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`Molecular Biology of
`
`THE CELL
`
`Fifth Edition
`
`LCY Biotechnology Holding, Inc.
`Ex. 1008
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`Molecular Biology of
`
`THE CELL
`
`Fifth Edition
`
`Bruce Alberts
`
`Alexander Johnson
`
`Julian Lewis
`
`Martin Raff
`
`Keith Roberts
`
`Peter Walter
`
`With problems by
`
`John Wilson
`
`Tim Hunt
`
`LCY Biotechnology Holding, Inc.
`Ex. 1008
`Page 5 of 240
`
`

`

`Garland Science
`Vice President: Denise Schanck
`Assistant Editor: Sigrid Masson
`Production Editor and Layout: Emma Jeffcock
`Senior Publisher: Jackie Harbor
`Illustrator: Nigel Orme
`Designer: Matthew McClements, Blink Studio, Ltd.
`Editors: Marjorie Anderson and Sherry Granum
`Copy Editor: Bruce Goatly
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`Permissions Coordinator: Mary Dispenza
`
`Cell Biology Interactive
`Artistic and Scientific Direction: Peter Walter
`Narrated by: Julie Theriot
`Production Design and Development: Michael Morales
`
`© 2008, 2002 by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff,
`Keith Roberts, and Peter Walter.
`© 1983, 1989, 1994 by Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff,
`Keith Roberts, and James D. Watson.
`
`Bruce Alberts received his Ph.D. from Harvard University and is Professor of
`Biochemistry and Biophysics at the University of California, San Francisco. For
`12 years, he served as President of the U.S. National Academy of Sciences (1993–2005).
`Alexander Johnson received his Ph.D. from Harvard University and is Professor of
`Microbiology and Immunology and Director of the Biochemistry, Cell Biology, Genetics,
`and Developmental Biology Graduate Program at the University of California, San
`Francisco. Julian Lewis received his D.Phil. from the University of Oxford and is a
`Principal Scientist at the London Research Institute of Cancer Research UK.
`Martin Raff received his M.D. from McGill University and is at the Medical Research
`Council Laboratory for Molecular Cell Biology and the Biology Department at University
`College London. Keith Roberts received his Ph.D. from the University of Cambridge and
`is Emeritus Fellow at the John Innes Centre, Norwich. Peter Walter received his Ph.D.
`from The Rockefeller University in New York and is Professor and Chairman of the
`Department of Biochemistry and Biophysics at the University of California, San
`Francisco, and an Investigator of the Howard Hughes Medical Institute.
`
`This book contains information obtained from authentic and highly regarded sources.
`Reprinted material is quoted with permission, and sources are indicated. A wide variety
`of references are listed. Reasonable efforts have been made to publish reliable data and
`information, but the author and the publisher cannot assume responsibility for the
`validity of all materials or for the consequences of their use.
`
`All rights reserved. No part of this book covered by the copyright heron may be
`reproduced or used in any format in any form or by any means—graphic, electronic, or
`mechanical, including photocopying, recording, taping, or information storage and
`retrieval systems—without permission of the publisher.
`
`Library of Congress Cataloging-in-Publication Data
`Molecular biology of the cell / Bruce Alberts … [et al.].-- 5th ed.
`p. cm
`ISBN 978-0-8153-4105-5 (hardcover)---ISBN 978-0-8153-4106-2 (paperback)
`1. Cytology. 2. Molecular biology. I. Alberts, Bruce.
`QH581.2 .M64 2008
`571.6--dc22
`
`2007005475 CIP
`
`Published by Garland Science, Taylor & Francis Group, LLC, an informa business,
`270 Madison Avenue, New York NY 10016, USA, and 2 Park Square, Milton Park,
`Abingdon, OX14 4RN, UK.
`
`Printed in the United States of America
`
`15 14 13 12 11 10 9 8 7 6 5 4 3 2
`
`LCY Biotechnology Holding, Inc.
`Ex. 1008
`Page 6 of 240
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`

`

`Chapter 3
`
`Proteins
`
`When we look at a cell through a microscope or analyze its electrical or bio-
`chemical 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 nearly all the cell’s functions. Thus, enzymes provide the intricate
`molecular surfaces in a cell that promote 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 mes-
`sages from one cell to another, or act as signal integrators that relay sets of sig-
`nals 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.
`
`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 devel-
`oped and fine-tuned over billions of years of evolutionary history. 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 deter-
`mines its function in a cell.
`
`The Shape of a Protein Is Specified by Its Amino Acid Sequence
`
`There are 20 types of amino acids in proteins, each with different chemical prop-
`erties. A protein molecule is made from a long 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, each with its
`own particular amino acid sequence.
`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 (“water-fearing”), others are negatively or positively charged, some
`readily form covalent bonds, and so on. Panel 3–1 (pp. 128–129) shows their
`atomic structures and Figure 3–2 lists their abbreviations.
`
`3
`
`In This Chapter
`
`THE SHAPE AND
`STRUCTURE OF PROTEINS
`
`125
`
`PROTEIN FUNCTION
`
`152
`
`125
`
`LCY Biotechnology Holding, Inc.
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`

`126
`
`Chapter 3: Proteins
`
`OH
`
`O O
`
`H
`
`CH2
`
`H N C
`+
`
`C
`
`H H
`
`+
`
`O O
`
`tyrosine (Tyr)
`
`O
`
`O
`
`C
`
`H
`
`CH2
`
`+
`
`H N C
`+
`
`C
`
`H H
`
`O
`
`O
`
`aspartic acid (Asp)
`
`leucine (Leu)
`
`H H
`
`+
`H N C
`
`C
`
`+
`
`H
`
`CH2
`
`CH
`
`H3C
`
`CH3
`
`methionine (Met)
`
`O O
`
`C
`
`H
`
`H
`
`+
`H N C
`
`CH2
`CH2
`
`S C
`
`H3
`
`H
`
`H2O
`
`H2O
`
`H2O
`
`Figure 3–1 The components
`of a protein. A protein
`consists of a polypeptide
`backbone with attached side
`chains. Each type of protein
`differs in its sequence and
`number of amino acids;
`therefore, it is the sequence
`of the chemically different
`side chains that makes each
`protein distinct. The two ends
`of a polypeptide chain are
`chemically different: the end
`carrying the free amino group
`+, also written NH2) is the
`(NH3
`amino terminus, or
`N-terminus, and that carrying
`the free carboxyl group
`(COO–, also written COOH) is
`the carboxyl terminus or
`C-terminus. The amino acid
`sequence of a protein is
`always presented in the
`N-to-C direction, reading
`from left to right.
`
`O
`
`O
`
`C
`
`CH2
`
`O
`
`side chains
`
`H H O
`
`OH
`
`CH2
`
`C N C
`
`C N C
`
`C N C
`
`C
`
`polypeptide backbone
`
`H
`
`H
`
`+
`H N C
`
`amino terminus
`or N-terminus
`
`SCHEMATIC
`
`carboxyl terminus
`or C-terminus
`
`O O
`
`H
`
`H H
`
`O
`
`H H
`
`peptide
`bonds
`
`CH2
`
`CH
`
`H3C
`
`CH3
`
`peptide bond
`
`polypeptide backbone
`
`CH2
`CH2
`
`S C
`
`H3
`
`nonpolar
`side chain
`
`polar side chain
`
`SEQUENCE
`
`Met
`
`Asp
`
`Leu
`
`Tyr
`
`As discussed in Chapter 2, atoms behave almost as if they were hard spheres
`with a definite radius (their van der Waals radius). The requirement that no two
`atoms overlap limits greatly the possible bond angles in a polypeptide chain
`(Figure 3–3). This constraint and other steric interactions severely restrict the
`possible three-dimensional arrangements of atoms (or conformations). Never-
`theless, a long flexible chain, such as a protein, can still fold in an enormous
`number of ways.
`The folding of a protein chain is, however, further constrained by many dif-
`ferent sets of weak noncovalent bonds that form between one part of the chain
`and another. These involve atoms in the polypeptide backbone, as well as atoms
`in the amino acid side chains. There are three types of weak bonds: hydrogen
`bonds, electrostatic attractions, and van der Waals attractions, as explained in
`Chapter 2 (see p. 54). Individual noncovalent bonds are 30–300 times weaker
`than the typical covalent bonds that create biological molecules. But many weak
`bonds acting in parallel can hold two regions of a polypeptide chain tightly
`together. In this way, the combined strength of large numbers of such noncova-
`lent bonds determines the stability of each folded shape (Figure 3–4).
`
`LCY Biotechnology Holding, Inc.
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`

`127
`
`Figure 3–2 The 20 amino
`acids found in proteins. Each
`amino acid has a three-letter
`and a one-letter abbreviation.
`There are equal numbers of
`polar and nonpolar side
`chains; however, some side
`chains listed here as polar are
`large enough to have some
`non-polar properties (for
`example, Tyr, Thr, Arg, Lys). For
`atomic structures, see Panel
`3–1 (pp. 128–129).
`
`THE SHAPE AND STRUCTURE OF PROTEINS
`
`AMINO ACID
`
`SIDE CHAIN
`
`AMINO ACID
`
`SIDE CHAIN
`
`nonpolar
`nonpolar
`nonpolar
`nonpolar
`nonpolar
`nonpolar
`nonpolar
`nonpolar
`nonpolar
`nonpolar
`
`A G V L I P F M W C
`
`Alanine
`Glycine
`Valine
`Leucine
`Isoleucine
`Proline
`Phenylalanine
`Methionine
`Tryptophan
`Cysteine
`
`Ala
`Gly
`Val
`Leu
`Ile
`Pro
`Phe
`Met
`Trp
`Cys
`
`negative
`negative
`positive
`positive
`positive
`uncharged polar
`uncharged polar
`uncharged polar
`uncharged polar
`uncharged polar
`
`D E R K H N Q S T Y
`
`Asp
`Glu
`Arg
`Lys
`His
`Asn
`Gln
`Ser
`Thr
`Tyr
`
`Aspartic acid
`Glutamic acid
`Arginine
`Lysine
`Histidine
`Asparagine
`Glutamine
`Serine
`Threonine
`Tyrosine
`
`POLAR AMINO ACIDS
`
`NONPOLAR AMINO ACIDS
`
`A fourth weak force also has a central role in determining the shape of a pro-
`tein. As described in Chapter 2, hydrophobic molecules, including the nonpolar
`side chains of particular amino acids, tend to be forced together in an aqueous
`environment in order to minimize their disruptive effect on the hydrogen-
`bonded network of water molecules (see p. 54 and Panel 2–2, pp. 108–109).
`Therefore, an important factor governing the folding of any protein is the distri-
`bution of its polar and nonpolar amino acids. The nonpolar (hydrophobic) side
`chains in a protein—belonging to such amino acids as phenylalanine, leucine,
`valine, and tryptophan—tend to cluster in the interior of the molecule (just as
`hydrophobic oil droplets coalesce in water to form one large droplet). This
`enables them to avoid contact with the water that surrounds them inside a cell.
`In contrast, polar groups—such as those belonging to arginine, glutamine, and
`histidine—tend to arrange themselves near the outside of the molecule, where
`they can form hydrogen bonds with water and with other polar molecules (Fig-
`ure 3–5). Polar amino acids buried within the protein are usually hydrogen-
`bonded to other polar amino acids or to the polypeptide backbone.
`
`(A)
`
`amino acid
`
`(B)
`
`+180
`
`psi
`
`0
`
`–180
`–180
`
`0
`
`phi
`
`+180
`
`H
`
`Ca
`
`R3
`
`NH
`
`OC
`
`psi
`
`R2
`
`Ca
`
`H
`
`phi
`
`N H
`
`peptide bonds
`
`CO
`
`H
`
`Ca
`
`R1
`
`Figure 3–3 Steric limitations on the bond angles in a polypeptide chain. (A) Each amino acid contributes three bonds
`(red) to the backbone of the chain. The peptide bond is planar (gray shading) and does not permit rotation. By contrast,
`rotation can occur about the Ca–C bond, whose angle of rotation is called psi (y), and about the N–Ca bond, whose angle
`of rotation is called phi (f). By convention, an R group is often used to denote an amino acid side chain (green circles).
`(B) The conformation of the main-chain atoms in a protein is determined by one pair of f and y angles for each amino acid;
`because of steric collisions between atoms within each amino acid, most pairs of f and y angles do not occur. In this so-
`called Ramachandran plot, each dot represents an observed pair of angles in a protein. The cluster of dots in the bottom
`left quadrant represents all of the amino acids that are located in a-helix structures (see Figure 3–7A). (B, from
`J. Richardson, Adv. Prot. Chem. 34:174–175, 1981. With permission from Academic Press.)
`
`LCY Biotechnology Holding, Inc.
`Ex. 1008
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`
`

`

`128
`
`PANEL 3–1: The 20 Amino Acids Found in Proteins
`
`OPTICAL ISOMERS
`
`The a-carbon atom is asymmetric, which
`allows for two mirror image (or stereo-)
`isomers, L and D.
`
`+
`NH3
`
`L
`
`H
`
`Ca
`
`R
`
`COO–
`
`COO–
`
`+
`NH3
`
`D
`
`H
`
`Ca
`
`R
`
`Proteins consist exclusively of L-amino acids.
`
`THE AMINO ACID
`The general formula of an amino acid is
`
`a-carbon atom
`
`COOH
`
`carboxyl
`group
`
`side-chain group
`
`H
`
`RC
`
`amino
`group
`
`H2N
`
`R is commonly one of 20 different side chains.
`At pH 7 both the amino and carboxyl groups
`are ionized.
`
`COO
`
`H
`
`RC
`
`+
`
`H3N
`
`histidine
`
`(His, or H)
`
`CO
`
`H C
`
`CH2
`C
`
`N H
`
`HN
`
`CH
`
`arginine
`
`(Arg, or R)
`
`CO
`
`H C
`
`CH2
`
`CH2
`
`CH2
`
`NH
`
`N H
`
`BASIC SIDE CHAINS
`lysine
`
`(Lys, or K)
`
`CO
`
`H C
`
`CH2
`
`CH2
`
`CH2
`
`N H
`
`FAMILIES OF
`AMINO ACIDS
`
`The common amino acids
`are grouped according to
`whether their side chains
`are
`
` acidic
` basic
` uncharged polar
` nonpolar
`
`CH2
`
`+
`NH3
`
`This group is
`very basic
`because its
`positive charge
`is stabilized by
`resonance.
`
`C
`
`+H2N
`
`NH2
`
`NH+
`HC
`These nitrogens have a
`relatively weak affinity for an
`H+ and are only partly positive
`at neutral pH.
`
`These 20 amino acids
`are given both three-letter
`and one-letter abbreviations.
`
`Thus: alanine = Ala = A
`
`PEPTIDE BONDS
`
`Amino acids are commonly joined together by an amide linkage,
`called a peptide bond.
`
`Peptide bond: The four atoms in each gray box form a rigid
`planar unit. There is no rotation around the C–N bond.
`
`C
`
`O
`
`OH
`
`HCR
`
`N H
`
`CO
`
`H
`
`CN
`
`R
`
`carboxyl- or
`C-terminus
`
`H
`
`C
`
`COO–
`
`CH
`CH3 CH3
`
`H H
`
`NH
`
`H2O
`
`C O
`
`SH
`
`CH2
`C
`
`N H
`
`CO
`
`H C C
`
`H2
`
`C
`
`O
`
`OH
`
`R
`
`CN
`
`C
`
`H
`
`H H
`
`amino- or
`N-terminus
`
`+
`
`H3N
`
`HN
`
`CH
`
`HC
`
`NH+
`
`These two single bonds allow rotation, so that long chains of
`amino acids are very flexible.
`
`O
`
`OH
`
`H
`
`CN
`
`C
`
`R
`
`H H
`
`Proteins are long polymers
`of amino acids linked by
`peptide bonds, and they
`are always written with the
`N-terminus toward the left.
`The sequence of this tripeptide
`is histidine-cysteine-valine.
`
`LCY Biotechnology Holding, Inc.
`Ex. 1008
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`
`

`

`THE SHAPE AND STRUCTURE OF PROTEINS
`
`129
`
`ACIDIC SIDE CHAINS
`
`NONPOLAR SIDE CHAINS
`
`valine
`
`(Val, or V)
`
`CO
`
`H C
`
`N H
`
`CH
`CH3
`
`CH3
`
`alanine
`
`(Ala, or A)
`
`CO
`
`H C
`
`CH3
`
`N H
`
`leucine
`
`(Leu, or L)
`
`CO
`
`H C
`
`N H
`
`CH
`CH3
`
`CH2
`
`CH3
`
`CO
`
`H C
`
`CH2
`CH
`CH3
`
`CH3
`
`N H
`
`phenylalanine
`
`(Phe, or F)
`
`CO
`
`H C
`
`N H
`
`proline
`
`(Pro, or P)
`
`CO
`
`H C
`
`N
`
`glutamic acid
`
`(Glu, or E)
`
`CO
`
`H C
`
`CH2
`CH2
`
`C
`
`N H
`
`O
`
`O–
`
`aspartic acid
`
`(Asp, or D)
`
`CO
`
`H C
`
`CH2
`
`C
`
`N H
`
`O
`
`O–
`
`UNCHARGED POLAR SIDE CHAINS
`
`glutamine
`
`(Gln, or Q)
`
`CO
`
`H C
`
`N H
`
`asparagine
`
`(Asn, or N)
`
`CO
`
`H C
`
`CH2
`
`CH2
`
`CH2
`
`(actually an
`imino acid)
`
`CH2
`
`tryptophan
`
`(Trp, or W)
`
`CO
`
`H C
`
`CH2
`
`N H
`
`NH
`
`cysteine
`
`(Cys, or C)
`
`methionine
`
`(Met, or M)
`
`CO
`
`H C
`
`CH2
`CH2
`S
`
`CH3
`
`N H
`
`glycine
`
`(Gly, or G)
`
`CO
`
`H C
`
`H
`
`N H
`
`CO
`
`H C
`
`N H
`
`CH2
`SH
`Disulfide bonds can form between two cysteine side chains
`in proteins.
`
`CH2
`
`S
`
`S
`
`CH2
`
`CH2
`CH2
`
`C
`
`O
`
`NH2
`
`CH2
`
`C
`
`N H
`
`O
`
`NH2
`
`Although the amide N is not charged at
`neutral pH, it is polar.
`
`tyrosine
`
`(Tyr, or Y)
`
`CO
`
`H C
`
`CH2
`
`N H
`
`OH
`
`threonine
`
`(Thr, or T)
`
`CO
`
`CH3
`
`H C
`
`CH
`
`OH
`
`N H
`
`serine
`
`(Ser, or S)
`
`CO
`
`H C
`
`CH2
`
`OH
`
`N H
`
`The –OH group is polar.
`
`LCY Biotechnology Holding, Inc.
`Ex. 1008
`Page 11 of 240
`
`

`

`130
`
`Chapter 3: Proteins
`
`glutamic acid
`H
`CN
`H
`CH2
`CH2
`C
`
`CO
`
`O
`
`O
`
`H
`
`N
`+
`
`CH2
`CH2
`CH2
`CH2
`H
`CC
`N
`O
`H
`lysine
`
`H H
`
`electrostatic
`attractions
`
`+
`
`van der Waals attractions
`
`hydrogen bond
`
`R
`
`C
`
`H
`
`C
`
`O
`
`H
`
`C
`
`N
`
`O
`
`O
`C
`
`H
`C
`
`R
`
`H
`C
`
`H
`
`N
`
`R
`
`Figure 3–4 Three types of noncovalent
`bonds help proteins fold. Although a
`single one of these bonds is quite weak,
`many of them often form together to
`create a strong bonding arrangement, as
`in the example shown. As in the previous
`figure, R is used as a general designation
`for an amino acid side chain.
`
`valine
`
`O
`
`H
`
`CC
`
`N
`
`H
`C
`H
`C
`
`O
`
`C
`
`H
`
`alanine
`
`CH3
`CH3
`CH3
`CH3
`CH3
`H
`N
`
`H
`
`C
`C C
`H
`O
`
`N
`
`H
`
`valine
`
`Proteins Fold into a Conformation of Lowest Energy
`
`As a result of all of these interactions, most proteins have a particular three-
`dimensional structure, which is determined by the order of the amino acids in its
`chain. The final folded structure, or conformation, of any polypeptide chain is
`generally the one that minimizes its free energy. Biologists have studied protein
`folding in a test tube by using highly purified proteins. Treatment with certain
`solvents, which disrupt the noncovalent interactions holding the folded chain
`together, unfolds, or denatures, a protein. This treatment converts the protein
`into a flexible polypeptide chain that has lost its natural shape. When the dena-
`turing solvent is removed, the protein often refolds spontaneously, or renatures,
`into its original conformation (Figure 3–6). This indicates that the amino acid
`sequence contains all the information needed for specifying the three-dimen-
`sional shape of a protein, which is a critical point for understanding cell function.
`Each protein normally folds up into a single stable conformation. However,
`the conformation changes slightly when the protein interacts with other
`molecules in the cell. This change in shape is often crucial to the function of the
`protein, as we see later.
`Although a protein chain can fold into its correct conformation without out-
`side help, in a living cell special proteins called molecular chaperones often assist
`in protein folding. Molecular chaperones bind to partly folded polypeptide
`chains and help them progress along the most energetically favorable folding
`
`polar
`side chains
`
`nonpolar
`side chains
`
`hydrophobic
`core region
`contains
`nonpolar
`side chains
`
`polar side chains
`on the outside
`of the molecule
`can form hydrogen
`bonds to water
`
`unfolded polypeptide
`
`folded conformation in aqueous environment
`
`Figure 3–5 How a protein folds into a
`compact conformation. The polar amino
`acid side chains tend to gather on the
`outside of the protein, where they can
`interact with water; the nonpolar amino
`acid side chains are buried on the inside
`to form a tightly packed hydrophobic
`core of atoms that are hidden from water.
`In this schematic drawing, the protein
`contains only about 30 amino acids.
`
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`THE SHAPE AND STRUCTURE OF PROTEINS
`
`131
`
`Figure 3–6 The refolding of a
`denatured protein. (A) This type of
`experiment, first performed more
`than 40 years ago, demonstrates
`that a protein’s conformation is
`determined solely by its amino acid
`sequence. (B) The structure of urea.
`Urea is very soluble in water and
`unfolds proteins at high
`concentrations, where there is
`about one urea molecule for every
`six water molecules.
`
`(B)
`
`O C
`
`H2N
`
`NH2
`
`(A)
`
`EXPOSE TO A HIGH
`CONCENTRATION
`OF UREA
`
`REMOVE
`UREA
`
`purified protein
`isolated from
`cells
`
`denatured
` protein
`
`original conformation
`of protein re-forms
`
`pathway. In the crowded conditions of the cytoplasm, chaperones prevent the
`temporarily exposed hydrophobic regions in newly synthesized protein chains
`from associating with each other to form protein aggregates (see p. 388). How-
`ever, the final three-dimensional shape of the protein is still specified by its
`amino acid sequence: chaperones simply make the folding process more reliable.
`Proteins come in a wide variety of shapes, and they are generally between 50
`and 2000 amino acids long. Large proteins usually consist of several distinct pro-
`tein domains—structural units that fold more or less independently of each
`other, as we discuss below. Since the detailed structure of any protein is compli-
`cated, several different representations are used to depict the protein’s structure,
`each emphasizing different features.
`Panel 3–2 (pp. 132–133) presents four different representations of a protein
`domain called SH2, which has important functions in eucaryotic cells. Con-
`structed from a string of 100 amino acids, the structure is displayed as (A) a
`polypeptide backbone model, (B) a ribbon model, (C) a wire model that
`includes the amino acid side chains, and (D) a space-filling model. Each of the
`three horizontal rows shows the protein in a different orientation, and the
`image is colored in a way that allows the polypeptide chain to be followed from
`its N-terminus (purple) to its C-terminus (red). <GTGA>
`Panel 3–2 shows that a protein’s conformation is amazingly complex, even
`for a structure as small as the SH2 domain. But the description of protein struc-
`tures can be simplified because they are built up from combinations of several
`common structural motifs, as we discuss next.
`
`The a Helix and the b Sheet Are Common Folding Patterns
`When we compare the three-dimensional structures of many different protein
`molecules, it becomes clear that, although the overall conformation of each pro-
`tein is unique, two regular folding patterns are often found in parts of them.
`Both patterns were discovered more than 50 years ago from studies of hair and
`silk. The first folding pattern to be discovered, called the a helix, was found in
`the protein a-keratin, which is abundant in skin and its derivatives—such as
`hair, nails, and horns. Within a year of the discovery of the a helix, a second
`folded structure, called a b sheet, was found in the protein fibroin, the major
`constituent of silk. These two patterns are particularly common because they
`result from hydrogen-bonding between the N–H and C=O groups in the
`polypeptide backbone, without involving the side chains of the amino acids.
`Thus, many different amino acid sequences can form them. In each case, the
`protein chain adopts a regular, repeating conformation. Figure 3–7 shows these
`two conformations, as well as the abbreviations that are used to denote them in
`ribbon models of proteins.
`The core of many proteins contains extensive regions of b sheet. As shown in
`Figure 3–8, these b sheets can form either from neighboring polypeptide chains
`that run in the same orientation (parallel chains) or from a polypeptide chain
`that folds back and forth upon itself, with each section of the chain running in
`the direction opposite to that of its immediate neighbors (antiparallel chains).
`Both types of b sheet produce a very rigid structure, held together by hydrogen
`bonds that connect the peptide bonds in neighboring chains (see Figure 3–7D).
`
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`132
`
`PANEL 3–2: Four Different Ways of Depicting a Small Protein, the SH2 Domain <GTGA>
`
`(A) Backbone: Shows the overall organization of the polypeptide
`chain; a clean way to compare structures of related proteins.
`
`(B) Ribbon: Easy way to visualize secondary structures, such as
`a helices and b sheets.
`
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`THE SHAPE AND STRUCTURE OF PROTEINS
`
`133
`
`(Courtesy of David Lawson.)
`
`(C) Wire: Highlights side chains and their relative proximities; useful for
`predicting which amino acids might be involved in a protein's activity,
`particularly if the protein is an enzyme.
`
`(D) Space-filling: Provides contour map of the protein; gives a feel for the
`shape of the protein and shows which amino acid side chains are exposed
`on its surface. Shows how the protein might look to a small molecule,
`such as water, or to another protein.
`
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`

`134
`
`Chapter 3: Proteins
`
`R
`
`amino acid
`side chain
`
`R
`
`oxygen
`
`H-bond
`
`R
`
`R
`
`hydrogen
`
`R
`
`nitrogen
`
`R
`
`R
`
`carbon
`
`R
`
`R
`
`R
`
`R
`
`(A)
`
`carbon
`
`nitrogen
`
`R
`
`peptide
`bond
`
`oxygen
`
`R
`
`H-bond
`
`hydrogen
`
`R
`
`R
`
`R
`
`R
`
`R
`
`R
`
`(B)
`
`amino acid
`side chain
`
`carbon
`
`R
`
`R
`
`R
`
`R
`
`R
`
`(D)
`
`(E)
`
`a helix
`
`(C)
`
`0.54 nm
`
`carbon
`
`nitrogen
`
`0.7 nm
`
`b sheet
`
`(F)
`
`Figure 3–7 The regular conformation of the polypeptide backbone in the a helix and the b sheet. <GTAG> <TGCT>
`(A, B, and C) The a helix. The N–H of every peptide bond is hydrogen-bonded to the C=O of a neighboring peptide bond
`located four peptide bonds away in the same chain. Note that all of the N–H groups point up in this diagram and that all of
`the C=O groups point down (toward the C-terminus); this gives a polarity to the helix, with the C-terminus having a partial
`negative and the N-terminus a partial positive charge. (D, E, and F) The b sheet. In this example, adjacent peptide chains
`run in opposite (antiparallel) directions. Hydrogen-bonding between peptide bonds in different strands holds the
`individual polypeptide chains (strands) together in a b sheet, and the amino acid side chains in each strand alternately
`project above and below the plane of the sheet. (A) and (D) show all the atoms in the polypeptide backbone, but the
`amino acid side chains are truncated and denoted by R. In contrast, (B) and (E) show the backbone atoms only, while (C)
`and (F) display the shorthand symbols that are used to represent the a helix and the b sheet in ribbon drawings of proteins
`(see Panel 3–2B).
`
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`THE SHAPE AND STRUCTURE OF PROTEINS
`
`135
`
`An a helix is generated when a single polypeptide chain twists around on
`itself to form a rigid cylinder. A hydrogen bond forms between every fourth pep-
`tide bond, linking the C=O of one peptide bond to the N–H of another (see Fig-
`ure 3–7A). This gives rise to a regular helix with a complete turn every 3.6 amino
`acids. Note that the protein domain illustrated in Panel 3–2 contains two a
`helices, as well as a three-stranded antiparallel b sheet.
`Regions of a helix are especially abundant in proteins located in cell mem-
`branes, such as transport proteins and receptors. As we discuss in Chapter 10,
`those portions of a transmembrane protein that cross the lipid bilayer usually
`cross as an a helix composed largely of amino acids with nonpolar side chains.
`The polypeptide backbone, which is hydrophilic, is hydrogen-bonded to itself in
`the a helix and shielded from the hydrophobic lipid environment of the mem-
`brane by its protruding nonpolar side chains (see also Figure 3–78).
`In other proteins, a helices wrap around each other to form a particularly
`stable structure, known as a coiled-coil. This structure can form when the two
`(or in some cases three) a helices have most of their nonpolar (hydrophobic)
`side chains on one side, so that they can twist around each other with these side
`chains facing inward (Figure 3–9). Long rodlike coiled-coils provide the struc-
`tural framework for many elongated proteins. Examples are a-keratin, which
`forms the intracellular fibers that reinforce the outer layer of the skin and its
`appendages, and the myosin molecules responsible for muscle contraction.
`
`(A)
`
`(B)
`
`Protein Domains Are Modular Units from which Larger Proteins
`Are Built
`
`Even a small protein molecule is built from thousands of atoms linked together by
`precisely oriented covalent and noncovalent bonds, and it is extremely difficult to
`visualize such a complicated structure without a three-dimensional display. For
`
`Figure 3–8 Two types of b sheet
`structures. (A) An antiparallel b sheet
`(see Figure 3–7D). (B) A parallel b sheet.
`Both of these structures are common
`in proteins.
`
`11 nm
`
`a
`
`NH2
`
`d
`
`e
`
`a
`
`e
`
`d
`
`a
`
`g
`
`d
`
`a
`
`a
`
`d
`
`d
`
`g
`
`g
`
`c
`
`c
`
`g
`
`0.5 nm
`
`(A)
`
`stripe of
`hydrophobic
`“a” and “d”
`amino acids
`
`11 nm
`
`NH2
`
`NH2
`
`HOOC COOH
`
`(B)
`
`(C)
`
`Figure 3–9 A coiled-coil. <CGGA>
`(A) A single a helix, with successive amino
`acid side chains labeled in a sevenfold
`sequence, “abcdefg” (from bottom to top).
`Amino acids “a” and “d” in such a sequence
`lie close together on the cylinder surface,
`forming a “stripe” (red) that winds slowly
`around the a helix. Proteins that form
`coiled-coils typically have nonpolar amino
`acids at positions “a” and “d.” Consequently,
`as shown in (B), the two a helices can wrap
`around each other with the nonpolar side
`chains of one a helix interacting with the
`nonpolar side chains of the other, while the
`more hydrophilic amino acid side chains are
`left exposed to the aqueous environment.
`(C) The atomic structure of a coiled-coil
`determined by x-ray crystallography. The
`red side chains are nonpolar.
`
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`136
`
`Chapter 3: Proteins
`
`this reason, biologists use various graphic and computer-based aids. A DVD that
`accompanies this book contains computer-generated images of selected pro-
`teins, displayed and rotated on the screen in a variety of formats.
`Biologists distinguish four levels of organization in the structure of a protein.
`The amino acid sequence is known as the primary structure. Stretches of
`polypeptide chain that form a helices and b sheets constitute the protein’s sec-
`ondary structure. The full three-dimensional organization of a polypeptide
`chain is sometimes referred to as the tertiary structure, and if a particular pro-
`tein molecule is formed as a complex of more than one polypeptide chain, the
`complete structure is designated as the quaternary structure.
`Studies of the conformation, function, and evolution of proteins have also
`revealed the central importance of a unit of organization distinct from these
`four. This is the protein domain, a substructure produced by any part of a
`polypeptide chain that can fold independently into a compact, stable structure.
`A domain usually contains between 40 and 350 amino acids, and it is the mod-
`ular unit from which many larger proteins are constructed.
`The different domains of a protein are often associated with different func-
`tions. Figure 3–10 shows an example—the Src protein kinase, which functions in
`signaling pathways inside vertebrate cells (Src is pronounced “sarc”). This pro-
`tein is considered to have three domains: the SH2 and SH3 domains have regu-
`latory roles, while the C-terminal domain is responsible for the kinase catalytic
`activity. Later in the chapter, we shall return to this protein, in order to explain
`how proteins can form molecular switches that transmit information through-
`out cells.
`Figure 3–11 presents ribbon models of three differently organized protein
`domains. As these examples illustrate, the polypeptide chain tends to cross the
`entire domain before making a sharp turn at the surface. The central core of a
`domain can be constructed from a helices, from b sheets, or from various com-
`binations of these two fundamental folding elements. <CAGT>
`The smallest protein molecules contain only a single domain, whereas
`larger proteins can contain as many as several dozen domains, often connected
`to each other by short, relatively unstructured lengths of polypeptide chain.
`
`Few of the Many Possible Polypeptide Chains Will Be Useful to
`Cells
`
`Since each of the 20 amino acids is chemically distinct and each can, in princi-
`ple, occur at any position in a protein chain, there are 20 ¥ 20 ¥ 20 ¥ 20 = 160,000
`different possible polypeptide chains four amino acids long, or 20n different
`possible polypeptide chains n amino acids long. For a typical protein length of
`
`SH3 domain
`
`N
`
`ATP
`
`C
`
`(A)
`
`SH2 domain
`
`(B)
`
`Figure 3–10 A protein formed from
`multiple domains. In the Src protein
`shown, a C-terminal domain with two
`lobes (yellow and orange) forms a protein
`kinase enzyme, while the SH2 and SH3
`domains perform regulatory functions.
`(A) A ribbon model, with ATP substrate in
`red. (B) A spacing-filling model, with ATP
`substrate in red. Note that the site that
`binds ATP is positioned at the interface of
`the two lobes that form the kinase. The
`detailed structure of the SH2 domain is
`illustrated in Panel 3–2 (pp. 132–133).
`
`LCY Biotechnology Holding, Inc.
`Ex. 1008
`