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.

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