Introduction to Biology Lecture 3 PDF

INTRODUCTION TO BIOLOGY BIO-106 Lecture-3  Eucaryotic Cells may have originated as Predators Eukaryotic cells are typically 10 times the length and 1000 times the volume of prokaryotic cells, although there is huge size variation with...

INTRODUCTION TO BIOLOGY BIO-106 Lecture-3  Eucaryotic Cells may have originated as Predators Eukaryotic cells are typically 10 times the length and 1000 times the volume of prokaryotic cells, although there is huge size variation within each category. They also possess a whole collection of features—a cytoskeleton, mitochondria, and other organelles—that set them apart from bacteria and archaea. When and how eukaryotes evolved these systems remains something of a mystery. Although eukaryotes, bacteria, and archaea must have diverged from one another very early in the history of life on Earth, the eukaryotes did not acquire all of their distinctive features at the same time (Figure 3–1). According to one theory, the ancestral eukaryotic cell was a predator that fed by capturing other cells. Such a way of life requires a large size, a flexible membrane, and a cytoskeleton to help the cell move and eat. The nuclear compartment may have evolved to keep the DNA segregated from this physical and chemical hurly-burly, so as to allow more delicate and complex control of the way the cell reads out its genetic information. 1 Figure 3-1: Where did eukaryotes come from? The eukaryotic, bacterial, and archaean lineages diverged from one another very early in the evolution of life on Earth. Some time later, eukaryotes are thought to have acquired mitochondria; later still, a subset of eukaryotes acquired chloroplasts. Mitochondria are essentially the same in plants, animals, and fungi, and therefore were presumably acquired before these lines diverged. 2  Eucaryotic Cells may have originated as Predators Such a primitive cell, with a nucleus and cytoskeleton, was most likely the sort of cell that engulfed the free-living, oxygen-consuming bacteria that were the likely ancestors of the mitochondria (Figure 3-2). This partnership is thought to have been established 1.5 billion years ago, when the Earth’s atmosphere first became rich in oxygen. A subset of these cells later acquired chloroplasts by engulfing photosynthetic bacteria (Figure 3-3). The likely history of these endosymbiotic events is illustrated in Figure 3-4. That single-celled eukaryotes can prey upon and swallow other cells is borne out by the behavior of many of the free-living, actively motile microorganisms called protozoans. Didinium, for example, is a large, carnivorous protozoan with a diameter of about 150 μm—roughly 10 times that of the average human cell. It has a globular body encircled by two fringes of cilia, and its front end is flattened except for a single protrusion rather like a snout (Figure 3-5A). 3 Figure 3-2: Mitochondria most likely evolved from engulfed bacteria. It is virtually certain that mitochondria originate from bacteria that were engulfed by an ancestral pre-eukaryotic cell and survived inside it, living in symbiosis with their host. Note that the double membrane of present-day mitochondria is thought to have been derived from the 4 plasma membrane and outer membrane of the engulfed bacterium. Figure 3-3: Chloroplasts almost certainly evolved from engulfed photosynthetic bacteria. The bacteria are thought to have been taken up by early eukaryotic cells that already contained mitochondria. 5 Figure 3.5 : One protozoan eats another. (A) The scanning electron micrograph shows Didinium on its own, with its circumferential rings of beating cilia and its “snout” at the top. (B) Didinium is seen ingesting another ciliated protozoan, a Paramecium. 6  Eucaryotic Cells may have originated as Predators Didinium swims at high speed by means of its beating cilia. When it encounters a suitable prey, usually another type of protozoan, it releases numerous small, paralyzing darts from its snout region. Didinium then attaches to and devours the other cell, inverting like a hollow ball to engulf its victim, which can be almost as large as itself (Figure 3-5B). Not all protozoans are predators. They can be photosynthetic or carnivorous, motile or sedentary. Their anatomy is often elaborate and includes such structures as sensory bristles, photoreceptors, beating cilia, stalk-like appendages, mouthparts, stinging darts, and muscle-like contractile bundles (Figure 3-6). Although they are single cells, protozoans can be as intricate and versatile as many multicellular organisms. Much remains to be learned about fundamental cell biology from studies of these fascinating life-forms. 7 Figure 3-6: An assortment of protozoans illustrates the enormous variety within this class of single-celled microorganisms. These drawings are done to different scales, but in each case the scale bar represents 10 μm. The organisms in (A), (C), and (G) are ciliates; (B) is a heliozoan; (D) is an amoeba; (E) is a dinoflagellate; and (F) is a euglenoid. 8  Model Organisms All cells are thought to be descended from a common ancestor, whose fundamental properties have been conserved through evolution. Thus, knowledge gained from the study of one organism contributes to our understanding of others, including ourselves. But certain organisms are easier than others to study in the laboratory. Some reproduce rapidly and are convenient for genetic manipulations; others are multicellular but transparent, so that one can directly watch the development of all their internal tissues and organs. For reasons such as these, large communities of biologists have become dedicated to studying different aspects of the biology of a few chosen species, pooling their knowledge to gain a deeper understanding than could be achieved if their efforts were spread over many different species. Although the roster of these representative organisms is continually expanding, a few stand out in terms of the breadth and depth of information that has been accumulated about them over the years—knowledge that contributes to our understanding of how all cells work. 9  Molecular Biologists have focused on E. Coli In molecular terms, we understand the workings of the bacterium Escherichia coli—E. coli for short—more thoroughly than those of any other living organism (Figure 3-7). This small, rod-shaped cell normally lives in the gut of humans and other vertebrates, but it also grows happily and reproduces rapidly in a simple nutrient broth in a culture bottle. Most of our knowledge of the fundamental mechanisms of life—including how cells replicate their DNA and how they decode these genetic instructions to make proteins— has come from studies of E. coli. Subsequent research has confirmed that these basic processes occur in essentially the same way in our own cells as they do in E. coli. 10 Figure 3-7: The bacterium Escherichia coli (E. coli ) has served as an important model organism. An electron micrograph of a longitudinal section is shown here; the cell’s DNA is concentrated in the lightly stained region. 11  Brewer’s Yeast is a Simple Eucaryotic Cell We tend to be preoccupied with eukaryotes because we are eukaryotes ourselves. But human cells are complicated and reproduce relatively slowly. To get a handle on the fundamental biology of eukaryotic cells, it is often advantageous to study a simpler cell that reproduces more rapidly. A popular choice has been the budding yeast Saccharomyces cerevisiae (Figure 3-8)—the same microorganism that is used for brewing beer and baking bread. S. cerevisiae is a small, single-celled fungus that is at least as closely related to animals as it is to plants. Like other fungi, it has a rigid cell wall, is relatively immobile, and possesses mitochondria but not chloroplasts. When nutrients are plentiful, S. cerevisiae reproduces almost as rapidly as a bacterium. Yet it carries out all the basic tasks that every eukaryotic cell must perform. Genetic and biochemical studies in yeast have been crucial to understanding many basic mechanisms in eukaryotic cells, including the cell-division cycle—the chain of events by which the nucleus and all the other components of a cell are duplicated and parceled out to create two daughter cells. The machinery that governs cell division has been so well conserved over the course of evolution that many of its components can function interchangeably in yeast and human cells. Darwin himself would no doubt have been stunned by this dramatic example of evolutionary conservation. 12 Figure 3-8: The yeast Saccharomyces cerevisiae is a model eukaryote. In this scanning electron micrograph, a few yeast cells are seen in the process of dividing, which they do by budding. Another micrograph of the same species is shown in Figure 3-9. 13 Figure 3-9: Yeasts are simple free-living eukaryotes. The cells shown in this micrograph belong to the species of yeast, Saccharomyces cerevisiae, used to make dough rise and turn malted barley juice into beer. As can be seen in this image, the cells reproduce by growing a bud and then dividing asymmetrically into a large mother cell and a small daughter cell; for this reason, they are called budding yeast. 14  Arabidopsis has been chosen out of 300,00 Species as a Model Plant Whereas bacteria, archaea, and eukaryotes separated from each other more than 3 billion years ago, plants, animals, and fungi diverged only about 1.5 billion years ago, and the different species of flowering plants less than 200 million years ago. The close evolutionary relationship among all flowering plants means that we can gain insight into their cell and molecular biology by focusing on just a few convenient species for detailed analysis. Out of the several hundred thousand species of flowering plants on Earth today, molecular biologists have focused their efforts on a small weed, the common wall cress Arabidopsis thaliana (Figure 3-10), which can be grown indoors in large numbers: one plant can produce thousands of offspring within 8–10 weeks. Because genes found in Arabidopsis have counterparts in agricultural species, studying this simple weed provides insights into the development and physiology of the crop plants upon which our lives depend, as well as into the evolution of all the other plant species that dominate nearly every ecosystem on Earth. 15 Figure 3-10: Arabidopsis thaliana, the common wall cress, is a model plant. This small weed has become the favorite organism of plant molecular and developmental biologists. 16  The Model Animal include Flies, Fish, Worms and Mice Multicellular animals account for the majority of all named species of living organisms, and the majority of animal species are insects. It is fitting, therefore, that an insect, the small fruit fly Drosophila melanogaster (Figure 3- 11), should occupy a central place in biological research. In fact, the foundations of classical genetics were built to a large extent on studies of this insect. More than 80 years ago, genetic analysis of the fruit fly provided definitive proof that genes—the units of heredity—are carried on chromosomes. In more recent times, Drosophila, more than any other organism, has shown us how the genetic instructions encoded in DNA molecules direct the development of a fertilized egg cell (or zygote) into an adult multicellular organism containing vast numbers of different cell types organized in a precise and predictable way. 17 Figure 3-11: Drosophila melanogaster is a favorite among developmental biologists and geneticists. Molecular genetic studies on this small fly have provided a key to the understanding of how all animals develop. 18  The Model Animal include Flies, Fish, Worms and Mice Drosophila mutants with body parts strangely misplaced or oddly patterned have provided the key to identifying and characterizing the genes that are needed to make a properly structured adult body, with gut, wings, legs, eyes, and all the other bits and pieces in their correct places. These genes—which are copied and passed on to every cell in the body—define how each cell will behave in its social interactions with its sisters and cousins, thus controlling the structures that the cells can create. Moreover, the genes responsible for the development of Drosophila have turned out to be amazingly similar to those of humans—far more similar than one would suspect from outward appearances. Thus, the fly serves as a valuable model for studying human development and disease. 19  The Model Animal include Flies, Fish, Worms and Mice Another widely studied organism is the nematode worm Caenorhabditis elegans (Figure 3- 12), a harmless relative of the eelworms that attack the roots of crops. Smaller and simpler than Drosophila, this creature develops with clockwork precision from a fertilized egg cell into an adult that has exactly 959 body cells (plus a variable number of egg and sperm cells)—an unusual degree of regularity for an animal. We now have a minutely detailed description of the sequence of events by which this occurs—as the cells divide, move, and become specialized according to strict and predictable rules. And a wealth of mutants are available for testing how the worm’s genes direct this developmental ballet. Some 70% of human genes have some counterpart in the worm, and C. elegans, like Drosophila, has proved to be a valuable model for many of the developmental processes that occur in our own bodies. Studies of nematode development, for example, have led to a detailed molecular understanding of apoptosis, a form of programmed cell death by which surplus cells are disposed of in all animals—a topic of great importance for cancer 20 research. Figure 3-12: Caenorhabditis elegans is a small nematode worm that normally lives in the soil. Most individuals are hermaphrodites, producing both sperm and eggs (the latter of which can be seen along the underside of the animal). C. elegans was the first multicellular organism to have its complete genome sequenced. 21  The Model Animal include Flies, Fish, Worms and Mice Another organism that is providing molecular insights into developmental processes, particularly in vertebrates, is the zebrafish. Because this creature is transparent for the first 2 weeks of its life, it provides an ideal system in which to observe how cells behave during development in a living animal (Figure 3-13). Mammals are among the most complex of animals, and the mouse has long been used as the model organism in which to study mammalian genetics, development, immunology, and cell biology. Thanks to modern molecular biological techniques, it is now possible to breed mice with deliberately engineered mutations in any specific gene, or with artificially constructed genes introduced into them. In this way, one can test what a given gene is required for and how it functions. Almost every human gene has a counterpart in the mouse, with a similar DNA sequence and function. Thus, this animal has proven an excellent model for studying genes that are important in both human health and disease. 22 Figure 3-13: Zebrafish are popular models for studies of vertebrate development. (A) These small, hardy, tropical fish are a staple in many home aquaria. But they are also ideal for developmental studies, as their transparent embryos (B) make it easy to observe cells moving and changing their characters in the living organism as it develops. 23  Biologists also directly study Human Beings and their Cells Humans are not mice—or fish or flies or worms or yeast—and so we also study human beings themselves. Like bacteria or yeast, our individual cells can be harvested and grown in culture, where we can study their biology and more closely examine the genes that govern their functions. Given the appropriate surroundings, most human cells—indeed, most cells from animals or plants—will survive, proliferate, and even express specialized properties in a culture dish. Experiments using such cultured cells are sometimes said to be carried out in vitro (literally, “in glass”) to contrast them with experiments on intact organisms, which are said to be carried out in vivo (literally, “in the living”). Although not true for all types of cells, many types of cells grown in culture display the differentiated properties appropriate to their origin: fibroblasts, a major cell type in connective tissue, continue to secrete collagen; cells derived from embryonic skeletal muscle fuse to form muscle fibers, which contract spontaneously in the culture dish; nerve cells extend axons that are electrically excitable and make synapses with other nerve cells; and epithelial cells form extensive sheets, with many of the properties of an intact epithelium 24 (Figure 3-14). Figure 3-14: Cells in culture often display properties that reflect their origin. (A) Phase-contrast micrograph of fibroblasts in culture. (B) Micrograph of cultured myoblasts, some of which have fused to form multinucleate muscle cells that spontaneously contract in culture. (C) Cultured epithelial cells forming a cell sheet.  Biologists also directly study Human Beings and their Cells Because cultured cells are maintained in a controlled environment, they are accessible to study in ways that are often not possible in vivo. For example, cultured cells can be exposed to hormones or growth factors, and the effects that these signal molecules have on the shape or behavior of the cells can be easily explored. Although naturally occurring mutations in any given human gene are rare, the consequences of many mutations are well documented. This is because humans are unique among animals in that they report and record their own genetic defects: in no other species are billions of individuals so intensively examined, described, and investigated. Nevertheless, the extent of our ignorance is still daunting. The mammalian body is enormously complex, being formed from thousands of billions of cells, and one might despair of ever understanding how the DNA in a fertilized mouse egg cell makes it generate a mouse rather than a fish, or how the DNA in a human egg cell directs the development of a human rather than a mouse. 26  Biologists also directly study Human Beings and their Cells Yet the revelations of molecular biology have made the task seem eminently approachable. As much as anything, this new optimism has come from the realization that the genes of one type of animal have close counterparts in most other types of animals, apparently serving similar functions (Figure 3-15). We all have a common evolutionary origin, and under the surface it seems that we share the same molecular mechanisms. Flies, worms, fish, mice, and humans thus provide a key to understanding how animals in general are made and how their cells work. 27 Figure 3-15: Different species share similar genes. The human baby and the mouse shown here have similar white patches on their foreheads because they both have defects in the same gene (called Kit), which is required for the development and maintenance of some pigment cells. 28  Comparing Genome Sequences reveals Life’s common Heritage At a molecular level, evolutionary change has been remarkably slow. We can see in present- day organisms many features that have been preserved through more than 3 billion years of life on Earth—about one-fifth of the age of the universe. This evolutionary conservatism provides the foundation on which the study of molecular biology is built. To set the scene for the chapters that follow, therefore, we end this chapter by considering a little more closely the family relationships and basic similarities among all living things. This topic has been dramatically clarified in the past few years by technological advances that have allowed us to determine the complete genome sequences of thousands of organisms, including our own species. The first thing we note when we look at an organism’s genome is its overall size and how many genes it packs into that length of DNA. Prokaryotes carry very little superfluous genetic baggage and, nucleotide-for-nucleotide, they squeeze a lot of information into their relatively small genomes. 29  Comparing Genome Sequences reveals Life’s common Heritage E. coli, for example, carries its genetic instructions in a single, circular, double-stranded molecule of DNA that contains 4.6 million nucleotide pairs and 4300 genes. The simplest known bacterium contains only about 500 genes, but most prokaryotes have genomes that contain at least 1 million nucleotide pairs and 1000–8000 genes. With these few thousand genes, prokaryotes are able to thrive in even the most hostile environments on Earth. The compact genomes of typical bacteria are dwarfed by the genomes of typical eukaryotes. The human genome, for example, contains about 700 times more DNA than the E. coli genome, and the genome of an amoeba contains about 100 times more than ours (Figure 3-16). The rest of the model organisms we have described have genomes that fall somewhere in between E. coli and human in terms of size. S. cerevisiae contains about 2.5 times as much DNA as E. coli; Drosophila has about 10 times more DNA per cell than yeast; and mice have about 20 times more DNA per cell than the fruit fly (Table 3-1). 30 Figure 3-16: Organisms vary enormously in the size of their genomes. Genome size is measured Figure 1–40 Organisms vary enormously in nucleotide pairs of DNA in the size of their genomes. Genome size per haploid genome, that is measured in nucleotide pairs of DNA per is, per single copy of the haploid genome, that is, per single copy genome. (The body cells of of the genome. (The body cells of sexually sexually reproducing reproducing organisms such as ourselves organisms such as are generally diploid: they contain two ourselves are generally copies of the genome, one inherited from diploid: they contain two the mother, the other from the father.) copies of the genome, one Closely related organisms can vary widely inherited from the mother, in the quantity of DNA in their genomes (as the other from the father.) indicated by the length of the green bars), Closely related organisms even though they contain similar numbers can vary widely in the of functionally distinct genes. (Adapted from quantity of DNA in their T.R. Gregory, 2008, Animal Genome Size genomes (as indicated by Database: www.genomesize.com) the length of the green bars), even though they contain similar numbers of functionally distinct genes. 31 Table 3-1: Some model organisms and their genomes 32  Comparing Genome Sequences reveals Life’s common Heritage In terms of gene numbers, however, the differences are not so great. We have only about six times as many genes as E. coli. Moreover, many of our genes—and the proteins they encode—fall into closely related family groups, such as the family of hemoglobins, which has nine closely related members in humans. Thus, the number of fundamentally different proteins in a human is not very many times more than in a bacterium, and the number of human genes that have identifiable counterparts in the bacterium is a significant fraction of the total. This high degree of “family resemblance” is striking when we compare the genome sequences of different organisms. When genes from different organisms have very similar nucleotide sequences, it is highly probable that both descended from a common ancestral gene. Such genes (and their protein products) are said to be homologous. Now that we have the complete genome sequences of many different organisms from all three domains of life—archaea, bacteria, and eukaryotes—we can search systematically for homologies that span this enormous evolutionary divide. By taking stock of the common inheritance of all living things, scientists are attempting 33 to trace life’s origins back to the earliest ancestral cells.  Genomes contain more than just Genes Although our view of genome sequences tends to be “gene-centric,” our genomes contain much more than just genes. The vast bulk of our DNA does not code for proteins or for functional RNA molecules. Instead, it includes a mixture of sequences that help regulate gene activity, plus sequences that seem to be dispensable. The large quantity of regulatory DNA contained in the genomes of eukaryotic multicellular organisms allows for enormous complexity and sophistication in the way different genes are brought into action at different times and places. Yet, in the end, the basic list of parts—the set of proteins that the cells can make, as specified by the DNA—is not much longer than the parts list of an automobile, and many of those parts are common not only to all animals, but also to the entire living world. That DNA can program the growth, development, and reproduction of living cells and complex organisms is truly amazing. 34  Essential Cell Biology Fourth Edition 2014 Bruce Alberts, Dennis Bray, Karen Hopkin, Reading Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts and Peter Walter Taylor and Francis NY USA 35 Thank you 36