Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

109
Proteins
chapter
3
When we look at a cell through a microscope or analyze its electrical or biochemical
activity, we are, in essence, observing proteins. Proteins constitute most
of a cell’s dry mass. They are not only the cell’s building blocks; they also execute
the majority of the cell’s functions. Thus, proteins that are enzymes provide
the intricate molecular surfaces inside a cell that catalyze its many chemical
reactions. Proteins embedded in the plasma membrane form channels and
pumps that control the passage of small molecules into and out of the cell. Other
proteins carry messages from one cell to another, or act as signal integrators that
relay sets of signals inward from the plasma membrane to the cell nucleus. Yet
others serve as tiny molecular machines with moving parts: kinesin, for example,
propels organelles through the cytoplasm; topoisomerase can untangle knotted
DNA molecules. Other specialized proteins act as antibodies, toxins, hormones,
antifreeze molecules, elastic fibers, ropes, or sources of luminescence. Before
we can hope to understand how genes work, how muscles contract, how nerves
conduct electricity, how embryos develop, or how our bodies function, we must
attain a deep understanding of proteins.
In This Chapter
The Shape and Structure
of Proteins
Protein function
THE SHAPE AND STRUCTURE OF PROTEINS
From a chemical point of view, proteins are by far the most structurally complex
and functionally sophisticated molecules known. This is perhaps not surprising,
once we realize that the structure and chemistry of each protein has been
developed and fine-tuned over billions of years of evolutionary history. The theoretical
calculations of population geneticists reveal that, over evolutionary time
periods, a surprisingly small selective advantage is enough to cause a randomly
altered protein sequence to spread through a population of organisms. Yet, even
to experts, the remarkable versatility of proteins can seem truly amazing.
In this section, we consider how the location of each amino acid in the long
string of amino acids that forms a protein determines its three-dimensional shape.
Later in the chapter, we use this understanding of protein structure at the atomic
level to describe how the precise shape of each protein molecule determines its
function in a cell.
The Shape of a Protein Is Specified by Its Amino Acid Sequence
There are 20 different of amino acids in proteins that are coded for directly in an
organism’s DNA, each with different chemical properties. A protein molecule
is made from a long unbranched chain of these amino acids, each linked to its
neighbor through a covalent peptide bond. Proteins are therefore also known as
polypeptides. Each type of protein has a unique sequence of amino acids, and
there are many thousands of different proteins in a cell.
The repeating sequence of atoms along the core of the polypeptide chain is
referred to as the polypeptide backbone. Attached to this repetitive chain are
those portions of the amino acids that are not involved in making a peptide bond
and that give each amino acid its unique properties: the 20 different amino acid
side chains (Figure 3–1). Some of these side chains are nonpolar and hydrophobic