancers.
Disorders and Diseases When the normal structure of DNA is altered (a process called a mutation), the number of proteins produced and/or the functions of proteins may be affected. At one extreme, a mutation may cause no problem at all to the person involved. At the other extreme, it may cause devastating damage to the person and result in genetic disease or cancer.
Mutations are changes in the normal sequence of bases in the DNA that carry the information to build a protein or that regulate the amount of protein to be produced. There are different types of mutations, such as the alteration of one base into another, the deletion of one or many bases, or the insertion of bases that were not in the sequence previously. Mutations can have many different causes, such as ultraviolet rays, X rays, mutagenic chemicals, invading viruses, or even heat. Sometimes mutations are caused by mistakes made during the process of DNA replication or cell division. Cells have several systems that constantly repair mutations, but occasionally some of these alterations slip by and become permanent.
Mutations may affect protein structure in several ways. The protein may be too short or too long, with amino acids missing or new ones added. It might have new amino acids substituting for the correct ones. Sometimes as small a change as one amino acid can have noticeable effects. In any of these cases, changes in the amino acid sequence of a protein may drastically affect the way the protein interacts with itself and folds itself into a three-dimensional structure. If a protein does not assume the correct three-dimensional structure, its function may be impaired. It is important to note that how severely a protein’s function is affected by a mutation depends on which amino acids are involved. Some amino acids are more important than others in maintaining a protein’s shape and function. A change in amino acid sequence may have virtually no effect on a protein or it may destroy that protein’s ability to function.
If a mutation occurs that affects the regulation of a particular protein, that gene may be perfectly normal and the protein may be fully functional, but it may exist in the cell in an improper amount—too much, too little, or even none at all. It is important to note that the overproduction of a protein, as well as its underproduction or absence, can be harmful to the cell or to the person in general. The genetic disease known as Down syndrome, for example, is the result of the overproduction of many proteins at the same time.
The term “genetic disease” is used for a heritable disease that can be passed from parent to child. The mutation responsible for the disease is contributed by the parents to the affected child via the sperm or the egg or (as is usually the case) both. The parents are, for the most part, quite unaffected. Because all creatures more complex than bacteria have at least two copies of all their genes, a person may carry a mutated gene and be perfectly healthy because the other normal gene compensates by producing adequate amounts of normal protein. If two individuals carrying the same mutated gene produce a child, that child has a chance of obtaining two mutant genes—one from each parent. Every cell in that child’s body carries the error with no normal genes to compensate, and every cell that would normally use that gene must produce an abnormal protein or abnormal amounts of that protein. The medical consequences vary, depending on which gene is affected and which protein is altered. The following are two specific examples of genetic diseases in which the connection between specific mutations
and the disease states are well documented.
Sickle cell disease is a genetic disease that results from an error in the gene that carries the information for the protein beta globin. Beta globin is one of the building blocks of hemoglobin, the molecule that binds to and carries oxygen in the red blood cells. The error or mutation is a surprisingly small one and serves to illustrate the fact that the replacement of even a single amino acid can change the chemical nature and function of a protein. Normal beta globin has a glutamic acid as the sixth amino acid in the protein chain. The mutation of a single base in the DNA changes the coded information such that the amino acid valine replaces glutamic acid as the sixth position in the protein chain. This single alteration causes the hemoglobin in the red blood cell to crystallize under conditions of low oxygen concentration. As the crystals grow, they twist and deform the normally flexible and disk-shaped red blood cells into rigid sickle shapes. These affected cells lose their capacity to bind and hold oxygen, thereby causing anemia, and their new structure can cause blockages in small capillaries of the circulatory system, causing pain and widespread organ damage. There is no safe and effective treatment or cure for this condition.
Phenylketonuria (PKU) is caused by a mutation in the gene that controls the synthesis of the protein phenylalanine hydroxylase (PAH). There are several mutations of the PAH gene that can lead to a drastic decrease in PAH activity (by greater than 1 percent of normal activity). Some are changes in one base that lead to the replacement of a single amino acid for another. For example, one of the most common mutations in the PAH gene is the alteration of a C to a T that results in amino acid number 408 changing from an arginine to a tryptophan. Some mutations are deletions of whole sequences of bases in the gene. One such deletion removes the tail end of the gene. In any case, the amino acid structure of PAH is altered significantly enough to remove its ability to function. Without this protein, the amino acid phenylalanine cannot be converted into tyrosine, another useful amino acid. The problem is not a shortage of tyrosine, since there is plenty in most foods, but rather an accumulation of undesirable products that form as the unused phenylalanine begins to break down. Since developing brain cells are particularly sensitive to these
products, the condition can cause mental retardation unless treated immediately after birth. While there is no cure, the disease is easily diagnosed and treatment is simple. The patient must stay on a diet in which phenylalanine is restricted. Food products that contain the artificial sweetener aspartame (NutraSweet) must have warnings to PKU patients printed on them since phenylalanine is a major component of aspartame.
Perspective and Prospects Genetics is a young science whose starting point is traditionally considered to be 1866, the year in which Gregor Mendel published his work on hereditary patterns in pea plants. While he knew nothing of DNA or its structure, Mendel showed mathematically that discrete units of inheritance, which are now called genes, existed as pairs in an organism and that different combinations of these units determined that organism’s characteristics. Unfortunately, Mendel’s work was ahead of its time and thus ignored until rediscovered by several researchers simultaneously in 1900.
DNA itself was discovered in 1869 by Friedrich Miescher, who extracted it from cell nuclei but did not realize its importance as the carrier of hereditary information. Chromosomes were first seen in the 1870’s as threadlike structures in the nucleus, and because of the precise way they are replicated and equally parceled out to newly divided cells, August Weismann and Theodor Boveri, in the 1880’s, postulated that chromosomes were the carriers of inheritance.
In 1900, Hugo de Vries, Karl Correns, and Erich Tschermak von Seysenegg—all plant biologists who were working on patterns of inheritance—independently rediscovered Mendel’s work. De Vries had in the meantime discovered mutation around 1890 as a source of hereditary variation, but he did not postulate a mechanism. Mendel’s theories and the then-current knowledge of chromosomes merged perfectly. Mendel’s units of inheritance were thought somehow to be carried on the chromosomes. Pairs of chromosomes would carry Mendel’s pairs of hereditary units, which, in 1909, were dubbed “genes.”
At that point, genes were still a theoretical concept and had not been proved to be carried on the chromosomes. In 1909, Thomas Hunt Morgan began the work that would provide that proof and allow the mapping of specific genes to specific areas of a chromosome. The nature of a gene, or how it expressed itself, was still a mystery. In 1941, George Beadle and Edward Tatum proved that genes regulated the production of proteins, but the nature of genes was still in debate. There were two candidates for the chemical substance of genes; one was protein and the other was the deceptively simple DNA. In 1944, Oswald Avery proved in experiments with pure DNA that DNA was indeed the molecule of inheritance. In 1953, James D. Watson and Francis Crick, using the work of Rosalind Franklin, elucidated the chemical structure of the double helix, and soon after, Matthew Meselson and Franklin Stahl proved that DNA replicated itself. By the end of the 1950’s, RNA was being implicated in protein synthesis, and much of the mechanism of translation was postulated by Marshall Nirenberg and Johann Matthaei in 1961.
Craig Mello and Andrew Fire were awarded the 2006 Nobel Prize in Physiology or Medicine for their discovery of siRNA and for their research on the RNAi system. In 1993, Victor Ambros was the first person to describe miRNA. Both siRNA and micro RNA have possible therapeutic use. Clinical trials involving siRNA and miRNA are in progress. Examples are the use of siRNA in the treatment of macular degeneration, an age-related eye disorder, and the use of miRNA in the treatment of chronic hepatitis C. The major barriers to the use of these molecules are inefficient delivery to target cells and off-target effects.
The concept of heritable genetic disease is also a relatively recent one. The first direct evidence that a mutation can result in the production of an altered protein came in 1949 with studies on sickle cell disease. Since then, thousands of genetic diseases have been characterized. The advent in the 1970’s of recombinant DNA technology, which allows the direct manipulation of DNA, has greatly increased the knowledge of these diseases, as well as demonstrated the genetic influences in maladies such as cancer and behavioral disorders. This technology has led to vastly improved diagnostic methods and therapies while pointing the way toward potential cures.
Bibliography
Campbell, Neil A., et al. Biology: Concepts and Connections. 6th ed. San Francisco: Pearson/Benjamin Cummings, 2008. This classic introductory textbook provides an excellent discussion of essential biological structures and mechanisms. Its extensive and detailed illustrations help to make even difficult concepts accessible to the nonspecialist. Of particular interest are the chapters constituting the unit titled “The Gene.”
Drlica, Karl. Understanding DNA and Gene Cloning: A Guide for the Curious. 4th ed. Hoboken, N.J.: Wiley, 2004. This book for the uninitiated explains the basic principles of genetic mechanisms without requiring knowledge of chemistry. The first third is especially good on the fundamentals, but the remainder may be too deep for some readers.
Frank-Kamenetskii, Maxim D. Unraveling DNA: The Most Important Molecule of Life. Translated by Lev Liapin. Rev. ed. Reading, Mass.: Addison-Wesley, 1997. This very readable book provides an excellent history of the discovery of DNA. Also describes the nature of DNA and discusses genetic engineering and the ethical questions that surround its use.
Glick, Bernard, Jack J. Pasternak, and Cheryl L. Patten. Molecular Biotechnology: Principles and Applications of Recombinant DNA. 4th ed. Washington, D.C.: ASM Press, 2010. Explores the scientific principles of recombinant DNA technology and its wide-ranging use in industry, agriculture, and the pharmaceutical and biomedical sectors.
Gonick, Larry, and Mark Wheelis. The Cartoon Guide to Genetics. Rev. ed. New York: Collins Reference, 2007. An effective mixture of humor and fact makes this book a nonthreatening reference on genetics. Presented using historical context, it covers DNA and RNA structure and function and much more.
Gribbin, John. In Search of the Double Helix. New York: Bantam Books, 1985. Gribbin is a renowned science writer who is capable of explaining complex subjects in a way that anyone can understand. In this book, he goes from Charles Darwin’s theories to quantum mechanics in his rendition of the history of the discovery of DNA. Very readable.
Hofstadter, Douglas R. “The Genetic Code: Arbitrary?” In Metamagical Themas: Questing for the Essence of Mind and Pattern. New York: Basic Books, 1985. While only a thirty-page chapter in a large book, this piece by Hofstadter is an excellent and thought-provoking explanation of transcription and translation written for the nonscientist.
Micklos, David A., Greg A. Freyer, and David A. Crotty. DNA Science: A First Course. 2d ed. Cold Springs Harbor, N.Y.: Cold Springs Harbor Press, 2003. Text that combines an introductory discussion of the principles of genetics, DNA structure and function, and methods for analyzing DNA with twelve laboratory experiments that illustrate the basic techniques of DNA restriction, transformation, isolation, and analysis.
Nicholl, Desmond S. T. Introduction to Genetic Engineering. 3d ed. New York: Cambridge University Press, 2008. A valuable textbook for the nonspecialist and anyone interested in genetic engineering. It provides an excellent foundation in molecular biology and builds on that foundation to show how organisms can be genetically engineered.
Paddison, Patrick J., and Peter J. Voght. RNA Interference. New York: Springer, 2008. A comprehensive book about the field of RNA interference that includes detailed and updated mechanistic descriptions of the RNAi process.
Watson, James D., and Andrew Berry. DNA: The Secret of Life. New York: Knopf, 2004. Nobel Prize-winning scientist Watson guides readers through the rapid advances in genetic technology and what these advances mean for modern life. Covers all aspects of the genome in a readable fashion.
