`
`Gilead 2010
`
`IfMAK v. Gilead
`IPR2018-oo125
`
`3
`
`lunaque ‘
`
`' 1E.Vne
`
`NEW. 3
`
`3
`
`Gilead 2010
`I-MAK v. Gilead
`IPR2018-00125
`
` 1
`
`

`

` Biochemistry
`
`
`University of Pennsylvania
`
`
`
` indie xi Veel
`
`
`
`Veel
`
`
`
`
`
`Swarthmore College, Emeritus
`
`€avleiie
`
`,
`
`a
`
`
`
`Seattle Pacific University
`
`
`
` 2
`
`

`

`
`
`
`scholar, teacher, friend
`
`Vice—President & Executive Publisher Kaye Pace
`Associate Publisher
`Petra Recter
`Marketing Manager
`Amanda Wainer
`Assistant Editor
`Alyson Rentrop
`Senior Production Editor
`Sandra Dumas
`Production Manager
`Dorothy Sinclair
`Director of Creative Services
`Harry Nolan
`Cover Design
`Madelyn Lesure
`Text Design
`Laura C. Ierardi
`Photo Department Manager
`Hilary Newman
`Photo Editors
`Hilary Newman, Sheena Goldstein
`Illustration Editor
`Sigmund Malinowski
`Pathways of Discovery Portraits
`Wendy Wray
`Senior Media Editor
`Thomas Kulesa
`Production Management Services
`Suzanne Ingrao/Ingrao Associates
`
`Background Photo Cover Credit: Lester Lefkowitz/Getty Images
`Inset Photo Credits: Based on X—ray structures by (left to right) Thomas Steitz,Yale
`University; Daniel Koshland, Jr., University of California at Berkeley; Emmanual
`Skordalakis and James Berger, University of California at Berkeley; Nikolaus Grigorieff
`and Richard Henderson, MRC Laboratory of Molecular Biology, U.K.;Thomas Steitz, Yale
`University.
`
`This book was set in 10/12 Times Ten by Aptara and printed and bound by
`Courier/KendallvilleThe cover was printed by Phoenix Color Corporation.
`
`This book is printed on acid free paper.
`
`1)
`
`Copyright © 2008 by Donald Voet, Judith G. Voet, and Charlotte W. Pratt. All rights
`reserved
`
`No part of this publication may be reproduced. stored in a retrieval system or transmitted
`in any form or by any means, electronic, mechanical, photocopying, recording, scanning or
`otherwise, except as permitted under Sections 107 or 1108 of the 1976 United States
`Copyright Act, without either the prior written permission of the Publisher, or authoriza—
`tion through payment of the appropriate per-copy fee to the Copyright Clearance Center,
`Inc, 222 Rosewood Drive, Danvers, MA 01923, website www.copyright.com. Requests to
`the Publisher for permission should be addressed to the Permissions Department, John
`Wiley & Sons, Inc, 111 River Street, Hoboken, NJ 07030—5774, (201)748-6011, fax (201)748-
`6008, website http://www.wiley.com/go/perniissions.
`
`To order books or for customer service, please call l-800—CALL WILEY (2256945).
`
`ISBN—l3
`
`978—0470—12930—2
`
`Printed in the United States of America
`1.0
`9
`8
`7
`6 5
`
`
`
`
`
`
`
` 3
`
`

`

`Nucleotides,
`Nucleic Acids,
`and Genetic
`
`Information
`
`A DNA molecule consists of two strands that wind around a central
`
`image
`axis, shown here as a glowing wire. [lllustration, Irving Geis.
`from the lrving Geis Collection/Howard Hughes Medical Institute.
`Rights owned by HHMI. Reproduction by permission only}
`
`B. Genes Direct Protein Synthesis
`
`MEDEA aesouaces
`-
`(Available at www.wiley.com/college/voet)
`Guided Exploration 1. Overview of transcription and translation
`Guided Exploration 2. DNA sequence determination by the chain-terminator
`method
`Guided Exploration 3. PCR and site—directed mutagenesis
`Interactive Exercise 1. Three-dimensional structure of DNA
`Animated Figure 3-26. Construction of a recombinant DNA molecule
`Animated Figure 3-27. Cloning with bacteriophage h
`Animated Figure 3-30. Site—directed mutagenesis
`7 Kinemage Exercise 2-1. Structure of DNA
`-‘ Kinemage Exercise 2-2. Watson~Crick base pairs
`Bioinformatics Exercises Chapter 3. Databases for the Storage and “Mining” of
`Genome Sequences
`
`CHAPEER CQNTEN'Fg
`
`Nucleic Acid
`
`1 Nucleotides
`'
`2 IntrOducnon t0
`Structure
`A- NUCIElC ACldS Are Polymers Ol Nucleotides
`B. DNA Forms a Double Helix
`(5- RNA l5 a Single-Stranded Nucleic Add
`Overview of Nucleic Acid Function
`A. DNA Carries Genetic information
`
`.
`.
`.
`NUCISIC ACld Sequencmg
`A. Restriction Endonucleases Cleave DNA at
`Specific Sequences
`B. Electrophoresis Separates Nucleic Acids
`
`C. DNA Is Sequenced by the Chain—Terminator
`Method
`
`D. Entire Genomes Have Been Sequenced
`E Evolution Results from Sequence Mutations
`.
`-
`Manipulatlng DNA ..
`A“ ClonequNA ls an AmphflEd Copy
`3' 3:1]: LI
`rarles Are Collections Of Cloned
`c DNA ls Amplified b
`the Poi merase Chain
`y
`' Reaction
`y
`. Recombinant DNA Technology Has
`Numerous Practical Applications
`
`.
`.
`.
`.
`.
`.
`espite obv10us differences in lifestyle and macroscopic appear—
`. ance, organisms exhibit striking Similarit
`at the molecular level.
`The structures and metabolic activities, of all cells rely on a
`mmon set of molecules that includes amino acids, carbohydrates, lipids,
`d nucleotides, as well as their polymeric forms. Each type of compound
`be described in terms of its chemical makeup, its interactions with
`er molecules, and its physiological function. We begin our survey of bio—
`lecules. with a discussion of the nucleotides and their polymers, the
`etc acxds.
`
`lflcally, they participate in oxidation—reduction reactions, energy
`Sfer, intracellular signaling, and biosynthetic reactions. Their polymers,
`nucleic acids DNA and RNA, are the primary players in the storage
`
` 4
`
`

`

`
`
`40
`
`a
`
`Chapter 3 Nucleotides, Nucleic Acids, and Genetic Information
`
`and decoding of genetic information. Nucleotides and nucleic acids also
`perform structural and catalytic roles in cells. No other class of molecules
`participates in such varied functions or in so many functions that are es-
`sential for life.
`
`Evolutionists postulate that the appearance of nucleotides permitted
`the evolution of organisms that could harvest and store energy from their
`surroundings and, most importantly, could make copies of themselves.
`Although the chemical and biological details of early life—forms are the
`subject of. speculation, it is incontrovertible that life as we know it is
`inextricably linked to the chemistry of nucleotides and nucleic acids.
`In this Chapter, we briefly examine the structures of nucleotides and the
`nucleic acids DNA and RNA. We also consider how the chemistry of these
`molecules allows them to carry biological information in the form of a
`sequence of nucleotides. This information is expressed by the transcription
`of a segment of DNA to yield RNA, which is then translated to form
`protein. Because a cell’s structure and function ultimately depend on its
`genetic makeup, we discuss how genomic sequences provide information
`about evolution, metabolism, and disease. Finally, we consider some of the
`techniques used in manipulating DNA in the laboratory. In later chapters,
`we will examine in greater detail the participation of nucleotides and
`nucleic acids in metabolic processes. Chapter 24 includes additional infor—
`mation about nucleic acid structures, DNA’s interactions with proteins, and
`DNA packaging in cells, as a prelude to several chapters discussing the
`roles of nucleic acids in the storage and expression of genetic information.
`
`
`
`,Nucleetides
`
`Nucleotides are ubiquitous molecules with considerable structural diversity.
`There are eight common varieties of nucleotides, each composed of a nitroge—
`nous base linked to a sugar to which at least one phosphate group is also
`attached. The bases of nucleotides are planar, aromatic, heterocyclic mole-
`cules that are structural derivatives of either purine or pyrimidine (although
`they are not synthesized in vivo from either of these organic compounds).
`
`6
`
`N1/
`2
`\3
`N
`
`4|
`
`R
`98
`N
`\
`H
`
`4
`N? 5
`2
`6
`\1
`N
`
`
`
`Purine
`
`Pyrimidine
`
`
`
`LEARNING OBJECTIVE
`
`a Become familiar with the structures and
`
`nomenclature of the eight common
`nucleotides.
`
`
`
`
`
`
`
`
`The most common purines are adenine (A) and guanine (G), and the
`major pyrimidines are cytosine (C), uracil (U), and thymine (T). The
`purines form bonds to a five—carbon sugar (a pentose) via their N9 atoms,
`whereas pyrimidines do so through their N1 atoms (Table 3—1).
`In ribonucleotides, the pentose is ribose, while in deoxyribonucleotides
`(or just deoxynucleotides), the sugar is 2’-de0xyrib0se (i.e., the carbon at
`position 2’ lacks a hydroxyl group).
`5’
`HO—CH2 O
`
`OH
`
`in, HM
`
`OH
`
`V m
`
`5'
`HO”CH2 O
`
`OH on
`
`Ribose
`
`OH H
`
`Deoxyribose
`
`5
`
` 5
`
`

`

`Section 3—1 Nucleotides
`
`name; and Abbiamm 'o‘f Nucleic Acid Bases, Nucleosidespand Niiél'eétidésww
`
`
`
`Formula
`
`Base
`(X = H)
`
`Nucleoside
`(X = ribose“)
`
`Nucleotide”
`(X = ribose phosphate“)
`
`
`
`
`
`
`
`
`
`N/
`N
`Adenine
`Adenosine
`Adenylic acid
`k i
`\>
`,
`Ade
`Ado
`Adenosine monophosphate
`\
`
`
`N
`N
`A
`A
`AMP
`
`
`
`
`
`H2N
`
`171
`
`
`
`
`Guanylic acid
`Guanosine
`Guanine
`N
`H\N
`X l
`>
`Gua
`Guo
`Guanosine monophosphate
`N
`G
`G
`GMP
`
`
`
`
`
`
`Cytidylic acid
`Cytidine monophosphate
`CMP
`
`N/
`A l
`N
`
`O
`
`Cytosine
`Cyt
`c
`
`Cytidine
`Cyd
`C
`
`
`
`
`
`
`H\N
`A I
`N
`
`O
`
`Uracil
`Ura
`U
`
`Uridine
`Ui‘d
`U
`
`Uridylic acid
`Uridine monophosphate
`UMP
`
`H
`
`CH3
`
`
`
`
`
`
`
`Deoxythymidylic acid
`Deoxythymidine
`Thymine
`Deoxythymidine monophosphate
`dThd
`Thy
`O
`N
`T
`dT
`dTMP
`
`
`
`- ”The presence of a 2’—deoxyribose unit in place of ribose, as occurs in DNA, is implied by the prefixes “deoxy” or “d.” For example. the deoxynu—
`cleoside of adenine is deoxyadenosine or dA. However, for thymine—containing residues, which rarely occur in RNA, the prefix is redundant and
`_ may be dropped The presence of a ribose unit may be explicitly implied by the prefix “ribo.”
`‘ [The position of the phosphate group in a nucleotide may be explicitly specified as in, for example. 3’—AMP and 5’-GMP.
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`Note that the “primed” numbers refer to the atoms of the pentose;
`“unprimed” numbers refer to the atoms of the nitrogenous base.
`,
`In a ribonucleotide or a deoxyribonucleotide, one or more phosphate
`
`groups are bonded to atom C3’ or atom C5’ of the pentose to form
`
`El- 3’~nucleotide or a 5’~nucleotide, respectively (Fig. 3—1). When the
`
`PEIOSPhate group is absent, the compound is known as a nucleoside. A
`enuCleotide can therefore be called a nucleoside—5’-phosphate.
`
`:ucleotides most commonly contain one to three phosphate groups at the
`
`:5, position and are called nucleoside monophosphates, diphosphates,
`
`nd triphosphates.
`,
`,
`
`(a) A 5’»ribonucleotide
`:glgure 3-1 : Chemical structures of nucleotides.
`
`_,
`(b) a 3’-deoxynucleotide. The purine or pyrimidine base is linked to C1’ of
`e pentose and at least one phosphate (red) is also attached. A nucleoside
`Insists only of a base and a
`entose
`--
`-
`-
`,
`p
`_,
`,
`
`,
`
`,_
`
`
`
`(a)
`5’
`‘
`”ZOgPO—CHz o
`[HI'
`ill/H,
`HWH
`0H 0H
`5’-Ribonucleotide
`
`(b)
`
`
`
`H
`
`5,
`HO—CHZ o
`% Hy
`H
`3
`2
`”203130
`H
`3’-Deoxynucleotide
`
`
`
` 6
`
`

`

`
`
`42
`
`Chapter 3 Nucleotides, Nucleic Acids, and Genetic Information
`
`Glucose
`
`’
`
`V
`
`ADPA
`
`NHZ
`
`N /
`
`\
`
`l
`
`crigou
`l
`o
`,.
`
`.
`
`H
`
`OH
`
`H
`
`HO
`
`
`
`a
`N
`O
`O
`}
`OflPHO-“P-‘Or—CHZ O
`O”
`O~
`H H
`H
`
`H
`OH
`
`HO
`
`In this nucleotide
`@ Figure 3-2 - ADP—glucose.
`derivative, glucose (blue) is attached to adenosine
`(black) by a diphosphate group (red).
`
`‘
`
`N
`
`N
`
`\>
`
`The structures, names, and abbreviations of the common bases, nucleo~
`sides, and nucleotides are given in Table 3-1. Ribonucleotides are
`components of RNA (ribonucleic acid), Whereas deoxynucleotides are com-
`ponents of DNA (deoxyribonucleic acid). Adenine, guanine, and cytosine
`occur in both ribonucleotides and deoxynucleotides (accounting for six of
`the eight common nucleotides), but uracil primarily occurs in ribonu-
`cleotides and thymine occurs in deoxynucleotides. Free nucleotides, which
`are anionic, are almost always associated with the counterion Mg2+ in cells.
`
`Nucleatides Participate in Metabolic Reactions. The bulk of the nu—
`cleotides in any cell are found in polymeric forms, as either DNA or RNA,
`whose primary functions are information storage and transfer. However,
`free nucleotides and nucleotide derivatives perform an enormous variety of
`metabolic functions not related to the management of genetic information.
`Perhaps the best known nucleotide is adenosine triphosphate (ATP), a
`nucleotide containing adenine, ribose, and a triphosphate group. ATP is
`often mistakenly referred to as an energy—storage molecule, but it is
`more accurately termed an energy carrier or energy transfer agent. The
`process of photosynthesis or the breakdown of metabolic fuels such as
`carbohydrates and fatty acids leads to the formation of ATP from
`adenosine diphosphate (ADP):
`
`Adenosine
`
`typically linked to the nucleotide through a mono- or diphosphate group.
`
`
`
`O
`O
`H
`H
`0
`HPOf+ HO—P—O—P‘O‘CHZ O
`0—
`O"
`H H
`H
`
`H
`OH OH
`
`2
`
`<
`
`o
`
`o
`
`o
`
`NH2
`
`N /
`
`K:NK/l/LI‘?
`
`N\
`
`ll
`ll
`1|
`‘O~1|3—O—1|’—O-El’-O—CH2 O
`O“
`0—
`O“
`H H
`H
`
`H
`OH OH
`
`+
`
`H20
`
`Adenosine diphosphate (ADP)
`
`Adenosine triphosphate (ATP)
`
`ATP diffuses throughout the cell to provide energy for other cellular work,
`such as biosynthetic reactions, ion transport, and cell movement. The
`chemical potential energy of ATP is made available when it transfers one
`(or two) of its phosphate groups to another molecule. This process can be
`represented by the reverse of the preceding reaction, namely, the hydro-
`lysis of ATP to ADP. (As we shall see in later chapters, the interconver—
`sion of ATP and ADP in the cell is not freely reversible, and free phos—
`phate groups are seldom released directly from ATP.) The degree to which
`ATP participates in routine cellular activities is illustrated by calculations
`indicating that while the concentration of cellular ATP is relatively
`moderate (~5 mM), humans typically recycle their own weight of ATP
`each day.
`Nucleotide derivatives participate in a wide variety of metabolic
`processes. For example, starch synthesis in plants proceeds by repeated
`additions of glucose units donated by ADP—glucose (Fig. 3—2). Other
`nucleotide derivatives, as we shall see in later chapters, carry groups that
`undergo oxidation~reduction reactions. The attached group, which may be
`a small molecule such as glucose (Fig. 3—2) or even another nucleotide, is
`
` CHECK YOUR UNDERSTANDING
`Describe the general structure of a nucleoside
`and a nucleotide.
`Describe the difference between a
`ribonucleotide and a deoxyribonucleotide.
`
`
`
`
`
` 7
`
`

`

`
`
`Understand what you don't know
`
`WileyPLUS for the new third edition of FUNDAMENTALS OF BIOCHEMISTRY now offers
`
`over 750 conceptually-based online question's, organized by chapter and topic. These original
`
`questions were created by Biochemistry Professors at University of Alberta, and have been
`tested and used since 2000.
`'
`‘
`-
`
`‘1
`
`
`wasps}.
`
`* Damn: Vast. Fundamentalsréf Bloch
`
`
`Barrio Masts-realms
`
`
`Home '=' Mad.$tudv8?m€t§cn
`Asslgnmem . Grafietlook
`
`
`> Open Assignment
`
`
`a asses,H_,, H“,
`
`
`lilm: 0r Emit} mm
`
` Whlch an. ufthe following xlatcmentx ah
`
`zhapmra assignment
`
`Whi<h or the following dumb“ the anti
`What is the primary driving force in the formation of lipid bilayors and proteln tertiary structure?
`irregular loops of H<onduv structure to
`whim or on follcvlnq omlno anid roxldu
`
`A domaln is:
`Energy released when additional ion pairs are formed.
`
`. The exclusion of non‘polar substances from aqueous solution.
`
`Wham an irregular incandary structure:
`The formation of van dor Wadls interactions between neighbouring groups.
`
` Whith of tho following statcmlntx is NOT
`
`. Energy released when additional hydrogen bonds are formed.
`
`whkh ol‘tho following mm of emlno in
`
`
`which or rm Golloulng statement: about
`which of the following statement: about ..
`#1. What ea the, pr‘l’rm‘n‘y driving: turn» in m s’nmmmn of mm: bile...
`thh or": or the running momma; er
`Cnmpnru the nlphx-hollx vlth the strudu
`x INCORRECTr The energy that formation of ion pairs might contribute to the folding process class not
`,
`whlrh one oflhe (alloying segment; at
`compensate for the reduced entropy of the side chains involved and the loss of the salvation free energy.
`What intimately dmrmlnu m. unique r
`:
`which ofthu follow:my sum of amino u
`_
`.
`,
`.
`.
`_
`_
`_
`~
`‘
`_
`.
`Wh(y. or m renewing mm”, m you;
`What Is the primary drlvmg force in the formation of lipid hlleyers and protein tertiary structure?
`‘
`What oss‘r distinqulshes irregular neon:
`W“‘5 °th “"9”" “mm” “mm ‘
`
`9 780470 12 9 3 0‘2
`
`
`
`_
`
`,
`
`,
`
`‘
`
`O The formatlon of van der Waals Interactlons between nelghbourlng groups.
`(‘3. The exclusion of non~polar substances from aqueous solution.
`(gt Energy released when additional ion pairs are Formed.
`(f Energy released when additional hydrogen bonds are formed.
`
`
`
`
`
`Now in WileyPLUS, these questions offer practice with instant intelligent feedback that explains
`why an answer choice is right or wrong.
`
`WileyPLUS also contains:
`0 Complete online version of FUNDAMENTALS OF BlOCHEMlSTRY,
`Third Edition
`
`'
`
`0 Guided Explorations and Interactive Exercises that enhance
`comprehension through animated graphics and narration
`
`flAnimated Figures from the text
`
`- Bioinformatics Exercises
`
`0 Case studies
`
`s 3D molecular models
`
`W.Wiley.com/college/V0et
`
`ISBN 978-0-470-1293D“2
`
` 8
`
`