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Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002.

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Biochemistry. 5th edition.

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Chapter 4Exploring Proteins

In the preceding chapter, we saw that proteins play crucial roles in nearly all biological processes—in catalysis, signal transmission, and structural support. This remarkable range of functions arises from the existence of thousands of proteins, each folded into a distinctive three-dimensional structure that enables it to interact with one or more of a highly diverse array of molecules. A major goal of biochemistry is to determine how amino acid sequences specify the conformations of proteins. Other goals are to learn how individual proteins bind specific substrates and other molecules, mediate catalysis, and transduce energy and information.

The purification of the protein of interest is the indispensable first step in a series of studies aimed at exploring protein function. Proteins can be separated from one another on the basis of solubility, size, charge, and binding ability. When a protein has been purified, the amino acid sequence can be determined. The strategy is to divide and conquer, to obtain specific fragments that can be readily sequenced. Automated peptide sequencing and the application of recombinant DNA methods are providing a wealth of amino acid sequence data that are opening new vistas. To understand the physiological context of a protein, antibodies are choice probes for locating proteins in vivo and measuring their quantities. Monoclonal antibodies able to probe for specific proteins can be obtained in large amounts. The synthesis of peptides is possible, which makes feasible the synthesis of new drugs, functional protein fragments, and antigens for inducing the formation of specific antibodies. Nuclear magnetic resonance (NMR) spectroscopy and x-ray crystallography are the principal techniques for elucidating three-dimensional structure, the key determinant of function.

The exploration of proteins by this array of physical and chemical techniques has greatly enriched our understanding of the molecular basis of life and makes it possible to tackle some of the most challenging questions of biology in molecular terms.

4.0.1. The Proteome Is the Functional Representation of the Genome:

Many organisms are yielding their DNA base sequences to gene sequencers, including several metazoans. The roundworm Caenorhabditis elegans has a genome of 97 million bases and about 19,000 protein-encoding genes, whereas that of the fruit fly Drosophilia melanogaster contains 180 million bases and about 14,000 genes. The incredible progress being made in gene sequencing has already culminated in the elucidation of the complete sequence of the human genome, all 3 billion bases with an estimated 40,000 genes. But this genomic knowledge is analogous to a list of parts for a car—it does not explain how the parts work together. A new word has been coined, the proteome, to signify a more complex level of information content, the level of functional information, which encompasses the type, functions, and interactions of proteins that yield a functional unit.

The term proteome is derived from proteins expressed by the genome. Whereas the genome tells us what is possible, the proteome tells us what is functionally present—for example, which proteins interact to form a signal-transduction pathway or an ion channel in a membrane. The proteome is not a fixed characteristic of the cell. Rather, because it represents the functional expression of information, it varies with cell type, developmental stage, and environmental conditions, such as the presence of hormones. The proteome is much larger than the genome because of such factors as alternatively spliced RNA, the posttranslational modification of proteins, the temporal regulation of protein synthesis, and varying protein-protein interactions. Unlike the genome, the proteome is not static.

An understanding of the proteome is acquired by investigating, characterizing, and cataloging proteins. An investigator often begins the process by separating a particular protein from all other biomolecules in the cell.

Milk, a source of nourishment for all mammals, is composed, in part, of a variety of proteins.


Milk, a source of nourishment for all mammals, is composed, in part, of a variety of proteins. The protein components of milk are revealed by the technique of MALDI-TOF mass spectrometry, which separates molecules on the basis of their mass to charge (more...)


4.1 The Purification of Proteins Is an Essential First Step in Understanding Their Function

4.2 Amino Acid Sequences Can Be Determined by Automated Edman Degradation

4.3 Immunology Provides Important Techniques with Which to Investigate Proteins

4.4 Peptides Can Be Synthesized by Automated Solid-Phase Methods

4.5 Three-Dimensional Protein Structure Can Be Determined by NMR Spectroscopy and X-Ray Crystallography



Selected Readings

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Copyright © 2002, W. H. Freeman and Company.
Bookshelf ID: NBK21181


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