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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 3Protein Structure and Function

Proteins are the most versatile macromolecules in living systems and serve crucial functions in essentially all biological processes. They function as catalysts, they transport and store other molecules such as oxygen, they provide mechanical support and immune protection, they generate movement, they transmit nerve impulses, and they control growth and differentiation. Indeed, much of this text will focus on understanding what proteins do and how they perform these functions.

Several key properties enable proteins to participate in such a wide range of functions.


Proteins are linear polymers built of monomer units called amino acids. The construction of a vast array of macromolecules from a limited number of monomer building blocks is a recurring theme in biochemistry. Does protein function depend on the linear sequence of amino acids? The function of a protein is directly dependent on its threedimensional structure (Figure 3.1). Remarkably, proteins spontaneously fold up into three-dimensional structures that are determined by the sequence of amino acids in the protein polymer. Thus, proteins are the embodiment of the transition from the one-dimensional world of sequences to the three-dimensional world of molecules capable of diverse activities.


Proteins contain a wide range of functional groups. These functional groups include alcohols, thiols, thioethers, carboxylic acids, carboxamides, and a variety of basic groups. When combined in various sequences, this array of functional groups accounts for the broad spectrum of protein function. For instance, the chemical reactivity associated with these groups is essential to the function of enzymes, the proteins that catalyze specific chemical reactions in biological systems (see Chapters 8–10).


Proteins can interact with one another and with other biological macromolecules to form complex assemblies. The proteins within these assemblies can act synergistically to generate capabilities not afforded by the individual component proteins (Figure 3.2). These assemblies include macro-molecular machines that carry out the accurate replication of DNA, the transmission of signals within cells, and many other essential processes.


Some proteins are quite rigid, whereas others display limited flexibility. Rigid units can function as structural elements in the cytoskeleton (the internal scaffolding within cells) or in connective tissue. Parts of proteins with limited flexibility may act as hinges, springs, and levers that are crucial to protein function, to the assembly of proteins with one another and with other molecules into complex units, and to the transmission of information within and between cells (Figure 3.3).

Crystals of human insulin.


Crystals of human insulin. Insulin is a protein hormone, crucial for maintaining blood sugar at appropriate levels. (Below) Chains of amino acids in a specific sequence (the primary structure) define a protein like insulin. These chains fold into well-defined (more...)

Figure 3.1. Structure Dictates Function.

Figure 3.1

Structure Dictates Function. Image mouse.jpg A protein component of the DNA replication machinery surrounds a section of DNA double helix. The structure of the protein allows large segments of DNA to be copied without the replication machinery dissociating from the (more...)

Figure 3.2. A Complex Protein Assembly.

Figure 3.2

A Complex Protein Assembly. An electron micrograph of insect flight tissue in cross section shows a hexagonal array of two kinds of protein filaments. [Courtesy of Dr. Michael Reedy.]

Figure 3.3. Flexibility and Function.

Figure 3.3

Flexibility and Function. Image mouse.jpg Upon binding iron, the protein lactoferrin undergoes conformational changes that allow other molecules to distinguish between the iron-free and the iron-bound forms.


3.1 Proteins Are Built from a Repertoire of 20 Amino Acids

3.2 Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains

3.3 Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops

3.4 Tertiary Structure: Water-Soluble Proteins Fold Into Compact Structures with Nonpolar Cores

3.5 Quaternary Structure: Polypeptide Chains Can Assemble Into Multisubunit Structures

3.6 The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure


Appendix: Acid-Base Concepts


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: NBK21177


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