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MEDIA GUIDE

FOURTH EDITION

ESSENTIAL
CELL BIOLOGY
Bruce Alberts
Dennis Bray
Karen Hopkin
Alexander Johnson
Julian Lewis
Martin Raff
Keith Roberts
Peter Walter

The teaching and learning resources for instructors and students are
available online. The instructors resources are password protected and
available only to qualified instructors. The student resources are available to everyone. The resources can be accessed from:
t*OTUSVDUPSTXXXHBSMBOETDJFODFDPNJOTUSVDUPST
t4UVEFOUTXXXHBSMBOETDJFODFDPN&$#TUVEFOUT

INSTRUCTOR RESOURCES
www.garlandscience.com/instructors

The Art of Essential Cell Biology, Fourth Edition


5IFJNBHFTGSPNUIFCPPLBSFBWBJMBCMFJOCPUI1PXFS1PJOUBOE+1&(GPSmats. The images have been optimized for displayed on a computer. The
search feature on the website allows the figures to be searched by figure
name, figure number, or by keywords in the figure legend from the book.

Figure-Integrated Lecture Outlines


For instructors who would like a head start creating lectures for their
courses, the section headings, concept headings, and figures from the text
have been integrated into PowerPoint presentations.

Animations and Videos


There are over 130 animations and videos available to both students and
JOTUSVDUPST5IFZBSFBWBJMBCMFPOUIF*OTUSVDUPST3FTPVSDFTJUFJOUXPGPSmats: WMV and QuickTime. The WMV-formatted movies may be used by
instructors who wish to integrate the movies into PowerPoint presentations on Windows computers; the QuickTime formatted movies may be
used in PowerPoint for Apple computers, or in Keynote presentations.
The movies can easily be downloaded to your computer using the download button on the movie preview page.

Question Bank
The question bank, written by Linda Huang, University of Massachusetts,
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formats. These formats include multiple choice, fill-in-the-blank, true-false,
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approximately 60-70 questions, a number of which will be suitable for use
with personal response systems (that is, clickers). The text of the question
bank is available in Microsoft Word format. The question bank is also
available pre-loaded into computerized test-generation software. The test
generation software can also be used to upload the contents of the question bank into a learning management system.

References
5IFi3FGFSFODFTwBSFBSJDIDPMMFDUJPOPGKPVSOBMBOESFWJFXBSUJDMFTGPSSFGerence and suggested reading assignments. They have been adapted from
the detailed references of Molecular Biology of the Cell and organized by the
table of contents for Essential Cell Biology. 5IFi3FGFSFODFTw1%'EPDVNFOU
is available on both the instructor and student websites.

Medical Topics Guide


This document highlights medically relevant topics covered throughout the
book, and will be particularly useful for instructors with a large number of
premedical, health science, or nursing students.

Blackboard and LMS Integration


The movies, book images, and student assessments that accompany
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UIBUGBDJMJUBUFTCVMLVQMPBEJOHPGUFYUCPPLSFTPVSDFTJOUP#MBDLCPBSEBOE
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PCUBJOFEPOB%7%GSPNZPVSTBMFTSFQSFTFOUBUJWFPSCZFNBJMJOHTDJFODF!
garland.com.

STUDENT RESOURCES

www.garlandscience.com/ECB4-students

Animations and Videos


There are 130+ movies that cover a broad range of cell biology topics.
The movies review key concepts from the book and illuminate the cellular microcosm.

Student Self-Assessments
The website contains a variety of tools designed to help students assess
their understanding of the material covered in the book:
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comprehension.
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number of animations and respond to specific questions about the
concepts and molecular details..
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available in the book.
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of conceptual understanding or to think from an experimental
perspective.

Cell Explorer
This application contains interactive micrographs that highlight important cellular structures.

Flashcards
The key terms presented at the end of each chapter can be reviewed
using the flashcards application.

Glossary
The complete glossary from the book is available on the website; terms
in the glossary can be searched or the entire glossary can be browsed.

References
A set of references is available for each chapter for further reading and
exploration.

Adobe and Acrobat are either registered trademarks or trademarks of Adobe


Systems Incorporated in the United States and/or other countries.
PowerPoint and Windows are trademarks of Microsoft Corporation in the United
States and/or other countries.
Mac OS X , QuickTime, and iPod are registered trademarks of Apple Inc.

ESSENTIAL CELL BIOLOGY WEBSITE VIEWING GUIDE

INTRODUCTION
The Essential Cell Biology Student Website
www.garlandscience.com/ECB4-students

As never before, new imaging and computer technologies have increased


our access to the inner workings of living cells. We have tried to capture
some of the excitement of these advances on the Essential Cell Biology
website. The site contains over one hundred and fifty video clips, animations, molecular structures, and high-resolution micrographsall
designed to complement the material in the individual book chapters.
Nearly all items are accompanied by a short narration that introduces
and explains key concepts. Our intent is to provide students and instructors with an opportunity to observe living cells and molecules in action,
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dynamics of the cellular and molecular world.
One cannot watch cells crawling, dividing, segregating their chromosomes, or rearranging their surface without a sense of wonder at the
molecular mechanisms that underlie these processes. We hope that the
Essential Cell Biology website will motivate and intrigue students while
reinforcing basic concepts covered in the text, and thereby will make the
learning of cell biology both easier and more rewarding. We also hope
that instructors can use these visual resources in the classroom to illuminate, not only the course material, but also the beauty and wonder
of this microcosm. We designed animations to bring to life some of the
more complicated figures in the book. Many of the videos provide visual demonstrations of topics that can be difficult to appreciate, such as
membrane fluidity, and the high-resolution micrographs allow students
to explore some magnificent cell images in detail. We have also created
three-dimensional models of some of the most interesting molecules,
presented in short tutorials.
The contents of the Essential Cell Biology website represent the work of
numerous laboratories around the world that provided video clips from
original research, animation segments, micrographs, and molecular
data. We are deeply indebted to the scientists who generously made this
material available to us.

Using the Movie Callouts


5IF UFYU PG &TTFOUJBM $FMM #JPMPHZ  'PVSUI &EJUJPO DPOUBJOT iNPWJF DBMMouts that directly link the content of the book to movies on the Essential
Cell Biology website. The movie callouts are integrated throughout the
book to indicate when relevant movies are available on the Essential
Cell Biology website. The callouts are similar to the callouts for figures
in the text, except that they indicate a particular movie is available. The
movie callouts and figure callouts are in different colors and are easy to
distinguish.
The website contains a field where you can enter the movie number
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field, that particular movie will play. You can also browse all the media by
chapter, but we hope this feature will allow students to easily integrate
the media resources on the website into study with the book.

ECB4 WEBSITE TABLE OF CONTENTS


Chapter 1








1.9











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Chlamydomonas
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Chapter 2

2.2
2.3







Energy, Catalysis, and Biosynthesis

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Chapter 4












Chemical Components of Cells

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Chapter 3








The Fundamental Units of Life

Protein Structure and Function

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11




















18

18
18







21








24












6










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Chapter 5 DNA and Chromosomes

33





















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Chapter 6 DNA Replication, Repair, and Recombination

36







6.7













39







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Chapter 7 From DNA to Protein: How Cells Read the Genome

42





































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Chapter 8 Control of Gene Expression

49



















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Chapter 9 How Genes and Genomes Evolve

52















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Chapter 10 Modern Recombinant DNA Technology

54

















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Chapter 11 Membrane Structure

57

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60







Chapter 12 Transport Across Cell Membranes

63

12.1
12.2





12.8

12.10

63






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68

Aquaporins
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12.12 Neuronal Pathfinding
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Chapter 13 How Cells Obtain Energy From Food

72



















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Chapter 14 Energy Generation in Mitochondria and Chloroplasts 78


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Chapter 15 Intracellular Compartments and Protein Transport

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Chapter 16 Cell Signaling

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Chapter 17 Cytoskeleton
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17.11 Listeria Parasites
17.12 Heart Tissue
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Chapter 18 The Cell-Division Cycle


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18.8 Mitosis
18.9 Apoptosis
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100


101

102
102



105
105
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110







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Chapter 19 Sexual Reproduction and the Power of Genetics


19.1






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116
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Chapter 20 Cell Communities: Tissues, Stem Cells, and Cancer 119


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11

1.1

Developing Egg Cells

This frog egg cell has been fertilized and starts dividing. The first cell
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same time divide and develop in almost perfect synchrony.
After a day or two, embryonic development is completed and tadpoles
hatch from the eggs.

From "From Egg to Tadpole"


Jeremy Pickett-Heaps and Julianne
Pickett-Heaps
Cytographics (www.cytographics.com)

1.2

Keratocyte Dance

Keratocytes, found on the scales of fish, are specialized for very rapid
motility in order to heal scratches.
Video editing and concept: Justin Reichman
Music: Freudenhaus Audio Productions (www.fapsf.com)

Mark S. Cooper
University of Washington

1.3

Crawling Amoeba

This single-celled amoeba crawls around by using actin polymerization


to push out pseudopods, or false feet, to explore new territory. At the
same time, organelles move in complex patterns within the cell.
Reproduced by copyright permission of CELLS alive!, CDROM and Video Library,
19982001.

CELLS alive!
www.cellsalive.com

12

1.4

Cytoplasmic Streaming

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mitochondria move in a constant stream along cytoskeletal tracks.
Although the complex network of the cytoskeleton cannot be seen, a
few of the cytoskeletal tracks are visible.
This circulation of the cytosol and organelles within the cell is called
cytoplasmic streaming. The rate of streaming is affected by exposure to
light, temperature, and pH.
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many of the cells.

1.5

Kristina Yu Exploratorium
www.exploratorium.edu

Cytoplasmic Crowding

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concentrated in the lightly stained region.
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electron microscopy cannot clearly resolve the individual molecules in
a densely packed cell, nor show them in motion, computer simulations
have been developed to visualize the molecular environment.
Zooming in to a small portion of the cytoplasm, this computer
simulation shows 50 different types of the most abundant
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with one another, and are swept to and fro by random thermal motion.
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bump into other molecules. The larger molecules stay in place relative
to the smaller ones, but continuously move as they are pushed around
and interact with other molecules in this densely packed microcosm.
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motion in the cytoplasm; in real time, it would be impossible to follow
the slowed-down movements shown here.
The empty spaces in this environment are filled by water molecules
which were omitted from the simulation.

Adrian Elcock
University of Iowa Carver College of Medicine

13

1.6

Swimming Eutreptiella

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flagellate, which uses both flagella and pronounced cell shape changes
to swim.

Richard E. Triemer
Rutgers, State University of New Jersey

1.7

Beating Heart Cell

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the cell contracts, it pulls on the substratum which becomes wrinkled.
Although individual heart cells can beat with their own rhythms, they
are coordinated in an intact heart so that all cells beat synchronously.
Reproduced from: CELLebration, 1995, edited by Rachel Fink, produced and
distributed by Sinauer Associates, Inc., by copyright permission of Barbara Danowski.
Barbara Danowski
Union College
Kyoko Imanaka-Yoshida
Mie University
Jean Sanger and Joseph Sanger
University of Pennsylvania School of
Medicine

1.8

Plant Cells

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Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

14

1.9

Chlamydomonas

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The University of Lethbridge, Canada

1.10

Liver Cell: View 1

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Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

1.11

Liver Cell: View 2

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reticulum

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Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

15

1.12

Liver Cell: View 3

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Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

1.13

Liver Cell: View 4

4IPXNF


t (PMHJBQQBSBUVT

t QMBTNBNFNCSBOFT

t MZTPTPNF

t NJUPDIPOESJB

Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

1.14

Liver Cell: View 5

4IPXNF


t OVDMFBSFOWFMPQF

t OVDMFBSQPSFDPNQMFY

t SJCPTPNFTCPVOEUPPVUFSOVDMFBSNFNCSBOF

t SPVHIFOEPQMBTNJDSFUJDVMVN

Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

16

1.15

Quiz: Chapter 1

*OXIBUXBZBSFBMMDFMMTBMJLF


t 5IFZBSFSPVOEJOTIBQF

t 5IFZBSFBCPVUBUFOUIPGBNJMMJNFUFSJOEJBNFUFS

t 5IFZTUPSFUIFJSHFOFUJDJOTUSVDUJPOTJO%/"

t 5IFZSFRVJSF%/"UPMJWF

1.16

Concept Questions: Chapter 1

&VLBSZPUJDDFMMTDPOUBJONVMUJQMFNFNCSBOFFODMPTFEPSHBOFMMFT)PX
NJHIUIBWFUIJTBSSBOHFNFOUFWPMWFE 8IBUFWJEFODFTVQQPSUTZPVS
UIFPSZ
One theory is that an ancestral eukaryotic cell was a predator that fed
by capturing other cells...

1.17

Challenge Question: Chapter 1

/"4"IBTBTLFEZPVUPEFTJHOBNPEVMFUIBUXJMMJEFOUJGZTJHOTPGMJGFPO
.BST8IBUXJMMZPVSNPEVMFMPPLGPS
4VDINPEVMFTBSFHFOFSBMMZEFTJHOFEUPMPPLGPSPSHBOJDNPMFDVMFT
characteristic of life. The first Mars probe analyzed soil samples...

Image courtesy of Ira Herskowitz and


Eric Schabatach.

17

1.18

Flashcards: Chapter 1

archaea


t

POFPGUIFUXPEJWJTJPOTPGQSPLBSZPUFT PGUFOGPVOEJOIPTUJMF
environments such as hot springs or concentrated brine. (See
also bacteria.)

bacteria (singular bacterium)




t

1.19

POFPGUIFUXPEJWJTJPOTPGQSPLBSZPUFTTPNFTQFDJFTDBVTF
disease.

References: Chapter 1

"OEFSTTPO4(& 
5IFCBDUFSJBMXPSMEHFUTTNBMMFSScience
o
#SFOOFS4 +BDPC'.FTFMTPO. 
"OVOTUBCMFJOUFSNFEJBUF
carrying information from genes to ribosomes for protein synthesis.
Nature 190:576581.

KEY TERMS
archaeon
bacterium
cell
chloroplast
chromosome
cytoplasm
cytoskeleton

18

2.1

Glucose

A glucose molecule is a six carbon sugar, consisting of a total of


BUPNT
*UJTWFSZQPMBSEVFUPJUTIZESPYZMHSPVQTUPXIJDIXBUFSNPMFDVMFTDBO
hydrogen bond.
#ZDPOWFOUJPO DBSCPOBUPNTBSFTIPXOJOHSBZ PYZHFOJOSFEBOE
hydrogen in white.

2.2

Palmitic Acid

This molecule of palmitic acid contains a long tail of 16 carbons bonded


UPIZESPHFOBUPNT*UJTUIJTIZESPDBSCPOUBJMUIBUHJWFTUIFNPMFDVMFJUT
overall hydrophobic character.
*ODPOUSBTU UIFPYZHFODPOUBJOJOHDBSCPYZMHSPVQPOUIFPUIFSFOEJT
very polar.

2.3

ATP

ATP molecules store and supply energy for cellular processes. An ATP
molecule contains three building blocks: the flat purine ring system
containing multiple nitrogen atoms shown in blue, the ribose sugar in
the middle, and the three phosphate groups with the phosphorus atoms
shown in yellow.

19

2.4

Noncovalent Interactions

Molecules in solution undergo random thermal movements and may


encounter each other frequently if the concentration is sufficiently high.
*GUXPNPMFDVMFTXJUIQPPSMZNBUDIFETVSGBDFTDPMMJEF POMZBGFXXFBL
bonds will form between them. Thermal motion of the molecules rapidly
breaks these bonds apart, and the molecules separate.
*GUIFTVSGBDFTPGUXPNPMFDVMFTBSFXFMMNBUDIFE NBOZXFBLCPOET
will form between the two. The bonds hold the molecules together for a
MPOHUJNFCFGPSFUIFSNBMKPMUJOHUFBSTUIFNBQBSU
Tightly bound molecules will spend most of their time associated
although they will go through cycles of association and dissociation.
The affinity of the two molecules for one another is a measure of the
relative time they spend bound together.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

2.5

Quiz: Chapter 2

1. What is the smallest particle of an element that still retains its


EJTUJODUJWFDIFNJDBMQSPQFSUJFT


t 1SPUPO

t "UPN

t .PMFDVMFT

2.6

Concept Questions: Chapter 2

%FTDSJCFUIFLFZGFBUVSFTPGUIFGPMMPXJOHDIFNJDBMJOUFSBDUJPOTJPOJD
bonds, covalent bonds, hydrogen bonds, van der Waals attractions,
FMFDUSPTUBUJDBUUSBDUJPOT8IJDIBSFUIFTUSPOHFTU
*POJDCPOETBSFGPSNFEXIFOFMFDUSPOTBSFEPOBUFECZPOFBUPNUP
another.

20

2.7

Challenge Questions: Chapter 2

5IFNPMFDVMBSXFJHIUPGFUIBOPM $)3$)20)
JTBOEJUTEFOTJUZJT
HDN3.



A. How many 12-oz (355-mL) bottles of 5% beer could a 70-kg


QFSTPOESJOLBOESFNBJOVOEFSUIFMFHBMMJNJU "LHQFSTPO
DPOUBJOTBCPVUMJUFSTPGXBUFS*HOPSFUIFNFUBCPMJTNPG
ethanol, and assume...

2.8

Flashcards: Chapter 2

acid


t

BNPMFDVMFUIBUSFMFBTFTBQSPUPOXIFOEJTTPMWFEJOXBUFSUIJT
dissociation generates hydronium (H3O+) ions, thereby
lowering the pH.

amino acid


2.9

t

TNBMMPSHBOJDNPMFDVMFDPOUBJOJOHCPUIBOBNJOPHSPVQBOEB
carboxyl...

References: Chapter 2

"CFMFT3) 'SFZ1"+FODLT81 


#JPDIFNJTUSZ#PTUPO+POFT
#BSUMFUU
Atkins PW (1996) Molecules. New York: WH Freeman.

KEY TERMS
acid
amino acid
atom
atomic weight
ATP
Avogadros number
base

21

3.1

Analogy of Enzyme Catalysis

&OWJTJPOBNPMFDVMF IFSFTZNCPMJ[FECZUIFCBMM UIBU JOQSJODJQMF DBO


react in four different ways.
To undergo any of these reactions, the molecule must overcome an
activation energy barrier that is of a characteristic height for each of the
possible reactions.
This can be achieved, for example, by putting more energy into the
TZTUFN TVDIBTXIFOIFBUJTBEEFE*OUIFFYBNQMFTIPXOIFSF UIF
molecule will enter many different reaction paths by overcoming similar
activation energy barriers.
An enzyme, in contrast, reduces the activation energy barrier of only
one specific reaction path. An enzyme therefore allows reactions to
proceed at normal temperatures and directs them into one desired
pathway.

3.2

Random Walk

%SJWFOCZUIFSNBMFOFSHZ NPMFDVMFTBSFDPOTUBOUMZJONPUJPO XIJDI


allows them to diffuse through cells in a random walk. Our simulation
shows the degree to which a small sugar molecule on the left and a
larger protein on the right explore the interior space of a cell, here
shown as a cube with a 10 micrometer side. The animation represents
one second in real time.
Note that the paths of the molecules in the second simulation are
different from those in the first, thus showing the randomness of this
motion.
Final composition: Blink Studio Ltd. (www.blink.uk.com)

3.3

Quiz: Chapter 3

8IBUJTUIFNFBTVSFPGEJTPSEFSJOBTZTUFNDBMMFE


t 'SFFFOFSHZ

t &OUSPQZ

t &OUIBMQZ

22

3.4

Concept Questions: Chapter 3

8IBUJTUIFEJGGFSFODFCFUXFFODBUBCPMJTNBOEBOBCPMJTN (JWFBO
example of each.
$BUBCPMJDQBUIXBZTCSFBLEPXOGPPETUVGGTJOUPTNBMMFSNPMFDVMFTUP
generate energy for the cell; anabolic pathways use energy to drive the
synthesis of

3.5

Challenge Question: Chapter 3

The organic chemistry of living cells is said to be special for two


reasons: it occurs in an aqueous environment and it accomplishes some
WFSZDPNQMFYSFBDUJPOT#VUEPZPVTVQQPTFJUJTSFBMMZBMMUIBUNVDI
different from the organic chemistry carried out in the top laboratories
JOUIFXPSME 8IZPSXIZOPU

3.6

Flashcards: Chapter 3

BDFUZM$P" BDFUZMDPFO[ZNF"

t

BDUJWBUFEDBSSJFSUIBUEPOBUFTUIFDBSCPOBUPNTJOJUTSFBEJMZ
transferable acetyl group to many metabolic reactions,
including the citric acid cycle and fatty acid biosynthesis; the
BDFUZMHSPVQJTMJOLFEUPDPFO[ZNF" $P"


KEY TERMS
acetyl CoA
activated carrier
activation energy
ADP, ATP
anabolism
biosynthesis
catabolism

23

3.7

References: Chapter 3

"ULJOT18 
5IF4FDPOE-BX&OFSHZ $IBPTBOE'PSN/FX:PSL
4DJFOUJmD"NFSJDBO#PPLT
"ULJOT18%F1BVMB+% 
1IZTJDBM$IFNJTUSZGPSUIF-JGF
4DJFODFT0YGPSE0YGPSE6OJWFSTJUZ1SFTT

24

4.1

Viewing Proteins: SH2

Protein structures can be displayed in many different ways. A small


QSPUFJOEPNBJO DBMMFEUIF4)EPNBJO JTVTFEIFSFUPEFNPOTUSBUF
the different ways in which a protein structure can be displayed. The
backbone view shows the path of the polypeptide chain. The chain is
DPMPSFECMVFBUJUT$UFSNJOVT
The ribbons view accents helices and sheets. These secondary
structure elements determine the fold of most polypeptide chains.
TUSBOETBSFTIPXOBTBSSPXTQPJOUJOHGSPNUIF/UPUIF$UFSNJOVT 
and helices are shown as twisted cylinders.
*OBwireframe presentation, the covalent bonds between all of the
atoms in the polypeptide are shown as sticks.

PDB ID number *: 1SHA

A spacefill view depicts each atom in the polypeptide as a solid sphere.


The radius of the sphere represents the van der Waals radius of the
atom. The coloring scheme follows the same rainbow spectrum used
CFGPSFXJUIUIF/UFSNJOVTSFEBOEUIF$UFSNJOVTCMVF
*OUIJTTQBDFmMMWJFXEJGGFSFOUBUPNTJOUIFQPMZQFQUJEFDIBJOBSFDPMPSFE
BDDPSEJOHUPFMFNFOU#ZDPOWFOUJPO DBSCPOJTDPMPSFEHSBZ OJUSPHFO
blue, oxygen red, and sulfur yellow.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

4.2

Helix

The helix is one of the most common secondary structures in


QSPUFJOT"NJOPBDJETJEFDIBJOTQSPKFDUPVUXBSETGSPNUIFQPMZQFQUJEF
backbone that forms the core of the helix. The chain is stabilized in this
conformation by hydrogen bonds between the backbone amino group
of one amino acid and the backbone carbonyl group of another amino
acid that is four positions away. These interactions do not involve side
chains. Thus many different sequences can adopt an helical structure.
helices are regular cylindrical structures. One full turn occurs every
3.6 residues and extends the length of the helix by approximately
0.5 nm.
4FDPOEBSZTUSVDUVSFTBSFPGUFOSFQSFTFOUFEJODBSUPPOGPSNUPDMBSJGZUIF
VOEFSMZJOHTUSVDUVSFPGBQSPUFJO*OUIJTSFQSFTFOUBUJPO UIFUXJTUFE%
ribbon follows the path of the peptide backbone.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)
Source: Glactone (www.chemistry.gsu.edu/glactone)

PDB ID source: Glactone

25

4.3

Coiled-Coil

*OBUZQJDBMDPJMFEDPJMUXP helices wrap around each other to form a


stable structure. One side of each helix contains mostly aliphatic amino
acids, such as leucines and valines, while the other side contains mostly
polar residues. Helices containing distinct hydrophobic and polar sides
BSFDBMMFEBNQIJQBUIJD*OBDPJMFEDPJM UXPBNQIJQBUIJDIFMJDFTBSF
aligned so their hydrophobic sides snuggle tightly together in the center,
with their polar faces exposed to the solvent.
A triple coiled-coil is another stable structure formed by IFMJDFT*O
this case, three amphipathic helices twist around a central axis. The
hydrophobic sides of all three helices face the center of the coil, creating
a stable hydrophobic core.
$PJMFEDPJMTBSFPGUFOGPVOEJOFMPOHBUFE mCSPVTQSPUFJOT"USJQMF
DPJMFEDPJMJTUIFNBKPSTUSVDUVSBMUIFNFJOmCSJOPHFO BQSPUFJOJOWPMWFE
in blood clotting. The fibrous nature of this protein is intimately related
to its ability to form clots.

PDB ID number *: GCN4 leucine zipper


(2ZTA); Trimeric coiled-coil domain of
chicken cartilage matrix protein (1AQ5);
Native chicken fibrinogen (1EI3)

Molecular modelling and animation: Timothy Driscoll, Molvisions


Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

4.4

Sheet

The TIFFUJTBOPUIFSDPNNPOTFDPOEBSZTUSVDUVSF*ODPOUSBTUUP
an helix, it is formed by hydrogen bonds between backbone atoms
POBEKBDFOUSFHJPOTPGUIFQFQUJEFCBDLCPOF DBMMFE strands. These
interactions do not involve side chains. Thus, many different sequences
can form a sheet.
A sheet is a regular and rigid structure often represented as a series of
nBUUFOFEBSSPXT&BDIBSSPXQPJOUTUPXBSETUIFQSPUFJOT$UFSNJOVT*O
the example shown here the two middle strands run parallelthat is, in
the same directionwhereas the peripheral strands are antiparallel.
The amino acid side chains from each strand alternately extend
above and below the sheet, thereby allowing each side to have
distinct properties from the other. sheets are usually twisted and not
completely flat.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

PDB ID number *: 1PGB

26

4.5

Oligomeric Proteins

Many proteins are composed of multiple polypeptide chains, or


TVCVOJUT5IF$SPSFQSFTTPS GPSFYBNQMF JTBIPNPEJNFSGPSNFEPGUXP
JEFOUJDBMTVCVOJUT5IFTVCVOJUTKPJOJOBIFBEUPIFBEGBTIJPOBTUXP
small sheetsone from each subunitzipper up and form a larger
sheet.
The enzyme neuraminidase is composed of four identical subunits
BSSBOHFEJOBTRVBSF&BDIQBJSPGUXPTVCVOJUTJTIFMEUPHFUIFSJOIFBE
to-tail fashion, by repeated use of the same binding interaction. This
becomes clear when the polypeptide chains are colored in a rainbow
pattern, so that the same regions of each subunit have the same colors.
All subunits adhere to each other through contacts between the orange
and light-blue regions.
)FNPHMPCJOJTBUFUSBNFSJDQSPUFJOUIBUUSBOTQPSUTPYZHFO*UJT
composed of two subunits and two closely related subunits. Oxygen
CJOETUPIFNFHSPVQTJOUIFQSPUFJO XIJDIBSFTIPXOJOSFE&BDI
subunit can sense whether neighboring subunits contain bound oxygen.
The protein subunits therefore communicate with one another through
the interfaces that hold them together.

PDB ID number *: Cro repressor protein


from bacteriophage lambda (5CRO);
Neuraminidase of influenza virus (1NN2);
Deoxy human hemoglobin (1A3N); p53
tetramerization domain (1C26)

The tumor suppressor protein p53 is a tetramer of four identical


TVCVOJUT&BDIQTVCVOJUDPOUBJOTBTJNQMFUFUSBNFSJ[BUJPOEPNBJO
composed of a single strand connected to an helix. The tetrameric
form of p53 assembles as a dimer of dimers. Two copies of p53 interact
via strands, forming a twostranded sheet. Two such dimers interact
via their helices to form the tetrameric assembly.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

4.6

Disulfide Bonds

%JTVMmEFCPOETTUBCJMJ[FUIFTUSVDUVSFPGNBOZQSPUFJOTCZGPSNJOH
JOUSBNPMFDVMBSCSJEHFT*OUIJTFYBNQMF mWFEJTVMmEFCPOETi[JQVQw
the center of a protease inhibitor. Most extracellular proteins contain
disulfide bonds.
%JTVMmEFCPOETBSFGPSNFECZPYJEBUJPOPGUXPDZTUFJOFSFTJEVFT
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)
PDB ID number *: 1BI6

27

4.7

Antibodies

"OUJCPEJFTPGUIFJNNVOPHMPCVMJO(DMBTTBSF:TIBQFEHMZDPQSPUFJOT
that circulate in the blood stream. They bind to and inactivate foreign
NPMFDVMFTUIFBOUJHFOTBOENBSLUIFNGPSEFTUSVDUJPO&BDI*H(
molecule consists of two light chains and two heavy chains. The heavy
chains have carbohydrates attached. The regions of the antibody that
bind to antigens are located at the very tips of the two arms.
&BDIBSNPGUIFBOUJCPEZJTDPNQPTFEPGGPVSEPNBJOT5XPBSFDBMMFE
the variable domains, contributed by the heavy and light chains, and
hence called VH and VL. The variable domains are attached to two
constant domains, again one each from the heavy and light chains, and
IFODFDBMMFE$HBOE$L.
Variable and constant domains share a similar structure, called the
*HGPME&BDIEPNBJODPOTJTUTPGBQBJSPGCFUBTIFFUT POFXJUIUISFF
strands and one with five. A single covalent disulfide bridge holds the
two sheets together, which results in a rigid and very stable domain.
As their name implies, the variable domains vary in amino acid
sequence from one antibody molecule to another, thus providing the
vast diversity in structure required by the immune system. The antigen
binding site in the variable domains is composed of hypervariable
MPPQTUIBUBSFFTQFDJBMMZTVTDFQUJCMFUPTFRVFODFWBSJBUJPOT4FRVFODF
variations in the hypervariable loops are responsible for the specificity
of antibodies to particular antigens.
Antigens bind to the tip of each antibody arm, generally two molecules
QFSBOUJCPEZ*OUIFFYBNQMFTIPXOIFSF UIFBOUJHFOCJOETUPUIF
antibody via a large contact surface, providing a tight and highly specific
association.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

4.8

Lysozyme Reaction

The lysozyme enzyme cleaves polysaccharide chains. First, the enzyme


and substrate associate, forming an enzyme-substrate complex. The
enzyme catalyzes a hydrolysis reaction that cleaves the substrate into
products, which are quickly released, allowing the enzyme to catalyze
another reaction.
The cleft in the enzyme holds six sugar residues of a polysaccharide.
The hydrolysis reaction occurs between residues.
Looking at the details of the reaction in solution, the sugar residues
adopt their most stable three-dimensional conformation. However,
after the polysaccharide enters into the enzymesubstrate complex, the
enzyme forces the sugar shown on the left into a strained conformation
that more closely resembles the transition state of the reaction.
Two amino acids within the enzyme facilitate the reaction. A glutamic
acid donates a proton to sugar on the right and an aspartic acid attacks
UIF$DBSCPOBUPNPGUIFTVHBSPOUIFMFGU5IFBUUBDLPOUIF$DBSCPO
results in a transient covalent bond between the sugar and the amino
acid, and hydrolysis of the sugar-sugar bond

PDB ID number *: Compilation of


immunoglobin G1 & immunoglobin Fc and
fragment B of Protein A complex (2IG2 &
1FC2); FabD1.3-lysozyme complex (1FDL)

28
The deprotonated glutamic acid then polarizes a water molecule,
drawing a proton away from it. This allows the water oxygen to attack
UIF$DBSCPO CSFBLJOHUIFTVHBSBTQBSUBUFCPOE
*OUIJTXBZ UIFUXPBNJOPBDJETBSFSFUVSOFEUPUIFJSPSJHJOBMTUBUFT 
forming the enzyme-product complex. The enzyme and products
dissociate.
Storyboard and Animation: Sumanas, Inc., (www.sumanasinc.com)

4.9

Lysozyme Structure

Lysozyme is a small enzyme that binds to polysaccharide chains and


CSFBLTUIFNBQBSUCZIZESPMZTJT*UIBTUXPTUSVDUVSBMEPNBJOT0OF
domain is composed mostly of helices, while the other domain is
composed mostly of strands. The interface between the two domains
forms a cleft in which the substrate binds. The structure shown here
contains one of the products of the hydrolysis reaction.
Lysozyme acts as a catalyst by adding a molecule of water to the bond
between two sugars, breaking the bond. This reaction is catalyzed by
two strategically positioned amino acid side chains in the enzymes
active site: glutamate 35 and aspartate 52. The highlighted group on the
reaction product shown here would have formed the bond cleaved in
the reaction.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

4.10

EF-Tu

&MPOHBUJPOGBDUPS5VIBTUISFFEPNBJOT XIJDIBSFDPNQBDUMZBSSBOHFE
JOJUT(51CPVOETUBUF)FSFXFTIPXUIFTVSGBDFPGUIFQSPUFJOXJUI
each of its domains in a different color.
3FHJPOTPGBMMUISFFQSPUFJOEPNBJOTDPOUSJCVUFUPUIFU3/"CJOEJOHTJUF
An important dynamic element in the structure of elongation factor Tu
is the switch helix.
"T(51JTIZESPMZ[FEBOEUIFHBNNBQIPTQIBUFJTSFMFBTFE UIFTXJUDI
helix rearranges.
5IJTJOUVSOMFBETUPBNBKPSTUSVDUVSBMSFBSSBOHFNFOUPGUIFUISFF
QSPUFJOEPNBJOT XIJDIEJTSVQUTUIFU3/"CJOEJOHTJUF
5IVTVQPO(51IZESPMZTJT UIFU3/"JTSFMFBTFEGSPNFMPOHBUJPOGBDUPS
Tu.
Animation: Graham Johnson, Fivth Element (www.fivth.com)

PDB ID number *: 1LSZ

29

4.11

The Safe Crackers

*OEJWJEVBMQSPUFJOTPGUFODPMMBCPSBUFBTTVCVOJUTPGMBSHFQSPUFJO
assemblies,
in which their individual activities may be coordinated.
&OFSHFUJDBMMZGBWPSBCMFDIBOHFTJOTVCTUSBUFTCPVOEUPPOFPSNPSF
subunits,
such as the hydrolysis of ATP, lead to orderly movements throughout the
protein complex that accomplish a specific task.

Original illustrations and storyboard:


Nigel Orme and Christopher Thorpe

4.12

Sickle Cell Anemia

4JDLMFDFMMBOFNJBJTBHFOFUJDEJTFBTFUIBUBGGFDUTIFNPHMPCJO UIF
oxygen transport molecule in the blood. The disease gets its name from
UIFTIBQFPGUIFSFECMPPEDFMMTVOEFSMPXPYZHFODPOEJUJPOT4PNFSFE
blood cells become sickle-shaped and these elongated cells get stuck in
small blood vessels so that parts of the body dont get the oxygen they
OFFE4JDLMFDFMMBOFNJBJTDBVTFECZBTJOHMFMFUUFSDIBOHFJOUIF%/"
This in turn alters one of the amino acids in the hemoglobin protein.
Valine sits in a position where glutamic acid should be. The valine
makes the hemoglobin molecules stick together when oxygen tension is
low, forming long fibers that distort the shape of the red blood cells, and
this brings on an attack.
Animation produced for DNA Interactive (www.dnai.org) 2003 Howard Hughes
Medical Institute (www.hhmi.org) All rights reserved.

4.13 Anatomy of a PDB File


Three dimensional structures of macromoleculesthat have been
EFUFSNJOFECZ/.3PSYSBZDSZTUBMMPHSBQIZBSFBSDIJWFEJOQSPUFJO
EBUBCBTFmMFT PS1%#mMFTGPSTIPSU
&BDI1%#mMFCFHJOTXJUIBEFTDSJQUJPOPGUIFNPMFDVMF DSFEJUTUP
the authors who solved the structure and experimental details of the
analysis. Next, the file lists the amino acid sequence of the protein.
5IFIFBSUPGUIF1%#mMFEFmOFTUIFQSFDJTFQPTJUJPOPGFBDIBUPNPGUIF
TUSVDUVSFJOUISFFEJNFOTJPOBMTQBDF&BDIBUPNJTEFTDSJCFEJO
a separate line. The first few columns define the atom as part of a
particular amino acid in the sequence. The later columns list a set of
x, y, and z coordinates that precisely locate the atom in the structure.
1SPHSBNTTVDIBT3BTNPMPS$IJNF VTFEPOUIJT$% EJSFDUMZSFBE1%#
files and use the coordinates to build three dimensional models on your
DPNQVUFSTDSFFO1%#mMFTBSFTUPSFEJOQVCMJDMZBDDFTTJCMFEBUBCBTFT
BOEDBOCFSFBEJMZEPXOMPBEFEGSPNUIF*OUFSOFU

Graham Johnson
Fivth Element (www.fivth.com)

30

4.14

MHC Class I: Protein Form and Function

$MBTT*.BKPS)JTUPDPNQBUJCJMJUZ$PNQMFYQSPUFJOTEJTQMBZTIPSU
peptides, or antigens, derived from normal cell proteins. PeptideMPBEFE.)$QSPUFJOTBSFMPDBUFEPOUIFDFMMTVSGBDFXIFSFUIFZDBO
CFFYBNJOFECZQBTTJOH5DFMMTPGUIFJNNVOFTZTUFN5IF.)$
complex has two subunits. The smaller subunit, 2 microglobulin,
resembles an immunoglobulin domain. The larger a subunit also has
an immunoglobulin-like domain which is linked to a head domain
containing the antigen-binding groove.
5IFBOUJHFOCJOEJOHHSPPWFJOUIF.)$IFBEEPNBJOJTCVJMUGSPNUXP
walls composed of long helices that rest on a floor composed of an
eight stranded sheet. The peptide on display fits snugly between the
helices in the groove.
The peptide backbone is bound at both ends by highly conserved
SFHJPOTPGUIF.)$QSPUFJO4PNFQFQUJEFTJEFDIBJOTFYUFOE
downwards into specific binding pockets in the groove, while other
QFQUJEFTJEFDIBJOTQSPKFDUVQXBSETXIFSFUIFZDBOCFSFDPHOJ[FECZ
T cells.
.)$DMBTT*QSPUFJOTEJTQMBZUIFJSCPVOEQFQUJEFTPOUIFDFMMTVSGBDFGPS
JNNVOFTVSWFJMMBODF*NNVOFDFMMT DBMMFEDZUPUPYJDPSLJMMFS5DFMMT GPS
FYBNQMF FYQSFTT5DFMMSFDFQUPSTUIBUCJOEUPUIF.)$IFBEEPNBJO
BOEUIFCPVOEQFQUJEF*GUIFDFMMFYQSFTTJOHUIF.)$QSPUFJOEJTQMBZT
a peptide foreign to the immune system, the T cell is activated by this
SFDFQUPS.)$JOUFSBDUJPO5IFBDUJWBUFE5DFMMUIFOQSPDFFETUPEFTUSPZ
UIFBCOPSNBMDFMM$VUBXBZWJFXTPGUIJTQFQUJEFCPVOE.)$QSPUFJO
complexed with a T-cell receptor reveal the exquisite precision with
which the interacting surfaces fit together.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

PDB ID number *: MHC class I molecule


(1A1M); Human T-cell receptor, viral peptide
and Hla-A 0201 complex (1AO7)

31

4.15

MHC Class II: Protein Form and Function

.)$DMBTT**QSPUFJOTIBWFBOPWFSBMMTJNJMBSTUSVDUVSFUP.)$DMBTT
*QSPUFJOT BMUIPVHIUIFJSTVCVOJUTUSVDUVSFJTEJTUJODU.)$DMBTT**
proteins are composed of two subunits that contribute to the structure
of the head domain containing the antigen-binding groove.
"TBSVMF .)$DMBTT**QSPUFJOTCJOEMPOHFSQFQUJEFTUIBO.)$DMBTT*
proteins. As seen in this comparison, the different shape of the antigen
CJOEJOHHSPPWFBMMPXTUIFFOETPGUIFQFQUJEFUPTUJDLPVU.)$DMBTT
**QSPUFJOTEJTQMBZQFQUJEFTPOUIFTVSGBDFTPGTQFDJBMJ[FEBOUJHFO
presenting cells and activate a different class of immune cells, called
helper T cells.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

4.16

Quiz: Chapter 4

)PXNBOZEJGGFSFOUBNJOPBDJETBSFVTFEJONBLJOHQSPUFJOT


t 

t 

t 

4.17

Concept Questions: Chapter 4

%FTDSJCFUIFQSJNBSZBOETFDPOEBSZTUSVDUVSFTPGQSPUFJOT
The primary structure of a protein is its amino acid sequence. Amino
acids are held together in a chain by peptide bonds. This polypeptide
chain can then fold into different shapes; these patterns constitute

PDB ID number *: Compilation of MHC class


I molecule & MHC class II/superantigen
complex (1A1M & 2SEB)

32

4.18

Challenge Question: Chapter 4

24ZOUIFTJTPGUIFQVSJOFOVDMFPUJEFT".1BOE(.1QSPDFFETCZB
CSBODIFEQBUIXBZTUBSUJOHXJUISJCPTFQIPTQIBUF 31
BTTIPXO
schematically in the figure below. Using the principles of feedback
inhibition, propose a regulatory strategy for this pathway that ensures
BOBEFRVBUFTVQQMZPGCPUI".1BOE(.1BOEy

Image courtesy of Robert Grant, Stephan


Crainic, and James M. Hogle

4.19

Flashcards: Chapter 4

active site


t

SFHJPOPOUIFTVSGBDFPGBOFO[ZNFUIBUCJOETUPBTVCTUSBUF
molecule and catalyzes its chemical transformation.

allosteric


t

4.20

EFTDSJCFTBQSPUFJOUIBUDBOFYJTUJONVMUJQMFDPOGPSNBUJPOTy

References: Chapter 4

"OmOTFO$# 
1SJODJQMFTUIBUHPWFSOUIFGPMEJOHPGQSPUFJODIBJOT
Science 181:223230.
#SBZ% 
'MFYJCMFQFQUJEFTBOEDZUPQMBTNJDHFMTGenome Biol
6:106109.

KEY TERMS
active site
allosteric
helix
amino acid sequence
antibody
antigen
sheet

33

5.1

DNA Structure

5XP%/"TUSBOETJOUFSUXJOFUPGPSNBEPVCMFIFMJY&BDITUSBOEIBTB
backbone composed of phosphates and sugars to which the bases are
attached. The bases form the core of the double helix, while the sugar
phosphate backbones are on the outside. The two grooves between the
CBDLCPOFTBSFDBMMFEUIFNBKPSBOENJOPSHSPPWFCBTFEPOUIFJSTJ[FT
.PTUQSPUFJOo%/"DPOUBDUTBSFNBEFJOUIFNBKPSHSPWF CFDBVTFUIF
minor groove is too narrow.
5IF%/"CBDLCPOFJTBTTFNCMFEGSPNSFQFBUJOHEFPYZSJCPTFTVHBS
VOJUTUIBUBSFMJOLFEUISPVHIQIPTQIBUFHSPVQT&BDIQIPTQIBUFDBSSJFT
BOFHBUJWFDIBSHF NBLJOHUIFFOUJSF%/"CBDLCPOFIJHIMZDIBSHFEBOE
polar.
A cyclic base is attached to each sugar. The bases are planar and extend
out perpendicular to the path of the backbone. Pyrimidine bases are
DPNQPTFEPGPOFSJOHBOEQVSJOFCBTFTPGUXPSJOHT"EKBDFOUCBTFT
BSFBMJHOFETPUIBUUIFJSQMBOBSSJOHTTUBDLPOUPQPGPOFBOPUIFS#BTF
stacking contributes significantly to the stability of the double helix.
*OBEPVCMFIFMJY FBDICBTFPOPOFTUSBOEJTQBJSFEUPBCBTFPO
UIFPUIFSTUSBOEUIBUMJFTJOUIFTBNFQMBOF*OUIFTFCBTFQBJSJOH
interactions, guanine always pairs with cytosine, and thymine with
adenine.
"($QBJSJTTUBCJMJ[FECZUISFFIZESPHFOCPOETGPSNFECFUXFFOBNJOP
BOEDBSCPOZMHSPVQTUIBUQSPKFDUGSPNUIFCBTFT
*ODPOUSBTU BO"5QBJSJTTUBCJMJ[FECZUXPIZESPHFOCPOET
5IFTQFDJmDJUZPGCBTFQBJSJOHUIBUJT $BMXBZTQBJSJOHXJUI( BOE"
always pairing with Tensures that the two strands are complementary.
5IJTJTJNQPSUBOUGPS%/"SFQMJDBUJPOBOEUSBOTDSJQUJPO
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

5.2

Chromosome Coiling

*OUIJTBOJNBUJPOXFMMTFFUIFXBZPVS%/"JTUJHIUMZQBDLFEVQUP
fit into the nucleus of every cell. The process starts with assembly of
a nucleosome, which is formed when eight separate histone protein
TVCVOJUTBUUBDIUPUIF%/"NPMFDVMF5IFDPNCJOFEUJHIUMPPQPG%/"
BOEQSPUFJOJTUIFOVDMFPTPNF4JYOVDMFPTPNFTBSFDPJMFEUPHFUIFSBOE
these then stack on top of each other. The end result is a fiber of packed
nucleosomes known as chromatin.
Animation produced for DNA Interactive (www.dnai.org) 2003 Howard Hughes
Medical Institute (www.hhmi.org) All rights reserved.

PDB ID number *: 132D

34

5.3

Liver Cell: View 6

4IPXNF


t OVDMFBSFOWFMPQF

t OVDMFBSQPSF

t FVDISPNBUJO

t IFUFSPDISPNBUJO

Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

5.4

Quiz: Chapter 5

8IJDICBTFQBJSTBSFGPVOEJO%/"


t "$BOE5(

t "5BOE$(

t "(BOE$5

t "6BOE$(

5.5

Media Assessment: DNA Structure

8IJDIJT/05USVFPG%/"TUSVDUVSF


t

5XP%/"TUSBOETJOUFSUXJOFUPGPSNBEPVCMFIFMJY

t

&BDITUSBOEIBTBCBDLCPOFDPNQPTFEPGQIPTQIBUFTBOE
sugars.

t

5IFOVDMFPUJEFCBTFTSBEJBUFPVUXBSEJOUPUIFHSPPWFT

t

5IF%/"CBDLCPOFJTOFHBUJWFMZDIBSHFE

35

5.6

Concept Questions: Chapter 5

%FTDSJCFUIFMFWFMTPGQBDLJOHUIBUPDDVSJOBFVLBSZPUJDDISPNPTPNF
5IF%/"EPVCMFIFMJYXJOETBSPVOEIJTUPOFQSPUFJOTUPGPSN
nucleosomes. The nucleosomes are then pulled together into a compact
chromatin fiber by interaction with the linker histone H1

5.7

Challenge Question: Chapter 5

25IFDIFNJDBMTUSVDUVSFTGPSBO"5BOEB($CBTFQBJSBSFTIPXOJO
the figure below, along with their points of attachment to the sugarphosphate backbones.
"*OEJDBUFUIFQPTJUJPOTPGUIFNBKPSBOENJOPSHSPPWFTPGUIF%/"
helix on these representations.

5.8

Flashcards: Chapter 5

base pair




t



UXPDPNQMFNFOUBSZOVDMFPUJEFTJOBO3/"PSB%/"NPMFDVMF
UIBUBSFIFMEUPHFUIFSCZIZESPHFOCPOETGPSFYBNQMF (XJUI
$ BOE"XJUI5PS6

cell cycle


5.9

t

UIFPSEFSMZTFRVFODFPGFWFOUTCZXIJDIBDFMMEVQMJDBUFTy

References: Chapter 5

8BUTPO+%$SJDL')$ 
.PMFDVMBSTUSVDUVSFPGOVDMFJDBDJET
A structure for deoxyribose nucleic acids. Nature 171:737738.
+JO+ $BJ: -J#FUBM 
*OBOEPVUIJTUPOFWBSJBOUFYDIBOHFJO
chromatin. Trends Biochem Sci 30:680687.

KEY TERMS
base pair
cell cycle
centromere
chromatin
chromatin-remodeling complex
chromosome
complementary

36

6.1

DNA Polymerase

%/"QPMZNFSBTFGBJUIGVMMZSFQMJDBUFT%/"CZVTJOHUIFOVDMFPUJEF
sequence of the template strand, colored yellow, to select each new
nucleotide to be added to the 3 end of a growing strand, colored gray.
*OUIJTBOJNBUJPO UIFEJGGFSFOUEPNBJOTPG%/"QPMZNFSBTFBSFDPMPSFE
differently.
#FGPSFBOVDMFPUJEFDBOCFJODPSQPSBUFEJOUP%/"BUUIF end of the
growing strand, the blue finger domain of the polymerase moves inward
to correctly position the nucleoside triphosphate. A pyrophosphate
group is released when each nucleotide is added.
*OUIJTWJFX UIFEFUBJMTPGOVDMFPUJEFTFMFDUJPOBUUIFBDUJWFTJUFBSF
shown with the incoming nucleoside triphosphate and the template
nucleotide in light blue. The growing strand is green, and the template
strand is red. When the finger domain moves inward, the nucleoside
triphosphate is tested for its ability to form a proper base pair with the
template nucleotide. When a base pair forms, the active site residues
catalyze the covalent addition of the new nucleotide to the 3 hydroxyl
group on the growing strand, and the entire process repeats at speeds
up to 500 nucleotides per second.

PDB ID number *: Human DNA polymerase


beta complexed with gapped DNA (1BPX);
Compilation of human DNA polymerase beta
complexed with gapped DNA & human DNA
polymerase beta complexed with gapped
DNA and ddCTP (1BPX & 1BPY)

On rare occasions, approximately once every 10,000 nucleotide


additions, the polymerase makes an error and incorporates a nucleotide
that does not form a proper base pair onto the end of the growing
strand. When this occurs, the polymerase changes conformation,
and transfers the end of the growing strand to a second active site on
the polymerase, where the erroneous, added nucleotide is removed.
The polymerase then flips back to its original conformation, allowing
QPMZNFSJ[BUJPOUPDPOUJOVF"TBSFTVMU TVDIBTFMGDPSSFDUJOH%/"
polymerase will make a mistake only about once every 107 to 108
nucleotide pairs.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

6.2

DNA Helicase

Helicases separate nucleic acid duplexes into their component strands


using energy from ATP hydrolysis.
5IFDSZTUBMTUSVDUVSFPGUIJT%/"IFMJDBTFGSPNCBDUFSJPQIBHF
T7, reveals an hexagonal arrangement of six identical subunits.
4VSQSJTJOHMZ UIFSJOHJTOPUTJYGPMETZNNFUSJD CVUJTTMJHIUMZTRVJTIFE
A model for the mechanism of how the enzyme might work explains
this structural asymmetry. Of the six potential ATP binding sites, two
PQQPTJOHPOFTCJOE"51UJHIUMZ UXPBSFNPSFMJLFMZUPCJOE"%1BOE
phosphate, and two are empty. These three states may interconvert in
a coordinate fashion as ATP is hydrolyzed, creating a ripple effect that
continuously runs around the ring.
#FDBVTFPGUIFTFDPOGPSNBUJPOBMDIBOHFT UIFMPPQTUIBUFYUFOEJOUP
UIFDFOUFSIPMFPGUIFSJOHUIBUBSFQSPQPTFEUPCJOE%/"PTDJMMBUFVQ
and down, as seen in this cross section. The oscillating loops might pull
B%/"TUSBOEUISPVHIUIFDFOUSBMIPMF UIVTVOXJOEJOHUIFEPVCMFIFMJY
in the process.
A frontal view shows the full dynamics of this fascinating protein
machine.

Dale B. Wigley and Martin R. Singleton


Imperial Cancer Research Fund
Tom Ellenberger
Harvard Medical School
Michael R. Sawaya
University of California, Los Angeles

37

6.3

Sliding Clamp

4MJEJOHDMBNQTBMMPX%/"QPMZNFSBTFTUPSFNBJOBUUBDIFEUPUIFJS%/"
UFNQMBUF*OUIJTXBZ %/"QPMZNFSBTFDBOTZOUIFTJ[FMPOHTUSFUDIFTPG
%/"FGmDJFOUMZXJUIPVUGBMMJOHPGGUIFUFNQMBUF%/"5IFNVMUJTVCVOJU
DMBNQGPSNTBSJOHUIBUFODJSDMFTUIF%/"IFMJYJUTTUSVDUVSFUIVT
relates to its function in a most intuitive way.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)
PBD ID number *: 1QE4

6.4

Replication I

Using computer animation based on molecular research, we are able


UPQJDUVSFIPX%/"JTSFQMJDBUFEJOMJWJOHDFMMT:PVBSFMPPLJOHBUBO
assembly line of amazing miniature biochemical machines that are
QVMMJOHBQBSUUIF%/"EPVCMFIFMJYBOEDSBOLJOHPVUBDPQZPGFBDI
TUSBOE5IF%/"UPCFDPQJFEFOUFSTUIFQSPEVDUJPOMJOFGSPNCPUUPN
MFGU5IFXIJSMJOHCMVFNPMFDVMBSNBDIJOFJTDBMMFEBIFMJDBTF*UTQJOT
UIF%/"BTGBTUBTBKFUFOHJOFBTJUVOXJOETUIFEPVCMFIFMJYJOUPUXP
strands. One strand is copied continuously and can be seen spooling
off to the right. Things are not so simple for the other strand because
JUNVTUCFDPQJFECBDLXBSET*UJTESBXOPVUSFQFBUFEMZJOMPPQT BOE
DPQJFEPOFTFDUJPOBUBUJNF5IFFOESFTVMUJTUXPOFX%/"NPMFDVMFT
Animation produced for DNA Interactive (www.dnai.org) 2003 Howard Hughes
Medical Institute, (www.hhmi.org) All rights reserved.

6.5

Replication II

*OBSFQMJDBUJPOGPSL UXP%/"QPMZNFSBTFTDPMMBCPSBUFUPDPQZUIF
MFBEJOHTUSBOEUFNQMBUFBOEUIFMBHHJOHTUSBOEUFNQMBUF%/"
*OUIJTQJDUVSF UIF%/"QPMZNFSBTFUIBUQSPEVDFTUIFMBHHJOHTUSBOE
IBTKVTUmOJTIFEBO0LB[BLJGSBHNFOU
5IFDMBNQUIBULFFQTUIFMPXFS%/"QPMZNFSBTFBUUBDIFEUPUIFMBHHJOH
TUSBOEEJTTPDJBUFT BOEUIF%/"QPMZNFSBTFUFNQPSBSJMZSFMFBTFTUIF
MBHHJOHTUSBOEUFNQMBUF%/"
"TUIF%/"IFMJDBTFDPOUJOVFTUPVOXJOEUIFQBSFOUBM%/" UIFQSJNBTF
CFDPNFTBDUJWBUFEBOETZOUIFTJ[FTBTIPSU3/"QSJNFSPOUIFHSPXJOH
lagging strand.
5IF%/"QPMZNFSBTFCJOETUPUIF%/"BHBJOBOECFDPNFTMPDLFEJOCZ
the clamp.

Original illustrations and storyboard:


Nigel Orme and Christopher Thorpe

38
5IFQPMZNFSBTFVTFTUIF3/"QSJNFSUPCFHJOBTIPSUDPQZPGUIF
MBHHJOHTUSBOEUFNQMBUF%/"
5IFQPMZNFSBTFTUBMMTXIFOJUSFBDIFTUIF3/"QSJNFSPGUIFQSFDFEJOH
Okazaki fragment, and the entire cycle repeats.
Music: Christopher Thorpe

6.6

Telomere Replication

5IFFOETPGMJOFBSDISPNPTPNFTQPTFVOJRVFQSPCMFNTEVSJOH%/"
SFQMJDBUJPO#FDBVTF%/"QPMZNFSBTFTDBOPOMZFMPOHBUFGSPNBGSFF
hydroxyl group, the replication machinery builds the lagging strand by
BCBDLTUJUDIJOHNFDIBOJTN3/"QSJNFSTQSPWJEF -hydroxyl groups at
regular intervals along the lagging strand template.
Whereas the leading strand elongates continuously in the 5 -to-3
direction all the way to the end of the template, the lagging strand stops
short of the end.
&WFOJGBmOBM3/"QSJNFSXFSFCVJMUBUUIFWFSZFOEPGUIF
chromosome, the lagging strand would not be complete.
The final primer would provide a 3 0)HSPVQUPTZOUIFTJ[F%/" CVU
the primers would later need to be removed. The 3 -hydroxyl groups on
BEKBDFOU%/"GSBHNFOUTQSPWJEFTUBSUJOHQMBDFTGPSSFQMBDJOHUIF3/"
XJUI%/")PXFWFS BUUIFFOEPGUIFDISPNPTPNFUIFSFJTOP -OH
HSPVQBWBJMBCMFUPQSJNF%/"TZOUIFTJT
#FDBVTFPGUIJTJOBCJMJUZUPSFQMJDBUFUIFFOET DISPNPTPNFTXPVME
progressively shorten during each replication cycle. This endreplication problem is solved by the enzyme telomerase. The ends
PGDISPNPTPNFTDPOUBJOB(SJDITFSJFTPGSFQFBUTDBMMFEBUFMPNFSF
Telomerase recognizes the tip of an existing repeat sequence. Using an
3/"UFNQMBUFXJUIJOUIFFO[ZNF UFMPNFSBTFFMPOHBUFTUIFQBSFOUBM
strand in the 5 -to-3 direction, and adds additional repeats as it moves
down the parental strand.
5IFMBHHJOHTUSBOEJTUIFODPNQMFUFECZ%/"QPMZNFSBTFBMQIB XIJDI
DBSSJFTB%/"QSJNBTFBTPOFPGJUTTVCVOJUT*OUIJTXBZ UIFPSJHJOBM
information at the ends of linear chromosomes is completely copied in
UIFOFX%/"
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

39

6.7

Holliday Junction

5IF)PMMJEBZKVODUJPO BOJNQPSUBOUJOUFSNFEJBUFTUSVDUVSFJO
IPNPMPHPVT%/"SFDPNCJOBUJPO JTGPSNFEXIFOUXPIPNPMPHPVT
EPVCMFTUSBOEFE%/"NPMFDVMFTSFDJQSPDBMMZFYDIBOHF%/"TUSBOET
5IJTKVODUJPODBOCFWJTVBMJ[FEEJSFDUMZJOUIFFMFDUSPONJDSPTDPQF
*OUIFDFMM UIJTKVODUJPOJTGPSNFEBOETUBCJMJ[FECZBTQFDJmDHSPVQ
of helicase proteins, seen here in the background, which use ATP
IZESPMZTJTUPNPWFUIFKVODUJPOVQBOEEPXOUIF%/" BTTIPXOJOUIJT
animation.
Electron microscopy:
David Dressler
University of Oxford
Huntington Potter
University of South Florida
Molecular animation:
David A. Waller
Astbury Centre for Structural Molecular
Biology, University of Leeds
David Rice, Peter Artymiuk, John Rafferty,
and David Hargreaves
Krebs Institute, University of Sheffield

6.8

Quiz: Chapter 6

$POTJEFSUIFQSPDFTTUIBUBDFMMVTFTUPSFQMJDBUFJUTEPVCMFTUSBOEFE
%/"UPNBLFDPQJFTGPSEBVHIUFSDFMMT8IJDITUBUFNFOUEFTDSJCFTUIF
%/"JOEBVHIUFSDFMMT


t

5IFEPVCMFIFMJYJOPOFEBVHIUFSDFMMDPOTJTUTPGUXPTUSBOET
that were originally in the parent cell, while the double helix in
the other daughter cell consists of two newly made strands.




t


5IFUXPTUSBOETPGUIFEPVCMFIFMJDFTJOCPUIEBVHIUFSDFMMT
DPOTJTUPGTFHNFOUTPGOFXBOEQBSFOUBM%/"

t

5IFEPVCMFIFMJDFTJOFBDIEBVHIUFSDFMMDPOTJTUPGPOF
parental strand and one newly made strand.

40

6.9

Media Assessment: Replication Fork

8IJDIFO[ZNFJTSFTQPOTJCMFGPSQSPEVDJOHUIFOFXMZTZOUIFTJ[FE%/"
TUSBOE


t

%/"QSJNBTF

t

3/"QSJNBTF

t

%/"IFMJDBTF

t

%/"QPMZNFSBTF

6.10

Concept Questions: Chapter 6

%VSJOHSFQMJDBUJPO BSFUIFTBNFOVNCFSPG3/"QSJNFSTSFRVJSFEGPS
UIFTZOUIFTJTPGUIFMFBEJOHBOEUIFMBHHJOHTUSBOET &YQMBJOZPVS
reasoning.
/P0OUIFMFBEJOHTUSBOE POF3/"QSJNFSJTOFFEFEPOMZUPTUBSU
replication at a replication origin; once a replication fork has been
FTUBCMJTIFE UIF%/"y

6.11

Challenge Question: Chapter 6

*G%/"QPMZNFSBTFSFRVJSFTBQFSGFDUMZQBJSFEQSJNFSJOPSEFSUPBEEUIF
next nucleotide, how is it that any mismatched nucleotides escape the
QPMZNFSBTFBOECFDPNFTVCTUSBUFTGPSNJTNBUDISFQBJSFO[ZNFT
$MFBSMZ %/"QPMZNFSBTFTNVTUCFBCMFUPFYUFOEBNJTNBUDIFEy

41

6.12

Flashcards: Chapter 6

%/"MJHBTF



FO[ZNFUIBUSFTFBMTOJDLTUIBUBSJTFJOUIFCBDLCPOFPGB%/"
NPMFDVMFJOUIFMBCPSBUPSZ DBOCFVTFEUPKPJOUPHFUIFSUXP%/"
fragments.

%/"SFQBJS
collective term for the enzymatic processes that correct

6.13

References: Chapter 6

$PPQFS(. #SVEOP. 4UPOF&4FUBM 


$IBSBDUFSJ[BUJPOPG
evolutionary rates and constraints in three mammalian genomes.
Genome Reso
$SPX+' 
5IFPSJHJOT QBUUFSOTBOEJNQMJDBUJPOTPGIVNBO
spontaneous mutation. Nature Rev Genet o

KEY TERMS
cancer
DNA ligase
DNA polymerase
DNA repair
DNA replication
homologous recombination
lagging strand

42

7.1

RNA Structure

-JLF%/" 3/"TUSBOETBMTPQBJSUPGPSNBEPVCMFIFMJY5IFQBJSFE
OVDMFPUJEFCBTFTBSFQBDLFEJOUIFNJEEMFPGBO3/"IFMJY TVSSPVOEFE
by the backbone.
5IF3/"IFMJYIBTBEJGGFSFOUHFPNFUSZUIBOBTUBOEBSE%/"IFMJY
'PSFYBNQMF UIF3/"IFMJYIBTBIPMFEPXOUIFNJEEMFBOEBMTPB
TJHOJmDBOUMZOBSSPXFSBOEEFFQFSNBKPSHSPPWF
The backbone is composed of repeating ribose sugars and phosphate
groups.
Unlike the 2 EFPYZSJCPTFVTFEJO%/" SJCPTFIBTBIZESPYZMHSPVQ
attached to the 2 carbon. This extra hydroxyl group influences the
TFDPOEBSZTUSVDUVSF*UJTUPPCVMLZUPBMMPX3/"UPGPMEMJLF%/" XIJDI
JTUIFQSJNBSZSFBTPOXIZBO3/"IFMJYIBTBEJGGFSFOUTUSVDUVSF
#BTFQBJSJOHCFUXFFOTUSBOETJTTJNJMBSUPUIBUJO%/" FYDFQUUIBU
adenine pairs with uracil instead of thymine. Uracil is never used in
%/""TJO%/"B($CBTFQBJSJOHJO3/"IBTUISFFIZESPHFOQPOET
Th A-U pair like the A-T pair has two hydrogen bonds.
3/"TUSBOETPGUFOGPMEJOUPDPNQMFYTUSVDUVSFT*OUIJTTUFNMPPQ
TUSVDUVSF BMTPDBMMFEBO3/"IBJSQJO BTJOHMFTUSBOEFE3/"NPMFDVMF
folds back onto itself.
5IFTUFNBUUIFCPUUPNJTBDMBTTJDBM3/"IFMJY#BTFTJOUIF
single-stranded loop, in contrast, are either exposed or engaged in
nonstandard interactions.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

7.2

Transcription

5SBOTDSJQUJPOJTUIFQSPDFTTCZXIJDI%/"JTDPQJFEJOUP3/"JOUIFmSTU
TUFQPGHFOFFYQSFTTJPO*UCFHJOTXJUIBCVOEMFPGGBDUPSTBTTFNCMJOHBU
UIFTUBSUPGBHFOF UIBUJT BMJOFBSTFRVFODFPG%/"JOTUSVDUJPOT IFSF
shown stretching away to the left. The assembled factors include an
3/"QPMZNFSBTF UIFCMVFNPMFDVMF4VEEFOMZ 3/"QPMZNFSBTFJTMFU
HP SBDJOHBMPOHUIF%/"UPSFBEUIFHFOF"TJUVO[JQTUIFEPVCMFIFMJY 
it copies one of the two strands. The yellow chain snaking out of the
UPQJTUIF3/" BDPQZPGUIFHFOFUJDNFTTBHF5IFOVDMFPUJEFCVJMEJOH
CMPDLTUIBUBSFVTFEUPNBLFUIF3/"FOUFSUISPVHIBOJOUBLFIPMFJO
UIFQPMZNFSBTF*OUIFBDUJWFTJUFPGUIFFO[ZNF UIFZBSFUIFONBUDIFE
UPUIF%/" OVDMFPUJEFCZOVDMFPUJEF UPDPQZUIF"T $T 5TBOE(T
PGUIFHFOF5IFPOMZEJGGFSFODFJTUIBUJOUIF3/"DPQZ UIZNJOFJT
replaced with the closely related base uracil, commonly abbreviated U.
You are watching this process, called transcription, in real time.
Animation produced for DNA Interactive (www.dnai.org) 2003 Howard Hughes
Medical Institute (www.hhmi.org) All rights reserved.

PDB ID number *: RNA duplex containing


a purine-rich strand (1RRR); RNA tetraloop
(1AFX)

43

7.3

RNA Polymerase II

&VDBSZPUJD3/"QPMZNFSBTF**USBOTDSJCFTBMMNFTTFOHFS3/"NPMFDVMFT
JOUIFDFMM*UJTBIVHFDPNQMFYPGUFOEJGGFSFOUQSPUFJOTVCVOJUT5IF
active site of the enzyme lies at the interface between the two largest
TVCVOJUT*OUIJTTUSVDUVSFBTIPSUTUSFUDIPGB%/"3/"IFUFSPEVQMFY
was co-crystallized. New nucleotides would be continually added to the
3 IZESPYZMHSPVQPGUIF3/"TIPXOJOSFE
*OUIFBDUJWFTJUFPG3/"QPMZNFSBTF** BTJOHMFTUSBOEFE%/"UFNQMBUF
JTUSBOTDSJCFEJOUPBDPNQMFNFOUBSZ3/"USBOTDSJQU5IFJOJUJBMQSPEVDU
JTB%/"3/"IZCSJEGSPNXIJDIUIFOFXMZTZOUIFTJ[FE3/"TUSBOEJT
TUSJQQFEPGG*UMFBWFTUIFQPMZNFSBTFWJBBOFYJUHSPPWFPOUIFQSPUFJOT
surface.

PDB ID number *: 1I6H

"QPSFPOUIFCBDLTJEFPG3/"QPMZNFSBTF**FYUFOETGSPNUIFQSPUFJO
surface all the way to the active site. The nucleotide triphosphates used
UPCVJMEUIFHSPXJOH3/"USBOTDSJQUFOUFSUIFQPMZNFSBTFUISPVHIUIJT
pore.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

7.4

TATA-Binding Protein

&VDBSZPUJDUSBOTDSJQUJPOCFHJOTXIFO3/"QPMZNFSBTF**CJOETUPUIF
promoter region of a gene. A crucial part of this initiation process is
the recognition and binding of the TATA sequence, a short stretch of
%/"SJDIJOUIZNJOFBOEBEFOJOFOVDMFPUJEFT5IFTVCVOJUPG3/"
QPMZNFSBTF**UIBUCJOETUPUIF5"5"TFRVFODFJTDBMMFEUIF5"5"
binding protein.
5IF5"5"CJOEJOHQSPUFJOCJOETUP%/"VTJOHBOFJHIUTUSBOEFECFUB
TIFFUUIBUSFTUTBUPQUIF%/"IFMJYMJLFBTBEEMF5XPQSPUFJOMPPQT
ESBQFEPXOUIFTJEFTPGUIF%/"MJLFTUJSSVQT
#JOEJOHPGUIF5"5"CJOEJOHQSPUFJOJOUSPEVDFTBTFWFSFLJOLJOUIF
%/"CBDLCPOF5IJTLJOLESBNBUJDBMMZCFOETUIF%/"IFMJYCZOFBSMZ
ninety degrees and is thought to provide a signal to assemble the rest of
the transcription complex at the initiation site.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

PDB ID number *: TATA element ternary


complex (1VOL); Compilation of TATA
element ternary complex & Gal4 complex
with DNA (1VOL & 1D66)

44

7.5

RNA Splicing

&VDBSZPUJDHFOFTUZQJDBMMZDPOUBJOJOUSPOT XIJDIIBWFUPCFSFNPWFE
after transcription.
#FGPSFUIF3/"USBOTDSJQUMFBWFTUIFOVDMFVT UIFDFMMTQMJDFTPVUUIF
intron sequences. A few short nucleotide sequences provide the cell
with cues of what to remove. The elaborate molecular machine that
carries out this task is called the spliceosome.
"CSBODIQPJOUCJOEJOHQSPUFJO ##1
BOEBIFMQFSQSPUFJO 6"'

SFDPHOJ[FUIFCSBODIQPJOUTJUFXJUIJOUIFJOUSPO BOEBO3/"BOE
QSPUFJODPNQMFY DBMMFEBTO3/1 SFDPHOJ[FTUIF splice site by forming
CBTFQBJSTXJUIJOJU/FYU BOPUIFSTO3/1CBTFQBJSTXJUIUIFCSBODI
TJUF EJTQMBZJOHUIFCPVOEQSPUFJOT"EEJUJPOBMTO3/1TOPXDPNFJOUP
QMBZBOETFWFSBM3/"SFBSSBOHFNFOUTPDDVSUPCSFBLBQBSUUIF6
6CBTFQBJSTBOEBMMPXUIF6TO3/1UPEJTQMBDF6BUUIF splice
KVODUJPO
Now in position, a conserved adenine nucleotide in the intron attacks
the 5 TQMJDFTJUF DVUUJOHUIFTVHBSQIPTQIBUFCBDLCPOFPGUIF3/"5IF
end of the intron covalently bonds to the adenine nucleotide forming a
lariat structure.
The spliceosome rearranges to bring together the exons, allowing the
3 hydroxyl group of the first exon to react with the 5 end of the other.
"GUFSUIFUXPFYPOTBSFKPJOFEJOUPBDPOUJOVPVTTFRVFODF UIFMBSJBUJT
released and degraded.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

7.6

tRNA

"MMU3/"TIBWFBDIBSBDUFSJTUJD-TIBQF XJUIBOBNJOPBDJEBUUBDIFEUP
the 3 end at the tip of the shorter arm. The anticodon loop is positioned
at the opposing end of the molecule and contains the anticodon base
triplet.
The amino acid, a phenylalanine in this case, is covalently attached to
BDPOTFSWFETFRVFODF $$" UIBUJTDPNNPOUPUIF terminus of all
U3/"T
The anticodon is comprised of three nucleotides complementary to
UIFDPEPOJOUIFN3/"5IFCBTFTBSFFYQPTFE BOEBSFUIVTGSFFMZ
BDDFTTJCMFGPSCBTFQBJSJOHEVSJOHQSPUFJOTZOUIFTJT*OUIJTFYBNQMF 
UIFBOUJDPEPOTFRVFODFJT("" XIJDIXPVMENBUDIB66$DPEPOPOB
NFTTFOHFS3/" TQFDJGZJOHQIFOZMBMBOJOF
5IFDIBSHJOHPGU3/"TXJUIUIFDPSSFDUBNJOPBDJETJTDBSSJFEPVUCZ
BNJOPBDZMU3/"TZOUIFUBTFT"TSFWFBMFEJOUIFDVUBXBZWJFX UIF
DPNQMFYPGQIFOZMBMBOJOFU3/"XJUIJUTDPHOBUFTZOUIFUBTFTIPXT
an extensive contact surface that includes recognition sites for the
BOUJDPEPOCBTFUSJQMFU5IFU3/"T$$"FOEJTEFFQMZCVSJFEJOUIF
enzyme.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

PDB ID number *: Phe-tRNA, elongation


factor Ef-Tu: Gdpnp ternary complex (1TTT);
Yeast aspartyl-tRNA synthetase (1ASY)

45

7.7

Translation I

8IFOUIFN3/"JTDPNQMFUF JUTOBLFTPVUPGUIFOVDMFVTJOUP
the cytosol. Then in a dazzling display of choreography, all the
DPNQPOFOUTPGBNPMFDVMBSNBDIJOFMPDLUPHFUIFSBSPVOEUIF3/"UP
GPSNBNJOJBUVSFGBDUPSZDBMMFEBSJCPTPNF*UUSBOTMBUFTUIFHFOFUJD
JOGPSNBUJPOJOUIF3/"JOUPBTUSJOHPGBNJOPBDJETUIBUXJMMCFDPNF
BQSPUFJOU3/"NPMFDVMFTuUIFHSFFOUSJBOHMFTuCSJOHFBDIBNJOPBDJE
to the ribosome. The amino acids are the small red tips attached to the
U3/"T5IFSFBSFEJGGFSFOUU3/"TGPSFBDIPGUIFUXFOUZBNJOPBDJET 
each of them carrying a three-letter nucleotide code that is matched to
UIFN3/"JOUIFNBDIJOF/PXXFDPNFUPUIFIFBSUPGUIFQSPDFTT
*OTJEFUIFSJCPTPNF UIFN3/"JTQVMMFEUISPVHIMJLFBUBQF5IFDPEF
for each amino acid is read off, three letters at a time, and matched to
UISFFDPSSFTQPOEJOHMFUUFSTPOUIFU3/"T8IFOUIFSJHIUU3/"QMVHTJO 
the amino acid it carries is added to the growing protein chain. You are
watching the process in real time. After a few seconds the assembled
QSPUFJOTUBSUTUPFNFSHFGSPNUIFSJCPTPNF3JCPTPNFTDBONBLFBOZ
LJOEPGQSPUFJO*UKVTUEFQFOETPOXIBUHFOFUJDNFTTBHFZPVGFFEJOPO
UIFN3/"*OUIJTDBTF UIFFOEQSPEVDUJTIFNPHMPCJO5IFDFMMTJOPVS
bone marrow churn out a hundred trillion molecules of it per second!
And as a result, our muscles, brain and all the vital organs in our body
receive the oxygen they need.
Animation produced for DNA Interactive (www.dnai.org) 2003 Howard
HughesMedical Institute (www.hhmi.org) All rights reserved.

7.8

Translation II

To extend a growing polypeptide chain the ribosome must select the


DPSSFDUBNJOPBDJETUIBUBSFTQFDJmFECZUIFNFTTFOHFS3/"
"OBNJOPBDZMU3/"CPVOEUPFMPOHBUJPOGBDUPS5V &'5VGPSTIPSU 
FOUFSTUIFGSFF"TJUFPOUIFSJCPTPNF*GUIFBOUJDPEPOPGUIFDIBSHFE
U3/"EPFTOPUNBUDIUIFDPEPOJOUIFNFTTFOHFS3/" UIFU3/"JT
SFKFDUFE
5IFQSPDFTTPGUSJBMBOEFSSPSSFQFBUTVOUJMUIFDPSSFDUU3/"JTJEFOUJmFE
&MPOHBUJPOGBDUPS5VIZESPMZ[FTJUTCPVOE(51BOEEJTTPDJBUFT*GUIF
U3/"JTDPSSFDUMZNBUDIFEBOESFNBJOTCPVOEGPSBMPOHFOPVHIUJNF JU
is committed to be used in protein synthesis.
The ribosome catalyzes the formation of the new peptide bond and
VOEFSHPFTBESBNBUJDDPOGPSNBUJPOBMDIBOHF&MPOHBUJPOGBDUPS(CJOET
UPUIFSJCPTPNF)ZESPMZTJTPG(51CZFMPOHBUJPOGBDUPS(TXJUDIFTUIF
ribosome back to the state in which it can accept the next incoming
U3/"

46

7.9

Translation: Atomic View

The crystal structure of the ribosome reveals many insights into the
molecular mechanism of translation.
Zooming in on the large ribosomal subunit shows highly evolutionarily
DPOTFSWFE3/"CBTFTMJOJOHUIFBDUJWFTJUFPGUIFQFQUJEZMUSBOTGFSBTF
center, which catalyzes polypeptide bond formation. There are no
ribosomal proteins in the vicinity; peptide bond formation is catalyzed
JOBOFOWJSPONFOUFYDMVTJWFMZNBEFPGSJCPTPNBM3/"
5IFaFOEPGBU3/"DIBSHFEXJUIBOBNJOPBDJEJTCPVOEJOUIFBDUJWF
site. This amino acid represents the carboxy-terminal amino acid of a
growing polypeptide chain on an actively translating ribosome with the
QFQUJEZMU3/"CPVOEUPUIF1TJUFPOUIFSJCPTPNF$POTFSWFECBTFT
DPNNPOUPUIFaFOEPGBMMU3/"TCBTFQBJSXJUIUIFSJCPTPNBM3/"UP
position the amino acid precisely.

T. Martin Schmeing
Thomas A. Steitz
Howard Hughes Medical Institute, Yale
University

5IFJODPNJOHBNJOPBDJEMJOLFEUPJUTSFTQFDUJWFU3/"CJOETDMPTFMZ 
again held precisely by base pairing interactions between a conserved
CBTFPOUIFU3/"BOESJCPTPNBM3/""OFUXPSLPGIZESPHFOCPOET
positions the reactive groups with the precise geometry required to
catalyze peptide bond formation.
5IFFNQUZEFBDZMBUFEU3/"JTSFMFBTFEGSPNUIF1TJUF
%VSJOHUIFAUSBOTMPDBUJPOTUFQPGQSPUFJOTZOUIFTJT UIFPUIFSU3/" 
now containing the growing polypeptide chain, moves from the A- to
the P-site, where it will be waiting for the next incoming amino acid to
repeat the polymerization cycle.
The different states of the reaction cycle shown in this animation are
based on actual crystal structures, in which large ribosomal subunits
XFSFDSZTUBMMJ[FEXJUIWBSJPVTBNJOPBDZMU3/"BOBMPHTCPVOEUPUIFN 
mimicking the discrete steps in the reaction cycle.

7.10

Polyribosome

"TTPPOBTBNFTTFOHFS3/"NPMFDVMFJTUSBOTQPSUFEGSPNUIFOVDMFVT
to the cytoplasm, ribosomes begin to translate the sequence into amino
BDJET5ZQJDBMMZ NBOZSJCPTPNFTUSBOTMBUFUIFN3/"TJNVMUBOFPVTMZ
&BDISJCPTPNFCFHJOTBUUIF FOEPGUIFN3/"BOEQSPHSFTTFTTUFBEJMZ
toward the 3 end. New ribosomes attach to the 5 end at the same rate
as the previous ones move out of the way. These multiple initiations
allow the cell to make much more protein from a single message than
if one ribosome had to complete the task before another could begin.
When a ribosome reaches a stop codon, the ribosome and the new
QSPUFJOEJTTPDJBUFGSPNFBDIPUIFSBOEGSPNUIFN3/"5IJTFMFDUSPO
micrograph depicts a membrane-bound polyribosome from a eucaryotic
cell.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

Electron Microscopy:
John Heuser
Washington University in St. Louis

47

7.11

Ribosome Ratchet

$PNQBSJTPOPGUXPTUBUFTPGBCBDUFSJBMSJCPTPNF FJUIFSXJUIUIF
JOJUJBUPSG.FUU3/"CPVOEPSXJUIFMPOHBUJPOGBDUPS&'(CPVOE SFWFBMT
the significant conformational changes that the ribosome is thought to
undergo during each elongation cycle. The ratchet-like rearrangements
at the interface between the two ribosomal subunits may help move the
N3/"BOEU3/"TUISPVHIUIFSJCPTPNFEVSJOHQSPUFJOTZOUIFTJT
The models shown here are a computer reconstruction made from
many thousands of images of single ribosomes in vitreous ice that were
observed with an electron microscope.
Animation: Amy Heagle Whiting, Howard Hughes Medical Institute, Health Research
Incorporated at the Wadsworth Center, State University of New York at Albany
Final composition: Graham Johnson, Fivth Element (www.fivth.com)
Funded, in part, by NIGMS and NCRR, National Institutes of Health

7.12

Quiz: Chapter 7

8IBUJTUIFiDFOUSBMEPHNBw


t (FOFUJDJOGPSNBUJPOnPXTGSPN3/"UP%/"UPQSPUFJO

t (FOFUJDJOGPSNBUJPOnPXTGSPN3/"UPQSPUFJOUP%/"

t (FOFUJDJOGPSNBUJPOnPXTGSPN%/"UP3/"UPQSPUFJO

t (FOFUJDJOGPSNBUJPOnPXTGSPN%/"UPQSPUFJOUP3/"

t (FOFUJDJOGPSNBUJPOnPXTGSPNQSPUFJOUP3/"UP%/"

t (FOFUJDJOGPSNBUJPOnPXTGSPNQSPUFJOUP%/"UP3/"

7.13

Media Assessment: Translation

5IFJOGPSNBUJPOJOBON3/"JTEFDPEFECZ


t

%/"

t

3/"QPMZNFSBTFT

t

SJCPTPNFT

t

BNJOPBDJET

Joachim Frank and Rajendra K. Agrawal


Howard Hughes Medical Institute
Health Research Incorporated at the
Wadsworth Center, State University of New
York at Albany

48

7.14

Concept Questions: Chapter 7

$PNQBSFIPXFVLBSZPUFTBOEQSPLBSZPUFTUSBOTDSJCF%/"UP3/"
#BDUFSJBDPOUBJOBTJOHMFUZQFPG3/"QPMZNFSBTF XIFSFBTFVLBSZPUJD
DFMMTIBWFUISFFEJGGFSFOUUZQFTPG3/"QPMZNFSBTF FBDIPGXIJDI
USBOTDSJCFTEJGGFSFOUUZQFTPGHFOFT1SPLBSZPUJD3/"QPMZNFSBTFy

7.15

Challenge Question: Chapter 7

8IBUBSFUIFSPMFTPGHFOFSBMUSBOTDSJQUJPOGBDUPSTJO3/"QPMZNFSBTF
**NFEJBUFEUSBOTDSJQUJPO BOEXIZBSFUIFZSFGFSSFEUPBTAHFOFSBM 
(FOFSBMUSBOTDSJQUJPOGBDUPSTQMBZTFWFSBMSPMFTJOQSPNPUJOH
USBOTDSJQUJPOCZ3/"QPMZNFSBTF**5IFZIFMQQPTJUJPOUIF3/"y

Image courtesy of Ulrich Scheer

7.16

Flashcards: Chapter 7

alternative splicing



t


UIFQSPEVDUJPOPGEJGGFSFOUN3/"T BOEQSPUFJOT
GSPNUIF
TBNFHFOFCZTQMJDJOHJUT3/"USBOTDSJQUTJOEJGGFSFOUXBZT

BNJOPBDZMU3/"TZOUIFUBTF


t

7.17

EVSJOHQSPUFJOTZOUIFTJT BOFO[ZNFUIBUBUUBDIFTUIFDPSSFDU

References: Chapter 7

"EBNT3- 8FOUF43 


6ODPWFSJOHOVDMFBSQPSFDPNQMFYJUZXJUI
innovation. Cell 152(6): 1218-21.
#FOUMFZ%- 
3VMFTPGFOHBHFNFOUDPUSBOTDSJQUJPOBMSFDSVJUNFOU
PGQSFN3/"QSPDFTTJOHGBDUPSTCurr Opin Cell Biol 17:251256.

KEY TERMS
alternative splicing
aminoacyl-tRNA synthetase
anticodon
codon
exon
gene
gene expression

49

8.1

Homeodomain

Homeodomains are found in many transcription regulatory proteins and


NFEJBUFUIFJSCJOEJOHUP%/""TJOHMFIPNFPEPNBJODPOTJTUTPGUISFF
overlapping helices packed together by hydrophobic forces. Helix 2
BOEIFMJYDPNQSJTFUIF%/"CJOEJOHFMFNFOU BIFMJYUVSOIFMJYNPUJG
Amino acids in the recognition helix make important, sequence-specific
DPOUBDUTXJUICBTFTJOUIF%/"NBKPSHSPPWF
Three side chains from the recognition helix form hydrogen bonds with
CBTFTJOUIF%/""IZESPHFOCPOEJTBTUSPOH OPODPWBMFOUJOUFSBDUJPO
that forms when two neighboring electronegative atoms, like oxygen
and nitrogen, share a single hydrogen.
*OBEEJUJPOUPUIFDPOUBDUTCFUXFFOUIFSFDPHOJUJPOIFMJYBOEUIFCBTFT
JOUIF%/"NBKPSHSPPWF BOBSHJOJOFSFTJEVFGSPNBnFYJCMFMPPQPGUIF
protein contacts bases in the minor groove.

PBD ID number *: 1APL

Molecular modelling and animation: Timothy Driscoll, Molvisions


Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

8.2

Zinc Finger Domain

;JODmOHFSEPNBJOTBSFTUSVDUVSBMNPUJGTVTFECZBMBSHFDMBTTPG%/"
binding proteins. They use centrally coordinated zinc atoms as crucial
structural elements. The zinc atom is coordinated by two cystine
residues from the sheet and two histidine residues from the a helix.
A single zinc finger domain is only large enough to bind a few bases of
%/""TBSFTVMU [JODmOHFSTBSFPGUFOGPVOEJOUBOEFNSFQFBUTBTQBSU
PGBMBSHFS%/"CJOEJOHSFHJPO
5IFIFMJDBMSFHJPOPGFBDI[JODmOHFSSFTUTJOUIFNBKPSHSPPWFPGUIF
%/""NJOPBDJETJEFDIBJOTQSPKFDUPVUGSPNUIFIFMJYBOEDPOUBDU
CBTFTJOUIF%/"5IFJEFOUJUJFTPGUIFTFTJEFDIBJOTEFUFSNJOFUIF
QSFDJTF%/"TFRVFODFSFDPHOJ[FECZFBDI[JODmOHFS"TTFNCMJOH
different zinc finger motifs allows precise control over the sequence
specificity of the protein.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com

PDB ID number *: Zinc finger DNA-binding


domain (1ZNF); Zif268-DNA complex (1ZAA)

50

8.3

Leucine Zipper

A leucine zipper domain is comprised of two long, intertwined


helices. Hydrophobic side chains extend out from each helix into the
space shared between them. Many of these hydrophobic side chains
are leucines, giving this domain its name. A spacefilling view reveals
the tight packing of side chains between the leucine zipper helices; this
makes the domain especially stable.
&YUFOTJPOTPGUIFUXPMFVDJOF[JQQFSIFMJDFTTUSBEEMFUIF%/"NBKPS
HSPPWF4JEFDIBJOTGSPNCPUIIFMJDFTFYUFOEJOUPUIFHSPPWFUPDPOUBDU
%/"CBTFT
The specific interactions between side chains and bases are hydrogen
CPOET*OUIJTFYBNQMF BOBSHJOJOFSFTJEVFNBLFTUXPDPOUBDUTXJUIB
guanine base.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

8.4

Quiz: Chapter 8

1. Which of the following statements is not true about the differences


CFUXFFOMJWFSDFMMTBOELJEOFZDFMMTJOUIFTBNFPSHBOJTN


t 5IFZDPOUBJOUIFTBNFHFOFT CVUFYQSFTTUIFNEJGGFSFOUMZ

t 5IFZDPOUBJOEJGGFSFOUHFOFT

t 5IFZDPOUBJOEJGGFSFOUTFUTPGQSPUFJOT

8.5

Concept Questions: Chapter 8

*OE. coli, how does the tryptophan repressor control the expression of
HFOFTJOUIFUSZQPQFSPO 8IBUXPVMEIBQQFOJGBNVUBUJPOSFOEFSFE
UIFSFQSFTTPSQSPUFJOVOBCMFUPCJOEUSZQUPQIBO &YQMBJOZPVSBOTXFS
*OOPSNBMDFMMT XIFODPODFOUSBUJPOTPGUIFBNJOPBDJEUSZQUPQIBOBSF
low

PDB ID number *: 1YSA

51

8.6

Challenge Question: Chapter 8

24PNFHFOFSFHVMBUPSZQSPUFJOTCJOEUP%/"BOEDBVTFUIFEPVCMF
IFMJYUPCFOEBUBTIBSQBOHMF4VDIACFOEJOHQSPUFJOTDBOBGGFDUUIF
JOJUJBUJPOPGUSBOTDSJQUJPOXJUIPVUDPOUBDUJOHUIF3/"QPMZNFSBTF UIF
HFOFSBMUSBOTDSJQUJPOGBDUPST PSBOZHFOFSFHVMBUPSZQSPUFJO$BOZPV
devise a plausible explanation for how such proteins might

8.7

Flashcards: Chapter 8

cell memory


t

UIFBCJMJUZPGEJGGFSFOUJBUFEDFMMTBOEUIFJSEFTDFOEBOUTUP
maintain their identity.

combinatorial control


8.8

t

EFTDSJCFTUIFXBZJOXIJDIHSPVQTPGUSBOTDSJQUJPOSFHVMBUPST
work

References: Chapter 8

$BNQCFMM,) .D8IJS+ 3JUDIJF8"8JMNVU* 


4IFFQDMPOFECZ
nuclear transfer from a cultured cell line. Natureo
%BWJETPO&) 
5IF3FHVMBUPSZ(FOPNF(FOF3FHVMBUPSZ/FUXPSLT
JO%FWFMPQNFOUBOE&WPMVUJPO#VSMJOHUPO ."&MTFWJFS

KEY TERMS
combinatorial control
differentiation
DNA methylation
epigenetic inheritance
gene expression
long noncoding RNA
microRNA (miRNA)

52

9.1 Conjugation
In this electron micrograph, one bacterium is seen contacting another
through a protein filament known as a sex pilus. Such contact initiates a
type of bacterial mating in which one bacteriumthe donor with the sex
pilitransfers DNA to a recipient, which lacks sex pili.
After the initial contact, the sex pilus retracts, reeling in the recipient
cell. Thus brought into intimate contact, the two cells form a
cytoplasmic bridge to consummate the encounter.
The donor cell contains a circular piece of DNA, called an F plasmid,
that is transferred to the recipient. The recipient acquires the F plasmid
through a process of DNA nicking and DNA synthesis.
Because the F plasmid contains all the genes required for making
sex pili and for transferring the DNA, both resulting bacteria are now
potential DNA donors.
The F plasmid can also bring along other genes from the donors
chromosome, thereby allowing for a potentially extensive genetic
transfer between the two cells.

9.2

Quiz: Chapter 9

1. Which of the following is not a mechanism of genetic variation?


Mutation within the coding sequence of a gene

Mutation within the regulatory DNA of a gene

Purifying selection

Gene duplication and divergence

Exon shuffling

9.3 Concept Questions


Analysis of a sample of skin cells reveals that the cells harbor mutations
that may cause cancer. Should the owner of these skin cells be
concerned that the mutations will be passed along to his/her offspring?
In sexually reproducing multicellular organisms, such as humans, only

53

9.4

Challenge Question: Chapter 9

4VQQPTFUIBUZPVBSFVOBCMFUPSFQBJSUIFEBNBHFUP%/"DBVTFECZ
the loss of purine bases. This defect causes the accumulation of about
NVUBUJPOTQFSEBZJOUIF%/"PGFBDIPGZPVSDFMMT"TUIFBWFSBHF
EJGGFSFODFJO%/"TFRVFODFTCFUXFFOIVNBOTBOEDIJNQBO[FFTJT
about 1%, it is only a matter of time until you turn into a chimp...

Image courtesy of R.C. Williams and


H.W. Fisher

9.5

Flashcards: Chapter 9

Alu sequence


9.6

t

GBNJMZPGNPCJMFHFOFUJDFMFNFOUTUIBUDPNQSJTFTBCPVU
of the human genome; this short, repetitive sequence is no
longer mobile on its own, but requires enzymes encoded by
other elements to transpose.

References: Chapter 9

"MGPEJ+ -JOECMBE5PI,  


$PNQBSBUJWFHFOPNJDTBTBUPPMUP
understand evolution and disease. Genome Res 23(7): 1063-8.
#BU[FS."%FJOJOHFS1- 
"-6SFQFBUTBOEIVNBOHFOPNJD
diversity. Nature Rev Genet 3:370379.

KEY TERMS
Alu sequence
conserved synteny
copy-number variation
divergence
exon shuffling
gene duplication and divergence
gene family

54

10.1

Polymerase Chain Reaction

5IFQPMZNFSBTFDIBJOSFBDUJPO PS1$3 BNQMJmFTBTQFDJmD%/"


fragment from a complex mixture.
'JSTU UIFNJYUVSFJTIFBUFEUPTFQBSBUFUIF%/"TUSBOET5XPEJGGFSFOU
specific oligonucleotide primers are added that are complementary to
short sequence stretches on either side of the desired fragment. After
MPXFSJOHUIFUFNQFSBUVSF UIFQSJNFSTIZCSJEJ[FUPUIF%/"XIFSF
they bind specifically to the ends of the desired target sequence. A heat
TUBCMF%/"QPMZNFSBTFBOEOVDMFPUJEFUSJQIPTQIBUFTBSFBEEFE5IF
polymerase extends the primers and synthesizes new complementary
%/"TUSBOET"UUIFFOEPGUIJTmSTUDZDMF UXPEPVCMFTUSBOEFE%/"
molecules are produced that contain the target sequence.
This cycle of events is repeated. The mixture is again heated to melt
UIFEPVCMFTUSBOEFE%/"5IFQSJNFSTBSFIZCSJEJ[FEBOEUIF%/"
polymerase synthesizes new complementary strands.
"UUIFFOEPGUIFTFDPOEDZDMF GPVSEPVCMFETUSBOEFE%/"NPMFDVMFT
BSFQSPEVDFEUIBUDPOUBJOUIFUBSHFUTFRVFODF*OUIFUIJSEDZDMF UIF
NJYUVSFJTIFBUFE UIFQSJNFSTBSFIZCSJEJ[FEBOE%/"QPMZNFSBTF
synthesizes new complementary strands. At the end of the third cycle,
FJHIUEPVCMFTUSBOEFE%/"NPMFDVMFTBSFQSPEVDFEUIBUDPOUBJOUIF
target sequence. Two of these molecules are precisely the length of the
UBSHFUTFRVFODF*OGVUVSFDZDMFTUIJTQPQVMBUJPOJODSFBTFTFYQPOFOUJBMMZ
$ZDMFIFBUJOH IZCSJEJ[BUJPO %/"TZOUIFTJT
"UUIFFOEPGUIFmGUIDZDMFUIFSFBSFEPVCMFTUSBOEFE%/"GSBHNFOUT
of the correct length and 10 longer ones.
$ZDMF   
After 30 cycles there are over 1 billion fragments of the correct length
but only 60 longer ones. The product therefore consists of essentially
pure target sequence.

10.2

Quiz: Chapter 10

*OUIFMBCPSBUPSZ %/"NPMFDVMFTDBOCFDVUBUTQFDJmDTFRVFODFT
using:


t 67MJHIU

t 3FTUSJDUJPOOVDMFBTFT

t %/"MJHBTF

t -BTFSUXFF[FST

Original illustrations, storyboard and music:


Christopher Thorpe

55

10.3

Media Assessment: Polymerase Chain Reaction

%VSJOHB1$3DZDMF UIFTBNQMFJTIFBUFEUP


t

BMMPXUIFQSJNFSTUPBUUBDIUPUIFUFNQMBUF%/"

t

BDUJWBUFUIFQPMZNFSBTF

t

TFQBSBUFUIF%/"TUSBOET

t

UVSOPGGUIFQPMZNFSBTF

10.4

Concept Questions: Chapter 10

8IBUJTUIFEJGGFSFODFCFUXFFOBHFOPNJDMJCSBSZBOEBD%/"MJCSBSZ
"HFOPNJDMJCSBSZJTBDPMMFDUJPOPG%/"GSBHNFOUTUIBUSFQSFTFOUTUIF
FOUJSFHFOPNFPGBHJWFOPSHBOJTN"D%/"MJCSBSZ POUIFPUIFSIBOE 
represents only the coding sequences of a genome.

10.5

Challenge Question: Chapter 10

Q: The cells in an individual animal contain nearly identical genomes.


*OBOFYQFSJNFOU BUJTTVFDPNQPTFEPGNVMUJQMFDFMMUZQFTJTmYFEBOE
TVCKFDUFEUPJOTJUVIZCSJEJ[BUJPOXJUIB%/"QSPCFUPBQBSUJDVMBSHFOF
To your surprise, the hybridization signal is much stronger in some cells
UIBUJOPUIFST&YQMBJOUIJTSFTVMU

56

10.6

Flashcards: Chapter 10

D%/"MJCSBSZ



t


DPMMFDUJPOPG%/"GSBHNFOUTTZOUIFTJ[FEVTJOHBMMPGUIF
N3/"TQSFTFOUJOBQBSUJDVMBSUZQFPGDFMMBTBUFNQMBUF

DPNQMFNFOUBSZ%/" D%/"

t

10.7

%/"NPMFDVMFTZOUIFTJ[FEGSPNBON3/"NPMFDVMFBOE
therefore

References: Chapter 10

"EBNT.% $FMOJLFS4& )PMU3"FUBM 


5IFHFOPNFTFRVFODFPG
Drosophila melanogaster. Science 287:21852195.
&NNFSU#VDL.3 #POOFS3' 4NJUI1%FUBM 
-BTFSDBQUVSF
microdissection. Scienceo

KEY TERMS
cDNA
cDNA library
dideoxy (Sanger) DNA sequencing
DNA cloning
DNA library
DNA ligase
DNA microarray

57

11.1

Fluidity of the Lipid Bilayer

To demonstrate the fluidity of the lipid bilayer, a piece of the plasma


membrane of this neuronal cell is pulled out with laser tweezers.
3FNBSLBCMZ NPWJOHUIJTNFNCSBOFUVCVMFSBQJEMZCBDLBOEGPSUIEPFT
not rupture the plasma membrane, which flows quickly to adapt to the
mechanical distortion.
Music: Christopher Thorpe

Steven M. Block
Stanford University

11.2

Lipids and Lipid Bilayer

Phospholipids contain a head group, choline in this case, that is


attached via a phosphate group to a 3-carbon glycerol backbone.
Two fatty acid tails are attached to the remaining two carbons of the
glycerol.
The head groups and the phosphate are polar, that is, they prefer to be
in an aqueous environment.
*ODPOUSBTUUIFGBUUZBDJEUBJMTBSFIZESPQIPCJD UIBUJT UIFZBSFSFQFMMFE
from water. The fatty acid tails on phospholipids can be saturated, with
no double bonds, or unsaturated, with one or more double bonds. The
double bonds are usually in the cis-configuration, which introduces
sharp kinks. When forming a bilayer, unsaturated fatty acid tails pack
MPPTFMZ XIJDIBMMPXTUIFCJMBZFSUPSFNBJOnVJE*GUIFSFXFSFOPEPVCMF
bonds, bilayers would solidify to a consistency resembling bacon
grease.
$IPMFTUFSPMJTBOPUIFSMJQJEDPNQPOFOUPGNPTUDFMMNFNCSBOFT*UIBTB
hydroxyl group, a tiny polar head group so to speak, attached to a rigid
IZESPQIPCJDUBJM$IPMFTUFSPMDBOmMMHBQTCFUXFFOQIPTQIPMJQJETBOE
thus stabilizes the bilayer.
*OBMJQJECJMBZFS MJQJETBSSBOHFUIFNTFMWFTTPUIBUUIFJSQPMBSIFBET
are exposed to water and their hydrophobic tails are sandwiched in the
middle.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Source: Beckman Institute, The Theoretical Biophysics Group University of Illinois
Urbana-Champaign
H. Heller, M. Schaefer, K. Schulten. Molecular dynamics simulation of a bilayer of
200 lipids in the gel and in the liquid-crystal phases. Journal of Physical Chemistry
97:83438360, 1993.
Lipidat Database (www.lipidat.chemistry.ohio-state.edu/)

PDB ID source: Compact lipid molecule


structure (Beckman Institute); Compilation
of saturated and unsaturated fatty acids and
cholesterol (Lipidat)

58

11.3

Membrane Disruption by Detergent

When detergent is added to this red blood cell, its membrane ruptures,
and the cytosol spills out.

Steven M. Block
Stanford University

11.4

Bacteriorhodopsin

#BDUFSJPSIPEPQTJOJTBOBCVOEBOUMJHIUESJWFOQSPUPOQVNQGPVOEJO
the membrane of Halobacter halobium, a purple archeon that lives in
TBMUNBSTIFTJOUIF4BO'SBODJTDP#BZ"SFB#BDUFSJPSIPEPQTJOJTB
multipass membrane protein that traverses the plasma membrane of
the cell with seven long helices. The helices surround a chromophore,
retinal, that is covalently attached to the polypeptide chain and gives the
protein and cells their characteristic purple color.
3FUJOBMJTBMPOH VOTBUVSBUFEIZESPDBSCPODIBJOUIBUJTDPWBMFOUMZ
attached to a lysine side chain of the protein. When retinal absorbs
a photon of light, one of its double bonds isomerizes from a trans
to a cis configuration, thus changing the shape of the molecule. The
change in retinals shape causes conformational rearrangements in the
surrounding protein.
The light-induced isomerization of retinal is the key event in proton
pumping.
*OUIFFYDJUFETUBUF SFUJOBMJTQPTJUJPOFETPUIBUJUDBOUSBOTGFSBQSPUPO
to an aspartate side chain, aspartate 85, that is positioned towards
the extracellular side of the protein. Aspartate 85 quickly hands off
the proton to the extracellular space via a bucket brigade of water
molecules. The now negatively-charged retinal takes up a proton from
another aspartate, aspartate 96; this one is positioned towards the
cytosolic face of the protein. Upon re-protonation, the retinal returns
to the ground state. Aspartate 96 replenishes its lost proton from the
cytosol, and the cycle can repeat. The net result: for each photon
absorbed, one proton is pumped out of the cell.
Molecular modelling by Tiago Barros, University of California at Berkeley

59

11.5

Membrane Effects in a Red Blood Cell

3FECMPPEDFMMTNVTUEFGPSNXIFOUIFZTRVFF[FUISPVHITNBMMCMPPE
WFTTFMT*OUIJTFYQFSJNFOUBSFECMPPEDFMMJTQVTIFEBOEEFGPSNFEXJUI
MBTFSUXFF[FST*URVJDLMZTQSJOHTCBDLUPJUTPSJHJOBMTIBQFCFDBVTFJU
has an extremely tough cytoskeleton to which the plasma membrane
is anchored. When the cell is placed in high-salt solution, however,
UIFTIBQFDIBOHFTESBNBUJDBMMZ%SJWFOCZUIFEJGGFSFODFJOPTNPUJD
pressure, water rushes out of the cell causing spike-like protrusions to
form as the cell collapses.

Steven M. Block
Stanford University
Henry Bourne and John Sedat
University of California, San Francisco
Orion Weiner
Harvard Medical School

11.6

FRAP

The lateral mobility of membrane proteins can be measured in


MJWJOHDFMMTCZ'3"1 XIJDITUBOETGPSnVPSFTDFODFSFDPWFSZBGUFS
photobleaching.
For this purpose, membrane proteins are often expressed as fusion
QSPUFJOTXJUIUIFHSFFOnVPSFTDFOUQSPUFJO('1BOEPCTFSWFEXJUIB
fluorescence microscope.
A selected area of the cell is then bleached with a strong, computer
controlled beam of laser light.
Those membrane proteins that are not anchored and therefore can
diffuse in the plane of the membrane, quickly exchange places with
their neighbors and fill back in the bleached area.
From the rate of this fluorescence recovery, the diffusion constant of the
protein can be calculated.
)FSF ('1JTGVTFEUPBNFNCSBOFQSPUFJOUIBUMJFTJOUIFNFNCSBOF
network of the endoplasmic reticulum.
After bleaching, we observe quick recovery of the fluorescence, showing
that the protein is very mobile in the plane of the membrane.
The same experiment can be repeated using a protein that is firmly
BODIPSFEBOEOPUGSFFUPEJGGVTF)FSF XFPCTFSWF('1GVTFEUP
a protein of the inner nuclear membrane that binds tightly to the
meshwork of the nuclear lamina.
After photobleaching, no fluorescence recovery can be seen over the
same time frame.
Final composition: Blink Studio Ltd. (www.blink.uk.com)
Video reproduced from: The Journal of Cell Biology 138:11931206, Figure 4B, 1997.
The Rockefeller University Press

Jennifer Lippincott-Schwartz
NICHD, National Institutes of Health

60

11.7

Rolling Leucocytes

Leucocytes are white blood cells that help fight infection. At sites of
JOKVSZ JOGFDUJPO PSJOnBNNBUJPO DZUPLJOFTBSFSFMFBTFEBOETUJNVMBUF
FOEPUIFMJBMDFMMTUIBUMJOFBEKBDFOUCMPPEWFTTFMT
The endothelial cells then express surface proteins, called selectins.
4FMFDUJOTCJOEUPDBSCPIZESBUFTEJTQMBZFEPOUIFNFNCSBOFPGUIF
leucocytes, causing them to stick to the walls of the blood vessels. This
binding interaction is of sufficiently low affinity that the leucocytes can
literally roll along the vessel walls in search for points to exit the vessel.
There, they adhere tightly, and squeeze between endothelial cells
without disrupting the vessel wallsthen crawl out of the blood vessel
JOUPUIFBEKBDFOUDPOOFDUJWFUJTTVF
Here, leucocyte rolling is observed directly in an anaesthetized mouse.
The up and down movement of the frame is due to the mouses
breathing. Two blood vessels are shown: the upper one is an artery
with blood flowing from right to left. The lower one is a veinwith
blood flowing from left to right. Leucocytes only adhere to the surface of
veins; they do not crawl out of arteries.

Marko Salmi and Sami Tohka


MediCity Research Laboratory, University of
Turku, Finland.

4PNFMFVDPDZUFTBSFmSNMZBUUBDIFEBOEBSFJOUIFQSPDFTTPGDSBXMJOH
through the vessel walls, whereas others have already left the vessel
and are seen in the surrounding connective tissue.
When the blood flow is stopped temporarily by gently clamping the
vessels, we can appreciate how densely both vessels are filled with red
CMPPEDFMMT3FECMPPEDFMMTEPOPUJOUFSBDUXJUIUIFWFTTFMXBMMTBOE
move so fast under normal flow that we cannot see them. When the
blood flow is restored, some of the leucocytes continue rolling, whereas
all noninteracting cells are immediately washed away by the shear.
Animation: Blink Studio Ltd. (www.blink.uk.com)

11.8

Laser Tweezers

The light of a laser beam that is focused into a cone through a


NJDSPTDPQFPCKFDUJWFFYFSUTTNBMMGPSDFTUIBUDBOUSBQQBSUJDMFTXJUI
high refractive indices near the focal point. This experimental set-up is
DBMMFEAMBTFSUXFF[FST*UDBOCFVTFEUPNPWFTNBMMQBSUJDMFT JODMVEJOH
cells and organelles.

Christopher Thorpe

61

11.9

Quiz: Chapter 11

8IJDIJTOPUGPVOEJOBDFMMNFNCSBOF


t -JQJE

t %/"

t 1SPUFJO

t $IPMFTUFSPM

11.10 Media Assessment: Lipids and Lipid Bilayer


The image of a lipid bilayer shows:


t

IZESPQIJMJDIFBEHSPVQTCVSJFEJOUIFJOUFSJPSPGUIFCJMBZFS

t

GBUUZBDJEUBJMTGBDJOHUIFDZUPTPMBOEUIFFYUSBDFMMVMBSTQBDF

t

GBUUZBDJEUBJMTCVSJFEJOUIFJOUFSJPSPGUIFCJMBZFS

t

#PUI"BOE#

11.11 Concept Questions: Chapter 11


8IZEPNFNCSBOFMJQJETGPSNBCJMBZFS
Membrane lipids, such as phospholipids, have both hydrophilic and
IZESPQIPCJDQBSUTBOEBSFTVCKFDUUPUXPDPOnJDUJOHGPSDFTUIF
hydrophilic heads are attracted to water, while the hydrophobic tails

62

11.12 Challenge Question: Chapter 11


.BSHBSJOFJTNBEFGSPNWFHFUBCMFPJMCZBDIFNJDBMQSPDFTT%PZPV
suppose this process converts saturated fatty acids to unsaturated ones,
PSWJDFWFSTB &YQMBJOZPVSBOTXFS
Vegetable oil is converted to margarine by reduction of double bonds...

11.13 Flashcards: Chapter 11


amphipathic


t

IBWJOHCPUIIZESPQIPCJDBOEIZESPQIJMJDSFHJPOT BTJOB
phospholipid or a detergent molecule.

bacteriorhodopsin


t

QJHNFOUFEQSPUFJOGPVOEJOBCVOEBODFJOUIFQMBTNB
membrane

11.14 References: Chapter 11


#SFUTDIFS.43BGG.$ 
.BNNBMJBOQMBTNBNFNCSBOFTNature
o
'JFEMFS4 #SPFDLFS+ ,FMMFS4 
1SPUFJOGPMEJOHJONFNCSBOFTCell
Mol Life Sci 67(11): 1179-98.

KEY TERMS
amphipathic
bacteriorhodopsin
cholesterol
detergent
glycocalyx
lipid bilayer
membrane domain

63

12.1

Aquaporins

This image from a computer simulation shows a cross section of a lipid


CJMBZFSXJUIXBUFSNPMFDVMFTPOFBDITJEF#FDBVTFXBUFSNPMFDVMFTBSF
small and uncharged, they can diffuse directly across the bilayer. This
simulation shows that water molecules occasionally and spontaneously
move into the hydrophobic core of the bilayer, even in the absence of
any channel protein. The lipid bilayer, therefore, is semi-permeable to
water.
The total concentration of solute particles inside the cell generally
exceeds the concentration of solute particles outside the cell, creating
an osmotic gradient that drives the diffusion of water molecules from
outside the cell, across the membrane, and into the cell.
As the simulation runs, observe the water molecules being bounced
around by thermal energy as they move randomly in the bilayer.
Although the water molecules will ultimately travel from the area of
low solute concentration to high solute concentration, and thus into the
cell, the likelihood of their entering the hydrophobic domain of the lipid
bilayer is very small.
To allow water to move more readily across the membrane, many cell
types, such as the epithelial cells of the kidney, use specialized channels
called aquaporins. Aquaporins selectively conduct water molecules, but
OPUJPOTPSPUIFSTPMVUFT BDSPTTUIFDFMMNFNCSBOF*OUIJTDPNQVUFS
simulation, we can see the helices of an aquaporin tetramer spanning
the plasma membrane; each monomer in the tetramer is a separate
channel through which water molecules can diffuse.
*OBDSPTTTFDUJPOPGBOBRVBQPSJODIBOOFM XFTFFUIBUUIFDIBOOFMIBT
a narrow poreone that is large enough for a single water molecule
to pass, but too small for hydrated ions to enter. One of the water
molecules is colored yellow to help track its path through the channel.
The water molecules move through the channel single-file, oriented by
JOUFSBDUJPOTXJUIUIFPUIFSXBUFSNPMFDVMFTBOEUIFDIBOOFMXBMM*OUIF
center of the pore are two strategically placed asparagines that serve
as a selectivity filter that prevents protons from passing through the
channel.
*OUIJTFYQFSJNFOU XIJDIQSPWFEUIFGVODUJPOBMOBUVSFPGBRVBQPSJOT 
UIFGSPHFHHPOUIFMFGUXBTJOKFDUFEXJUIN3/"FODPEJOHBRVBQPSJO 
and the egg on the right was used as a control. The eggs were
transferred from an isotonic solution (in which ions are at an equal
concentration inside and outside the cell) to a hypotonic salt solution
(which has a low concentration of ions). This has no effect on the
control egg because its membrane is poorly permeable to water.
However, the egg expressing aquaporins quickly begins to swell and
eventually bursts as water rushes down the osmotic gradient. This
experiment demonstrates the role aquaporins play in channeling water
across cell membranes.

Movie I
Jochen Hub & Bert de Groot
Max Planck Institute for Biophysical
Chemistry
Large Influence of Cholesterol on Solute
Partitioning into Lipid Membranes
Christian L. Wennberg, David van der
Spoel, and Jochen S. Hub
J. Am. Chem. Soc. 134, 53515361 (2012)
Movie II
Jochen Hub
Georg-August-Universitt Gttingen
Movie III
Gregory Preston

64

12.2

Na+-K+ Pump

Animal cells store energy in the form of ion gradients across the cell
NFNCSBOF*OUIFDZUPTPM UIFTPEJVNJPODPODFOUSBUJPOJTLFQUMPX
relative to the extracellular fluid, and conversely the potassium ion
concentration in the cytosol is kept high.
Like water behind a dam, these gradients harbor potential energy that
the cell taps to fuel cellular work.
Animal cells use a membrane pump, called the sodiumpotassium
pump, to maintain these ion gradients. To begin the pumping cycle,
sodium ions enter binding sites on the cytosolic side of the pump.
Although there are three sodium-binding sites on this pump, for
simplicity only one is illustrated here.
Pumping sodium against its concentration gradient requires energy,
which is provided by cleaving ATP. ATP transfers a phosphate group to
the pump in a high-energy linkage.
Phosphorylation causes a dramatic change in the pumps conformation,
so that the sodium ions become exposed and released outside of the
cell. This action also exposes binding sites for potassium ions in the
pump. Although there are two potassium-binding sites, for simplicity
only one is shown here.
#JOEJOHPGUIFQPUBTTJVNJPOTUSJHHFSTSFMFBTFPGUIFQIPTQIBUFHSPVQ
and the return of the pump to its initials conformation. The potassium
is then released inside the cell, and the cycle repeats. A complete cycle
takes about 10 milliseconds.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

12.3

Transport by Carrier Proteins

$FMMTQPTTFTTBWBSJFUZPGNFNCSBOFQSPUFJOTUPGFSSZTPMVUFTBDSPTTUIF
membrane. One type of transporter, called a uniport, carries only one
type of solute, selectively bringing it from one side of the membrane to
the other.
*ODPOUSBTUUPVOJQPSUT DPVQMFEUSBOTQPSUFSTDBSSZUXPUZQFTPGTPMVUFT
*GCPUITPMVUFTBSFNPWJOHJOUIFTBNFEJSFDUJPOBDSPTTUIFNFNCSBOF 
the transporter is called a symport.
*OUIJTFYBNQMF UIFTPMVUFSFQSFTFOUFECZUIFDJSDMFJTDBSSJFEEPXO
its concentration gradient, from high concentration to low. The energy
released by the movement of this solute drives the movement of the
other solute, represented by the square, against its concentration
gradient, from low to high concentration.
When the coupled transporter moves solutes in opposite directions
across the membrane, it is called an antiport.
*OUIJTFYBNQMF UIFTPMVUFSFQSFTFOUFECZUIFDJSDMFJTUSBOTQPSUFEEPXO
its concentration gradient, fueling the transport of the other solute
(represented by the triangle) against its concentration gradient, that is
from low to high concentration.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

65

12.4

Glucose Uptake

One important task for cells lining the lumen of the gut is the uptake of
glucose produced by digestion of food. Yet glucose is typically higher in
concentration inside the cells than in the gut, and therefore transporting
it into the cell requires energy. To this end, a glucosesodium symport
harvests the energy stored in the sodium gradient to pump glucose into
the cell.
According to one model, sodium and glucose can both bind to the
pump, but the binding of one makes the binding of the other more
effective. When the binding sites of the symport are open to the lumen
of the gut, the high sodium concentration makes sodium very likely to
bind, and thus glucose will bind more efficiently.
#FDBVTFUIFDPOGPSNBUJPOBMDIBOHFPGUIFUSBOTQPSUFSXJMMPOMZPDDVS
when both sodium and glucose binding sites are filled, both solutes
are transported across the membrane in strict unison and are released
together into the cell.
On the cytosolic side of the membrane, the solutes could, in principle,
also bind and thus be exported again by the same route that brought
them into the cell. However, while there is plenty of glucose inside the
cell, there is very little sodium. Therefore, the binding of both types of
solutes only occurs very rarely, such that most of the glucose molecules
that enter the cell will not leave by the same route. The import is
therefore unidirectional.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

12.5

Potassium Channel

The bacterial potassium channel is a multipass transmembrane protein


JOUIFQMBTNBNFNCSBOF*UJTCVJMUGSPNGPVSJEFOUJDBMTVCVOJUTUIBU
are arranged symmetrically. A pore in the center of the protein allows
selective passage of potassium ions across the membrane.
Four rigid protein loops, one contributed by each subunit, form a
selectivity filter at the narrowest part of the pore. This structure is
responsible for the channels high degree of selectivity for potassium
ions over sodium ions.
*OUIFTFMFDUJWJUZmMUFS DBSCPOZMHSPVQTMJOFUIFXBMMTPGUIFQPSF5IFTF
carbonyl groups are spaced precisely to interact with an unsolvated
potassium ion, balancing the energy required to remove its hydration
shell. Passage of a sodium ion through the channel is energetically
unfavorable because the sodium is too small for optimal interaction
with the carbonyl groups.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

PDB ID number *: 1BL8

66

12.6

Hair Cells I

5IFTPVOETFOTJUJWFDFMMTXJUIJOPVSFBSTBSFDBMMFEIBJSDFMMT&BDIIBT
a tuft of spiky extensions called stereocilia on its upper surface, and
each sends signals to auditory nerve fibers through its basal surface.
The hair cells are embedded in a layer of supporting cells and are
sandwiched between two sheets of extracellular matrixthe tectorial
NFNCSBOFBOEUIFCBTJMBSNFNCSBOF4PVOEWJCSBUJPOTDBVTFUIF
basilar membrane to vibrate, and this motion pushes the stereocilia
against the tectorial membrane. The stereocilia tilt, triggering an
electrical response in the hair cell. The activated hair cell, in turn,
activates the auditory nerve cells.
The hair cell membrane contains mechanically gated channels. These
channels are closed when the stereocilia are not tilted. However, when
they tilt, a linking filament from one stereocilium to a channel on the
neighboring stereocilium pulls at the channel, opening it. Positively
charged ions flow into the cell, depolarizing the membrane.

12.7

Hair Cells II

5IFTUFSFPDJMJBUIBUQSPKFDUGSPNIBJSDFMMTWJCSBUFJOSFTQPOTFUPTPVOE
waves.
)FSFUIFCVOEMFPGTUFSFPDJMJBQSPKFDUJOHGSPNBTJOHMFIBJSDFMMJT
pushed with laser tweezers to simulate this movement. Movement
opens stressactivated ion channels in the plasma membrane, leading
to membrane depolarization. This is translated into the perception of
sound.
Moving an individual stereocilium demonstrates the flexible attachment
of these structures to the cell body.
Music: Christopher Thorpe

67

12.8

Action Potentials

The fundamental task of a nerve cell is to receive, conduct, and transmit


signals. Neurons propagate signals in the form of action potentials,
which can travel great distances along an axon without weakening.
To transmit an action potential over such a distance without weakening
requires that the signal is continuously reamplified along the way.
The central molecular players in this process are the voltage-gated
sodium channels, which undergo a cycle of finely choreographed
conformational changes. When an action potential passes, sodium
DIBOOFMTPQFOJOSFTQPOTFUPUIFNFNCSBOFEFQPMBSJ[BUJPO4PEJVN
ions rush into the axon, further depolarizing its membrane. Within a
fraction of a thousandth of a second, however, the sodium channels
switch to a new, inactivated state, in which they are closed but now
BMTPSFGSBDUPSZUPSFPQFOJOH*OUIJTXBZ UIFNFNCSBOFQPUFOUJBM
can recover quickly after an action potential has passed. The sodium
channels then reconvert to the closed state, ready to be opened again
when the next action potential is encountered.
Lets examine the changing state of the sodium channel during an
action potential. When no stimulus is present, the sodium channels
remain closed and the electrical potential measured across the
membrane remains constant. However, if a depolarizing stimulus is
applied by a brief pulse of electric current, the membrane will start to
EFQPMBSJ[FBXBZGSPNUIFSFTVMUJOHQPUFOUJBMPGBCPVUoN74PNF
of the sodium channels will open, permitting sodium ions to enter
UIFBYPOBMPOHUIFJSDPODFOUSBUJPOHSBEJFOU*GUIFEFQPMBSJ[BUJPO
is sufficient, even more sodium channels open, and the membrane
potential rapidly approaches the equilibrium potential for sodium (about
N7
"UUIJTQPJOU UIFTPEJVNDIBOOFMTDMPTF BEPQUJOHUIFJOBDUJWF
conformation, where the channel is unable to open again even though
the membrane potential is still depolarized. The sodium channels
will remain in this inactivated state until a few milliseconds after the
membrane potential returns to its initial negative value.
The action potential is propagated along the length of the axon in only
POFEJSFDUJPO#ZFYBNJOJOHUIFNFNCSBOFQPUFOUJBMBOEUIFTUBUFPG
the sodium channels along a length of the axon, we can see why this
is so. As a depolarizing stimulus (represented in orange) reaches our
section of the membrane, sodium channels open and current flows into
UIFBYPO5IJTJOUVSOEFQPMBSJ[FTBEKBDFOUTFDUJPOTPGUIFNFNCSBOF
SFQSFTFOUFEJOCMVF
DBVTJOHBEKBDFOUTPEJVNDIBOOFMTUPPQFO BOE
UIFBDUJPOQPUFOUJBMJTUIVTQSPQBHBUFEBMPOHUIFBYPO4PEJVNDIBOOFM
inactivation prevents the depolarization from spreading backward along
the axon.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

68

12.9

Synaptic Signaling

Neurons transmit chemical signals across synapses, like the ones


shown in this electron micrograph. We can identify the dendrite
of the receiving, or postsynaptic cell, as well as two presynaptic
nerve terminals loaded with synaptic vesicles. Note the narrow cleft
separating the pre- and postsynapitic cells.
The synapse converts the electrical signal of the action potential in
the presynaptic cell into a chemical signal. When an action potential
SFBDIFTBOFSWFUFSNJOBM JUPQFOTWPMUBHFHBUFE$B2+ channels in the
QMBTNBNFNCSBOF BMMPXJOH$B2+ ions to flow into the terminal. The
JODSFBTFE$B2+ in the nerve terminal stimulates synaptic vesicles to fuse
with the plasma membrane, releasing their neurotransmitter cargo into
the synaptic cleft.

Electron Microscopy:
Cedric S. Raine
Albert Einstein College of Medicine

The released neurotransmitters diffuse across the synaptic cleft where


they bind to and open the transmitter-gated ion channels in the plasma
membrane of the postsynaptic cell. The resulting ion flows depolarize
the plasma membrane of the postsynaptic cell, thereby converting the
neurotransmitters chemical signal back into an electrical one that
can be propagated as a new action potential. The neurotransmitter is
quickly removed from the synaptic clefteither by enzymes that destroy
it, or by reuptake into the nerve terminals or neighboring cells.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

12.10 Optogenetics
Photosynthetic green algae, like the Chlamydomonas reinhardtii seen
here, use light-gated channels in their plasma membranes to sense
sunlight and navigate toward it.
*OSFTQPOTFUPCMVFMJHIU BDIBOOFMJOUIFNFNCSBOFPG
Chlamydomonascalled channelrhodopsinopens and allows Na+
to flow into the cell. This depolarizes the plasma membrane and,
ultimately, modulates the beating of the flagella that algae use to swim.
$IBOOFMSIPEPQTJOTGVODUJPOFWFOXIFOUIFZBSFBSUJmDJBMMZUSBOTGFSSFE
into other, excitable cell types, such as neurons, which then become
responsive to light.

Movie I

*OBDPNQFMMJOHFYQFSJNFOU UIFHFOFFODPEJOHDIBOOFMSIPEPQTJO
was introduced into a select subpoplation of neurons in a mouse
hypothalamus, a region of the brain involved in many functions,
including the control of aggression.

George Witman
University of Massachusetts, Worcester

The scientists then implanted a tiny fiber optic cable into the mouses
brain, in order to control the flow of blue light to the modified neurons.

Gregory J. Pazour
University of Massachusetts Medical School

This technique, called optogenetics, allows scientists to study neurons


and neural circuits in live animals.

Movies II & II

*OUIJTWJEFPGSPNUIFFYQFSJNFOU POUIFMFGU JTBNVUBUFE NBMFNPVTF


with a fiber optic cable attached to its brain. On the right is a female
mouse.
When the light from the fiber optic cable is off, the male engages in
normal mating behavior with the female. However, when the light is
switched on, the mouse immediately becomes aggressive, and violently
attacks his female companion. When the light is turned back off, the
mouse returns to normal behavior.

Anthony G. Moss
Auburn University

Dayu Lin
New York University Langone Medical
Center

69
"TJNJMBSSFTQPOTFJTFMJDJUFEXIFOBOJOBOJNBUFPCKFDU JOUIJTJOTUBODF
an inflated rubber glove, is introduced to the cage.
The mouse largely ignores the glove when the light is off. However,
when the light turns on, the mouse immediately attacks the glove. Once
the light is switched back off, the mouse resumes its normal behavior.
Optogenetics may hold the potential to revolutionize the field of
neurobiology by allowing neuroscientists to analyze with remarkable
precision the neurons and circuits underlying complex behaviors.

12.11 Neurite Outgrowth


Neuronal precursor cells, taken from the hippocampus of an embryonic
rodent brain, differentiate in culture and send out long extensions,
called neurites, that could later become dendrites or axons.
These neurites are pulled out of the cell body by growth cones that can
crawl independently over the substratum. Occasionally, a growth cone
detatches from the substratum and the neurite retracts.
New growth cones can grow from the sides of existing neurites, forming
branches.
Final composition: Blink Studio Ltd. (www.blink.uk.com)

Frank B. Gertler and Lorene Lanier


Massachusetts Institute of Technology

12.12 Neuronal Pathfinding


*OUIFFNCSZPOJDCSBJOPGUIFGSPHXenopus, neurons extend axons
from the eye to connect to appropriate target cells in the midbrain.
&BSMZJOFNCSZPHFOFTJT UIFTFDPOOFDUJPOTIBWFUPCFNBEFQSPQFSMZ
(SPXUIDPOFTBUUIFUJQTPGUIFFMPOHBUJOHBYPOTHVJEFDFMMTJOUIFSJHIU
direction.
(SPXUIDPOFTFMPOHBUFUPXBSEUIFJSUBSHFUTCZFYUFOEJOHBOESFUSBDUJOH
UIJOQSPDFTTFT DBMMFEmMPQPEJB*OUIJTXBZ UIFHSPXUIDPOFTQSPCFUIFJS
FOWJSPONFOU GPS HVJEBODF *O UIJT DBTF  UIFZ DSPTT QBUIT BT DVFT MFBE
them on unerring courses toward their targets.
After entering the appropriate part of the midbrain, the optic tectum, the
axons slow down and send out branches, which can sample numerous
target neurons and establish synaptic connections.
These two axons took six hours to grow to their targets less than a millimeter away.
Final Composition: Allison Bruce

Sonia Witte and Christine E. Holt


University of Cambridge

70

12.13 Quiz: Chapter 12


1. Which of the following membrane transport proteins forms tiny
hydrophilic pores in the membrane through which solutes can pass by
EJGGVTJPO


t "USBOTQPSUFS

t "DIBOOFM

t "QVNQ

12.14 Media Assessment: Action Potential


What is the principle ion involved in membrane depolarization during
BOBDUJPOQPUFOUJBM


t

)+

t

$M

t

$B2+

t

/B+

12.15 Concept Questions: Chapter 12


)PXEPQMBOUTLFFQUIFJSTUFNTBOEMFBWFTGSPNXJMUJOH 
The rigidity of plants ultimately stems from the movement of water.
Water, like any molecule, tends to travel down its concentration
gradient when it diffuses across a cell membrane.

71

12.16 Challenge Question: Chapter 12


Q: Your boss is coming to dinner! All you have for a salad is some
wilted, day-old lettuce. You vaguely recall that there is a trick to
SFKVWFOBUJOHXJMUFEMFUUVDF CVUZPVDBOUSFNFNCFSXIBUJUJT4IPVME
you soak the lettuce in salt water, soak it in tap water, or soak it in
TVHBSXBUFS PSNBZCFKVTUTIJOFBCSJHIUMJHIUPOJUBOEIPQFUIBU
QIPUPTZOUIFTJTXJMMQFSLJUVQ

Image courtesy of Olaf Mundigl and


Pietro de Camilli

12.17 Flashcards: Chapter 12


action potential


t

USBWFMJOHXBWFPGFMFDUSJDBMFYDJUBUJPODBVTFECZSBQJE 
transient, self-propagating depolarization of the plasma
membrane in a neuron or other excitable cell; also called
a nerve impulse.

12.18 References: Chapter 12


Al-Awqati Q (1999) One hundred years of membrane permeability: does
0WFSUPOTUJMMSVMF Nature Cell Biol&o&
(PVBVY&BOE.BD,JOOPO3 
1SJODJQMFTPGTFMFDUJWFJPOUSBOTQPSU
in channels and pumps. Scienceo

KEY TERMS
action potential
active transport
antiport
axon
Ca2+ pump (or Ca2+-ATPase)
channel
coupled pumps

72

13.1

Glycolysis

$FMMTCSFBLEPXOGPPENPMFDVMFT TVDIBTHMVDPTF UISPVHINVMUJTUFQ


QBUIXBZT*OUIFQSPDFTTPGHMZDPMZTJT UIFCSFBLEPXOPGPOFHMVDPTF
molecule into two three-carbon molecules produces a net gain of energy
UIBUJTDBQUVSFECZUIFNPMFDVMFT"51BOE/"%)*OFVDBSZPUFT UIF
breakdown product, pyruvate, is imported into mitochondria, where it
ultimately feeds into the citric acid cycle and the electron transport chain.
(MZDPMZTJTJOWPMWFTBTFRVFODFPGTUFQT*OUIFmSTUUISFFTUFQT 
FOFSHZJOUIFGPSNPG"51JTJOWFTUFEUPCFSFDPVQFEMBUFS*OUIFGPVSUI
and fifth steps, this energy allows glucose to be split into two smaller
molecules from which energy can be harnessed efficiently. And in the last
mWFTUFQT FOFSHZJTSFMFBTFETUFQXJTFBT"51BOE/"%)5IFFMFHBOU
chemistry that evolved to catalyze these reactions ensures that energy is
released in small portions that can be efficiently captured. Less controlled
combustion reactions would release most of the energy as heat.
*OUIFmSTUTUFQ UIFFO[ZNFIFYPLJOBTFVTFT"51UPQIPTQIPSZMBUF
glucose. This investment of energy primes glucose for energy-releasing
reactions later in glycolysis.
5IFSFTVMUJOHNPMFDVMFJTHMVDPTFQIPTQIBUF"%1JTSFMFBTFE5IJTmSTU
step of glycolysis is irreversible.
*OUIFTFDPOETUFQPGHMZDPMZTJT UIFFO[ZNFQIPTQIPHMVDPTFJTPNFSBTF
catalyzes the opening of the ring form of glucose 6-phosphate to the
open chain form.
The same enzyme then performs a reversible reaction in which the
carbonyl group of glucose 6-phosphate changes position from the first
carbon to the second carbon in the chain.
This reaction involves a water molecule, which donates a hydrogen ion
to the carbonyl oxygen.
The hydrogen ion is then retrieved from the hydroxyl group on the
TFDPOEDBSCPO DSFBUJOHBOFXXBUFSNPMFDVMF*OUIFQSPDFTT GSVDUPTF
6-phosphate is formed.
The same enzyme, phosphoglucose isomerase, catalyzes the formation
of fructose 6-phosphate into its ring form.
*OUIFUIJSETUFQPGHMZDPMZTJT UIFFO[ZNFQIPTQIPGSVDUPLJOBTFVTFT"51
UPQIPTQIPSZMBUFGSVDUPTFQIPTQIBUF"%1JTSFMFBTFEBOEUIFNPMFDVMF
fructose 1,6-bisphosphate is formed.
This third step, in which the second phosphorylation event occurs,
JTJSSFWFSTJCMFBOEJTBNBKPSSFHVMBUPSZQPJOUJOUIFDPNNJUNFOUUP
glycolysis.
The phosphorylations in steps 1 and 3 represent an investment of energy
that will be paid back in the later stages of the pathway.
4UFQPGHMZDPMZTJTCFHJOTXJUIUIFPQFOJOHPGUIFSJOHGPSNPGGSVDUPTF
1,6- bisphosphate into its open chain form.
*OUIJTTUFQ UIFFO[ZNFBMEPMBTFDMFBWFTGSVDUPTF CJTQIPTQIBUFJOUP
two molecules.
One molecule that is formed is the 3-carbon glyceraldehyde 3-phoshate.
The enzyme performs additional reactions on the second 3-carbon
molecule. The second molecule is dihydroxyacetone phosphate.
*OTUFQPGHMZDPMZTJT UIFFO[ZNFUSJPTFQIPTQIBUFJTPNFSBTFDBUBMZ[FT
the isomerization of dihyroxyacetone phosphate into glyceraldehyde
3-phosphate.

73
The catalytic mechanism of this enzyme is very similar to that of
phosphoglucose isomerase, back in step 2. The result is two molecules
of glyceraldehyde 3-phosphate.
All of the subsequent steps of glycolysis will occur twiceonce for
each molecule of glyceraldehyde 3-phosphate. These are the energy
generation steps of gylcolysis.
*OTUFQ UIFFO[ZNFHMZDFSBMEFIZEFQIPTQIBUFEFIZESPHFOBTFVTFT
/"%+ to oxidize glyceraldehyde 3-phosphate. The resulting molecule is
connected to the enzyme by a high-energy thioester bond.
A molecule of inorganic phosphate displaces the high-energy thioester
bond, forming a high-energy acyl-anhydride bond. The resulting
molecule is 1,3-bisphosphoglycerate.
*OUIFTFWFOUITUFQ UIFFO[ZNFQIPTQIPHMZDFSBUFLJOBTF
dephosphorylates 1,3-bisphosphoglycerate. The high-energy phosphate
JTUSBOTGFSSFEUP"%1 GPSNJOH"515IFDBSCPONPMFDVMFJTOPX
QIPTQIPHMZDFSBUF#FDBVTFUIJTSFBDUJPOPDDVSTUXJDF PODFGPSFBDI
3-carbon molecule, a total of 2 ATPs are generated. At this point the
energy investment from the first three steps has been paid back.
*OUIFFJHIUITUFQ QIPTQIPHMZDFSBUF XIJDIIBTBSFMBUJWFMZMPXGSFF
energy of hydrolysis, is transformed by the enzyme phosphoglycerate
mutase into 2- phosphoglycerate.
*OUIFOJOUITUFQ UIFFO[ZNFFOPMBTFSFNPWFTBXBUFSNPMFDVMFGSPN
2-phosphoglycerate, creating phosphoenolpyruvate. The loss of water
redistributes energy within the molecule, creating a phosphate group
with an extremely high free-energy of hydrolysis.
*OUIFUFOUIBOEMBTUTUFQPGHMZDPMZTJT UIFFO[ZNFQZSVWBUFLJOBTF
USBOTGFSTUIFIJHIFOFSHZQIPTQIBUFHSPVQUP"%1 GPSNJOH"51BOE
pyruvate.
*OUIFTFDPOEIBMGPGHMZDPMZTJT NBOZPGUIFSFBDUJPOTSFMFBTFFOFSHZ 
DBQUVSFEJOUIFGPSNPG"51BOE/"%)0WFSBMMUIFOFUFOFSHZQSPEVDFE
in glycolysis from a single molecule of glucose is two molecules of ATP
BOEUXPNPMFDVMFTPG/"%)
The chemistry of glycolysis is conserved all the way from bacteria to
animal cells.
Chemistry Consultant: Patricia S. Caldera-Muoz
Storyboard and Animation: Sumanas, Inc. (www.sumansinc.com)

74

13.2

Citric Acid Cycle

$FMMTCSFBLEPXOGPPENPMFDVMFT TVDIBTHMVDPTF UISPVHINVMUJ


step pathways. For example, in the process of glycolysis, breakdown
of glucose molecules releases energy that is captured by the energy
DBSSJFSNPMFDVMFT TVDIBT"51BOE/"%)"CSFBLEPXOJOUFSNFEJBUF 
pyruvate, is imported into mitochondria, where it is converted into
BDFUZM$P"BOEGFEJOUPUIFDJUSJDBDJEDZDMF"DFUZM$P"DBOBMTPCF
generated by breakdown of fats or amino acids.
*OUIJTDJSDVMBSSFBDUJPOQBUIPGUIFDJUSJDBDJEDZDMF DBSCPOBUPNTBSF
burnedthat is, oxidizedand released one-by-one as the waste
QSPEVDUDBSCPOEJPYJEF*OUIJTXBZ FOFSHZJTSFMFBTFETUFQXJTFBOE
DBQUVSFECZFOFSHZDBSSJFST JODMVEJOH/"%)/"%)GVOOFMTFOFSHZUP
the electron transport chain in the inner mitochondrial membrane. This
fuels the proton gradient that is then used for the production of ATP, the
cells primary energy currency.
The molecule that enters the citric acid cycle is the 2-carbon compound
BDFUZM$P""DFUZM$P"KPJOTXJUIUIFDBSCPOPYBMPBDFUBUFUPDSFBUF
the 6-carbon citrate.
8FMMUSBDLUIFDBSCPOTGSPNBDFUZM$P"XJUIBSFEDPMPS5IFUXP
carbon atoms from oxaloacetate marked in blue will be released during
this cycle to form carbon dioxide.
*OUIFOFYUTUFQPGUIFDZDMF DJUSBUFSFBSSBOHFTUPGPSNJTPDJUSBUF/PUF
that the hydroxyl group is in a different position in these two molecules.
*OUIFOFYUTUFQ FOFSHZJTDBQUVSFECZBO/"%)NPMFDVMF BOEB
NPMFDVMFPGDBSCPOEJPYJEFJTSFMFBTFE*OUIJTSFBDUJPO JTPDJUSBUFJT
converted to aketoglutarate. The hydroxyl-bound carbon is stripped
of its hydrogen atoms, resulting in a carbonyl group. One of these
IZESPHFOBUPNTJTQJDLFEVQCZ/"%+UPGPSN/"%) BOEBOPUIFSJT
released as a proton. The carbon and 2 oxygen atoms are then released
BT$02, creating the 5-carbon aketoglutarate.
5IFOFYUSFBDUJPOBMTPQSPEVDFT/"%)BOESFMFBTFT$02. The
LFUPHMVUBSBUFGSPNUIFQSFWJPVTSFBDUJPOJTDPOWFSUFEUPTVDDJOZM$P"
by the addition of the coenzyme A. The enzyme for this reaction adds a
high-energy thioester bond to coenzyme A, releasing the carbon and 2
PYZHFOBUPNTBOEDPOWFSUJOH/"%+UP/"%)
5IFOFYUSFBDUJPOSFMFBTFTFOPVHIFOFSHZUPGPSN(51 BOFOFSHZ
DBSSZJOHNPMFDVMFSFMBUFEUP"51*OUIJTSFBDUJPO TVDDJOZM$P"JT
converted into succinate. The release of the coenzyme A group provides
UIFFOFSHZUPDPNCJOF(%1BOEJOPSHBOJDQIPTQIBUFJOUP(51
Note that succinate is symmetrical molecule. The two end carbons are
chemically identical, and the two carbons in the middle are chemically
identical. For convenience we will continue tracing only the 2 carbons
depicted in the upper half of the molecule.
*OUIFOFYUTUFQ BNPMFDVMFPG'"%)2JTQSPEVDFE'"%)2 MJLF/"%) 
is an energy carrier that feeds high-energy electrons to the electron
USBOTQPSUDIBJO*OUIJTSFBDUJPO TVDDJOBUFJTDPOWFSUFEUPGVNBSBUF
)ZESPHFOBUPNTGSPNTVDDJOBUFBSFTUSJQQFEPGGBOEEPOBUFEUP'"%UP
QSPEVDF'"%)2.
*OUIFOFYUSFBDUJPO GVNBSBUFDPNCJOFTXJUIBXBUFSNPMFDVMF5IF
resulting molecule is malate, with the water molecule added across the
two central carbons.
5IFOFYUTUFQQSPEVDFTUIFmOBM/"%)NPMFDVMF*OUIJTSFBDUJPO 
malate is converted to oxaloacetate. The carbon carrying the hydroxyl

75
group is converted to a carbonyl group. This reaction releases hydrogen
BUPNTBOEDPOWFSUT/"%+UP/"%) SFMFBTJOHBQSPUPO BOEQSPEVDJOH
the four-carbon oxaloacetate.
Oxaloacetate is thus replenished and can take part in another cycle,
returning to step 1. Note the new position of the red carbon atoms,
XIJDIPSJHJOBUFEGSPNUIFBDFUZM$P"JOUIFQSFWJPVTDZDMF*O
TVCTFRVFOUDZDMFT UIFTFDBSCPOTXJMMFWFOUVBMMZCFMPTUBT$02. The
green labels indicate the positions of the new carbons added during this
new cycle.
Chemistry Consultant: Patricia S. Caldera-Muoz
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

13.3

Quiz: Chapter 13

1. The energy released by oxidizing glucose is saved in the high-energy


bonds of:


t "%1BOEPUIFSBDUJWBUFEDBSSJFSNPMFDVMFT

t "51BOEPUIFSBDUJWBUFEDBSSJFSNPMFDVMFT

t (51BOEPUIFSBDUJWBUFEDBSSJFSNPMFDVMFT

t )20BOE$02.

13.4

Media Assessment: Glycolysis

The end product of glycolysis is:




t

UXPNPMFDVMFTPGQZSVWBUF

t

POFNPMFDVMFPGQZSVWBUF

t

POFNPMFDVMFPGQIPTQIPFOPMQZSVWBUF

t

UXPNPMFDVMFTPGQIPTQIPFOPMQZSVWBUF

76

13.5

Concept Questions: Chapter 13

*GBDFMMJTEFQSJWFEPGPYZHFO DBOJUDPOUJOVFUPQSPEVDFFOFSHZGSPN
UIFCSFBLEPXOPGHMVDPTF &YQMBJO
:FT*OBFSPCJDDFMMT HMVDPTFJTCSPLFOEPXOCZBTFSJFTPGDIFNJDBM
reactions, starting with glycolysis and ending with oxidative
phosphorylation...

13.6

Challenge Question: Chapter 13

*OUIFBCTFODFPGPYZHFO DFMMTDPOTVNFHMVDPTFBUBIJHI TUFBEZSBUF


When oxygen is added, glucose consumption drops precipitously and is
then maintained at the lower rate. Why is glucose consumed at a high
SBUFJOUIFBCTFODFPGPYZHFOBOEBUBMPXSBUFJOJUTQSFTFODF

Image courtesy of Peter Tontonoz and


Ronald M. Evans

13.7

Flashcards: Chapter 13

anabolic pathway


t

TFSJFTPGFO[ZNFDBUBMZ[FESFBDUJPOTCZXIJDIMBSHFCJPMPHJDBM
molecules are synthesized from smaller subunits; usually
requires an input of energy.

KEY TERMS
acetyl CoA
ADP, ATP
anabolic pathways
catabolism
cell respiration
citric acid cycle
electron-transport chain

77

13.8

References: Chapter 13

$SBNFS8",OBGG%# 
&OFSHZ5SBOTEVDUJPOJO#JPMPHJDBM
.FNCSBOFT/FX:PSL4QSJOHFS7FSMBH
%JTNVLFT($ ,MJNPW77 #BSBOPW47FUBM 
5IFPSJHJO
PGBUNPTQIFSJDPYZHFOPO&BSUI5IFJOOPWBUJPOPGPYZHFOJD
photosyntheis. Proc Nat Acad Sci USA 98:21702175.

78

14.1

Tomogram of Mitochondrion

A mitochondrion contained in a one-half micrometer thick section


of chicken brain is viewed with a high voltage electron microscope.
When the section is tilted in the microscope, it can be viewed from
many different angles, and a large amount of three-dimensional detail
CFDPNFTBQQBSFOU*NBHFTGSPNTVDIBTFSJFTPGUJMUFEWJFXTDBOCF
used to calculate a three-dimensional reconstruction, or tomogram, of
the mitochondrion.
The tomogram of the same tissue slice is shown here as a series of
stacked images. The movie steps through the images one by one, from
the bottom of the stack, to the top, and back. This allows us to trace
individual membranes in three-dimensions.
To create a three-dimensional model, membranes in an individual
TMJDFPGUIFUPNPHSBNBSFUSBDFE*OUIJTDBTFUIFJOOFSNFNCSBOF
is traced in light blue, where it parallels the outer membrane, and
traced in yellow, where it folds into the cristae that protrude into the
mitochondrial interior. The tracings from all sections are then modeled
as three-dimensional surfaces, and displayed as a three-dimensional
NPEFMCZBDPNQVUFSQSPHSBN4VDIBNPEFMDBOOPXCFWJFXFEGSPN
any angle.
*OUIJTWJFX POMZGPVSDSJTUBFBSFTIPXOBOEUIFPUIFSTBSFPNJUUFE
The cristae are colored differently and show the variety of shapes and
connections to the inner membrane in a single mitochondrion.
The model also shows the reconstitution of the outer mitochondrial
membrane, represented in dark blue, as well as two fragments of
FOEPQMBTNJDSFUJDVMVN3FHJPOTPGTVDIDMPTFQSPYJNJUZCFUXFFOUIF
two organelles are quite frequently seen in cells. Note that there is
no continuity between the mitochondrial and endoplasmic reticulum
membranes. Lipids are thought to be shuttled between the two
organelles by special carrier proteins that operate in this gap.
Final composition: Graham Johnson, Fivth Element (www.fivth.com)

14.2

Electron-Transport Chain

The mitochondrion is the site of most of the cells energy production.


After food molecules are processed in the cytosol, they enter the
NJUPDIPOESJPO XIFSFUIFZBSFGVSUIFSCSPLFOEPXO*OUIFDJUSJDBDJE
cycle, the molecules are stripped of high-energy electrons, which are
EPOBUFEUPDBSSJFSNPMFDVMFT TVDIBT/"%)
The carrier molecules transfer the high-energy electrons to a chain of
proteins, called the electron transport chain, which is embedded in the
inner mitochondrial membrane. The chain acts as a pump, using the
energy of the electrons to move protons from one side of the membrane
to the other. The pumping creates a proton gradient across the
membrane, which the mitochondrion can tap to make the fuel molecule
ATP.
5IFFMFDUSPOUSBOTGFSCFHJOTBUBNVMUJQSPUFJODPNQMFYDBMMFEUIF/"%)
dehydrogenase complex. This complex has a higher affinity for electrons
UIBO/"%) BOEFBTJMZTUSJQTBXBZUIFIJHIFOFSHZFMFDUSPOT"TUIF
electrons are transferred from one protein to another in the complex,
energy is released and used to pump protons across the membrane.

Terrence G. Frey
San Diego State University
Guy Perkins
University of California, San Diego

79
&MFDUSPOTBSFUIFOUSBOTGFSSFEUPVCJRVJOPOF BEJGGFSFOUDBSSJFSUIBU
shuttles them to the next way station, called the cytochrome b-c1
DPNQMFY XIJDIBHBJOQVNQTQSPUPOTBTUIFZnPXUISPVHIJU#FDBVTF
each complex in the chain has a higher affinity for the electrons
than the previous one, the electrons keep moving through the chain
unidirectionally.
Finally, cytochrome c delivers the electrons to the cytochrome oxidase
complex, a third proton pump. The cycle repeats until the cytochrome
PYJEBTFDPNQMFYIBTBDDVNVMBUFEFMFDUSPOT
From there, they are handed over to molecular oxygen. Oxygen takes
up the electrons as it combines with protons, forming water as product,
thereby completing the step-wise path of the combustion of the food
molecules.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

14.3

ATP SynthaseA Molecular Turbine

ATP synthase is a molecular machine that works like a turbine to


convert the energy stored in a proton gradient into chemical energy
stored in the bond energy of ATP.
The flow of protons down their electrochemical gradient drives a rotor
UIBUMJFTJOUIFNFNCSBOF*UJTUIPVHIUUIBUQSPUPOTnPXUISPVHIBO
entry open to one side of the membrane and bind to rotor subunits.
Only protonated subunits can then rotate into the membrane, away
from the static channel assembly. Once the protonated subunits have
completed an almost full circle, and have returned to the static subunits,
an exit channel allows them to leave to the other side of the membrane.
*OUIJTXBZ UIFFOFSHZTUPSFEJOUIFQSPUPOHSBEJFOUJTDPOWFSUFEJOUP
mechanical, rotational energy.
The rotational energy is transmitted via a shaft attached to the rotor that
penetrates deep into the center of the characteristic lollipop head, the
F1 ATPase, which catalyzes the formation of ATP.
The F1 ATPase portion of ATP synthase has been crystallized.
*UTNPMFDVMBSTUSVDUVSFTIPXTUIBUUIFQPTJUJPOPGUIFDFOUSBMTIBGU
influences the conformation and arrangement of the surrounding
TVCVOJUT*UJTUIFTFDIBOHFTUIBUESJWFUIFTZOUIFTJTPG"51GSPN"%1
*OUIJTBOJNBUFENPEFM EJGGFSFOUDPOGPSNBUJPOBMTUBUFTBSFMJOFEVQBT
a temporal sequence as they would occur during rotation of the central
shaft.
-JLFBOZFO[ZNF "51TZOUIBTFDBOXPSLJOFJUIFSEJSFDUJPO*GUIF
concentration of ATP is high and the proton gradient low, ATP synthase
will run in reverse, hydrolyzing ATP as it pumps protons across the
membrane.
To show the rotation of the central shaft, a short fluorescent actin
mMBNFOUXBTFYQFSJNFOUBMMZBUUBDIFEUPJU4JOHMFmMBNFOUTBUUBDIFEUP
single F1 ATPases can be visualized in the microscope.
When ATP is added, the filament starts spinning, directly demonstrating
the mechanical properties of this remarkable molecular machine.
Animation: Graham Johnson, Fivth Element (www.fivth.com)

80

14.4

ATP SynthaseDisco

4VCVOJUT


$FOUFS HBNNBTVCVOJU
5PZPLJ"NBOP

-FGU CFUBTVCVOJU
)JSPZVLJ/PKJ

3JHIU CFUBTVCVOJU
4BUPTIJ15TVOPEB

#BDL CFUBTVCVOJU
.BTBLJ4IJCBUB

Dance direction: Nagatsuta Bon-Odori


Camera work and production: Hiroyuki Noji

14.5

Bacterial Flagellum

Many species of bacteria propel themselves through their environment


by spinning helical motorized flagella. Rhodobacter cells have one
flagellum each, whereas E. coli cells have multiple flagella that rotate
JOCVOEMFT&BDInBHFMMVNDPOTJTUTPGBIFMJDBMmMBNFOUUIBUJT
nanometers wide and up to 15 microns long and spins on the order of
100 times per second. These animations show a series of schematized
and speculative models about how bacterial flagella might function and
assemble.
Just outside of the cell wall, the filament is connected to a flexible
rotating hook.
The filament, the hook, and a structure called the basal body (located
below the cells surface) make up the three parts of the flagellum. The
basal body consists of a rod and a series of rings embedded in the inner
membrane, the peptidoglycan layer, and the outer membrane.
4PNFPGUIFSJOHTNBLFVQUIFnBHFMMBSNPUPS XIJDIDBOCFEJWJEFE
JOUPUXPNBKPSQBSUTUIFTUBUPS XIJDIJTBUUBDIFEUPUIFQFQUJEPHMZDBO
layer and, as its name implies, remains stationary, and the rotor, which
rotates.
The motor derives its power from a proton gradient across the
NFNCSBOF*OUIJTFYBNQMF BIJHIDPODFOUSBUJPOPGQSPUPOTFYJTUT
outside and a low concentration exists inside the cell.
The protons flow through the interface between two types of proteins,
DBMMFE.PU"BOE.PU#UIBUNBLFVQUIFTUBUPS
.VUBUJPOBMTUVEJFTTVHHFTUUIBUBDPOTFSWFEBTQBSUJDBDJEJO.PU#
GVODUJPOTJOQSPUPODPOEVDUBODF&BDITUBUPSDPOUBJOTUXP.PU#
proteins and therefore also contains two of these important aspartic
acids.
Although the molecular mechanism of rotation is not known, one
possible model describes protons moving through the channels in the
TUBUPSTBOECJOEJOHUPUIFBTQBSUJDBDJEJOUIF.PU#QSPUFJOT5IJT
binding causes a conformational change in MotA proteins, resulting in
the first power stroke that moves the rotor incrementally.
At the end of the first power stroke, the two protons are released into
the cytoplasm. The proton loss causes a second conformational change
that drives the second power stroke, once again engaging the rotor.
Although the mechanism for motor function is not yet certain, many
details of flagellar assembly have been determined.

Video: Howard C. Berg, Harvard University


3D Animation and Flagellar Structures:
Keiichi Namba, Protonic NanoMachine
Project, ERATO, JST & Osaka University

81
Flagella begin their assembly with structures in the inner membrane.
26 subunits of an integral membrane protein called FliF come together
JOUIFQMBTNBNFNCSBOFUPGPSNUIF.4SJOH5IF'MJ(QSPUFJOT
BTTFNCMFVOEFSUIF.4SJOH'MJ( BMPOHXJUI'MJ.BOE'MJ/QSPUFJOT 
make up the rotor.
Flagellar proteins destined to be part of the extracellular portion of
the flagellum are exported from the cell by a flagellum-specific export
pathway and assembled at the center.
.PU"BOE.PU#GPSNUIFTUBUJPOBSZQBSUPGUIFnBHFMMBSNPUPSUIF
TUBUPS#PUIBSFJOUFHSBMNFNCSBOFQSPUFJOT CVU.PU#JTBMTPBODIPSFE
to the rigid peptidoglycan layer, keeping the stator proteins fixed in
place.
The subunits of the rod portion of the rotor move up through the hollow
cylinder in the assembly and, assisted by cap proteins, build up the rod
in a proximal to distal fashion.
Another set of rings, called L and P rings, are found in gram negative
bacteria, such as E. coli. They penetrate the outer membrane forming a
bearing for the rod.
As the rod cap is exposed outside the L ring, it dissociates and is
replaced by a hook cap that guides the assembly of the hook proteins.
After the hook is assembled, the hook cap dissociates, and a series of
KVODUJPOQSPUFJOTBTTFNCMFCFUXFFOUIFIPPLBOEGVUVSFmMBNFOU
Finally, yet another cap is built and filament proteins assemble. Like the
rod and hook proteins, they travel through the hollow channel inside
the filament to reach the distal end. The cap rotates which causes the
subunits to build in a helical fashion. A complete filament can consist of
20,000 to 30,000 subunits.

14.6

Photosynthetic Reaction Center

The bacterial photosynthetic reaction center is a large complex of


four protein subunits. Three subunits, called the H, L, and M subunits,
contain hydrophobic helices that span the membrane and anchor
the complex. The fourth subunit is a cytochrome that is peripherally
attached.
&OFSHZUSBOTGFSUISPVHIUIFSFBDUJPODFOUFSJOWPMWFTQJHNFOUNPMFDVMFT
UIBUBSFPSHBOJ[FEJOUIFJOUFSJPSPGUIFQSPUFJODPNQMFY&YDJUFE
electrons generated after absorption of light move from centrally
located chlorophylls to pheophytins. From there they move to a
quinone, which is then released from the reaction center to feed the
FMFDUSPOTJOUPUIFFMFDUSPOUSBOTQPSUDIBJO&MFDUSPOTMPTUGSPNUIF
chlorophylls are replaced through a conduit of heme groups found in
the cytochrome subunit.
Molecular modelling and animation: Timothy Driscoll, Molvisions

PDB ID number *: 1DXR

82

14.7

Light Harvesting

*OQMBOUDFMMT DIMPSPQMBTUTDBSSZPVUQIPUPTZOUIFTJT5IFTFMBSHF 
dedicated organelles contain a variety of membrane components
UIBUDPOWFSUUIFFOFSHZJOMJHIUJOUPUIFFOFSHZDBSSJFST/"%1)BOE
ATP, which in turn fuel the production of sugars and other molecules
required by the cell.
$IMPSPQMBTUTIBWFUISFFEJTUJODUNFNCSBOFTZTUFNTBUXPNFNCSBOF
envelope akin to that surrounding mitochondria, and the internal
thylakoid membrane system. Within the thylakoid membranes large
antennae consisting of hundreds of light-absorbing chlorophyll
molecules capture light energy. When a chlorophyll molecule absorbs
light, the energy bumps from one chlorophyll molecule to another, until
it passes to a special pair of chlorophyll molecules in the reaction center
PGQIPUPTZTUFN**
*OUIFSFBDUJPODFOUFS UIFFOFSHZDBVTFTBOFMFDUSPOJODIMPSPQIZMM
UPKVNQUPBIJHIFSFOFSHZMFWFM5IJTKVNQJOJUJBUFTBMPOHTFSJFTPG
electron transfers. First, a neighboring molecule accepts the high-energy
FMFDUSPO*OUIFNFBOUJNF BOPUIFSOFJHICPSJOHNPMFDVMFEPOBUFTB
MPXFOFSHZFMFDUSPOUPUIFEFmDJFOUDIMPSPQIZMMNPMFDVMF*OUVSO UIJT
donor molecule receives a low-energy electron from water. After this
series of transfers occurs four times, two water molecules are split into
one molecule of oxygen and four protons.
The photosystem shares the thylakoid membranes with an electron
transport chain. When light bumps an electron out of the photosystem,
the electron is removed by a small diffusible carrier molecule. As shown
before, water replenishes lost electrons. The diffusible carrier molecule
brings the electrons to the cytochrome b6-f complex, which uses part
of the electrons energy to pump protons across the membrane. From
UIFSF UIFFMFDUSPOTUSBWFMUPQIPUPTZTUFN*
+VTUMJLFQIPUPTZTUFN** QIPUPTZTUFN*BCTPSCTMJHIUUISPVHIJUTPXO
antenna system and kicks electrons to an even higher energy level.
After two such high-energy electrons have been produced and delivered
UPGFSSFEPYJO/"%1SFEVDUBTF UIFZESJWFUIFSFEVDUJPOPG/"%1 UP
/"%1)
To make the system work, each member of the electron transport chain
has to be finely tuned to have an appropriate tendency to receive or
EPOBUFFMFDUSPOT NFBTVSFEBTBSFEPYQPUFOUJBM8IFOQIPUPTZTUFN**
is excited by light, it has a high tendency to donate electrons. The next
component is more likely to receive electrons. The loss of an electron
GSPNQIPUPTZTUFN**OPXNBLFTJUBOFYDFMMFOUFMFDUSPOBDDFQUPS 
receiving electrons from water. The next series of carriers in the chain
make better and better acceptors, drawing the electron through the
chain.
The released energy is used to generate a proton gradient that fuels
"51QSPEVDUJPO5IFHPBMPGQIPUPTZTUFN*JTUPEPOBUFBOFMFDUSPOUP
GFSSSPEPYJO/"%1SFEVDUBTF*OPSEFSGPSUIJTUPIBQQFO UIFFMFDUSPO
has to be bumped up to an even higher energy level than that absorbed
CZQIPUPTZTUFN**5PEPUIJT QIPUPTZTUFN*NVTUBCTPSCBOPUIFS
QIPUPOPGMJHIU5XPTVDIFMFDUSPOTFOFSHJ[FECZQIPUPTZTUFN*XJMM
QSPEVDFBNPMFDVMFPG/"%1)
'PSFWFSZUXPXBUFSNPMFDVMFTTQMJUCZQIPUPTZTUFN** FMFDUSPOTBSF
VMUJNBUFMZEPOBUFEUPQSPEVDF/"%1)
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

83

14.8

Quiz: Chapter 14

8IBUJTUIFNBJODIFNJDBMDVSSFODZJODFMMT


t (MVDPTF

t /"%)

t "51

t )JHIFOFSHZFMFDUSPOT

14.9

Media Assessment: Electron Transport Chain

The electron transport chain pumps protons:




t

BDSPTTUIFQMBTNBNFNCSBOF

t

BDSPTTUIFPVUFSNJUPDIPOESJBMNFNCSBOF

t

BDSPTTUIFJOOFSNJUPDIPOESJBMNFNCSBOF

t

PVUPGUIFNJUPDIPOESJPO

14.10 Concept Questions: Chapter 14


8IBUJTUIFEJGGFSFODFCFUXFFOQIPUPTZTUFNT*BOE**
1IPUPTZTUFN**EPOBUFTFMFDUSPOTUPBOFMFDUSPOUSBOTQPSUDIBJO5IFTF
electrons pass through a proton pump, which uses their movement to
generate an electrochemical proton gradient that ultimately produces
ATP

84

14.11 Challenge Question: Chapter 14


The uncoupler dinitrophenol was once prescribed as a diet drug to aid
in weight loss. How would an uncoupler of oxidative phosphorylation
QSPNPUFXFJHIUMPTT 8IZEPZPVTVQQPTFUIBUJUJTOPMPOHFSQSFTDSJCFE
An uncoupler promotes weight loss by decreasing the efficiency of

Image courtesy of Chan B. Park

14.12 Flashcards: Chapter 14


antenna complex


t

JODIMPSPQMBTUTBOEQIPUPTZOUIFUJDCBDUFSJB UIFQBSUPGUIF
membrane-bound photosystem that captures energy from
sunlight; contains an array of proteins that bind hundreds of
chlorophyll molecules and other photosensitive pigments.

14.13 References: Chapter 14


"CSBIBNT+1 -FTMJF"( -VUUFS38BMLFS+& 
4USVDUVSFBU
resolution of F1-ATPase from bovine heart mitochondria. Nature
370:621628.
#FSH)$ 
5IFSPUBSZNPUPSPGCBDUFSJBMnBHFMMBAnnu Rev Biochem


KEY TERMS
antenna complex
ATP synthase
carbon fixation
cell respiration
chemiosmotic coupling
chlorophyll
chloroplast

85

15.1

Nuclear Import

Nuclear import and export can be directly visualized in living cells that
FYQSFTTUIFHSFFOnVPSFTDFOUQSPUFJO('1GVTFEUPUIFHFOFSFHVMBUPSZ
protein NF-AT.
NF-AT is normally localized in the cytosol, and excluded from the
OVDMFVT#VUXIFOUIFDZUPTPMJDDBMDJVNDPODFOUSBUJPOJTSBJTFE /'"5
migrates to the nucleus.
This is done here experimentally by adding an ionophore that allows
calcium to enter the cells from the medium.
Upon removal of the ionophore, calcium levels return to normal and
NF-AT is exported from the nucleus.
3FBEEJUJPOPGUIFJPOPQIPSFUSJHHFSTSFJNQPSUPG/'"5

Frank McKeon
Harvard Medical School

Final composition: Allison Bruce

Futoshi Shibasaki
The Tokyo Metropolitan Institute of Medical
Science
Roydon Price
Harvard University
Annie Yang
Harvard Medical School

15.2

Mitochondrial Protein Import

.JUPDIPOESJBBSFPSHBOFMMFTUIBUIBWFUIFJSPXO%/"BOEDBONBLF
UIFJSPXOQSPUFJOT)PXFWFS BWBTUNBKPSJUZPGNJUPDIPOESJBMQSPUFJOT
are encoded in the nucleus and translated into protein in the cytosol.
Proteins made in the cytosol must therefore be sorted and selectively
delivered to their proper destinations.
Precursor proteins destined for a mitochondrion have a short segment
of amino acids, the signal sequence, that targets the proteins to
this organelle. The signal sequence has affinity for a receptor on
the mitochondrions surface and delivers the precursor protein to a
translocation apparatus for import.
At a contact site where the mitochondrions two membranes are close
together, the precursor protein snakes in an unfolded state through
two sequential protein translocators, one in each of the mitochondrial
NFNCSBOFT*OTJEFUIFNJUPDIPOESJPO DIBQFSPOFQSPUFJOTBSFSFRVJSFE
UPIFMQQVMMUIFQSPUFJOJO$IBQFSPOFQSPUFJOTCJOEUPUIFQSFDVSTPS
protein as it appears on the inside of the mitochondrion, and thereby
prevent the protein chain from backsliding through the translocation
tunnel.
Once inside, an enzyme, called a signal peptidase, cleaves the
signal sequence, which is no longer needed, from the precursor. The
chaperone proteins are released as the protein chain folds into its threedimensional structure.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

Electron Microscopy:
Daniel S. Friend

86

15.3

ER Tubules

The endoplasmic reticulum is a highly dynamic network of


interconnected tubules that spans the cytosol of a eukaryotic celllike a
spiders web.
The network is continually reorganizing with some connections being
broken while new ones are being formed.
Motor proteins moving along microtubules can pull out sections of
endoplasmic reticulum membranes to form extended tubules that then
fuse to form a network.

Part I: Jennifer Lippincott-Schwartz


NICHD, National Institutes of Health
Part II: Ron D. Vale
Howard Hughes Medical Institute
University of California, San Francisco

15.4 Protein Translocation


5IFFOEPQMBTNJDSFUJDVMVN PS&3
JTUIFNPTUFYUFOTJWFNFNCSBOF
TZTUFNJOFVDBSZPUJDDFMMT1SPUFJOTUSBOTQPSUFEUPUIF(PMHJBQQBSBUVT 
FOEPTPNFT MZTPTPNFT BOEUIFDFMMTVSGBDF BMMNVTUmSTUFOUFSUIF&3
from the cytosol.
"TBON3/"NPMFDVMFJTUSBOTMBUFEJOUPBQSPUFJO NBOZSJCPTPNFT
bind to it, forming a polyribosome. There are two separate populations
of polyribosomes in the cytosol that share the same pool of ribosomal
subunits.
Free ribosomes are unattached to any membrane. Membrane-bound
SJCPTPNFTCFDPNFSJWFUFEUPUIF&3NFNCSBOFBOEUSBOTMBUFQSPUFJOT
UIBUBSFUSBOTMPDBUFEJOUPUIF&35IFTFNFNCSBOFCPVOESJCPTPNFT
DPBUUIFTVSGBDFPGUIF&3 DSFBUJOHSFHJPOTDBMMFESPVHIFOEPQMBTNJD
reticulum.
5XPLJOETPGQSPUFJOTBSFNPWFEGSPNUIFDZUPTPMUPUIF&38BUFS
TPMVCMFQSPUFJOTDPNQMFUFMZDSPTTUIF&3NFNCSBOFBOEBSFSFMFBTFE
into the lumen, while transmembrane proteins only partially cross the
&3BOECFDPNFFNCFEEFEJOUIFNFNCSBOF
"MMUIFTFQSPUFJOTBSFEJSFDUFEUPUIF&3CZBTJHOBMTFRVFODFPGTNBMM
IZESPQIPCJDBNJOPBDJET5IFTJHOBMTFRVFODFJTHVJEFEUPUIF&3
NFNCSBOFXJUIBTJHOBMSFDPHOJUJPOQBSUJDMF PS431
XIJDICJOETUIF
&3TJHOBMTFRVFODFJOUIFOFXQSPUFJOBTJUFNFSHFTGSPNUIFSJCPTPNF
1SPUFJOTZOUIFTJTUIFOTMPXTEPXOVOUJMUIF431SJCPTPNFDPNQMFY
CJOETUPBO431SFDFQUPSJOUIF&3NFNCSBOF
5IF431JTUIFOSFMFBTFE QBTTJOHUIFSJCPTPNFUPBQSPUFJO
USBOTMPDBUJPODIBOOFMJOUIF&3NFNCSBOF5IVTUIF431BOE431
receptor function as molecular matchmakers, connecting ribosomes
UIBUBSFTZOUIFTJ[JOHQSPUFJOTDPOUBJOJOH&3TJHOBMTFRVFODFTUP
BWBJMBCMF&3USBOTMPDBUJPODIBOOFMT
*OBEEJUJPOUPEJSFDUJOHQSPUFJOTUPUIF&3 UIFTJHOBMTFRVFODFGVODUJPOT
to open the translocation channel. The signal peptide remains bound to
the channel while the rest of the protein chain is threaded through the
membrane as a large loop.
Once the protein has passed through the membrane it is released into
UIF&3MVNFO"GUFSUIFTJHOBMTFRVFODFIBTCFFODMFBWFEPGGCZBTJHOBM
peptidase

87
MPDBUFEPOUIFMVNJOBMTJEFPGUIF&3NFNCSBOFUIFTJHOBMQFQUJEFJT
then released from the translocation channel into the membrane and
rapidly degraded.
*UJTUIPVHIUUIBUBQSPUFJOTFSWJOHBTBQMVHUIFOCJOETGSPNUIF&3
MVNFOUPDMPTFUIFJOBDUJWFDIBOOFM#VUOPUBMMQSPUFJOTUIBUFOUFSUIF
&3BSFSFMFBTFEJOUPUIF&3MVNFOTPNFSFNBJOFNCFEEFEJOUIF&3
membrane as transmembrane proteins.
For claritys sake, the membrane-bound ribosome will be omitted to
JMMVTUSBUFUIFUSBOTMPDBUJPOPGUSBOTNFNCSBOFQSPUFJOTJOUPUIF&3
NFNCSBOF*OUIFTJNQMFTUDBTF UIBUPGBUSBOTNFNCSBOFQSPUFJOXJUI
a single membrane spanning segment, the N-terminal signal sequence
JOJUJBUFTUSBOTMPDBUJPO KVTUBTGPSBTPMVCMFQSPUFJO#VUUIFUSBOTGFS
process is halted by an additional sequence of hydrophobic amino acids,
a stop-transfer sequence, further in the polypeptide chain. The stoptransfer sequence is released laterally from the translocation channel
and drifts into the plane of the lipid bilayer, where it forms a membranespanning segment that anchors the protein in the membrane.
As a result, the translocated protein ends up as a transmembrane
protein inserted in the membrane with a defined orientation.
*OTPNFUSBOTNFNCSBOFQSPUFJOT BOJOUFSOBMTJHOBMTFRVFODFJTVTFEUP
TUBSUUIFQSPUFJOUSBOTGFS*OUIFTFDBTFTIZESPQIPCJDTJHOBMTFRVFODFT
are thought to work in pairs: an internal start-transfer sequence serves
to initiate translocation, which continues until a stop-transfer sequence
is reached; the two hydrophobic sequences are then released into the
bilayer, where they remain anchored.
*ODPNQMFYNVMUJQBTTQSPUFJOT JOXIJDINBOZIZESPQIPCJDSFHJPOT
span the bilayer, additional pairs of stop and start sequences come
into play: one sequence reinitiates translocation further down the
polypeptide chain, and the other stops translocation and causes
polypeptide release... and so on for subsequent starts and stops.
Thus, multipass membrane proteins are stitched into the lipid bilayer
as they are being synthesized, by a mechanism resembling a sewing
machine.
Storyboard and Animation: Thomas Dallman, Bioveo (www.bioveo.com)

15.5

Clathrin

&VDBSZPUJDDFMMTUBLFJOFYUSBDFMMVMBSNPMFDVMFTUISPVHIBQSPDFTTDBMMFE
endocytosis, in which the plasma membrane invaginates and pinches
off cargo-filled vesicles.
This movie shows a shows a series of electron micrographs that have
been artificially morphed to show the process of endocytosis as it may
occur.
The process involves a variety of molecules, including the cargo
molecules that the cell takes in; the receptors that capture the cargo
molecules; and molecules called adaptins that mediate contact between
the receptors and the clathrin molecules that act to shape the vesicle
forming at the plasma membrane.

88
*OUIFFMFDUSPONJDSPTDPQF JOEJWJEVBMDMBUISJONPMFDVMFTDBOCFTFFO
BTUISFFMFHHFETUSVDUVSFT DBMMFEUSJTLFMJPOT%VSJOHUIFBTTFNCMZPGB
$MBUISJODPBU UIFJOEJWJEVBMUSJTLFMJPOTDPNFUPHFUIFS JOUFSBDUUISPVHI
their leg domains, and ultimately form a closed cage.
Part I: Electron Micrograph, M.M. Perry and A.B. Gilbert
Part II: Animation and Storyboard, Sumanas, Inc. (www.sumanasinc.com)
Part III: Electron Micrograph, Ernst Ungewickell, Hanover Medical School
Part IV: Toms Kirchhausen, Harvard Medical School.
Animation: Alison Bruce

15.6

Cell Compartments

High voltage electron microscopy allows three-dimensionsional imaging


PGBTFHNFOUPGUIJTJOTVMJOTFDSFUJOHQBODSFBUJDDFMM3FMBUJWFMZUIJDL
slices of the cell are viewed in the microscope from different angles,
which allows us to reconstruct a three-dimensional image.
4UFQQJOHUISPVHIUIFJNBHFGSPNUIFUPQSFWFBMTUIFDPNQMFYJUZPGDFMM
structure.
'PDVTJOHPOUIF(PMHJBQQBSBUVT JOEJWJEVBMNFNCSBOFTDBOCFUSBDFE 
and we can appreciate the size and shape of various compartments.
Using these outlines, a computer can construct a three-dimensional
NPEFMPGUIFFOUJSFTFHNFOU)FSFXFTFFUIFTUBDLTPGUIF(PMHJ
apparatus, each traced in a different color. The cis(PMHJ XIFSFQSPUFJOT
are first delivered to the organelle, is light blue and the trans(PMHJ
network, where they exit, is light blue.
4IPXOJOEBSLCMVFBSFUIFTFDSFUPSZWFTJDMFTJOUPXIJDIJOTVMJOHFUT
packaged after leaving the trans (PMHJOFUXPSL
.BOZMJUUMFUSBOTQPSUWFTJDMFT TIPXOJOXIJUF TVSSPVOEUIF(PMHJ
apparatus. They transport cargo between the cisternae or back to the
endoplasmic reticulum.
When all the other organelles are combined into a single image, we
can see the incredible crowding of organelles in the cytosol. Here,
NJUPDIPOESJBBOENJDSPUVCVMFTBSFDPMPSFEHSFFO&OEPQMBTNJD
reticulum and ribosomes are shown in yellow. The purple organelles are
probably endosomes.
(JWFOUIJTBQQBSFOUDMVUUFS POFDBOOPUIFMQCVUXPOEFSIPXBMMUIFTF
components work in synchrony to allow the cell to achieve its tasks.

89

15.7

Constitutive Exocytosis Pathway

'MVPSFTDFOUMZMBCFMFENFNCSBOFQSPUFJOTTUBSUUIFJSKPVSOFZUPUIF
plasma membrane after synthesis in the endoplasmic reticulum.
They are first dispersed throughout the extensive membrane network of
the endoplasmic reticulum from where they move to exit sites that form
in random locations in the membrane network. At each of these sites,
the membrane proteins are concentrated and packaged into transport
WFTJDMFT$MVTUFSTPGUIFUSBOTQPSUWFTJDMFTGVTFUPGPSNUSBOTQPSU
intermediates.
At the next stage, transport intermediates move along microtubule
USBDLTUPUIF(PMHJBQQBSBUVTOFBSUIFDFOUFSPGUIFDFMM5IFNFNCSBOF
QSPUFJOTFYJUUIF(PMHJBQQBSBUVT5IFZNPWFJOUSBOTQPSUWFTJDMFTUIBU
are now pulled outward on microtubules, which deliver them to the
plasma membrane.

Jennifer Lippincott-Schwartz
NICHD, National Institutes of Health

&BDIUJNFB(PMHJEFSJWFEWFTJDMFGVTFTXJUIUIFQMBTNBNFNCSBOF JUT
content proteins disperse.
Video reproduced from: The Journal of Cell Biology 143:14851503, Figure 1A, 1998.
The Rockefeller University Press.

15.8

Exocytotic Transport

1BTTFOHFSQSPUFJOTFYJUJOHUIF(PMHJBQQBSBUVTPOUIFXBZUPUIFDFMM
surface are often packaged into tubular transport vesicles of significant
size.
4VDIUVCVMBSWFTJDMFTDBOCSBODIBOEGSBHNFOUCFGPSFUIFZGVTFXJUI
the plasma membrane.
The transport vesicles move along microtubules which are stained
here with a red fluorescent dye.
The green cell in the corner does not contain fluorescent microtubules.
Final composition: Blink Studio Ltd. (www.blink.uk.com)

Jennifer Lippincott-Schwartz
NICHD, National Institutes of Health
Patrick Keller and Kai Simons
European Molecular Biology Laboratory

90

15.9

Phagocytosis

Phagocytosis allows cells to take up large particles, such as these yeast


cells that are being engulfed by the slime mold Dictostelium.
Final composition: Blink Studio Ltd. (www.blink.uk.com)
Video reproduced from: M. Maniak, R. Rauchenberger, R. Albrecht, J. Murphy, and
G. Gerisch. Coronin involved in phagocytosis. Cell 83:91924. 1995, with
permission from Elsevier Science.

Markus Maniak
University of Kassel, Germany

15.10 Receptor-Mediated Endocytosis


$IPMFTUFSPMDJSDVMBUFTJOUIFCMPPETUSFBNBOEUIFOFOUFSTDFMMTCZB
QSPDFTTDBMMFESFDFQUPSNFEJBUFEFOEPDZUPTJT*OTUFBEPGDJSDVMBUJOH
freely, cholesterol molecules are derivatized and packed inside low
EFOTJUZMJQPQSPUFJOQBSUJDMFT PS-%-T"QSPUFJOBOEQIPTQIPMJQJEMBZFS
surrounds the cholesterol molecules. The protein portion is recognized
CZ-%-SFDFQUPSTPOUIFTVSGBDFPGDFMMT
"OBEBQUPSNPMFDVMF DBMMFEBEBQUJO CJOETUPUIFUBJMPGUIF-%-
receptor that protrudes into the cytosol. Adaptin recruits clathrin
molecules, which start coating the membrane. Assembly of the clathrin
coat causes the membrane to bend and invaginate, forming a vesicle
UIBUCVETPGGJOTJEFUIFDFMM UBLJOHXJUIJU-%-SFDFQUPSTBOEUIF-%-
particles bound to them.
Once inside the cell, the vesicle uncoats and fuses with the endosome,
the intracellular compartment that first receives all endocytosed
NBUFSJBM5IFFOEPTPNFIBTBMPXJOUFSOBMQ) XIJDIDBVTFTUIF-%-
receptors to release their cargo.
&NQUZ-%-SFDFQUPSTBSFSFDZDMFEUPUIFQMBTNBNFNCSBOFJOWFTJDMFT
UIBUCVEPGGGSPNUIFFOEPTPNF&BDI-%-SFDFQUPSNBLFTBSPVOE
trip from the plasma membrane to the endosome and back every 10
minutes.
.FBOXIJMF UIF-%-QBSUJDMFTOFFEUPCFEJTBTTFNCMFE5IFFOEPTPNBM
content is delivered to a lysosome, which contains hydrolytic enzymes
that can digest the particles. Free cholesterol is liberated together with
BNJOPBDJETBOETNBMMQFQUJEFTHFOFSBUFECZEJHFTUJPOPG-%-QSPUFJOT
The cholesterol is then released into the cytosol to be used in the
synthesis of new membranes.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

91

15.11 Endosome Fusion


*OUIFTFDFMMT nVPSFTDFOU3BCQSPUFJOIBTCFFOPWFSFYQSFTTFE3BC
binds to endosomes and promotes their fusion with one another,
thereby increasing the steady-state size of individual endosomal
compartments.
*OEJWJEVBMNFNCSBOFGVTJPOFWFOUTDBOCFPCTFSWFEBUIJHIFS
magnification.
Final composition: Blink Studio Ltd. (www.blink.uk.com)

Philip D. Stahl, Alejandro Barbieri and


Richard Roberts
Washington University School of Medicine
in St. Louis

15.12 Freeze Fracture of Yeast Cell


4IPXNF


t PVUFSOVDMFBSNFNCSBOF

t JOOFSOVDMFBSNFNCSBOF

t

OVDMFBSQPSFDPNQMFYFT

Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

15.13 Pancreas: View 1


4IPXNF


t DFMMPVUMJOFT

t OVDMFJ

t TFDSFUPSZWFTJDMFT

t NJDSPWJMMJ

Originally published in Freeze-Etch Histology: A Comparison between Thin Sections


and Freeze-Etch Replicas by Lelio Orci and Alain Perrelet. Springer-Verlag. New York,
1975.
Lelio Orci and Alain Perrelet

92

15.14 Pancreas: View 2


4IPXNF


t TFDSFUPSZWFTJDMFT

t QBODSFBUJDEVDU

t UJHIUKVODUJPOT

t DFOUSJPMFT

Originally published in Freeze-Etch Histology: A Comparison between Thin Sections


and Freeze-Etch Replicas by Lelio Orci and Alain Perrelet. Springer-Verlag. New York,
1975
Lelio Orci and Alain Perrelet

15.15 Pancreatic Secretory Cell


4IPXNF


t OVDMFBSMBNJOB

t PVUFSOVDMFBSNFNCSBOF

t OVDMFBSQPSFT

t &3MVNFO

Originally published in Freeze-Etch Histology: A Comparison between Thin Sections


and Freeze-Etch Replicas by Lelio Orci and Alain Perrelet. Springer-Verlag. New York,
1975.

15.16 Quiz: Chapter 15


1. The outer membrane of the nucleus is continuous with the membrane
PGXIJDIPUIFSPSHBOFMMF


t "NJUPDIPOESJPO

t 5IFFOEPQMBTNJDSFUJDVMVN

t 5IF(PMHJBQQBSBUVT

t "QFSPYJTPNF

Lelio Orci and Alain Perrelet

93

15.17 Concept Questions: Chapter 15


)PXEPNPMFDVMFTQBTTCFUXFFOUIFOVDMFVTBOEDZUPTPM 
Molecules enter and exit the nucleus through a structure called the
OVDMFBSQPSF4NBMM XBUFSTPMVCMFNPMFDVMFTDBOQBTTGSFFMZUISPVHI
the tangled meshwork of disordered polypeptides that fill the central
channel of the

15.18 Challenge Question: Chapter 15


5IFSPVHI&3JTUIFTJUFPGTZOUIFTJTPGNBOZEJGGFSFOUDMBTTFTPG
NFNCSBOFQSPUFJO4PNFPGUIFTFQSPUFJOTSFNBJOJOUIF&3 XIFSFBT
PUIFSTBSFTPSUFEUPDPNQBSUNFOUTTVDIBTUIF(PMHJBQQBSBUVT 
lysosomes, and the plasma membrane. One measure of the difficulty of
the sorting problem is the degree of purification that must be

15.19 Flashcards: Chapter 15


autophagy


t

NFDIBOJTNCZXIJDIBDFMMiFBUTJUTFMG wEJHFTUJOHNPMFDVMFT
and organelles that are damaged or obsolete.

clathrin


t

QSPUFJOUIBUNBLFTVQUIFDPBUPGBUZQFPGUSBOTQPSUWFTJDMF
that

15.20 References: Chapter 15


#MPCFM( 
*OUSBDFMMVMBSQSPUFJOUPQPHFOFTJTProc Natl Acad Sci USA
o
%F%VWF$ 
5IFPSJHJOPGFVLBSZPUFTBSFBQQSBJTBMNature Rev
Geneto

KEY TERMS
autophagy
chaperone protein
clathrin
coated vesicle
endocytosis
endomembrane system
endoplasmic reticulum (ER)

94

16.1

Calcium Signaling

*OUIJTFYQFSJNFOU HMJBMDFMMTGSPNUIFSBUCSBJOBSFHSPXOJODFMM
culture.
$BMDJVNDPODFOUSBUJPOTBSFWJTVBMJ[FEXJUIBnVPSFTDFOUEZFUIBU
CFDPNFTCSJHIUFSXIFODBMDJVNJPOTBSFQSFTFOU*OUIFQSFTFODFPG
small amounts of a neurotransmitter, individual cells light up randomly
as ion channels open up and allow calcium ions to enter the cell.
0DDBTJPOBMMZ DBMDJVNXBWFTBSFUSBOTNJUUFEUPBEKBDFOUDFMMTUISPVHI
HBQKVODUJPOTBUSFHJPOTXIFSFUIFDFMMTDPOUBDUFBDIPUIFS

Ann H. Cornell-Bell
Viatech Imaging
Steven Finkbeiner
Gladstone Institute of Neurological Disease
at the University of California, San Francisco
Mark S. Cooper
University of Washington
Stephen J. Smith
Stanford University School of Medicine

16.2

G-Protein Signaling

.BOZ(QSPUFJODPVQMFESFDFQUPSTIBWFBMBSHFFYUSBDFMMVMBSMJHBOE
binding domain.
When an appropriate protein ligand binds to this domain, the receptor
undergoes a conformational change that is transmitted to its cytosolic
SFHJPOT XIJDIOPXBDUJWBUFBUSJNFSJD(51CJOEJOHQSPUFJO PS(
protein for short).
"TUIFOBNFJNQMJFT BUSJNFSJD(QSPUFJOJTDPNQPTFEPGUISFFQSPUFJO
TVCVOJUTDBMMFEBMQIB CFUB BOEHBNNB#PUIUIFBMQIBBOEHBNNB
TVCVOJUTIBWFDPWBMFOUMZBUUBDIFEMJQJEUBJMTUIBUIFMQBODIPSUIF(
protein in the plasma membrane.
*OUIFBCTFODFPGBTJHOBM UIFBMQIBTVCVOJUIBTB(%1CPVOE BOEUIF
(QSPUFJOJTJOBDUJWF*OTPNFDBTFT UIFJOBDUJWF(QSPUFJOJTBTTPDJBUFE
with the inactive receptor, while, in other cases, as shown here, it only
CJOETBGUFSUIFSFDFQUPSJTBDUJWBUFE*OFJUIFSDBTF BOBDUJWBUFESFDFQUPS
JOEVDFTBDPOGPSNBUJPOBMDIBOHFJOUIFBMQIBTVCVOJU DBVTJOHUIF(%1
to dissociate.
(51 XIJDIJTBCVOEBOUJOUIFDZUPTPM DBOOPXSFBEJMZCJOEJOQMBDFPG
UIF(%1(51CJOEJOHDBVTFTBGVSUIFSDPOGPSNBUJPOBMDIBOHFJOUIF(
protein, activating both the alpha subunit and beta-gamma complex.
*OTPNFDBTFT BTTIPXOIFSF UIFBDUJWBUFEBMQIBTVCVOJUEJTTPDJBUFT
from the activated betagamma complex, whereas in other cases the
two activated components stay together.
*OFJUIFSDBTF CPUIPGUIFBDUJWBUFEDPNQPOFOUTDBOOPXSFHVMBUFUIF
activity of target proteins in the plasma membrane, as shown here for a

95
(51CPVOEBMQIBTVCVOJU5IFBDUJWBUFEUBSHFUQSPUFJOTUIFOSFMBZUIF
signal to other components in the signaling cascade.
&WFOUVBMMZ UIFBMQIBTVCVOJUIZESPMZTFTJUTCPVOE(51UP(%1 XIJDI
inactivates the subunit. This step is often accelerated by the binding
PGBOPUIFSQSPUFJO DBMMFEBSFHVMBUPSPG(QSPUFJOTJHOBMJOH PS3(4

5IFJOBDUJWBUFE (%1CPVOEBMQIBTVCVOJUOPXSFGPSNTBOJOBDUJWF
(QSPUFJOXJUIBCFUBoHBNNBDPNQMFY UVSOJOHPGGPUIFSEPXOTUSFBN
events.
As long as the signaling receptor remains stimulated, it can continue
UPBDUJWBUF(QSPUFJOT6QPOQSPMPOHFETUJNVMBUJPO IPXFWFS UIF
receptors eventually inactivate, even if their activating ligands remain
bound.
*OUIJTDBTF BSFDFQUPSLJOBTFQIPTQIPSZMBUFTUIFDZUPTPMJDQPSUJPOTPG
the activated receptor. Once a receptor has been phosphorylated in this
way, it binds with high affinity to an arrestin protein, which inactivates
UIFSFDFQUPSCZQSFWFOUJOHJUTJOUFSBDUJPOXJUI(QSPUFJOT
Arrestins also act as adaptor proteins, and recruit the phosphorylated
receptors to clathrin-coated pits, from where the receptors are
endocytosed, and afterwards they can either be degraded in lysosomes
or activate new signaling pathways.
Animation: Thomas Dallman, Bioveo (www.bioveo.com)

16.3

cAMP Signaling

Adenylyl cyclase is a membrane-bound enzyme whose catalytic domain


JTBDUJWBUFECZUIF(51CPVOEGPSNPGUIFTUJNVMBUPSZ(QSPUFJOBMQIB
TVCVOJU PS(BMQIBTGPSTIPSU

Activated adenylyl cyclase converts ATP to cyclic AMP which then
BDUTBTBTFDPOENFTTFOHFSUIBUSFMBZTUIFTJHOBMGSPNUIF(QSPUFJO
coupled receptor to other components in the cell.
*ONPTUBOJNBMDFMMT DZDMJD".1BDUJWBUFTDZDMJD".1EFQFOEFOU
QSPUFJOLJOBTF PS1,"
*OUIFJOBDUJWFTUBUF1,"DPOTJTUTPGBDPNQMFY
of two catalytic subunits and two regulatory subunits. The binding of
cyclic AMP to the regulatory subunits alters their conformation and
liberates the catalytic subunits which are now active and phosphorylate
specific target proteins.
*OTPNFFOEPDSJOFDFMMT GPSFYBNQMF UIFBDUJWBUFE1,"DBUBMZUJD
subunits enter the nucleus, where they phosphorylate a transcription
GBDUPSDBMMFE$3&#1IPTQIPSZMBUFE$3&#UIFOSFDSVJUTB$3&#CJOEJOH
protein. This complex activates transcription after binding to specific
regulatory regions that are present in the promoters of appropriate
target genes.
Animation: Thomas Dallman, Bioveo (www.bioveo.com)

Original illustrations:
Nigel Orme

96

16.4

Calcium Wave During Fertilization

When a sperm cell fuses with this sea urchin egg cell, calcium ions
begin rushing into the cell at the site of fusion.
*OUIFTFFYQFSJNFOUT DBMDJVNDPODFOUSBUJPOTBSFWJTVBMJ[FEBOE
measured with a fluorescent dye that becomes increasingly brighter the
more calcium is present.
#SJHIUOFTTJTUIFOUSBOTMBUFEJOUPBDPMPSTDBMF BOE JOUIJTUISFF
dimensional display, into peak heights, where red and high peaks
represent the highest calcium concentrations.
A second rise of the calcium concentration can be observed after
GFSUJMJ[BUJPO*UPDDVSTEVSJOHUIFNPWFNFOUTPGUIFTQFSNBOEFHH
pronuclei to meet and fuse near the center of the egg.
Final composition: Allison Bruce

Part I:
Carolyn A. Larabell
Lawrence Berkeley National Laboratory
Jeff Hardin
University of Wisconsin, Madison
Part II:
Michael Whitaker
University of Newcastle Upon Tyne
Isabelle Gillot
University of Nice-Sophia Antipolis

16.5

Calmodulin

$BMNPEVMJOJTBEVNCCFMMTIBQFEQSPUFJOGPSNFECZBTJOHMFQPMZQFQUJEF
DIBJO*UT/UFSNJOBMBOE$UFSNJOBMHMPCVMBSEPNBJOTBSFTFQBSBUFE
CZBOFYUFOEFEDFOUSBMIFMJY&BDIHMPCVMBSEPNBJODPOUBJOTUXPIJHI
affinity calcium-binding sites.
#JOEJOHPGGPVSDBMDJVNJPOTJOEVDFTNBKPSBMMPTUFSJDDIBOHFTJO
calmodulin.
Most notably, the two globular domains rotate relative to each other.
These conformational changes enable calmodulin to bind to target
proteins and regulate their activity.
3FNJOJTDFOUPGBCPBHSBCCJOHJUTQSFZ DBMDJVNCPVOEDBMNPEVMJO
captures helical peptides on target proteins by wrapping tightly around
them. To make this possible, the central helix of calmodulin breaks into
two helices now connected by a flexible loop. Although the calcium
ions remain tightly bound during this remarkable reaction, they are not
shown in the animated part of this movie.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)
Source: Intermediate structures provided by Eric Martz (www.umass.edu/microbio/
rasmol/) and calculated by the Yale University Morph Server, Mark Gerstein and
Werner Krebs (bioinfo.mbb.yale.edu/)

PDB ID number *: Calcium-free calmodulin


(1CFD); Compilation of calcium-free
calmodulin & calcium-bound calmodulin
(1CFD & 1OSA); Compilation of calcium
bound calmodulin & calcium-bound
calmodulin complexed with rabbit skeletal
myosin light chain kinase (1OSA & 2BBM)

97

16.6

Ras

5IF3BTQSPUFJOJTBSFQSFTFOUBUJWFFYBNQMFPGUIFMBSHFGBNJMZPG
(51BTFTUIBUGVODUJPOTBTNPMFDVMBSTXJUDIFT5IFOVDMFPUJEFCJOEJOH
TJUFPG3BTJTGPSNFECZTFWFSBMDPOTFSWFEQSPUFJOMPPQTUIBUDMVTUFSBU
POFFOEPGUIFQSPUFJO*OJUTJOBDUJWFTUBUF 3BTJTCPVOEUJHIUMZUP(%1
"TBNPMFDVMBSTXJUDI 3BTDBOUPHHMFCFUXFFOUXPDPOGPSNBUJPOBM
TUBUFTEFQFOEJOHPOXIFUIFS(%1PS(51JTCPVOE5XPSFHJPOT DBMMFE
switch 1 and switch 2, change conformation dramatically. The change
in conformational state allows other proteins to distinguish active
3BTGSPNJOBDUJWF3BT"DUJWF (51CPVOE3BTCJOETUP BOEBDUJWBUFT 
downstream target proteins in the cell signaling pathways.
A space-filling model shows that the conformational changes between
UIF(%1BOE(51CPVOEGPSNTPG3BTTQSFBEPWFSUIFXIPMFTVSGBDFPG
the protein. The two switch regions move the most.
3BTIZESPMZ[FT(51UPTXJUDIPGGUIBUJT UPDPOWFSUGSPNUIF(51
CPVOETUBUFUPUIF(%1CPVOETUBUF5IJTIZESPMZTJTSFBDUJPOSFRVJSFT
UIFBDUJPOPGB3BT(51BTFBDUJWBUJOHQSPUFJO PS3BT("1GPSTIPSU
3BT("1CJOETUJHIUMZUP3BTCVSZJOHUIFCPVOE(51*UJOTFSUTBO
arginine side chain directly into the active site. The arginine, together
XJUIUISFPOJOFBOEHMVUBNJOFTJEFDIBJOTPG3BTJUTFMG QSPNPUFTUIF
IZESPMZTJTPG(51

PDB ID number *: Compilation of c-H-Ras


p21 protein catalytic domain complex with
GDP & structure of p21-Ras complexed
with GTP at 100K (4Q21 & 1QRA);
Ras-Rasgap complex (1WQ1)

Molecular modelling and animation: Timothy Driscoll, Molvisions

16.7

Chemotaxis of Neutrophils

These human neutrophils, taken from the blood of a graduate student,


BSFNPCJMFDFMMTUIBUXJMMRVJDLMZNJHSBUFUPTJUFTPGJOKVSZUPIFMQmHIU
infection. They are attracted there by chemical signals that are released
by other cells of the immune system or by invading microbes.
*OUIJTFYQFSJNFOUUJOZBNPVOUTPGDIFNPBUUSBDUBOUBSFSFMFBTFEGSPNB
micropipette. When neutrophils sense these compounds they polarize
and move towards the source. When the source of the chemoattractant
is moved, the neutrophil immediately sends out a new protrusion, and
its cell body reorients towards the new location.
Henry Bourne and John Sedat
University of California, San Francisco
Orion Weiner
Harvard Medical School

98

16.8

Lymphocyte Homing

5PWJTVBMJ[FMZNQIPDZUFIPNJOHUPBTJUFPGJOKVSZ B[FCSBmTIMBSWB
was anaesthetized and its fin pierced with a needle to introduce a small
wound.
A vein is seen at the bottom of the frame.
#FDBVTFUIFmOJTWFSZUIJOBOEUSBOTQBSFOU XFDBOXBUDIEJSFDUMZBT
lymphocytes crawl out of the blood vessel and migrate towards the
wound.
They are attracted there by chemicals released from damaged cells,
invading bacteria, and other lymphocytes.
*OB[PPNFEPVUWJFXXFDBOBQQSFDJBUFUIBUMZNQIPDZUFJOWBTJPOJT
restricted to the wounded area.
The static cells that are dispersed in the connective tissue are
fibroblasts.
*OUIFTFNPWJFT NJOVUFTPGSFBMUJNFBSFDPNQSFTTFEJOUP
seconds.
Final composition: Blink Studio Ltd. (www.blink.uk.com)

16.9

Quiz: Chapter 16

1. When the hormone insulin is released into the bloodstream, what


GPSNPGDFMMUPDFMMTJHOBMJOHJTCFJOHVTFE


t &OEPDSJOF

t 1BSBDSJOF

t /FVSPOBM

t $POUBDUEFQFOEFOU

16.10 Media Assessment: G-Protein Signaling


8IFOB(QSPUFJOJTBDUJWBUFECZB(1$3 JU


t

SFMFBTFT(51BOECJOET(%1

t

SFMFBTFT(%1BOECJOET(51

t

IZESPMZ[FT(51

t

IZESPMZ[FT(%1

99

16.11 Concept Questions: Chapter 16


%FTDSJCFUIFUISFFNBJODMBTTFTPGDFMMTVSGBDFSFDFQUPST
The three main classes of cell-surface receptors are ion-channelDPVQMFESFDFQUPST (QSPUFJODPVQMFESFDFQUPST BOEFO[ZNFDPVQMFE
SFDFQUPST*PODIBOOFMDPVQMFESFDFQUPSTDIBOHFUIFQFSNFBCJMJUZPGUIF
plasma

16.12 Challenge Questions: Chapter 16


How is it that different cells can respond in different ways to exactly the
TBNFTJHOBMJOHNPMFDVMFFWFOXIFOUIFZIBWFJEFOUJDBMSFDFQUPST
$FMMTXJUIJEFOUJDBMSFDFQUPSTDBOSFTQPOEEJGGFSFOUMZUPUIFTBNFTJHOBM
molecule because of differences in the internal machinery...

Image courtesy of Michael Snyder

16.13 Flashcards: Chapter 16


adaptation


t

BEKVTUNFOUPGTFOTJUJWJUZGPMMPXJOHSFQFBUFETUJNVMBUJPOBMMPXT
a cell or organism to register small changes in a signal despite
a high background level of stimulation.

16.14 References: Chapter 16


#FO4IMPNP* :V)TV4 3BVDI3FUBM 
4JHOBMJOHSFDFQUPNFB
genomic and evolutionary perspective of plasma membrane receptors
involved in signal transduction. Sci STKE3&
#PVSOF)3 
(51BTFTBGBNJMZPGNPMFDVMBSTXJUDIFTBOEDMPDLT
Philos Trans R Soc Lond B Biol Scio

KEY TERMS
adaptation
adenylyl cyclase
Ca2+/calmodulin-dependent
protein kinase (CaM-kinase)
calmodulin
cell signaling
cyclic AMP

100

17.1

Intermediate Filaments

&VDBSZPUJDDFMMTDPOUBJOBDPNQMFYOFUXPSLPGmMBNFOUTJOUFSNFEJBUF
filaments, microtubules, and actin filamentsthat provide the cells with
strength, structure, and movement. Although all eucaryotic cells contain
microtubules and actin filaments, intermediate filaments are found only
in vertebrates and a number of other soft-bodied animals.
*OUFSNFEJBUFmMBNFOUTBSFGPVOEJOBOJNBMDFMMTUIBUSFRVJSFBMPUPG
TUSFOHUI TVDIBTUIFFQJUIFMJBMDFMMTPGUIFTLJO4PNFPGUIFTFmMBNFOUT
TQBOUIFMFOHUIPGUIFDFMM DPOOFDUJOHDFMMoDFMMKVODUJPOTDBMMFE
desmosomes.
These cables of intermediate filaments have a high tensile strength.
Without these filaments, stretching or pressure on the epithelial sheet
would cause it to rupture.

Electron Microscopy:
D.E. Kelly

&BDImMBNFOUJTSPQFMJLF DPOTJTUJOHPGUIJOOFSTUSBOETNBEFPGB
precise hierarchical arrangement of protein subunits. At the lowest
level, two monomers associate with each other to create a twisted
dimer.
Two dimers then line up to form a staggered tetramer. Note that the two
dimers are arranged in opposite orientations, with their amino terminal
ends away from each other, so that the two ends of the tetramer are
indistinguishable.
Tetramers then link end-to-end, thus building up one strand of an
intermediate filament.
A total of eight strands stack together and twist around each other
to create the intermediate filament. This stacking provides the
extensive lateral contacts between the strands that give the filament its
remarkable mechanical strength. An electron micrograph shows the
appearance of intermediate filaments that have been assembled in a
test tube.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

17.2

Dynamic Instability of Microtubules

Microtubules continually grow from this centrosome added to a cell


extract. Quite suddenly however, some microtubules stop growing and
then shrink back rapidly, a behavior called dynamic instability.
Music: Christopher Thorpe

Timothy Mitchison
Harvard Medical School

101

17.3

Microtubule Dynamics in vivo

&#JTBQSPUFJOUIBUCJOETUPUIF(51UVCVMJODBQBUUIFHSPXJOHFOET
of microtubules.
$FMMTFYQSFTTJOHBO('1&#GVTJPOQSPUFJOSFWFBMUIFTQFDUBDVMBS
dynamics of the microtubule cytoskeleton.
Note that many but not all microtubules in this cell grow from the
centrosome.
Only the ends of growing microtubules are visible in this experiment;
UIPTFUIBUBSFTUBUJDPSTISJOLJOHIBWFMPTUUIFJS(51UVCVMJODBQTBOE
EPOPUCJOE&#
*ODPOUSBTU XIFOBMMNJDSPUVCVMFTBSFMBCFMFEXJUI('1UVCVMJO UIFUSVF
extent of the microtubule cytoskeleton emerges.
#PUIHSPXJOHBOETISJOLJOHNJDSPUVCVMFTDBOCFPCTFSWFE

Yuko Mimori-Kiyosue
KAN Research Institute
Shoichiro Tsukita
Faculty of Medicine, Kyoto University

Final composition: Blink Studio Ltd. (www.blink.uk.com)

17.4

Microtubule and ER Dynamics

(PWFSOFECZUIFQSJODJQMFTPGEZOBNJDJOTUBCJMJUZ NJDSPUVCVMFT
constantly extend into the leading edge of a migrating cell and retract
again.
4VQFSJNQPTFEPOUIFEZOBNJDNJDSPUVCVMFDZUPTLFMFUPO TIPXOIFSFJO
red), the membrane network of the endoplasmic reticulum (shown here
in green) exhibits its own dynamic behavior as tubes are extended by
motor proteins on the microtubule tracks.
Video reproduced from: C.M. Waterman-Storer and E.D. Salmon. Endoplasmic
reticulum tubes are distributed in living cells by three distinct microtubule dependent
mechanisms. Current Biology 8:798806. 1998, with permission from Elsevier
Science.

Clare M. Waterman-Storer
The Scripps Research Institute
Edward D. (Ted) Salmon
University of North Carolina at Chapel Hill

102

17.5

Organelle Movement on Microtubules

*OUIJTFYQFSJNFOUBDFMMIPNPHFOBUFDPOUBJOJOHNBOZEJGGFSFOU
organelles is added to microtubules.
Motor proteins are normally attached to the organelles. When ATP
is added as a fuel for the motor proteins, some organelles bind
microtubules, and are moved along the tracks by their motors.
Most kinesin motors move towards the plus end of microtubules.
%ZOFJONPUPSTBMXBZTNPWFJOUIFPQQPTJUFEJSFDUJPO#PUINPUPST
are used to transport organelles, and occasionally a single organelle,
which must have both types of motor attached, can be seen to switch
directions.
The bi-directional traffic observed here is reminiscent of that in an intact
cell.

17.6

Nira Pollack
University of California, San Francisco
Ron D. Vale
Howard Hughes Medical Institute
University of California, San Francisco

Kinesin

The motor protein kinesin is a dimer with two identical motor heads.
&BDIIFBEDPOTJTUTPGBDBUBMZUJDDPSFBOEBOFDLMJOLFS*OUIFDFMM 
kinesins pull organelles along microtubule tracks. The organelle
attaches to the other end of the long coiled-coil that holds the two
motor heads together. The organelle is not shown here.
*OTPMVUJPO CPUILJOFTJOIFBETDPOUBJOUJHIUMZCPVOE"%1 BOENPWF
SBOEPNMZ ESJWFOCZ#SPXOJBONPUJPO8IFOPOFPGUIFUXPLJOFTJO
heads encounters a microtubule, it binds tightly. Microtubule binding
DBVTFT"%1UPCFSFMFBTFEGSPNUIFBUUBDIFEIFBE"51UIFOSBQJEMZ
enters the empty nucleotide binding site.
This nucleotide exchange triggers the neck linker to zipper onto the
catalytic core. This action throws the second head forward, and brings it
near the next binding site on the microtubule.
The attached trailing head hydrolyzes the ATP, and releases phosphate.
As the neck linker unzippers from the trailing head, the leading head
exchanges its nucleotide, and zippers its neck linker onto the catalytic
core, and the cycle repeats.
*OUIJTXBZ LJOFTJOEJNFSTNPWFQSPDFTTJWFMZ TUFQCZTUFQ BMPOHUIF
microtubule.
Animation: Graham Johnson, Fivth Element (www.fivth.com)
Animation reproduced with permission from Vale & Milligan, Science 288:8895,
Supplemental Movie 1. 2000 American Association for the Advancement of
Science.

Ron D. Vale
Howard Hughes Medical Institute
University of California, San Francisco
Ron Milligan
The Scripps Research Institute

103

17.7

Neutrophil Chase

/FVUSPQIJMTBSFXIJUFCMPPEDFMMTUIBUIVOUBOELJMMCBDUFSJB*O
this spread a neutrophil is seen in the midst of red blood cells.
Staphylococcus aureus bacteria have been added. The small clump of
bacteria releases a chemoattractant that is sensed by the neutrophil.
The neutrophil becomes polarized, and starts chasing the bacteria. The
bacteria, bounced around by thermal energy, move in a random path,
TFFNJOHUPBWPJEUIFJSQSFEBUPS&WFOUVBMMZ UIFOFVUSPQIJMDBUDIFTVQ
with the bacteria and engulfs them by phagocytosis.
Digital capture: Tom Stossel, Brigham and Womens Hospital, Harvard Medical
School

David Roger
Vanderbilt University

Music: Freudenhaus Audio Productions (www.fapsf.com)

17.8

Crawling Actin

Myosin motors can be attached to the surface of a glass slide.


Fluorescent actin filaments will bind to the motor domains of the
attached myosins. When ATP is added, the myosin motors move the
actin filaments.
This rapid movement can be observed in a fluorescence microscope as
the actin filaments appear to crawl across the slide.

James Spudich
Stanford University School of Medicine

104

17.9

Muscle Contraction

When a neuron stimulates a muscle cell, an action potential sweeps


over the plasma membrane of the muscle cell. The action potential
releases internal stores of calcium that flow through the muscle cell and
trigger a contraction.
Muscle cells have an elaborate architecture that allows them to
EJTUSJCVUFDBMDJVNJPOTRVJDLMZUISPVHIPVUUIFDZUPTPM%FFQUVCVMBS
invaginations of the plasma membrane, called T-tubules, criss-cross the
cell. When the cell is stimulated, a wave of depolarizationthat is an
action potentialspreads from the synapse over the plasma membrane
and via the T tubules deep into the cell. A voltage-sensitive protein
JOUIFTFNFNCSBOFTPQFOTBDBMDJVNSFMFBTFDIBOOFMJOUIFBEKBDFOU
TBSDPQMBTNJDSFUJDVMVN XIJDIJTUIFNBKPSDBMDJVNTUPSFJONVTDMF
cells, thereby releasing a burst of calcium ions all throughout the cytosol
of the cell.
Within a contractile bundle of a muscle cell, called a myofibril, the
DBMDJVNJOUFSBDUTXJUIQSPUFJOmMBNFOUTUPUSJHHFSDPOUSBDUJPO*OFBDI
contracting unit, or sarcomere, thin actin and thick myosin filaments
BSFKVYUBQPTFECVUDBOOPUJOUFSBDUJOUIFBCTFODFPGDBMDJVN5IJTJT
because myosin-binding sites on the actin filaments are all covered by
a rodshaped protein called tropomyosin. A calcium-sensitive complex,
called troponin, is attached to the end of each tropomyosin molecule.
When calcium floods the cell, troponin binds to it, moving tropomyosin
off the myosin-binding sites. Opening the myosin-binding site on the
actin filaments allows the myosin motors to crawl along the actin,
SFTVMUJOHJOBDPOUSBDUJPOPGUIFNVTDMFmCFS$BMDJVNJTUIFORVJDLMZ
returned to the sarcoplasmic reticulum by the action of a calcium pump.
Without calcium, myosin releases actin, and the filaments slide back to
their original positions.
Storyboard and Animation: Sumanas, Inc. (www.sumanasinc.com)

105

17.10 Myosin
Muscle myosin is a dimer with two identical motor heads that act
JOEFQFOEFOUMZ&BDINZPTJOIFBEIBTBDBUBMZUJDDPSFBOEBOBUUBDIFE
lever arm. A coiled-coil rod ties the two heads together, and tethers
them to the thick filament seen on top. The helical actin filament is
shown at the bottom.
*OUIFCFHJOOJOHPGUIFNPWJF UIFNZPTJOIFBETDPOUBJOCPVOE"%1
and phosphate, and have weak affinity for actin.
Once one of the heads docks properly onto an actin subunit, phosphate
is released. Phosphate release strengthens the binding of the myosin
head to actin, and also triggers the force-generating power stroke that
NPWFTUIFBDUJOmMBNFOU"%1UIFOEJTTPDJBUFT BOE"51CJOETUPUIF
empty nucleotide binding site, causing the myosin head to detach from
the actin filament.
On the detached head, ATP is hydrolyzed, which re-cocks the lever
arm back to its pre-stroke state. Thus, like a spring, the arm stores the
energy released by ATP hydrolysis, and the cycle can repeat.
The actin filament does not slide back after being released by the motor
head, because there are many other myosin molecules also attached to
it, holding it under tension.

Part I:
Ron D. Vale
Howard Hughes Medical Institute
University of California, San Francisco
Ron Milligan
The Scripps Research Institute
Part II:
Toshio Ando
Kanazawa University, Japan

The swing of the lever arm can be directly observed on single myosin
molecules, here visualized by high-speed atomic force microscopy.
Animation: Graham Johnson, Fivth Element (www.fivth.com)
Animation reproduced with permission from Vale & Milligan, Science 288:8895,
Supplemental Movie 1. 2000 American Association for the Advancement of
Science.

17.11 Listeria Parasites


This mammalian cell has been infected with pathogenic Listeria
monocytogenes. These bacteria move throughout the cytosol by
recruiting host cell actin which polymerizes and pushes them forward,
producing a comets tail in their wake.
Whenever a bacterium is pushed into the plasma membrane, it creates a
temporary protrusion and is then bounced back to continue its random
path.
*GXFMPPLDMPTFMZ XFDBOTFFBCBDUFSJVNEJWJEFJOTJEFUIFIPTUDFMM
*NNFEJBUFMZBGUFSTFQBSBUJPO UIFUXPEBVHIUFSDFMMTBTTFNCMFUIFJSPXO
actin tails and start moving about.
These bacteria can also form actin comet tails and move in cell extracts.
Here, the bacteria are expressing the green fluorescent protein, and
actin is labeled red with a fluorescent dye.
The dynamics of the actin tails, that propel the bacteria through the
cytosol, can be modeled, based on known biochemical and physical
properties of actin and actin filaments.
Final composition: Blink Studio Ltd. (www.blink.uk.com)
Video reproduced by permission from Nature Reviews Molecular Cell Biology 1:110
119. 2000 Macmillan Magazines Ltd.

Part I:
Julie A. Theriot
Stanford University School of Medicine
Daniel A. Portnoy
University of California, Berkeley
Part II:
Julie A. Theriot
Stanford University School of Medicine
Frederick S. Soo
Stanford University
Part III:
Jonathan B. Alberts
University of Washington, Seattle

106

17.12 Heart Tissue


4IPXNF


t FOEPUIFMJBMDFMMTVSSPVOEJOHCMPPEWFTTFM

t TNPPUINVTDMFDFMM

t CVEEJOHGVTJOHUSBOTDZUPUJDWFTJDMFT

t KVODUJPOTCFUXFFOFOEPUIFMJBMDFMMT

t XIJUFCMPPEDFMM

t CMPPEWFTTFM MVNFO

Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

17.13 Heart Muscle Cell


4IPXNF


t NJUPDIPOESJB

t .MJOF

t UIJOmMBNFOUT BDUJO

t SJCPTPNFT

t ;MJOF

t UIJDLmMBNFOUT NZPTJO

Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

17.14 Gut Epithelium: View 1


4IPXNF


t UJHIUKVODUJPOT

t EFTNPTPNFT

t DBSCPIZESBUFMBZFS

t BEIFTJPOCFMU

t NJDSPWJMMJ

Originally published in Freeze-Etch Histology: A Comparison between Thin Sections


and Freeze-Etch Replicas by Lelio Orci and Alain Perrelet, Springer-Verlag. New York,
1975

Lelio Orci and Alain Perrelet

107

17.15 Gut Epithelium: View 2


4IPXNF


t UJHIUKVODUJPO

t BEIFSFOTKVODUJPOT

t BDUJOmMBNFOUT

t BEIFTJPOCFMU

Originally published in Freeze-Etch Histology: A Comparison between Thin Sections


and Freeze-Etch Replicas by Lelio Orci and Alain Perrelet, Springer-Verlag.
New York, 1975.

Lelio Orci and Alain Perrelet

17.16 Gut Epithelium: View 3


4IPXNF


t BDUJOmMBNFOUT

t NJDSPWJMMJ

t QMBTNBNFNCSBOF

t DBSCPIZESBUFMBZFS

Originally published in Freeze-Etch Histology: A Comparison between Thin Sections


and Freeze-Etch Replicas by Lelio Orci and Alain Perrelet, Springer-Verlag.
New York, 1975

Lelio Orci and Alain Perrelet

17.17 Tracheal Epithelium


4IPXNF


t DJMJB

t NJDSPUVCVMFT

t NVDVTTFDSFUJOHDFMM

t NJDSPWJMMJ

Originally published in Freeze-Etch Histology: A Comparison between Thin Sections


and Freeze-Etch Replicas by Lelio Orci and Alain Perrelet, Springer-Verlag.
New York, 1975.

Lelio Orci and Alain Perrelet

108

17.18 Quiz: Chapter 17


8IJDIPGUIFGPMMPXJOHJTUIFNBJOGVODUJPOPGJOUFSNFEJBUFmMBNFOUT


t 5PQSPWJEFUSBDLTGPSHVJEJOHJOUSBDFMMVMBSUSBOTQPSU

t 5PFOBCMFUPDSBXM

t 5PFOBCMFDFMMTUPXJUITUBOEUIFNFDIBOJDBMTUSFTTUIBUPDDVST
when cells are stretched

17.19 Media Assessment: Muscle Contraction


8IBUUSJHHFSTUIFDPOUSBDUJPOPGBNVTDMFDFMM


t

(QSPUFJOTCJOEJOHUPBDUJOBOENZPTJO

t

"OBDUJPOQPUFOUJBMJOJUJBUFECZBOFSWFDFMM

t

"OJOnVYPGDBMDJVNJPOTJOUPUIFNVTMDFDFMM

t

"OFnVYPGDBMDJVNJPOTGSPNUIFOFSWFDFMM

17.20 Concept Questions: Chapter 17


8IBUJTEZOBNJDJOTUBCJMJUZBOEIPXJTJUDPOUSPMMFE 
%ZOBNJDJOTUBCJMJUZJTUIFSBQJETXJUDIJOHCFUXFFOHSPXUIBOE
shrinkage shown by microtubules. As free tubulin dimers are added to a
HSPXJOHNJDSPUVCVMF UIFZIZESPMZ[FUIFJS(51UP(%1y

109

17.21 Challenge Question: Chapter 17


Q: Polymerization of tubulin subunits into microtubules occurs with an
increase in the orderliness of the subunits (see figure below). Yet tubulin
polymerization occurs with an increase in entropy (decrease in order).
)PXDBOUIBUCF

Image courtesy of Albert Tousson

17.22 Flashcards: Chapter 17


actin filament



t


UIJO nFYJCMFQSPUFJOmMBNFOUNBEFGSPNBDIBJOPGHMPCVMBS
BDUJONPMFDVMFTBNBKPSDPOTUJUVFOUPGBMMFVLBSZPUJDDFMMT 
this cytoskeletal element is essential for cell movement and for
the contraction of muscle cells.

17.23 References: Chapter 17


%PHUFSPN.:VSLF# 
.FBTVSFNFOUPGUIFGPSDFWFMPDJUZ
relation for growing microtubules. Science 278:856860.
(BSOFS&$ $BNQCFMM$4.VMMJOT3% 
%ZOBNJDJOTUBCJMJUZJOB
%/"TFHSFHBUJOHQSPLBSZPUJDBDUJOIPNPMPHScience 306:10211025.

KEY TERMS
actin-binding protein
actin filament
cell cortex
centriole
centrosome
cilium
cytoskeleton

110

18.1

Cdk2

$ZDMJOEFQFOEFOULJOBTFT PS$ELTGPSTIPSU BSFDSVDJBMSFHVMBUPSZ


proteins in the cell cycle. When activated, these kinases transfer
phosphate groups from ATP to serine and threonine side chains on
UBSHFUQSPUFJOT8IFOJOBDUJWF UIFBDUJWFTJUFPG$ELTJTTUFSJDBMMZ
occluded by a loop, often referred to as the T loop.
As their name suggests, cyclin-dependent kinases are activated by
DZDMJOT$ZDMJOCJOEJOHUP$ELQVMMTUIF5MPPQBXBZGSPNUIFBDUJWFTJUF
and exposes the bound ATP, allowing it access to target proteins. Thus
B$ELDBOQIPTQIPSZMBUFUBSHFUQSPUFJOTPOMZXIFOJUJTJOBDZDMJO$EL
complex.
"UIJSEQSPUFJODBMMFEB$ELBDUJWBUJOHLJOBTFJTSFRVJSFEGPSGVMM
BDUJWBUJPOPG$EL5IJTLJOBTFBEETBQIPTQIBUFHSPVQUPBDSVDJBM
UISFPOJOFJOUIF5MPPQ UIFSFCZFOBCMJOH$ELUPCJOEUPBOE
phosphorylate its target proteins.
5BSHFUQFQUJEFTCJOEUPUIFBDUJWFTJUFPGUIFDZDMJO$ELDPNQMFYTPUIBU
the target serine or threonine side chains are precisely positioned with
respect to the phosphate of the bound ATP.
$ELJOIJCJUPSQSPUFJOT PS$,*T IFMQSFHVMBUFUIFSJTFBOEGBMMPGDZDMJO
$ELBDUJWJUZ4PNFJOIJCJUPSTMJLFUIFPOFTIPXOIFSFCJOEEJSFDUMZBU
the kinase active site and block kinase activity by interfering with ATP
binding. Other inhibitors bind near the active site and interfere with
substrate binding.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

18.2

Early Embryonic Cell Division

This video shows the remarkable synchrony of the early embryonic cell
divisions for the clawed frog Xenopus laevis. About 25 frog eggs were
fertilized simultaneously in this petri dish, and then filmed over the first
EP[FOSPVOETPGDFMMEJWJTJPO&BDIDFMMEJWJTJPODZDMFUBLFTBCPVU
25 minutes in real time. Not only do all the cells in each embryo divide
simultaneously, but the entire dish of embryos maintains essentially the
same clock time over several hours after fertilization.

PDB ID number *: Human Cyclindependent


kinase 2 (1HCK); Cyclin A/Cyclin-dependent
kinase 2 complex (1FIN); Phosphorylated
cyclin-dependent kinase 2 bound to cyclin
A (1JST); Phosphorylated Cdk2cyclin A
substrate peptide complex (1QMZ); p27/
cyclin A/Cdk2 complex (1JSU)

111

18.3

p53-DNA Complex

p53 is a tumor suppressor protein that prevents cells from dividing


inappropriately. Loss of p53 function is associated with many forms of
DBODFS5IF%/"CJOEJOHEPNBJOPGQJTGPMEFEBTB CBSSFM*UFYFSUT
JUTGVODUJPOCZCJOEJOHUP%/"BTBOFHBUJWFUSBOTDSJQUJPOBMSFHVMBUPS
5IFQ%/"JOUFSGBDFJTDPNQMFY*UJOWPMWFTTFWFSBMMPPQTBOEB
IFMJYUIBUFYUFOETGSPNUIFCCBSSFMDPSF3FTJEVFTGSPNPOFMPPQBOE
UIFIFMJYCJOEJOUIF%/"NBKPSHSPPWF"SHJOJOFGSPNBOPUIFS
MPPQNBLFTFYUFOTJWFDPOUBDUTXJUIUIF%/"CBDLCPOFBOE JOEJSFDUMZ
through water molecules, with bases in the minor groove. Mutations
JOBSHJOJOFBSFDPNNPOMZGPVOEJOUVNPSDFMMT4VDINVUBUJPOT
EJTSVQUUIFBCJMJUZPGQUPCJOE%/"
-PPQEPFTOPUCJOEUP%/"EJSFDUMZCVUJTFTTFOUJBMGPSDPSSFDUMZ
QPTJUJPOJOHBSHJOJOFPOUIF%/"5ISFFDZTUFJOFTBOEBIJTUJEJOF
from both loop 2 and loop 3 cooperate to sequester a zinc ion, forming
the rigid heart of a zinc finger motif. Mutations that disrupt interactions
in this motif are also common in tumor cells.
Molecular modelling and animation: Timothy Driscoll, Molvisions
Chime conversion and QuickTime production: Sumanas Inc. (www.sumanasinc.com)

18.4

Plant Cell Division

As this plant nucleus, taken from a blood lily, prepares to divide, the
chromosomes first condense during prophase. Next, they gradually line
up across the center of the mitotic spindle.
At the metaphase to anaphase transition, the sister chromatids of
every chromosome pair separate suddenly, in striking synchrony. The
chromosomes are pulled along the microtubules of the spindle to
opposite ends.
After chromosome separation, small vesicles line up in the center of the
spindle and fuse with each other to form a new cell wall between the
two daughter nuclei.
At telophase, the chromosomes decondense in the newly formed nuclei.

Andrew S. Bajer
Jadwiga A. Mol-Bajer
University of Oregon

112

18.5

Animal Cell Division

%JGGFSFOUJBMJOUFSGFSFODFDPOUSBTUNJDSPTDPQZJTVTFEIFSFUPWJTVBMJ[F
mitotic events in a lung cell grown in tissue culture.
*OEJWJEVBMDISPNPTPNFTCFDPNFWJTJCMFBTUIFSFQMJDBUFEDISPNBUJO
starts to condense.
The two chromatids in each chromosome remain paired as the
chromosomes become aligned on the metaphase plate.
The chromatids then separate and get pulled by the mitotic spindle into
the two nascent daughter cells.
The chromatin decondenses as the two new nuclei form and cytokinesis
continues to constrict the remaining cytoplasmic bridge until the two
daughter cells become separated.

Edward D. (Ted) Salmon and Victoria Skeen


University of North Carolina at Chapel Hill

Final composition: Blink Studio Ltd. (www.blink.uk.com)

Robert Skibbens
Lehigh University

Video reproduced from: The Journal of Cell Biology 122:859875, 1993. The
Rockefeller University Press

18.6

Mitotic Spindle

The mitotic spindle of a dividing human cell is reconstructed here in


its full beauty from multiple optical sections that were recorded with
BnVPSFTDFOUNJDSPTDPQF.JDSPUVCVMFTBSFTUBJOFEJOHSFFO %/"JT
stained in blue, and the kinetochoreswhere microtubules attach to the
%/"BSFTUBJOFEJOQJOL
Final composition: Blink Studio Ltd. (www.blink.uk.com)

Kevin F. Sullivan
The Scripps Research Institute

18.7

Mitotic Spindles in a Fly Embryo

*OBOFBSMZDrosophila embryo, nuclei divide rapidly and in perfect


TZODISPOZ*OUIJTFYQFSJNFOU CPUI%/"BOEUVCVMJOBSFWJTVBMJ[FEXJUI
different fluorescent dyes.
After the mitotic spindle has assembled, the microtubulesshown in
greenstart pulling the blue chromosomes to either pole.
The chromosomes decondense and fill the newly formed round nuclei.
*OQSFQBSBUJPOGPSUIFOFYUSPVOEPGNJUPTJT UIFDFOUSPTPNFTEVQMJDBUF
and migrate to opposite poles of each nucleus where they form new
mitotic spindles and the process repeats.
The whole embryo rhythmically contracts with each division cycle.

William Sullivan
University of California, Santa Cruz
Claudio E. Sunkel, Tatiana MoutinhoSantos, Paula Sampaio, Isabel Amorim and
Madalena Costa
Institute of Biologia Molecular and Cell
Biology, University of Porto, Portugal

113

18.8

Mitosis

*OUIJTNPWJF DSFBUFECZTQJOOJOHEJTLDPOGPDBMnVPSFTDFODF
microscopy, we observe a HeLa cell in late prophase. The membranes of
the endoplasmic reticulum and nuclear envelope are tagged green, and
the chromosomes, which have already replicated and condensed, are
red.
As the nuclear envelope breaks down during prometaphase, the
chromosomes attach to microtubules via their kinetochores and begin
to move. Note how the endoplasmic reticulum absorbs the nuclear
envelope, with which it is continuous, and maintains its integrity.
%VSJOHNFUBQIBTFUIFDISPNPTPNFTBMJHOBUUIFFRVBUPSPGUIFEJWJEJOH
cell.

Tom Kirchhausen
Harvard Medical School

At anaphase, the sister chromatids synchronously separate and are


pulled towards opposite poles of the dividing cell. Note that the space
occupied by the mitotic spindle between the separating chromosomes
FYDMVEFTUIF&3NFNCSBOF
%VSJOHUFMPQIBTFBOFXOVDMFBSFOWFMPQF XIJDIXFDBOOPXPCTFSWF 
reassembles around each set of chromosomes, resealing the nuclear
compartment.
And finally, during cytokinesis, the cytoplasm is divided in two by
a contractile ring of actin and myosin filaments, (which cannot be
observed here), that constrict the plasma membrane and create two
daughter cells.
After mitosis, the chromosomes in each daughter cell lose their distinct
shape as they de-condense.
When we play the movie again at a faster speed, we can better
appreciate the dynamics and beauty of the endoplasmic reticulum and
chromosomes during mitosis.

18.9

Apoptosis

Apoptosis, a form of programmed cell death, has been induced in these


DVMUVSFEDFMMT$FMMEFBUIJTDIBSBDUFSJ[FECZCMFCCJOHPGUIFQMBTNB
NFNCSBOFBOEGSBHNFOUBUJPOPGUIFOVDMFJ4VEEFOMZ DFMMTXFBLFO
attachment to the substratum that they have been growing on and
shrivel up without lysing.
*OUIFGPMMPXJOHNPWJFTXFPCTFSWFUIFQSPDFTTBUIJHIFSNBHOJmDBUJPO

Shigekazu Nagata,
Kyoto university
Sakura Motion Picture Company, 2007
Sakura Motion Picture Company

114

18.10 Interpretive Mitosis


Chromosomes: Mari Nishino, Han Li, Lisa Watson, Manisha Ray, Beatrice Wang,
Sarah Foss
Cleavage Furrow: Ryan Joseph, Ahnika Kline, Chris Cain, Arthur Millius
Centrosomes: Ben Engel, Andrew Houk
Camera Work: Will Ludington
Directed & Edited: Ben Engel

18.11 Mitotic Chromosomes


4IPXNF


t NJDSPUVCVMFT

t LJOFUJDPSF

t DISPNPTPNF

Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

18.12 Quiz: Chapter 18


1. Which two processes together constitute the M phase of the cell
DZDMF


t *OUFSQIBTFBOENJUPTJT

t .JUPTJTBOEDZUPLJOFTJT

t *OUFSQIBTFBOENFUBQIBTF

t 4QIBTFBOE(

115

18.13 Concept Questions: Chapter 18


Why are the kinases of the cell-cycle control system known as cyclinEFQFOEFOUQSPUFJOLJOBTFT 8IBUJTBDZDMJO BOEXIBUJTJUTSPMFJOUIF
DFMM
Kinases of the cell-cycle control system are called cyclin-dependent

18.14 Challenge Question: Chapter 18


One important role of Fas and Fas ligand is to mediate elimination
PGUVNPSDFMMTCZLJMMFSMZNQIPDZUFT*OBTUVEZPGQSJNBSZMVOH
and colon tumors, half the tumors were found to have amplified and
overexpressed a gene for a secreted protein that binds to Fas ligand.
How do you suppose that overexpression of this protein might

Image courtesy of Andrew Bajer

18.15 Flashcards: Chapter 18


anaphase


t

TUBHFPGNJUPTJTEVSJOHXIJDIUIFUXPTFUTPGDISPNPTPNFT
separate and are pulled toward opposite ends of the dividing
cell.

BOBQIBTFQSPNPUJOHDPNQMFY "1$

t

BQSPUFJODPNQMFYUIBUUSJHHFSTUIFTFQBSBUJPOPGTJTUFS
chromatids

18.16 References: Chapter 18


"SJBT&&8BMUFS+$ 
4USFOHUIJOOVNCFSTQSFWFOUJOH
rereplication via multiple mechanisms in eukaryotic cells. Genes Dev
o
)BSUXFMM-) $VMPUUJ+ 1SJOHMF+3FUBM 
(FOFUJDDPOUSPMPGUIFDFMM
division cycle in yeast. Science o

KEY TERMS
anaphase
anaphase-promoting complex
(APC)
apoptosis
aster
Bcl2 family
bi-orientation

116

19.1

Meiosis

(BNFUFT TVDIBTBTQFSNPSBOFHH BSFTQFDJBMJ[FEDFMMTVTFEJOTFYVBM


SFQSPEVDUJPO*OUIJTNJDSPHSBQIPGBDMBNFHH XFDBOTFFBMBSHF
number of sperm binding to its surface. Note the large difference in size
between these male and female gametes.
Although the sperm are much smaller than the egg, a single sperm has
the same number of chromosomes as the egg. When a single sperm
and egg fuse during fertilization, each contribute a set of chromosomes
to the resulting fertilized egg, called a zygote. The zygote will have the
same number of chromosomes as the other cells in the body, since each
parental gamete supplies a half-set of chromosomes.
(BNFUFTBSFDSFBUFEUISPVHIBTQFDJBMQSPDFTTPGDFMMEJWJTJPODBMMFE
NFJPTJT%VSJOHNFJPTJT BTJOHMFHFSNDFMMQSFDVSTPSXJUIUXPTFUTPG
DISPNPTPNFTNVTUEJWJEFUXJDFUPDSFBUFGPVSHBNFUFT&BDIPGUIF
four resulting gametes will have half the number of chromosomes as
the germ-cell precursor, and each of the gametes will be genetically
different from the other gametes.
*OPSEFSUPVOEFSTUBOEXIZNFJPUJDDFMMEJWJTJPOSFTVMUTJOHFOFUJDBMMZ
dissimilar gametes, we need to look more closely at the key molecular
events that occur during the meiotic cycle.
The germ-cell precursor begins with two complete sets of
DISPNPTPNFT BNBUFSOBMTFUBOEBQBUFSOBMTFU5ISPVHI%/"
replication, a complete copy of each set is made. The copies align with
the original set of chromosomes, and then link tightly, forming twin sets
of chromosomes, called sister chromatids.
The maternal and paternal sister chromatids then align on the
metaphase plate, where they form a set of four paired chromatids,
DBMMFEBCJWBMFOU$SPTTPWFSFWFOUTPDDVSCFUXFFOUIFOPOTJTUFS
chromatids, mixing chromosomal information at sites called chiasmata.
5IJTFYDIBOHFPGJOGPSNBUJPO DBMMFESFDPNCJOBUJPO JTBNBKPSTPVSDF
of genetic variation.
After recombination, the reshuffled chromatids separate, and eventually
UIFDFMMTEJWJEFDPNQMFUFMZ FOEJOH.FJUPUJD%JWJTJPO*
.FJUPUJD%JWJTJPO*JTGPMMPXFECZBTFDPOETUBHFPGDFMMEJWJTJPO .JUPUJD
%JWJTJPO**4JHOJmDBOUMZ UIJTTFDPOEEJWJTJPOPDDVSTXJUIPVU%/"
SFQMJDBUJPO4VCTFRVFOUMZ UIFGPVSSFTVMUJOHEBVHIUFSDFMMT UIFHBNFUFT 
will have one half the number of chromosomes as the parent cells and,
due to recombination, each gamete will be genetically different from the
others.
Animation: Graphic Pulse, Inc. (www.graphicpulse.com)

117

19.2

Sea Urchin Fertilization

A sea urchin egg during fertilization is visualized here simultaneously


by phase contrast microscopy and by fluorescence microscopy. The
egg contains a fluorescent dye that becomes brighter in the presence of
calcium ions.
When a sperm cell fuses with the egg, the fluorescence image shows
a wave of calcium ions that sweeps through the cytosol, starting from
the initial point of spermegg fusion. Following the path of the calcium
wave, we see a membrane, called the fertilization envelope, rising
from the cell surface. The fertilization envelope protects the fertilized
egg from the outside environment, and prevents the entry of additional
sperm. The rise in cytosolic calcium triggers an elevation of the
fertilization envelope through the process of exocytosis.
&YPDZUPTJTSFMFBTFTIZESPMZUJDFO[ZNFTTUPSFEJOWFTJDMFT"DUJPOPGUIF
released hydrolases causes a swelling of material surrounding the cell,
which in turn elevates the fertilization envelope.
&YPDZUPTJTDBOCFWJTVBMJ[FEEJSFDUMZJOUIJTTZTUFN'PSUIJTQVSQPTF 
the plasma membrane is labeled with a fluorescent dye, seen on the
SJHIU&BDIUJNFBWFTJDMFGVTFT JUMFBWFTBEFQSFTTJPOJOUIFQMBTNB
membrane which, in the optical sections shown, appears as a ring of
increased fluorescent staining.
On the left, differential interference contrast microscopy is used to
directly view the exocytic vesicles that underlie the plasma membrane.
The vesicles are visible here, because they are densely packed with
protein and consequently have a different refractive index from the
TVSSPVOEJOHNBUFSJBM&BDIUJNFBWFTJDMFFYPDZUPTFT JUEJTQFSTFTJUT
contents and disappears from the image. This effect is best seen when
XFTUFQCBDLBOEGPSUICFUXFFOBEKBDFOUGSBNFTPGUIFNPWJF

19.3

Quiz: Chapter 19

8IJDIPGUIFGPMMPXJOHJTUIFUFSNGPSWBSJBOUWFSTJPOTPGBHFOF


t .VUBUJPOT

t "MMFMFT

t )PNPMPHT

t 4JTUFSHFOFT

Mark Terasaki
University of Connecticut Health Center

118

19.4

Concept Questions: Chapter 19

)PXEPFTTFYVBMSFQSPEVDUJPOHFOFSBUFHFOFUJDEJWFSTJUZ
4FYVBMSFQSPEVDUJPOHFOFSBUFTHFOFUJDEJWFSTJUZJOTFWFSBMXBZT'JSTU 
during meiosis, the maternal and paternal homologs come together and
FYDIBOHF%/"TFHNFOUTUISPVHISFDPNCJOBUJPOy

19.5

Flashcards: Chapter 19

allele


t

BOBMUFSOBUJWFGPSNPGBHFOFGPSBHJWFOHFOF NBOZBMMFMFT
may exist in the gene pool of the species.

asexual reproduction


t

19.6

NPEFPGSFQSPEVDUJPOJOXIJDIPGGTQSJOHBSJTFGSPNBTJOHMF
parent

References: Chapter 19

#MBU: 1SPUBDJP36 )VOUFS/BOE,MFDLOFS/ 


1IZTJDBMBOE
functional interactions among basic chromosome organizational
features govern early steps of meiotic chiasma formation. Cell
111:791802.
)PFLTUSB3' 
&WPMVUJPOBSZCJPMPHZXIZTFYJTHPPENature
o

KEY TERMS
allele
asexual reproduction
bivalent
chiasma (plural chiasmata)
classical genetic approach
complementation test
crossing-over

119

20.1

Wound Healing

Fibroblasts grown in vitro in a culture dish form a confluent monolayer


PGDFMMT$FMMTJOBNPOPMBZFSBSFSFMBUJWFMZTUBUJDDPOUBDUJOHFBDIPUIFS
inhibits their migration.
4VDIDFMMMBZFSTDBOCFXPVOEFEFYQFSJNFOUBMMZCZTDSBUDIJOHUIFN
with a needle.
*OTVDIBOFYQFSJNFOU XFDBOPCTFSWFUIBUUIFmCSPCMBTUTBUUIFFEHF
of the wound become migratory and quickly move to repair the gap.
4VDIDFMMNJHSBUJPOJTJNQPSUBOUGPSXPVOESFQBJSJOBOJOUBDUPSHBOJTN
Animation: Blink Studio Ltd. (www.blink.uk.com)

20.2

Sheryl Denker and Diane Barber


University of California, San Francisco

Adhesion Junctions Between Cells

These epithelial cells express green fluorescent cadherin. They are


HSPXOBUMPXEFOTJUZ TPUIBUJTPMBUFEDFMMTDBOCFPCTFSWFE*OJUJBMMZ 
labeled cadherin is diffusely distributed over the whole cell surface.
As cells crawl around and touch each other, cadherin becomes
DPODFOUSBUFEBTJUGPSNTUIFBEIFTJPOKVODUJPOTUIBUMJOLBEKBDFOUDFMMT
&WFOUVBMMZ BTUIFDFMMEFOTJUZJODSFBTFTGVSUIFS UIFDFMMTCFDPNF
completely surrounded by neighbors and form a tightly packed sheet of
epithelial cells.
Music: Christopher Thorpe
Stephen J. Smith
Stanford University School of Medicine
Cynthia Adams
Finch University of Health Sciences and
Chicago Medical School
Yih-Tai Chen
Cellomics, Inc.
W. James Nelson
Stanford University School of Medicine

120

20.3

Drosophila Development

%VSJOHEFWFMPQNFOU BDrosophila embryo undergoes many complex


morphological changes. We first see migration of pole cells from the
posterior end. These cells are destined to become the germ cells of the
fly. A crest develops which separates a region that will develop into the
head, mouth parts, and fore gut. At this stage, the future tail end of the
CPEZJTGPMEFEPWFSPOUIFEPSTBMTJEF#PEZTFHNFOUTUIFOCFDPNF
defined.
The first three segments will give rise to the head and mouth parts,
the next three to the thorax, and the remaining ones to the abdomen.
&WFOUVBMMZ UIFSFBSFOEPGUIFFNCSZPXJMMSFUSBDUCBDLPOUPUIFWFOUSBM
TJEFBOETUSBJHIUFOPVUUIFFNCSZP%FWFMPQNFOUUPUIJTTUBHFUBLFT
about 10 hours.
We can appreciate the complexity of these events by morphing a series
of individual scanning electron micrographs into a continuous temporal
sequence: migration of pole cells; development of various surface
indentations, including openings to the air ducts, or tracheal tubes;
segmentation, and tail retraction.
A similar sequence viewed from the topor the dorsal side. Pole cells
migrate and then move into the interior as the hind gut invaginates. The
rear end is temporarily folded over onto the dorsal side and eventually
starts retracting to straighten out the embryo.

Thomas C. Kaufman
Howard Hughes Medical Institute
Indiana University, Bloomington
SEM:
Rudi Turner
Indiana University, Bloomington Morphing:
Michael Kaufmann, Jeffrey Giacoletti and
Chris Macri
Indiana University, Bloomington

&BSMZJOEFWFMPQNFOUXIFOTFFOGSPNUIFCPUUPNPSWFOUSBMTJEFB
deep groove forms during gastrulation, as mesodermal cells migrate
inward, where they become the precursor cells for many internal
organs. The groove then seals off as the cells that remain exterior zipper
up.
Final composition: Blink Studio Ltd. (www.blink.uk.com)

20.4

Early Zebrafish Development

The first divisions of a zebrafish egg occur synchronously about every 30


minutes and create a mass of cells sitting on top of a enormous yolk.
This blastoderm then begins to spread as a continuous sheath over the
yolk.
%VSJOHUIJTQSPDFTT TPNFDFMMTGSPNUIFFYUFSOBMMBZFSUVHJOUPUIF
interior of the embryo. They will eventually form the lining of the gut, as
well as the musculature, skeleton, and other internal tissues.
The first body segments, the head process and tail bud become visible.
The tail bud continues to extend, and we clearly see the eye develop.
17 hours into development, we can already see a recognizable
vertebrate emerging, wrapped around the ball of yolk that will nourish it
for the first few days of its existence.
Final composition: Blink Studio Ltd. (www.blink.uk.com)
Video reproduced from: R.O. Karlstrom and D.A. Kane, Development 123:461.
1996 The Company of Biologists Ltd.

Rolf O. Karlstrom
University of Massachusetts at Amherst
Donald A. Kane
University of Rochester, New York

121

20.5

Megakaryocyte

Megakaryocytes are the precursor cells from which blood platelets


derive. These gigantic cells undergo an elaborate fragmentation process
that pinches off portions of the cells cytoplasm. These fragments are
the platelets, which are then swept away in the blood stream. Platelets
BSFJNQPSUBOUGPSCMPPEDPBHVMBUJPOBUTJUFTPGJOKVSZ
Final composition: Blink Studio Ltd. (www.blink.uk.com)
Video reproduced from: The Journal of Cell Biology 147:12991312, 1999. The
Rockefeller University Press.

Joseph E. Italiano, Jr.


Brigham and Women's Hospital and
Harvard Medical School
Ramesh A. Shivdasani
Dana-Farbwe Cancer Institute and Harvard
Medical School

20.6

Embryonic Stem Cells

&NCSZPOJDTUFNDFMMTDBOEJGGFSFOUJBUFJOUPBOZDFMMUZQFJOUIFCPEZ
such as red blood cells, neurons or muscle cells.
When grown in culture and exposed to an appropriate cocktail of signal
molecules, previously homogeneous, undifferentiated embryonic stem
DFMMT PSHBOJ[FJOUPHSPVQTPGIJHIMZTQFDJBMJ[FEDFMMT3FNBSLBCMZ UIF
cells in these groups start contracting rhythmically and in synchrony,
indicating that they have formed a fully functional contractile apparatus
BOEDPOOFDUJOHKVODUJPOT DIBSBDUFSJTUJDPGNVTDMFDFMMT
('1FYQSFTTFEGSPNBIFBSUNVTDMFTQFDJmDQSPNPUFS TIPXTUIBUUIF
appropriate gene expression programs are selectively activated in the
beating cells

20.7

Bruce R. Conklin
Gladstone Institute of Cardiovascular
Disease, University of California, San
Francisco

Breast Cancer Cells

Normal human breast epithelial cells can be grown in cell culture. They
form structures that resemble the little sacs of cells from which the
NBNNBSZHMBOEJTCVJMU$FMMTBTTFNCMFJOUPBXFMMPSHBOJ[FE QPMBSJ[FE
FQJUIFMJVNUIBUGPSNTBDMPTFETQIFSFXJUIBOJOUFSOBMMVNFO*OUIF
mammary gland, this space would be connected to ducts, and the cells
would secrete milk into it.
#ZDPOUSBTU UIFTFIVNBOCSFBTUDBODFSDFMMTHSPXOVOEFSUIFTBNF
conditions, divide aggressively and in an uncontrolled fashion. They are
also more migratory and grow into disorganized clumps which would
form tumors in the body.
Final composition: Blink Studio Ltd. (www.blink.uk.com)

Mina J. Bissell, Karen Schmeichel, Hong Liu


and Tony Hansen
Lawrence Berkeley Laboratories

122

20.8

The Intestinal Crypt and APC Loss

The lining of the small intestine, like the lining of most of the gut, is
BTJOHMFMBZFSFEFQJUIFMJVN%FQFOEJOHVQPOMPDBUJPOJOUIFHVU UIF
epithelial cells, usually called enterocytes, help absorb nutrients from
UIFMVNFOPGUIFHVUPSBCTPSCXBUFSGSPNUIFJOUFTUJOBMDPOUFOUT*O
the small intestine, the surface of the lining of the gut is increased
enormously by thousands of villi that protrude into the lumen. Here
we see a single villus and its internal architecture. The surface of the
villus is covered by a single layer of enterocytes, which extend down
JOUPUIFDSZQUCFMPX4UFNDFMMTBUUIFCPUUPNPGUIFDSZQU MPDBUFE
between paneth cells, divide and make copies of themselves, and also
make transit-amplifying cells. The transit amplifying cells proliferate
rapidly and move up the walls of the crypt. As the cells migrate upwards
they begin to differentiate into goblet cells and enterocytes. While the
cells are moving up the sides of the villus, they carry out the essential
functions of the small intestine, notably absorption of nutrients. When
the differentiated cells reach the tip of the villus, they undergo apoptosis
and are shed into the lumen of the small intestine. The entire process
PGPVUNJHSBUJPOBOEDFMMEFBUIJTDPNQMFUFEJOKVTUUISFFUPGPVSEBZT
The process of out-migration and rapid cell replacement is a defense
mechanism against the development of colon cancer, since almost
all epithelial cells, including those that have accidentally sustained
mutations, are shed within days of their formation. Therefore, the only
mutations that can lead to the development of a cancer are those that
are retained in the crypt. This dictates that such mutations must block
the outmigration of mutant cells from the crypt. The outmigration
of transit amplifying cells from the bottom of the crypt depends on
UIFQSPUFJODBMMFEBEFOPNBUPVTQPMZQPTJTDPMJ PSTJNQMZ"1$*OUIF
BCTFODFPGGVODUJPOBM"1$ UIJTDPOUJOVPVTPVUNJHSBUJPOJTCMPDLFE 
leading to the accumulation of transit amplifying cells in the crypt.
*OUIJTBOJNBUJPOPGBOFYQFSJNFOU "1$MPTTJTBDIJFWFEUISPVHI
an induced gene inactivation, which appears to mimic the mutation
UIBUJOJUJBUFTNPTUHBTUSPJOUFTUJOBMUVNPST"1$JTVTVBMMZSFRVJSFEUP
inactivate the intracellular protein called -catenin; the inactivation of
-catenin permits the differentiation of the transit amplifying cells and
UIFJSDPOUJOVFEPVUNJHSBUJPOGSPNUIFCBTFPGUIFDSZQU*OUIFBCTFODF
PG"1$GVODUJPO  -catenin accumulates within the transit amplifying
cells, which blocks both their outmigration and differentiation.
The accumulated transit amplifying cells do not themselves form a
carcinoma. However, they and their descendants can now accumulate
additional mutations that will drive such cells progressively to become
full-fledged carcinoma cells.
Animation by Digizyme, Inc (www.digizyme.com)
Models, Animations, Surfacing, Composite: Eric Keller
Storyboard and Art Directions: Gael McGill
2009 by Hans Clevers

Hans Clevers
Hubrecht Institute

123

20.9

Angiogenesis

As a normal part of growth and development, the body must generate


OFXCMPPEWFTTFMTUPPYZHFOBUFUIFUJTTVFT*OBQSPDFTTDBMMFE
BOHJPHFOFTJT OFXWFTTFMTTQSPVUGSPNFYJTUJOHPOFT*OUIJTNPWJF XF
see endothelial cells sprouting to form new branches from the aorta
PGB[FCSBmTIFNCSZP&BDITQSPVUJTJOJUJBMMZGPSNFECZPOFPSBGFX
endothelial cells. The process begins when an endothelial cell of a
small vessel is activated by an angiogenic stimulus, such as vascular
FOEPUIFMJBMHSPXUIGBDUPS PS7&('
*OSFTQPOTFUPUIFTUJNVMVT UIF
endothelial cell becomes motile and extends filopodia that guide the
development of a capillary sprout. The leading or tip cell continues to
move away from the capillary as cells behind it migrate in and divide,
GPSNJOHBTUBML5IFTQSPVUCFHJOTUPIPMMPXPVU GPSNJOHBUVCF*OUIJT
process, pinocytic vesicles fuse with one another. The large vacuoles
formed in this way then fuse with one another, creating a lumen that
SVOTUISPVHIUIFDBQJMMBSZTQSPVU*ODVMUVSF FOEPUIFMJBMDFMMTCFIBWFJO
BTJNJMBSXBZUIFZTQPOUBOFPVTMZEFWFMPQJOUFSOBMWBDVPMFTUIBUKPJO
VQGSPNDFMMUPDFMM DSFBUJOHBTJOHMFMVNFOTIBSFECZNBOZDFMMT*OUIF
example shown here, the individual cells contain either a red or a green
fluorophore. Note that the areas of green and red are distincteven
though cells share a lumen, they do not share cytoplasm and remain
separate cells after the fusion events. Angiogenesis is critical not only in
normal development and wound healing, but also in the development
of tumors. A tumor must stimulate blood vessel formation to grow more
UIBOBGFXNJMMJNFUFSTJOTJ[F7&('JTBLFZBDUJWBUPSPGBOHJPHFOFTJT
in both normal cells and tumors. When cells within a tumor become
PYZHFOEFmDJFOU UIFZCFHJOUPFYQSFTT7&('7&('EJGGVTFTUISPVHI
the tissues, activating endothelial cells on nearby vessels. This results
JODBQJMMBSZTQSPVUJOH4PNFOFXDBODFSUIFSBQJFTBSFUBSHFUFEUPCMPDL
UIFBDUJPOPG7&(' XJUIWBSZJOHDMJOJDBMSFTVMUT

Movie I:
Brant M. Weinstein
National Institutes of Health
Movie II:
Georgina E. Davis
University of Missouri School of Medicine

20.10 Junction Between Two Muscle Cells


4IPXNF


t QMBTNBNFNCSBOFT

t EFTNPTPNFT

t ;EJTLT

t USBOTWFSTFUVCVMFTBOETBSDPQMBTNJDSFUJDVMVN

Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

124

20.11 Endothelial Cell in Liver


4IPXNF


t PVUMJOFPGFOEPUIFMJBMDFMM

t PVUMJOFPGTVSSPVOEJOHMJWFSDFMMT

t TFDSFUPSZWFTJDMFTXJUIDPOEFOTFEDPOUFOUQSPUFJOT

Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

20.12 Liver Cells: Sinusoid Space


4IPXNF


t NJDSPWJMMJPGIFQBUPDZUFT

t XIJUFCMPPEDFMM OFVUSPQIJM

t FOEPUIFMJBMDFMMT

t OVDMFVTPGOFVUSPQIJM

Doug Bray
The University of Lethbridge, Canada
Brian Oates and Cyprien Lomas
The University of British Columbia

20.13 Quiz: Chapter 20


4VQQPSUJWFUJTTVFT TVDIBTCPOFPSXPPE EFSJWFUIFJSTUSFOHUIGSPN


t DFMMT

t FYUSBDFMMVMBSNBUSJY

t DZUPTLFMFUBMmMBNFOUT

125

20.14 Concept Questions: Chapter 20


What would happen if fibroblasts produced mature collagen rather
UIBOQSPDPMMBHFO 8IBUXPVMEIBQQFOJGUIFSFXFSFOPQSPDPMMBHFO
QSPUFJOBTFTJOUIFFYUSBDFMMVMBSTQBDF 
$PMMBHFOJTTZOUIFTJ[FEBTBQSPDPMMBHFONPMFDVMFUIBUIBT
unstructured

20.15 Challenge Question: Chapter 20


Q: Mortality due to lung cancer was followed in groups of males in the
6OJUFE,JOHEPNGPSZFBST'JHVSFoTIPXTUIFDVNVMBUJWFSJTLPG
dying from lung cancer as a function of age and smoking habits for four
groups of males: those who never smoked, those who stopped at age
30, those who stopped at age 50, and those who continued...

20.16 Flashcards: Chapter 20


BEIFSFOTKVODUJPO


t

DFMMKVODUJPOUIBUIFMQTIPMEUPHFUIFSFQJUIFMJBMDFMMTJOBTIFFU
of epithelium; actin filaments inside the cell attach to its
cytoplasmic face.

20.17 References: Chapter 20


'VDIT& 
4DSBUDIJOHUIFTVSGBDFPGTLJOEFWFMPQNFOUNature
o
(BJFUUB( %FFSJODL5+ "EBNT43FUBM 
.VMUJDPMPSBOEFMFDUSPO
microscopic imaging of connexin trafficking. Science 296:503507.

KEY TERMS
adherens junction
apical
basal
basal lamina
cadherin
cancer
cell junction

126

GENERAL CREDITS
Artistic and scientific direction:
Peter Walter, Howard Hughes Medical Institute, University of California, San Francisco
Narrated by:
Julie Theriot, Stanford University School of Medicine
Produced by:
Michael Morales, Garland Science
Animation and video production:
Sumanas, Inc. (www.sumanasinc.com)
Blink Studio Ltd. (www.blink.uk.biz)
Graham Johnson, University of California, San Francisco
Allison Bruce
Thomas Dallman
Amy Heagle Whiting, Health Research Incorporated at the Wadsworth Center, State
University of New York at Albany
Michael Kusie (www.mkmstudio.com)
Graphic Pulse Inc. (www.graphicpulse.com)
Michael Morales and Lamia Harik, Garland Science
Peter Walter, Howard Hughes Medical Institute, University of California, San Francisco
High-resolution electron micrographs:
Doug Bray, The University of Lethbridge, Canada
Lelio Orci and Alain Perrelet
Brian Oates and Cyprien Lomas, The University of British Columbia
Audio recording and engineering:
Adam Rossi (www.ar-audio.com)
Johannes Luley, mysonictemple (www.mysonictemple.com)
Freudenhaus Audio Productions
Original music:
Freudenhaus Audio Productions
Christopher Thorpe
Adam Rossi
Licensed music and sound effects:
CSS Music (www.cssmusic.com)
Sounddogs (www.sounddogs.com)
Chemistry consultant:
Patricia S. Caldera-Muoz
Editorial Assistant:
Lamia Harik
Production Editor:
Emma Jeffcock of EJ Publishing
Marketing:
Adam Sendroff and Helen Boyd, Garland Science
Executive Producer:
Denise Schanck, Garland Science
2014 by Garland Science