Essential Cell Biology 5th edition

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124 CHAPTER 4 Protein Structure and Functionnewly synthesized,partially folded proteinschambercapchaperoneproteinone polypeptidechain is sequesteredby the chaperoneisolatedpolypeptidechain foldscorrectlycorrectly foldedprotein is releasedwhen capdissociatesFigure 4–9 Some chaperone proteins act as isolation chambers that help apolypeptide fold. In this case, the barrel of the chaperone provides an enclosedchamber in which a newly synthesized polypeptide chain can fold without the risk ofECB5 04.09aggregating with other polypeptides in the crowded conditions of the cytoplasm.This system also requires an input of energy from ATP hydrolysis, mainly for theassociation and subsequent dissociation of the cap that closes off the chamber.Proteins Come in a Wide Variety of Complicated ShapesProteins are the most structurally diverse macromolecules in the cell.Although they range in size from about 30 amino acids to more than10,000, the vast majority are between 50 and 2000 amino acids long.Proteins can be globular or fibrous, and they can form filaments, sheets,rings, or spheres (Figure 4−10). We will encounter many of these structuresthroughout the book.To date, the structures of about 100,000 different proteins have beendetermined (using techniques we discuss later in the chapter). Most proteinshave a three-dimensional conformation so intricate and irregularthat their structure would require the rest of the chapter to describe indetail. But we can get some sense of the intricacies of polypeptide structureby looking at the conformation of a relatively small protein, such asthe bacterial transport protein HPr.This small protein, only 88 amino acids long, facilitates the transportof sugar into bacterial cells. In Figure 4−11, we present HPr’s threedimensionalstructure in four different ways, each of which emphasizesdifferent features of the protein. The backbone model (see Figure 4−11A)shows the overall organization of the polypeptide chain and provides astraightforward way to compare the structures of related proteins. Theribbon model (see Figure 4−11B) shows the polypeptide backbone in away that emphasizes its most conspicuous folding patterns, which wedescribe in detail shortly. The wire model (see Figure 4−11C) includes thepositions of all the amino acid side chains; this view is especially usefulfor predicting which amino acids might be involved in the protein’s activity.Finally, the space-filling model (see Figure 4−11D) provides a contourmap of the protein surface, which reveals which amino acids are exposedon the surface and shows how the protein might look to a small moleculesuch as water or to another macromolecule in the cell.The structures of larger proteins—or of multiprotein complexes—are evenmore complicated. To visualize such detailed and intricate structures,scientists have developed various computer-based tools to emphasizedifferent features of a protein, only some of which are depicted inFigure 4–11. All of these images can be displayed on a computer screenand readily rotated and magnified to view all aspects of the structure(Movie 4.1).When the three-dimensional structures of many different protein moleculesare compared, it becomes clear that, although the overall
The Shape and Structure of Proteins125transportprotein HPrlysozymecatalasehemoglobinmyoglobinDNAdeoxyribonucleasecollagencytochrome cporinchymotrypsincalmodulinaspartatetranscarbamoylaseinsulinalcoholdehydrogenase5 nmFigure 4−10 Proteins come in a wide variety of shapes and sizes. Each folded polypeptide is shown as a space-filling model,represented at the same scale. In the top-left corner is HPr, the small transport protein featured in detail in Figure 4−11. The proteindeoxyribonuclease is shown bound to a portion of a DNA molecule (gray) for comparison.ECB5 e4.11-4.10
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ESSENTIALCELL BIOLOGYFIFTH EDITION
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W. W. Norton & Company has been ind
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viPrefaceanswer and others invite s
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viiiPrefaceDenise Schanck deserves
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ABOUT THE AUTHORSBRUCE ALBERTS rece
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xiiList of Chapters and Special Fea
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PrefacexvCONTENTSPreface vAbout the
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ContentsxviiThe Equilibrium Constan
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ContentsxixCHAPTER 6DNA Replication
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ContentsxxiPOST-TRANSCRIPTIONAL CON
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ContentsxxiiiCHAPTER 11Membrane Str
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ContentsxxvCHAPTER 14Energy Generat
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ContentsxxviiCHAPTER 16Cell Signali
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ContentsxxixCHAPTER 18The Cell-Divi
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ContentsxxxiGENETICS AS AN EXPERIME
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CHAPTER ONE1Cells: The FundamentalU
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Unity and Diversity of Cells3mechan
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Unity and Diversity of Cells5nucleo
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Cells Under the Microscope7The Inve
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Cells Under the Microscope9cytoplas
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The Prokaryotic Cell110.2 mm(200 µ
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The Prokaryotic Cell13SUPER-RESOLUT
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The Prokaryotic Cell15(A)HSV10 µmF
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The Eukaryotic Cell17nucleusnuclear
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The Eukaryotic Cell19chloroplastsch
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The Eukaryotic Cell21lysosomenuclea
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The Eukaryotic Cell23duplicatedchro
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PANEL 1-2 CELL ARCHITECTURE 25ANIMA
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Model Organisms27(C)(D)(A) (B) (E)
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Model Organisms29Figure 1-34 Drosop
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Model Organisms31INTRODUCE FRAGMENT
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Model Organisms33(A) (B) (C)50 µm
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Model Organisms35TABLE 1-2 SOME MOD
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Questions37• Free-living, single-
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CHAPTER TWO2Chemical Components of
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Chemical Bonds41number of protons.
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Chemical Bonds43+atoms+SHARING OFEL
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Chemical Bonds45Four electrons can
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Chemical Bonds47Because of the favo
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Chemical Bonds49Some Polar Molecule
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Small Molecules in Cells51with othe
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Small Molecules in Cells53optical i
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Small Molecules in Cells55can be re
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Small Molecules in Cells57O _O _ ph
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Macromolecules in Cells59Figure 2-3
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Macromolecules in Cells61ultracentr
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Macromolecules in Cells63BBAAthe su
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Questions65KEY TERMSacid electrosta
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67C-O COMPOUNDSMany biological comp
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69WATER AS A SOLVENTMany substances
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71ELECTROSTATIC ATTRACTIONSElectros
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Page 109 and 110: 75LIPID AGGREGATESFatty acids have
Page 111 and 112: 77ACIDIC SIDE CHAINSNONPOLAR SIDE C
Page 113 and 114: 79NOMENCLATUREThe names can be conf
Page 115 and 116: CHAPTER THREE3Energy, Catalysis, an
Page 117 and 118: The Use of Energy by Cells83(A) (B)
Page 119 and 120: The Use of Energy by Cells85ABraise
Page 121 and 122: The Use of Energy by Cells87H 2 OPH
Page 123 and 124: Free Energy and Catalysis89thermody
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Page 131 and 132: Free Energy and Catalysis97to the c
Page 133 and 134: Free Energy and Catalysis99Figure 3
Page 135 and 136: Activated Carriers and Biosynthesis
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Page 149: Questions115a kilocalorie (kcal) is
Page 152 and 153: 118 PANEL 4-1 A FEW EXAMPLES OF SOM
Page 154 and 155: 120 CHAPTER 4 Protein Structure and
Page 174 and 175: 140PANEL 4-2 MAKING AND USING ANTIB
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174 CHAPTER 5 DNA and ChromosomesTh
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176 CHAPTER 5 DNA and Chromosomes5
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178 CHAPTER 5 DNA and Chromosomes(A
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180 CHAPTER 5 DNA and ChromosomesFi
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182 CHAPTER 5 DNA and ChromosomesY
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184 CHAPTER 5 DNA and ChromosomesFi
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186 CHAPTER 5 DNA and Chromosomesli
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188 CHAPTER 5 DNA and ChromosomesTH
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190 CHAPTER 5 DNA and Chromosomeshe
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192 CHAPTER 5 DNA and Chromosomesge
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194CHAPTER 5DNA and Chromosomesform
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196 CHAPTER 5 DNA and ChromosomesQU
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198 CHAPTER 5 DNA and ChromosomesQU
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200 CHAPTER 6 DNA Replication and R
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202HOW WE KNOWTHE NATURE OF REPLICA
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204CHAPTER 6DNA Replication and Rep
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228 CHAPTER 7 From DNA to Protein:
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246HOW WE KNOWCRACKING THE GENETIC
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CHAPTER EIGHT8Control of Gene Expre
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An Overview of Gene Expression269(A
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How Transcription Is Regulated271de
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How Transcription Is Regulated273tr
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How Transcription Is Regulated275Li
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How Transcription Is Regulated277fo
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Generating Specialized Cell Types27
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Post-Transcriptional Controls287Alt
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Post-Transcriptional Controls289rib
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Post-Transcriptional Controls291At
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Questions293• MicroRNAs (miRNAs)
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Questions295specialized cells is ba
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298 CHAPTER 9 How Genes and Genomes
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324HOW WE KNOWCOUNTING GENESHow man
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5′ 3′5′3′330 CHAPTER 9 How
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CHAPTER TEN10Analyzing the Structur
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Isolating and Cloning DNA Molecules
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IIIIIIIIIIIIIDNA Cloning by PCR341D
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DNA Cloning by PCR343HEAT TOSEPARAT
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DNA Cloning by PCR345(A)ANALYSIS OF
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Sequencing DNA347single-stranded DN
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Sequencing DNA349repetitive DNAinte
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Exploring Gene Function351each loca
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Exploring Gene Function353(A)CONSTR
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Exploring Gene Function355E. coli,
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Exploring Gene Function357(A)(B)Fig
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Exploring Gene Function359fused to
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Exploring Gene Function361Figure 10
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Questions363• DNA sequencing tech
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CHAPTER ELEVEN11Membrane StructureA
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ECB5 e11.05/11.05The Lipid Bilayer3
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The Lipid Bilayer369hydrogen bondsC
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The Lipid Bilayer371sets a lower li
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The Lipid Bilayer373Figure 11-16 Ne
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Membrane Proteins375TRANSPORTERS AN
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Membrane Proteins377A Polypeptide C
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Membrane Proteins379Figure 11-26 SD
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Membrane Proteins381spectrin dimera
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Membrane Proteins383apical plasmame
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ECB5 e11.36/11.36Membrane Proteins3
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Questions387• Most cell membranes
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CHAPTER TWELVE12Transport Across Ce
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Principles of Transmembrane Transpo
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Principles of Transmembrane Transpo
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Transporters and Their Functions395
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Ion Channels and the Membrane Poten
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Ion Channels and Nerve Cell Signali
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Essential Concepts423• Ion channe
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Questions425QUESTION 12-18Amino aci
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428 CHAPTER 13 How Cells Obtain Ene
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436PANEL 13-1 DETAILS OF THE 10 STE
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442PANEL 13-2 THE COMPLETE CITRIC A
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444HOW WE KNOWUNRAVELING THE CITRIC
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CHAPTER FOURTEEN14Energy Generation
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Energy Generation in Mitochondria a
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Mitochondria and Oxidative Phosphor
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Molecular Mechanisms of Electron Tr
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Chloroplasts and Photosynthesis479c
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Chloroplasts and Photosynthesis481F
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Chloroplasts and Photosynthesis483T
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Chloroplasts and Photosynthesis485r
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Chloroplasts and Photosynthesis487s
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The Evolution of Energy-Generating
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Essential Concepts491(A)1 µm(B)Fig
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Questions493C. The electrochemical
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CHAPTER FIFTEEN15Intracellular Comp
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Membrane-Enclosed Organelles497mito
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Membrane-Enclosed Organelles499DNAm
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Protein Sorting501proteins that are
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Protein Sorting503they have the sam
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Protein Sorting505prospective nucle
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Protein Sorting507the first six mon
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Protein Sorting509mRNAgrowingpolype
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Vesicular Transport511hydrophobicst
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Vesicular Transport513(A)(C)25 nm(B
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Secretory Pathways515receptorcargo
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Secretory Pathways517KEY:= glucose=
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Secretory Pathways519cisGolginetwor
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Secretory Pathways521ERGolgiapparat
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Endocytic Pathways523protein in the
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Endocytic Pathways525shed their coa
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Endocytic Pathways527Figure 15−35
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Essential Concepts529• Nuclear pr
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Questions531their destination. Thus
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534 CHAPTER 16 Cell Signalingconsid
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536 CHAPTER 16 Cell Signalingcontac
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538 CHAPTER 16 Cell Signaling(A) he
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540 CHAPTER 16 Cell SignalingFigure
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544 CHAPTER 16 Cell SignalingTABLE
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548 CHAPTER 16 Cell Signalinga diff
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554 CHAPTER 16 Cell Signalingby mem
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556 CHAPTER 16 Cell Signalingouters
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ECB5 e16.32/16.29558 CHAPTER 16 Cel
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562 CHAPTER 16 Cell Signalinggrowth
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564CHAPTER 16Cell Signalinginvolve
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570 CHAPTER 16 Cell Signalingcyclas
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572 CHAPTER 16 Cell SignalingQUESTI
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574 CHAPTER 17 CytoskeletonFigure 1
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576 CHAPTER 17 Cytoskeleton(A)NH 2C
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578 CHAPTER 17 Cytoskeletonbasal ce
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582 CHAPTER 17 Cytoskeletonnucleati
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584 CHAPTER 17 Cytoskeleton(A)GROWI
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586 CHAPTER 17 CytoskeletonQUESTION
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588HOW WE KNOWPURSUING MICROTUBULE-
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594 CHAPTER 17 Cytoskeletonactin wi
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596 CHAPTER 17 Cytoskeletonof actin
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598 CHAPTER 17 Cytoskeletonplus end
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myofibrils602 CHAPTER 17 Cytoskelet
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606 CHAPTER 17 CytoskeletonThe cont
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608 CHAPTER 17 CytoskeletonQUESTION
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610 CHAPTER 18 The Cell-Division Cy
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616CHAPTER 18The Cell-Division Cycl
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628PANEL 18-1 THE PRINCIPAL STAGES
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ECB5 EQ18.14/Q18.14648 CHAPTER 18 T
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CHAPTER NINETEEN19Sexual Reproducti
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The Benefits of Sex653Figure 19−2
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Meiosis and Fertilization655In this
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Meiosis and Fertilization657(A)MITO
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Meiosis and Fertilization659duplica
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Meiosis and Fertilization661(A)(B)m
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Meiosis and Fertilization663gamete
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Mendel and the Laws of Inheritance6
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PANEL 19-1 SOME ESSENTIALS OF CLASS
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Genetics as an Experimental Tool677
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Exploring Human Genetics679With the
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Exploring Human Genetics681remainde
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Exploring Human Genetics683prevalen
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Exploring Human Genetics685Such lin
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Essential Concepts687and function a
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Questions689C. Genotype and phenoty
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CHAPTER TWENTY20Cell Communities: T
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Extracellular Matrix and Connective
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ECB5 e20.11-20.11Extracellular Matr
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Epithelial Sheets and Cell Junction
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Stem Cells and Tissue Renewal709cyt
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Stem Cells and Tissue Renewal711epi
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Stem Cells and Tissue Renewal713LUM
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Stem Cells and Tissue Renewal715SEL
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Stem Cells and Tissue Renewal717reg
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Cancer719normal epithelial cellprim
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Cancer721Figure 20−43 Cancer inci
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Cancer7232. Cancer cells can surviv
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Cancer725(B)(A)loss-of-function mut
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Cancer727(A)Figure 20-50 Colorectal
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Essential Concepts729Figure 20-53 A
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731It turns out that APC regulates
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Questions733KEY TERMSadherens junct
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AnswersChapter 1ANSWER 1-1 Trying t
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Answers A:3proteins, nucleic acids,
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Answers A:5B. The volume of the pag
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Answers A:7X YYYY Zenzyme lowers th
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Answers A:9ANSWER 3-16A. From Table
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Answers A:11on its surface; however
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Answers A:13rate (µmole/min)210 5
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Answers A:15transcriptionally inact
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Answers A:17HNNadenineNNHNH 2NH 2NO
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Answers A:19(A) NORMALsplicing173 b
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Answers A:21Figure A8-2minor groove
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5′ 3′3′Answers A:23proliferat
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Answers A:25that its function is ve
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Answers A:27additional fragments ge
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Answers A:29slightly water-soluble,
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Answers A:311 2 3 4OUTSIDEFigure A1
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Answers A:33ANSWER 12-21 The membra
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Answers A:35STEP1STEP2STEP3STEP4COO
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Answers A:37in their reduced form.
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Answers A:39D. Prokaryotic cells do
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Answers A:41cells that evolved. New
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Answers A:43ANSWER 16-14 Activation
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Answers A:45becomes localized by bi
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Answers A:47ANSWER 18-3 For multice
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Answers A:49overlapping interpolar
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Answers A:51large amounts of alcoho
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Answers A:53chromosome during a mei
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Answers A:55ANSWER 20-9A. False. Ga
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Glossaryacetyl CoAActivated carrier
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Glossary G:3Ca 2+ /calmodulin-depen
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Glossary G:5cyclic AMPSmall intrace
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Glossary G:7a chain of enzymatic re
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Glossary G:9homologousDescribes gen
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Glossary G:11membrane of a cell or
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Glossary G:13oxidative phosphorylat
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Glossary G:15as a molecular marker
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Glossary G:17stromaIn a chloroplast
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IndexNote: The index covers the tex
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IndexI:3BB lymphocytes/B cells 140F
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IndexI:5internal membranes 19, 365-
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IndexI:7cultured cell types 285cult
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IndexI:9endosomes 497-500, 507, 511
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IndexI:11familial hypertrophiccardi
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IndexI:13integrases 319integrinsin
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IndexI:15mitochondrial DNA 17, 245,
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IndexI:17oxaloacetate 110F, 142, 43
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IndexI:19pyrophosphate (PP i) 111,
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IndexI:21spindle poles 627F, 629F,
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IndexI:23water-splitting enzyme (ph
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