campbell 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

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.

Another theme seen in previous posts (Exploring Levels of Biological Organization) is the idea that the appropriate form of the function, which you'll recognize from everyday life, for example a screwdriver is suited to tighten or loosen screws, a hammer to pound nails. How a device works is correlated with its structure. AppJied to biology, this theme is a guide to
the anatomy ofJife at all its structural levels. An example from Figure 1.4 is seen in the leaf: Its thin, flat shape maximizes the amount of sunlight that can be captured by its chloroplasts.
Analyzing a biological structure gives us dues about what it does and how it works. Conversely, knowing the function of something provides insight into its construction. An example from the animal kingdom, the wing of a bird, provides additional instances ofthe structure-function theme (Figure 1.6), In exploring life on its different structural levels, we discover
functional beauty at every turn.

Wing bones have a honeycombed internal structure that is strong but lightweight


The flight muscles are controlled by neurons (nerve cells). which transmit signals. With long extenSions, neurons are espeCially well structured for communication within the body


The flight muscles obtain energy in a usable form from organelles called mitochondria. A mitochondrion has an inner membrane with many infoldings. Molecules embedded in the inner membrane carry out many of the steps in energy produdion, and the Illfoldings pack a large amount of this membrane into a small container.


A bird's wings have an aerodynamically efficient shape


source: Campbell and Reece book