3 13 The Three Domains of Life
wea25324_ch01_001-011.indd Page 9 10/19/10 12:03 PM user-f468 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile 1.3 The Three Domains of Life 9 These transplanted genes can alter the characteristics of the recipient organisms, so they may provide powerful tools for agriculture and for intervening in human genetic diseases. We will examine gene cloning in detail in Chapter 4. SUMMARY All cellular genes are made of DNA arranged in a double helix. This structure explains how genes engage in their three main activities: replication, carrying information, and collecting mutations. The complementary nature of the two DNA strands in a gene allows them to be replicated faithfully by separating and serving as templates for the assembly of two new complementary strands. The sequence of nucleotides in a gene is a genetic code that carries the information for making an RNA. Most of these are messenger RNAs that carry the information to protein-synthesizing ribosomes. The end result is a new polypeptide chain made according to the gene’s instructions. A change in the sequence of bases constitutes a mutation, which can change the sequence of amino acids in the gene’s polypeptide product. Genes can be cloned, allowing molecular biologists to harvest abundant supplies of their products. 1.3 The Three Domains of Life In the early part of the twentieth century, scientists divided all life into two kingdoms: animal and plant. Bacteria were considered plants, which is why we still refer to the bacteria in our guts as intestinal “flora.” But after the middle of the century, this classification system was abandoned in favor of a five-kingdom system that included bacteria, fungi, and protists, in addition to plants and animals. Then in the late 1970s, Carl Woese (Figure 1.14) performed sequencing studies on the ribosomal RNA genes of many different organisms and reached a startling conclusion: A class of organisms that had been classified as bacteria have rRNA genes that are more similar to those of eukaryotes than they are to those of classical bacteria like E. coli. Thus, Woese named these organisms archaebacteria, to distinguish them from true bacteria, or eubacteria. However, as more and more molecular evidence accumulated, it became clear that the archaebacteria, despite a superficial resemblance, are not really bacteria. They represent a distinct domain of life, so Woese changed their name to archaea. Now we recognize three domains of life: bacteria, eukaryota, and archaea. Like bacteria, archaea are prokaryotes— organisms without nuclei—but their molecular biology is actually more like that of eukaryotes than that of bacteria. Figure 1.14 Carl Woese. (Source: Courtesy U. of Ill at Urbana Champaign.) The archaea live in the most inhospitable regions of the earth. Some of them are thermophiles (“heat-lovers”) that live in seemingly unbearably hot zones at temperatures above 1008C near deep-ocean geothermal vents or in hot springs such as those in Yellowstone National Park. Others are halophiles (halogen-lovers) that can tolerate very high salt concentrations that would dessicate and kill other forms of life. Still others are methanogens (“methane-producers”) that inhabit environments such as a cow’s stomach, which explains why cows are such a good source of methane. In this book, we will deal mostly with the first two domains, because they are the best studied. However, we will encounter some interesting aspects of the molecular biology of the archaea throughout this book, including details of their transcription in Chapter 11. And in Chapter 24, we will learn that an archaeon, Methanococcus jannaschii, was among the first organisms to have its genome sequenced. All living things are grouped into three domains: bacteria, eukaryota, and archaea. Although the archaea resemble the bacteria physically, some aspects of their molecular biology are more similar to those of eukaryota. SUMMARY This concludes our brief chronology of molecular biology. Table 1.1 reviews some of the milestones. Although it is a very young discipline, it has an exceptionally rich history, and molecular biologists are now adding new knowledge at an explosive rate. Indeed, the pace of discovery in molecular biology, and the power of its techniques, has led many commentators to call it a revolution. Because some of the most important changes in medicine and agriculture over the next few decades are likely to depend on the manipulation of genes by molecular biologists, this revolution will touch everyone’s life in one way or another. Thus, you are wea25324_ch01_001-011.indd Page 10 10 10/19/10 12:03 PM user-f468 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Chapter 1 / A Brief History Table 1.1 1859 1865 1869 1900 Molecular Biology Time Line 1966 1970 Charles Darwin Gregor Mendel Friedrich Miescher Hugo de Vries, Carl Correns, Erich von Tschermak Archibald Garrod Walter Sutton, Theodor Boveri Thomas Hunt Morgan, Calvin Bridges A.H. Sturtevant H.J. Muller Harriet Creighton, Barbara McClintock George Beadle, E.L. Tatum Oswald Avery, Colin McLeod, Maclyn McCarty James Watson, Francis Crick, Rosalind Franklin, Maurice Wilkins Matthew Meselson, Franklin Stahl Sydney Brenner, François Jacob, Matthew Meselson Marshall Nirenberg, Gobind Khorana Hamilton Smith 1972 1973 1977 Paul Berg Herb Boyer, Stanley Cohen Frederick Sanger 1977 1993 Phillip Sharp, Richard Roberts, and others Victor Ambros and colleagues 1995 Craig Venter, Hamilton Smith 1996 Many investigators 1997 1998 Ian Wilmut and colleagues Andrew Fire and colleagues 2003 2005 Many investigators Many investigators 2007 Craig Venter and colleagues 2008 Jian Wang and colleagues 2008 David Bentley and colleagues 1902 1902 1910, 1916 1913 1927 1931 1941 1944 1953 1958 1961 Published On the Origin of Species Advanced the principles of segregation and independent assortment Discovered DNA Rediscovered Mendel’s principles First suggested a genetic cause for a human disease Proposed the chromosome theory Demonstrated that genes are on chromosomes Constructed a genetic map Induced mutation by x-rays Obtained physical evidence for recombination Proposed the one-gene/one-enzyme hypothesis Identified DNA as the material genes are made of Determined the structure of DNA Demonstrated the semiconservative replication of DNA Discovered messenger RNA Finished unraveling the genetic code Discovered restriction enzymes that cut DNA at specific sites, which made cutting and pasting DNA easy, thus facilitating DNA cloning Made the first recombinant DNA in vitro First used a plasmid to clone DNA Worked out methods to determine the sequence of bases in DNA and determined the base sequence of an entire viral genome (ϕX174) Discovered interruptions (introns) in genes Discovered that a cellular microRNA can decrease gene expression by base-pairing to an mRNA Determined the base sequences of the genomes of two bacteria: Haemophilus influenzae and Mycoplasma genitalium, the first genomes of free-living organisms to be sequenced Determined the base sequence of the genome of brewer’s yeast, Saccharomyces cerevisiae, the first eukaryotic genome to be sequenced Cloned a sheep (Dolly) from an adult sheep udder cell Discovered that RNAi works by degrading mRNAs containing the same sequence as an invading double-stranded RNA Reported a finished sequence of the human genome Reported the rough draft of the genome of the chimpanzee, our closest relative Used traditional sequencing to obtain the first sequence of an individual human (Craig Venter). Used “next generation” sequencing to obtain the first sequence of an Asian (Han Chinese) human. Used single molecule sequencing to obtain the first sequence of an African (Nigerian) human. embarking on a study of a subject that is not only fascinating and elegant, but one that has practical importance as well. F. H. Westheimer, professor emeritus of chemistry at Harvard University, put it well: “The greatest intellectual revolution of the last 40 years may have taken place in biology. Can anyone be considered educated today who does not understand a little about molecular biology?” Happily, after this course you should understand more than a little. wea25324_ch01_001-011.indd Page 11 10/19/10 12:03 PM user-f468 /Volume/204/MHDQ268/wea25324_disk1of1/0073525324/wea25324_pagefile Suggested Readings S U M M A RY Genes can exist in several different forms called alleles. A recessive allele can be masked by a dominant one in a heterozygote, but it does not disappear. It can be expressed again in a homozygote bearing two recessive alleles. Genes exist in a linear array on chromosomes. Therefore, traits governed by genes that lie on the same chromosome can be inherited together. However, recombination between homologous chromosomes occurs during meiosis, so that gametes bearing nonparental combinations of alleles can be produced. The farther apart two genes lie on a chromosome, the more likely such recombination between them will be. Most genes are made of double-stranded DNA arranged in a double helix. One strand is the complement of the other, which means that faithful gene replication requires that the two strands separate and acquire complementary partners. The linear sequence of bases in a typical gene carries the information for making a protein. The process of making a gene product is called gene expression. It occurs in two steps: transcription and 11 translation. In the transcription step, RNA polymerase makes a messenger RNA, which is a copy of the information in the gene. In the translation step, ribosomes “read” the mRNA and make a protein according to its instructions. Thus, a change (mutation) in a gene’s sequence may cause a corresponding change in the protein product. All living things are grouped into three domains: bacteria, eukaryota, and archaea. The archaea resemble bacteria physically, but their molecular biology more closely resembles that of eukaryota. SUGGESTED READINGS Creighton, H.B., and B. McClintock. 1931. A correlation of cytological and genetical crossing-over in Zea mays. Proceedings of the National Academy of Sciences 17:492–97. Mirsky, A.E. 1968. The discovery of DNA. Scientific American 218 (June):78–88. Morgan, T.H. 1910. Sex-limited inheritance in Drosophila. Science 32:120–22. Sturtevant, A.H. 1913. The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association. Journal of Experimental Zoology 14:43–59.