Basic Molecular Functions

Other chapters in this book look at how the structures of molecules permit them to carry out the processes that cells need to survive and build complex organisms. This section briefly introduces the relationship between DNA, RNA, and proteins and describes some of their basic functions. The easiest way to do so is probably to describe a day in the life of a typical cell.

Cells have to be flexible to survive, whether they live as single organisms in a pond or as parts of a vast human body. They need to move toward sources of food, to respond to changes in the environment, and to protect themselves from damaging substances (or predators) in the environment. These and a cell's other behaviors are carried out as a dialogue between the information in its genes and the environment. Its DNA sequence is like a huge library of user's manuals that has been in the writing since the beginning of life on Earth. The genome contains instructions that have helped the species survive over its entire evolutionary history. When circumstances change, the cell tries a different set of instructions, as if consulting a new user's manual. It shuts down some genes that it has been using and switches on another set, which changes its proteins and rebuilds molecular machines.

Changes in the cell are usually triggered by the environment. By "tasting" the molecules around it, the cell learns what to become. The tasting is done by proteins called receptors that float on the cell surface.

Foods have different, recognizable tastes because nerves in different parts of the tongue detect particular flavors, and all of these sensations are combined on their way to the brain. Environmental signals are also combined to have an effect on cell behavior. Cells have many types of receptor proteins, each able to detect a different "flavor" through a partner molecule called a ligand. Each type of cell produces a unique set of receptors, which enables it to taste some things but not others. Each environment tastes different because it contains a unique set of ligands. Muscles in the heart produce different ligands than do the linings of blood vessels, the bone marrow, or the brain. By interpreting combinations of signals, cells learn how to develop, when to divide, and even when to die.

Tasting is the first step in a process that tells a cell what to become and how to behave. Receptors send information into the cell via signaling pathways. These are information chains made of molecules that brush by each other, often binding for just an instant, just long enough to change each other's chemistry. Through signaling pathways particular molecules are triggered in a specific sequence, called a "cascade," which ends with the activation of certain genes. They work a bit like a telephone list that a teacher might use to get information to parents. Instead of calling every parent himself, the teacher calls one parent, who calls another, who calls the next parent on the list. Each bit of news reaches the same parents in the same order. Sometimes the lists are organized for speed: One person in the chain calls several. (If the teacher calls four parents, and each of them calls four more, a whole school of 1,000 pupils could be reached in just five steps.)

In the cell, information is passed from a receptor (teacher) to proteins (parents) using chemistry rather than telephone calls. When a signal triggers the same proteins in the same order it is called a pathway. Just as there are many receptors, there are many pathways. Signaling pathways cope with the same types of confusing situations that sometimes happen with telephone lists. One teacher may need to send out information to several classes. (Some receptors can trigger multiple pathways.) If there are three children in a family, a parent will be on three telephone lists. (One protein may belong to several pathways.) If a parent cannot reach the next person on the list, the chain may be interrupted (a broken or missing protein may block the signal). A child may use the list to make prank phone calls—just as cellular pathways can be abused. (Viruses often use receptor proteins, for example, to dock onto cells and gain entry through the membrane, much as if a telemarketer had found a copy of the telephone list.)

Eventually the information makes its way to the genes in the cell's large internal compartment, the nucleus—a bit like customer orders arriving at the kitchen of a restaurant. DNA contains the recipes for other molecules needed by the cell (RNAs and proteins). Information from signaling pathways switches on some genes and switches off others. This changes the set of molecules present in a cell, the way the arrival of new customers changes the food on restaurant tables. Tracking each order—identifying which receptor sends a certain signal, which proteins pass it along, and which genes are affected by the information—is the subject of a great deal of today's biological research.

Signaling pathways are involved in nearly everything that happens in the cell—good and bad. They can also break down. A protein may go missing, or it may get stuck in a "transmitting" mode where it broadcasts signals all the time, even when there has been no call from the receptor. If the pathway tells the cell to divide all the time, rather than alternating reproduction and resting phases, the result may be cancer.

One process that is controlled by signaling pathways is whether cells stick together in a tissue or migrate. The ability to switch on and off migratory behavior played an important role in the evolution of the first animals more than a billion years ago and is essential throughout the body of every animal alive today. When the signals that control this behavior break down, the result may be serious trouble, including cancer and metastases. An organism's body enters uncharted territory. Cancer resembles what happens all of the time in an embryo: Cells migrate to specific places to build new tissues. Tumors are like futile attempts by the body to build new organs that have no function and have not been shaped by evolution.

Signals trigger other types of molecular functions that are needed by cells. One is building the cell's architecture, which is crucial to its behavior. For example, the treelike structure of a neuron, with large networks of roots and branches, allows it to establish contact with other cells and communicate with them.

A red blood cell has to be small and flexible to navigate through tiny blood vessels called "capillaries." Muscles need pistonlike fibers to be able to expand and contract. Tubes and fibers made of protein complexes give cells these shapes.

A cell also needs to convert substances from the environment into what it needs to survive and make new copies of itself. Machines made of proteins and RNAs break down raw materials and glue them together in new ways, creating energy and nutrients. Another task is to protect the cell from dramatic changes in the environment and other dangers, such as invasions by viruses or bacteria.

Starting with chapter 2, The Molecules of Life shows how molecules work together to carry out these various tasks. The rest of chapter 1 is devoted to discussing some of the methods that have been developed to study molecules.

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