campbell book

As astronomers study newly discovered planets orbiting distant stars, they hope to find evidence of water on these far-off celestial bodies, for water is the substance that makes possible life as we know it here on Earth. All organisms familiar to us are made mostly of water and live in an environment dominated by water. Water is the biological medium here on Earth, and possibly on other planets as well.
Three-quarters of Earth's surface is submerged in water. Although most of this water is in liquid form, water is also present on Earth as ice and vapor. Water is the only common substance to exist in the natural environment in all three physical states of matter: solid, liquid, and gas. The abundance of water is a major reason Earth is habitable. In a classic book called The Fitness of the Environment, ecologist Lawrence Henderson highlights the importance of water to life. While acknowledging that life adapts to its environment through natural selection, Henderson emphasizes that for life to exist at all, the environment must first be a suitable abode.
Life on Earth began in water and evolved there for 3 billion years before spreading onto land. Modern life, even terrestrial (land-dwelling) life, remains tied to water. An living organisms require water more than any other substance. Human beings, for example, can survive for quite a few weeks without food, but only a week or so without water. Molecules of water partidpate in many chemical reactions necessary to sustain life.
Most cells are surrounded by water, and cells themselves are about 70-95% water.
What properties of the simple water molecule allow it to function as a support to all living organisms? In this chapter, you will learn how the structure of a water molecule allows it to interact with other molecules, including other water molecules. This ability leads to unique emergent properties that support and maintain living systems on our planet. Your objective in this chapter is to develop a conceptual understanding of how water contributes to the fitness of Earth for life.

The history of life, as documented by fossils and other evidence, is a saga of a changing Earth billions of years old, inhabited by an evolving cast of living forms (Figure 1.17). This evolutionary view of life came into sharp focus in November 1859, when Charles Robert Darwin published one of the most
important and influential books ever written. Entitled On the Origin of Species by Means of Natural Selection, Darwin's book was an immediate bestseller and soon made "Darwinism" almost synonymous with the concept of evolution (Figure 1.18)


The Origin of Species articulated two main points. First, Darwin presented evidence to support his view that contemporary species arose from a succession ofancestors. (We will discuss the evidence for evolution in detail in next Chapter.)
Darwin called this evolutionary history of species "descent with modification" It was an insightful phrase, as it captured the duality of life's unity and diversity-unity in the kinship among species that descended from common ancestors; diversity in the modifications that evolved as species branched from their common ancestors (Figure 1.19).
Darwin's second main point was to proposea mechanism for descent with modification. He called this evolutionary mechanism natural selection.
Darwin synthesized his theory of natural selection from observations that by themselves were neither new nor profound. Others had the pieces of the puzzle, but Darwin saw how they fit together. He started with the following observations from nature: Individuals in a population vary in their traits, many of which seem to be heritable (passed on from parents to offspring), Also, a population can produce far more off spring than can survive to produce offspring of their own. With more individuals than the environment can support, competition is inevitable. Lastly, species generally suit their environments.



For instance, birds living where tough seeds are a good food source may have especially strong beaks. Darwin made inferences from these observations to arrive at his theory of evolution. He reasoned that individuals with inherited traits that are best suited to the local environment are more likely to survive and reproduce than less fit individuals. Over many generations, a higher and higher proportion of individuals in a population will have the advantageous traits. Evolution occurs as the unequal reproductive success of individuals adapts the population to its environment.
Darwin called this mechanism of evolutionary adaptation "natural selection" because the natural environment "selects" for the propagation of certain traits. The example in Figure 1.20 illustrates the ability of natural selection to "edit" a population's heritable variations in color. We see the products of natural selection in the exquisite adaptations of various organisms to the special circumstances of their way of Hfe and their environment

The list of biological themes discussed under Concept 1.1 is not absolute; some people might find a shorter or longer list more useful. There is consensus among biologists, however, as to the core theme of biology: It is evolution. To quote one of the founders of modern evolutionary theory, Theodosius Dobzhansky, "Nothing in biology makes sense except in the light of evolution."
In addition to encompassing a hierarchy of size scales from molecules to the biosphere, biology extends across the great diversity of species that have ever lived on Earth. To understand Dobzhansky's statement, we need to discuss how biologists think about this vast diversity.

Organizing the Diversity of Life.
Diversity is a hallmark of life. Biologists have so far identified and named about 1.8 million species. To date, this diversity of life is known to include at least 6,300 species of prokaryotes (organisms with prokaryotic cells), 100,000 fungi, 290,000 plants, 52,000 vertebrates (animals with backbones), and 1 million insects (more than half of all known forms of life). Researchers identify thousands of additional species each year. Estimates of the total number of species range from about 10 million to over 100 million. Whatever the actual number, the enormous variety of life gives biology a very broad scope. Biologists face a major challenge in attempting to make sense of this variety (Picture 1).

Grouping Species: The Basic Idea
There is a human tendency to group diverse items according to similarities. For instance, perhaps you organize your music collection by artist. And then maybe you group the various artists into broader categories, such as rock, jazz, and classical.
In the same way, grouping species that are similar is natural for us. We may speak of squirrels and butterflies, though we recognize that many different species belong to each group. We may even sort groups into broader categories, such as rodents (which include squirrels) and insects (which include butterflies). Taxonomy, the branch of biology that names and classifies species, formalizes this ordering of species into groups of increasing breadth (see Picture 1).
You will learn more about this taxonomic scheme in Chapter 26. For now, we wm focus on kingdoms and domains, the broadest units of classification.

The Three Domains of Life
Until a few decades ago, most biologists adopted a taxonomic scheme that divided the diversity of life into five kingdoms: plants, animals, fungi, single-celled eukaryotic organisms, and prokaryotes. Since then, new methods, such as comparisons of DNA sequences from different species, have led to an ongoing reevaluation of the number and boundaries of kingdoms.
Researchers have proposed anywhere from six kingdoms to dozens of kingdoms. But as debate continues at the kingdom level, there is a consensus that the kingdoms of life can now be grouped into three even higher levels of classification called domains. The three domains are named Bacteria,
Archaea, and Eukarya (Picture 2, 3, and 4).

The organisms making up domain Bacteria and domain Archaea are all prokaryotic. Most prokaryotes are singlecelled and microscopic. In the five-kingdom system, bacteria and archaea were combined in a single kingdom because they shared the prokaryotic form of cell structure. But much evidence now supports the view that bacteria and archaea represent two very distinct branches of prokaryotic life, different in key ways that you'll learn about in Chapter 27. There is also evidence that archaea are at least as closely related to eukaryotic organisms as they are to bacteria.
All the eukaryotes (organisms with eukaryotic cells) are now grouped in domain Eukarya. In the era of the five-kingdom scheme, most single-celled eukaryotes, such as the microorganisms known as protozoans, were placed in a single kingdom, "Protista." Many biologists extended the boundaries of kingdom Protista to include some multicellular forms, such as seaweeds, that are closely related to certain unicellular protists. The recent  taxonomic trend has been to split the protists into several groups at the kingdom level. In addition to these protistan groups, domain Eukarya includes three kingdoms of multicellular eukaryotes: kingdoms Plantae, Fungi, and Animalia. These three kingdoms are distinguished partly by their modes of nutrition.
Plants produce theirown sugars and other foods byphotosynthesis. Fungi absorb dissolved nutrients from their surroundings; many decompose dead organisms and organic wastes (such as leaflitter and animal feces) and absorb nutrients from these sources. Animals obtain food by ingestion, which is the eating and digesting of other organisms. Animalia is, of course, the kingdom to which we belong.

Unity in the Diversity of Life
As diverse as life is, it also displays remarkable unity. Earlier we mentioned the similar skeletons of different vertebrate animals, but similarities are even more striking at the molecular and cellular levels. For example, the universal genetic language of DNA is common to organisms as different as bacteria and animals. Unity is also evident in many features of cell structure.
How can we account for life's dual nature of unity and diversity?
The process of evolution, explained next, illuminates both the similarities and differences in the world ofHfe and introduces another dimension of biology: historical time.



Picture 1: Classifying life . To help organize the diversity of life. biologists classify species into groups that are then combined into even broader groups, In the traditional "linnaean" system. species that are very closely related, such as polar bears and brown bears, are placed in the same genus; genera (plural) are grouped Into families; and so on. This example classifies the species Ursus americanus, the American black bear, (Alternative classification schemes will be discussed in detail in Chapter 26.)


Picture 2: DOMAIN BACTERIA. Bacteria are the most diverse and widespread prokaryotes and are now divided among multiple kingdoms, Each of the rod-shaped structures in this photo is a bacterial cell.


Picture 3: DOMAIN ARCHAEA. Many of the prokaryotes known as archaea live in Earth's extreme environments. such as salty lakes and boiling hot springs. Domain Archaea includes multiple kingdoms, The photo shows a colony composed of many cells.




source : campbell and reece book

A kind of supply-and-demand economy applies to many biological systems. Consider your muscles, for instance. When your muscle cells require more energy during exercise, they increase their consumption of the sugar molecules that provide fuel. In contrast, when you rest, a different set of chemical reactions converts surplus sugar to storage molecules.
Like most of the cell's chemical processes, those that decompose or store sugar are accelerated, or catalyzed, by the specialized proteins called enzymes. Each type ofenzyme catalyzes a specific chemical reaction. In many cases, these reactions are linked into chemical pathways, each step with its own enzyme. How does the cell coordinate its various chemical pathways? In our example ofsugar management, how does the cell match fuel supply to demand, regulating its opposing pathways of sugar consumption and storage? The key is the ability ofmany biological processes to self-regulate by a mechanism called feedback.
In feedback regulation, the output, or product, of a process regulates that very process. In life, the mostcommon form of regulation is negative feedback, in which accumulation of an end product of a process slows that process. For example, the cell's breakdown of sugar generates chemical energy in the form of a substance called ATP. When a cell makes more ATP than it can use, the excess ATP "feeds back" and inhibits an enzyme near the beginning of the pathway (figure 1a).
Though less common than processes regulated by negative feedback, there are also many biological processes regulated by positive feedback, in which an end product speeds up its production (figure 1b). The clotting of your blood in response to injury is an example. When a blood vessel is damaged, structures in the blood called platelets begin to aggregate at the site. Positive feedback occurs as chemicals released by the platelets attract more platelets. The platelet pile then initiates a complex process that seals the wound with a clot.
Feedback is a regulatory motifcommon to life at all levels, from the molecular level to ecosystems and the biosphere. Such regulation is an example of the integration that makes living systems much greater than the sum of their parts.


Negative feedback. ThiS three-step chemICal pathway converts substance A to substance D. A specific enzyme catalyzes each chemical reaction. Accumulation of the final product (OJ inhibits the first enzyme in the sequence. thus slowing down production of moreD.


Positive feedback. In a biochemical pathway regulated by positive feedback, a product stimulates an enzyme in the reaction sequence, incteasing the tate of production of the product.


source: Campbell and Reece book

The entire sequence of nucleotides in the human genome is now known, along with the genome sequences of many other organisms, including bacteria, archaea, fungi, plants, and animals. These accomplishments have been made possible by the development of new methods and DNA-sequencing machines.
The sequencing of the human genome is a scientific and technological achievement comparable to landing the Apollo astronauts on the moon in 1969. But itis only the beginning of an even bigger research endeavor, an effort to learn how the activities of the myriad proteins encoded by the DNA are coordinated in cells and whole organisms.
The best way to make sense of the deluge of data from genome-sequencing projeds and the growing catalog of known protein unctions is to apply a systems approach at the cellular and molecular levels. Figure 1 illustrates the results of a large study that mapped a network of protein interactions within a cell ofa fruit fly, a popular research organism.
The model is based on a database of thousands ofknown proteins and their known interactions with other proteins. For example, protein A may attach to and alter the activities of proteins B, C. and D, which then go on to interact with stit! other proteins. The figure maps these protein partnerships to their cellular locales.
The basics of the systems strategy are straightforward. First, it is necessary to inventory as many parts of the system as possible, such as all the known genes and proteins in a cell(an application of reductionism). Then it is necessary to investigate how each part behaves in relation to others in the working system-all the protein-protein interactions, in the case of our fly cell example. Finally, with the help of computers and specialized software, it is possible to pool all the data into the kind of system network pictured in Figure 1.
Though the basic idea ofsystems biology is simple, the practice is not, as you would expect from the complexity ofbiological systems. It has taken three key research developments to bring systems biology within reach. One is "high-throughput" technology, tools that can analyze biological materials very rapidly and produce enormous amounts of data. The automatic DNA-sequencing machines that made the sequencing of the human genome possible are examples of high-throughput devices. The second is bioinformatics, which is the use ofcomputational tools to store, organize, and analyze the huge volume of data that result from high-throughput methods. The third key development is the formation of interdisciplinary research teams-melting pots of diverse specialists that may include computer scientists, mathematicians, engineers, chemists, physicists, and, of course, biologists from a variety of fields.


A systems map of interactions among
proteins in a cell. This diagram maps 2,346 proteins (dots) and their network of interadions (lines connecting the proteins) in afruit fly cell. Systems biologists develop such models from huge databases of information about molecules and their interadions in the cell. A major goal of this systems approach is to use the models to predict how one change. such as an increase in the activity of a particular protein, can ripple through the cell's molecular circuitry to cause other changes. The tolal number of proteins in this type of cell is probably in the range of 4,000 10 7,000.

source: Campbell and Reece book

Inside the dividing cell in Figure 1.7 (on the previous page), you can see structures called chromosomes, which are stained with a blue-glowing dye. The chromosomes have almost all of the cell's genetic material, its DNA (short for deoxyribonucleic acid). DNA is the substance of genes, the units of inheritance that transmit information from parents to offspring.Your blood group (A, B, AB, or 0), for example, is the result of certain genes that you inherited from your parents.
DNA Structure and Function.
Each chromosome has one very long DNA molecule, with hundreds or thousands of genes arranged along its length. The DNA of chromosomes replicates as a cell prepares to divide, and each ofthe two cellular offspring inherits a complete set of genes.
Each of us began life as a single cell stocked with DNA inherited from our parents. Replication of that DNA with each round of cell division transmitted copies of it to our trillions of cells. In each cell, the genes along the length of the DNA molecules encode the information for building the cell's other molecules. In this way, DNA controls the development and maintenance ofthe entire organism and, indirectly, everything it does (Figure 1). The DNA serves as a central database.
The molecular structure ofDNA accounts for its ability to store information. Each DNA molecule is made up of two long chains arranged in a double helix. Each chain link is one of four kinds of chemical building blocks called nucleotides (Figure 2). The way DNA encodes information is analogous to the waywe arrange the letters ofthe alphabet into precise sequences with specific meanings. The word rat, for example, evokes a rodent; the words tar and art, which contain the same letters, mean very different things. Libraries are filled with books containing information encoded in varying sequences of only 26 letters. We can think of nucleotides as the alphabet of inheritance. Specific sequential arrangements of these four chemical letters encode the precise information in genes, which are typically hundreds or thousands of nucleotides long. One gene in a bacterial cell may be translated as "Build a certain component of the cell membrane. A particular human gene may mean "Make growth hormone".
More generally, genes like those just mentioned program the cell's production oflarge molecules called proteins. Other human proteins include a muscle cell's contraction proteins and the defensive proteins called antibodies. A class of proteins crucial to all cells are enzymes, which catalyze (speed up) specific chemical reactions. Thus, DNA provides the blueprints, and proteins serve as the tools that actually build and maintain the cell and carry out its activities.
The DNA of genes controls protein production indirectly, using a related kind ofmolecule called RNA as an intermediary.
The sequence of nucleotides along a gene is transcribed into RNA, which is then translated into a specific protein with a unique shape and function. In the translation process, all forms of life employ essentially the same genetic code. A particular sequence of nucleotides says the same thing to one organism as it does to another. Differences between organisms reflect differences between their nucleotide sequences.
Not all RNA in the cell is translated into protein. We have known for decades that some types ofRNA molecules are actually components of the cellular machinery that manufactures proteins. Recently, scientists have discovered whole new classes of RNA that play other roles in the cell, such as regulating the functioning of protein-coding genes.
The entire "library" of genetic instructions that an organism inherits is called its genome. A typical human cell has two similar sets of chromosomes, and each set has DNA totaling about 3 billion nucleotides. If the one-letter symbols for these nucleotides were written in letters the size of those you are now reading, the genetic text would fill about 600 books the size of this one. Within this genomic library of nucleotide sequences are genes for about 75,000 kinds of proteins and an as yet unknown number of RNA molecules.


Inherited DNA directs development of an organism.


(a)DNA double helix. This mcxlel shows each atom in a segment of DNA. Made up of two long chains of bUilding blocks called nucleotides, a DNA molecule takes the three-dimensional form of adouble helix.
(b)Single strand of DNA. These geometric shapes and letters are simple symbols for the nucleotides in asmall section of one chain of a DNA molecule Genetic information is encoded in specific sequences of the four types of nucleotides. (Their names are abbreviated here as A. T, C, and G.)

In life's structural hierarchy, the cell has a special place as the lowest level of organization that can perform all activities required for life. Moreover, the activities of organisms are all based on the activities ofcells. For instance, the division of cells to form new cells is the basis for all reproduction and for the growth and repair of multicellular organisms (Figure 1). To cite another example, the movement of your eyes as you read this line is based on activities of muscle and nerve cells. Even a global process such as the recycling ofcarbon is the cumulative product ofcellular activities, including the photosynthesis that occurs in the chloroplasts ofleafcells. Understanding how cells work is a major focus of biological research.
All cells share certain characteristics. For example, every cell is enclosed by a membrane that regulates the passage of materials between the cell and its surroundings. And every cell uses DNA as its genetic information. However, we can distinguish between two main forms ofcells: prokaryotic cells and eukaryotic cells. The cells of two groups of microorganisms called bacteria and archaea are prokaryotic. All other forms of life, including plants and animals, are composed of eukaryotic cells.


Aeukaryotic cell is subdivided by internal membranes into various membrane-enclosed organelles, such as the ones you see in image above and the chloroplast you saw in Figure on Exploring Levels of Biological Organization. In most eukaryotic cells, the largest organelle is the nucleus, which contains the cell's DNA. The other organelles are located in the cytoplasm, the entire region between the nucleus and outer membrane of the cell. As image above also shows, prokaryotic cells are much simpler and generally smaller than eukaryotic cells. In a prokaryotic cell, the DNA is not separated from the rest of the cell by enclosure in a membrane-bounded nucleus. Prokaryotic cells also lack the other kinds of membrane-enclosed organelles that characterize eukaryotic cells.
But whether an organism has prokaryotic or eukaryotic cells, its structure and function depend on cells.