3rd Ed Refs
Essential Cell Biology, Third Edition References
http://www.garlandscience.com/textbooks/0815341296/pdf/ECB3References.pdf
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Chapter 1
The Universal Features of Cells on Earth
Andersson SGE (2006) The bacterial world gets smaller.
Science 314:259–260.
Brenner S, Jacob F & Meselson M (1961) An unstable
intermediate carrying information from genes to
ribosomes for protein synthesis. Nature 190:576–
581.
Fraser CM, Gocayne JD, White O et al (1995) The
minimal gene complement of Mycoplasma
genitalium. Science 270:397–403.
Harris JK, Kelley ST, Spiegelman et al (2003) The
genetic core of the universal ancestor. Genome Res
13:407–413.
Koonin EV (2005) Orthologs, paralogs, and
evolutionary genomics. Annu Rev Genet 39:309–338.
Watson JD & Crick FHC (1953) Molecular structure of
nucleic acids. A structure for deoxyribose nucleic
acid. Nature 171:737–738.
Yusupov MM,Yusupova GZ, Baucom A et al (2001)
Crystal structure of the ribosome at 5.5 Å resolution.
Science 292:883–896.
Looking at Cells in the Light Microscope
Adams MC, Salmon WC, Gupton SL et al (2003) A highspeed
multispectral spinning‐disk confocal
microscope system for fluorescent speckle
microscopy of living cells. Methods 29:29–41.
Agard DA, Hiraoka Y, Shaw P & Sedat JW (1989)
Fluorescence microscopy in three dimensions. In
Methods in Cell Biology, vol 30: Fluorescence
Microscopy of Living Cells in Culture, part B (DL
Taylor, Y‐L Wang eds). San Diego: Academic Press.
Centonze VE (2002) Introduction to multiphoton
excitation imaging for the biological sciences.
Methods Cell Biol 70:129–48.
Chalfie M, Tu Y, Euskirchen G et al (1994) Green
fluorescent protein as a marker for gene expression.
Science 263:802–805.
Giepmans BN, Adams SR, Ellisman MH & Tsien RY
(2006) The fluorescent toolbox for assessing protein
location and function. Science 312:217–224.
Harlow E & Lane D (1988) Antibodies. A Laboratory
Manual. Cold Spring Harbor, NY: Cold Spring Harbor
Laboratory Press.
Haugland RP (ed) (1996) Handbook of Fluorescent
Probes and Research Chemicals, 8th ed. Eugene, OR:
Molecular Probes, Inc. (Available online at
http://www.probes.com/)
Jaiswai JK & Simon SM (2004) Potentials and pitfalls of
fluorescent quantum dots for biological imaging.
Trends Cell Biol 14:497–504.
Jares‐Erijman EA & Jovin TM (2003) FRET imaging.
Nature Biotech 21:1387–1395.
Lippincott‐Shwartz J, Altan‐Bonnet N & Patterson G
(2003) Photobleaching and photoactivation:
following protein dynamics in living cells. Nature Cell
Biol 5:S7–S14.
Minsky M (1988) Memoir on inventing the confocal
scanning microscope. Scanning 10:128–138.
Miyawaki A, Sawano A & Kogure T (2003) Lighting up
cells: labeling proteins with fluorophores. Nature Cell
Biol 5:S1–S7.
Parton RM & Read ND (1999) Calcium and pH imaging
in living cells. In Light Microscopy in Biology. A
Practical Approach, 2nd ed. (Lacey AJ ed) Oxford:
Oxford University Press.
Sako Y & Yanagida T (2003) Single‐molecule
visualization in cell biology. Nature Rev Mol Cell Biol
4:SS1–SS5.
Sekar RB & Periasamy A (2003) Fluorescence
resonance energy transfer (FRET) microscopy
imaging of live cell protein localizations. J Cell Biol
160:629–633.
Shaner NC, Steinbach PA & Tsien RY (2005) A guide to
choosing fluorescent proteins. Nature Methods
2:905–909.
Sheetz MP (ed) (1997) Laser Tweezers in Cell Biology.
Methods Cell Biol 55.
Sluder G & Wolf DE (2007) Video Microscopy 3rd ed.
Methods Cell Biol 81.
Stevens DJ & Allan (2003) Light Microscopy Techniques
for Live Cell Imaging. Science 300:82–86.
Tsien RY (2003) Imagining imaging’s future. Nature Rev
Mol Cell Rev 4:SS16–SS21.
Weiss DG, Maile W, Wick RA & Steffen W (1999) Video
microscopy. In Light Microscopy in Biology: A
Practical Approach, 2nd ed. (AJ Lacey ed) Oxford:
Oxford University Press.
White JG, Amos WB & Fordham M (1987) An
evaluation of confocal versus conventional imaging
of biological structures by fluorescence light
microscopy. J Cell Biol 105:41–48.
Zernike F (1955) How I discovered phase contrast.
Science 121:345–349.
Looking at Cells and Molecules in the Electron
Microscope
Allen TD & Goldberg MW (1993) High resolution SEM
in cell biology. Trends Cell Biol 3:203–208.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Baumeister W (2002) Electron tomography: towards
visualizing the molecular organization of the
cytoplasm. Curr Opin Struct Biol 12:679–684.
Böttcher B, Wynne SA & Crowther RA (1997)
Determination of the fold of the core protein of
hepatits B virus by electron cryomicroscopy. Nature
386:88–91.
Dubochet J, Adrian M, Chang J‐J et al (1988)
Cryoelectron microscopy of vitrified specimens. Q
Rev Biophys 21:129–228.
Frank J (2003) Electron microscopy of functional
ribosome complexes. Biopolymers 68:223–233.
Hayat MA (2000) Principles and Techniques of Electron
Microscopy, 4th ed. Cambridge: Cambridge
University Press.
Heuser J (1981) Quick‐freeze, deep‐etch preparation of
samples for 3D electron microscopy. Trends Biochem
Sci 6:64–68.
Lippincott‐Schwartz J & Patterson GH (2003)
Development and use of fluorescent protein markers
in living cells. Science 300:87–91.
McIntosh R, Nicastro D & Mastronarde D (2005) New
views of cells in 3D: an introduction to electron
tomography. Trends Cell Biol 15:43–51.
McDonald KL & Auer M (2006) High pressure freezing,
cellular tomography, and structural cell biology.
Biotechniques 41:137–139.
Pease DC & Porter KR (1981) Electron microscopy and
ultramicrotomy. J Cell Biol 91:287s–292s.
Unwin PNT & Henderson R (1975) Molecular structure
determination by electron microscopy of unstained
crystal specimens. J Mol Biol 94:425–440.
Chapter 2
The Chemical Components of a Cell
Abeles RH, Frey PA & Jencks WP (1992) Biochemistry.
Boston: Jones & Bartlett.
Atkins PW (1996) Molecules. New York: WH Freeman.
Branden C & Tooze J (1999) Introduction to Protein
Structure, 2nd ed. New York: Garland Science.
Bretscher MS (1985) The molecules of the cell
membrane. Sci Am 253:100–109.
Burley SK & Petsko GA (1988) Weakly polar
interactions in proteins. Adv Protein Chem 39:125–
189.
De Duve C (2005) Singularities: Landmarks on the
Pathways of Life. Cambridge: Cambridge University
Press.
Dowhan W (1997) Molecular basis for membrane
phospholipid diversity: Why are there so many
lipids? Annu Rev Biochem 66:199–232.
Eisenberg D & Kauzman W (1969) The Structure and
Properties of Water. Oxford: Oxford University Press.
Fersht AR (1987) The hydrogen bond in molecular
recognition. Trends Biochem Sci 12:301–304.
Franks F (1993) Water. Cambridge: Royal Society of
Chemistry.
Henderson LJ (1927) The Fitness of the Environment,
1958 ed. Boston: Beacon.
Neidhardt FC, Ingraham JL & Schaechter M (1990)
Physiology of the Bacterial Cell: A Molecular
Approach. Sunderland, MA: Sinauer.
Pauling L (1960) The Nature of the Chemical Bond, 3rd
ed. Ithaca, NY: Cornell University Press.
Saenger W (1984) Principles of Nucleic Acid Structure.
New York: Springer.
Sharon N (1980) Carbohydrates. Sci Am 243:90–116.
Stillinger FH (1980) Water revisited. Science 209:451–
457.
Tanford C (1978) The hydrophobic effect and the
organization of living matter. Science 200:1012–
1018.
Tanford C (1980) The Hydrophobic Effect. Formation of
Micelles and Biological Membranes, 2nd ed. New
York: John Wiley.
Chapter 3
Catalysis and the Use of Energy by Cells
Atkins PW (1994) The Second Law: Energy, Chaos and
Form. New York: Scientific American Books.
Atkins PW & De Paula JD (2006) Physical Chemistry for
the Life Sciences. Oxford: Oxford University Press.
Baldwin JE & Krebs H (1981) The Evolution of
Metabolic Cycles. Nature 291:381–382.
Berg HC (1983) Random Walks in Biology. Princeton,
NJ: Princeton University Press.
Dickerson RE (1969) Molecular Thermodynamics.
Menlo Park, CA: Benjamin Cummings.
Dill KA & Bromberg S (2003) Molecular Driving Forces:
Statistical Thermodynamics in Chemistry and
Biology. New York: Garland Science.
Dressler D & Potter H (1991) Discovering Enzymes.
New York: Scientific American Library.
Einstein A (1956) Investigations on the Theory of
Brownian Movement. New York: Dover.
Fruton JS (1999) Proteins, Enzymes, Genes: The
Interplay of Chemistry and Biology. New Haven: Yale
University Press.
Goodsell DS (1991) Inside a living cell. Trends Biochem
Sci 16:203–206.
Karplus M & McCammon JA (1986) The dynamics of
proteins. Sci Am 254:42–51.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Karplus M & Petsko GA (1990) Molecular dynamics
simulations in biology. Nature 347:631–639.
Kauzmann W (1967) Thermodynamics and Statistics:
with Applications to Gases. In Thermal Properties of
Matter Vol 2. New York: WA Benjamin, Inc.
Kornberg A (1989) For the Love of Enzymes.
Cambridge, MA: Harvard University Press.
Lavenda BH (1985) Brownian Motion. Sci Am 252:70–
85.
Lawlor DW (2001) Photosynthesis, 3rd ed. Oxford:
BIOS.
Lehninger AL (1971) The Molecular Basis of Biological
Energy Transformations, 2nd ed. Menlo Park, CA:
Benjamin Cummings.
Lipmann F (1941) Metabolic generation and utilization
of phosphate bond energy. Adv Enzymol 1:99–162.
Lipmann F (1971) Wanderings of a Biochemist. New
York: Wiley.
Nisbet EE & Sleep NH (2001) The habitat and nature of
early life. Nature 409:1083–1091.
Racker E (1980) From Pasteur to Mitchell: a hundred
years of bioenergetics. Fed Proc 39:210–215.
Schrödinger E (1944 & 1958) What is Life?: The
Physical Aspect of the Living Cell and Mind and
Matter, 1992 combined ed. Cambridge: Cambridge
University Press.
van Holde KE, Johnson WC & Ho PS (2005) Principles of
Physical Biochemistry, 2nd ed. Upper Saddle River,
NJ: Prentice Hall.
Walsh C (2001) Enabling the chemistry of life. Nature
409:226–231.
Westheimer FH (1987) Why nature chose phosphates.
Science 235:1173–1178.
Youvan DC & Marrs BL (1987) Molecular mechanisms
of photosynthesis. Sci Am 256:42–49.
Chapter 4
The Shape and Structure of Proteins
Anfinsen CB (1973) Principles that govern the folding
of protein chains. Science 181:223–230.
Bray D (2005) Flexible peptides and cytoplasmic gels.
Genome Biol 6:106–109.
Burkhard P, Stetefeld J & Strelkov SV (2001) Coiled
coils: a highly versatile protein folding motif. Trends
Cell Biol 11:82–88.
Caspar DLD & Klug A (1962) Physical principles in the
construction of regular viruses. Cold Spring Harb
Symp Quant Biol 27:1–24.
Doolittle RF (1995) The multiplicity of domains in
proteins. Annu Rev Biochem 64:287–314.
Eisenberg D (2003) The discovery of the alpha‐helix
and beta‐sheet, the principle structural features of
proteins. Proc Natl Acad Sci USA 100:11207–11210.
Fraenkel‐Conrat H & Williams RC (1955) Reconstitution
of active tobacco mosaic virus from its inactive
protein and nucleic acid components. Proc Natl Acad
Sci USA 41:690–698.
Goodsell DS & Olson AJ (2000) Structural symmetry
and protein function. Annu Rev Biophys Biomol
Struct 29:105–153.
Harrison SC (1992) Viruses. Curr Opin Struct Biol 2:293–
299.
Harrison SC (2004) Whither structural biology? Nature
Struct Mol Biol 11:12–15.
Hudder A, Nathanson L & Deutscher MP (2003)
Organization of mammalian cytoplasm. Mol Cell Biol
23:9318–9326.
International Human Genome Sequencing Consortium
(2001) Initial sequencing and analysis of the human
genome. Nature 409:860–921.
Meiler J & Baker D (2003) Coupled prediction of
protein secondary and tertiary structure. Proc Natl
Acad Sci USA 100:12105–12110.
Nomura M (1973) Assembly of bacterial ribosomes.
Science 179: 864–873.
Orengo CA & Thornton JM (2005) Protein families and
their evolution— a structural perspective. Annu Rev
Biochem 74:867–900.
Pauling L & Corey RB (1951) Configurations of
polypeptide chains with favored orientations around
single bonds: two new pleated sheets. Proc Natl
Acad Sci USA 37:729–740.
Pauling L, Corey RB & Branson HR (1951) The structure
of proteins: two hydrogen‐bonded helical
configurations of the polypeptide chain. Proc Natl
Acad Sci USA 37:205–211.
Ponting CP, Schultz J, Copley RR et al. (2000) Evolution
of domain families. Adv Protein Chem 54:185–244.
Trinick J (1992) Understanding the functions of titin
and nebulin. FEBS Lett 307:44–48.
Vogel C, Bashton M, Kerrison ND et al (2004)
Structure, function and evolution of multidomain
proteins. Curr Opin Struct Biol 14:208–216.
Zhang C & Kim SH (2003) Overview of structural
genomics: from structure to function. Curr Opin
Chem Biol 7:28–32.
Protein Function
Alberts B (1998) The cell as a collection of protein
machines: preparing the next generation of
molecular biologists. Cell 92:291–294.
Benkovic SJ (1992) Catalytic antibodies. Annu Rev
Biochem 61:29–54.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Berg OG & von Hippel PH (1985) Diffusion‐controlled
macromolecular interactions. Annu Rev Biophys
Biophys Chem 14:131–160.
Bhattacharyya RP, Remenyi A, Yeh BJ & Lim WA (2006)
Domains, motifs, and scaffolds: The role of modular
interactions in the evolution and wiring of cell
signaling circuits. Annu Rev Biochem 75:655–680.
Bourne HR (1995) GTPases: a family of molecular
switches and clocks. Philos Trans R Soc Lond B
349:283–289.
Braden BC & Poljak RJ (1995) Structural features of the
reactions between antibodies and protein antigens.
FASEB J 9:9–16.
Dickerson RE & Geis I (1983) Hemoglobin: Structure,
Function, Evolution and Pathology. Menlo Park, CA:
Benjamin Cummings.
Dressler D & Potter H (1991) Discovering Enzymes.
New York: Scientific American Library.
Eisenberg D, Marcotte, EM, Xenarios, I & Yeates TO
(2000) Protein function in the post‐genomic era.
Nature 405:823–826.
Fersht AR (1999) Structure and Mechanisms in Protein
Science: A Guide to Enzyme Catalysis. New York: WH
Freeman.
Johnson, LN & Lewis RJ (2001) Structural basis for
control by phosphorylation. Chem Rev 101:2209–
2242.
Kantrowitz ER & Lipscomb WN (1988) Escherichia coli
aspartate transcarbamoylase: the relation between
structure and function. Science 241:669–674.
Khosla C & Harbury PB (2001) Modular enzymes.
Nature 409:247–252.
Kim E & Sheng M (2004) PDZ domain proteins of
synapses. Nature Rev Neurosci 5:771–781.
Koshland DE, Jr (1984) Control of enzyme activity and
metabolic pathways. Trends Biochem Sci 9:155–159.
Kraut DA, Carroll KS & Herschlag D (2003) Challenges in
enzyme mechanism and energetics. Annu Rev
Biochem 72:517–571.
Krogan NJ, Cagney G, Yu H et al (2006) Global
landscape of protein complexes in the yeast
Saccharomyces cerevisisae. Nature 440:637–643.
Lichtarge O, Bourne HR & Cohen FE (1996) An
evolutionary trace method defines binding surfaces
common to protein families. J Mol Biol 257:342–358.
Marcotte EM, Pellegrini M, Ng HL et al (1999)
Detecting protein function and protein–protein
interactions from genome sequences. Science
285:751–753.
Monod J, Changeux JP & Jacob F (1963) Allosteric
proteins and cellular control systems. J Mol Biol
6:306–329.
Pawson T & Nash P (2003) Assembly of regulatory
systems through protein interaction domains.
Science 300:445–452.
Pavletich NP (1999) Mechanisms of cyclin‐dependent
kinase regulation: structures of Cdks, their cyclin
activators, and Cip and INK4 inhibitors. J Mol Biol
287:821–828.
Pellicena P & Kuriyan J (2006) Protein‐protein
interactions in the allosteric regulation of protein
kinases. Curr Opin Struct Biol 16:702–709.
Perutz M (1990) Mechanisms of Cooperativity and
Allosteric Regulation in Proteins. Cambridge:
Cambridge University Press.
Raushel F, Thoden, JB & Holden HM (2003) Enzymes
with molecular tunnels. Acc Chem Res 36:539–548.
Radzicka A & Wolfenden R (1995) A proficient enzyme.
Science 267:90–93.
Sato TK, Overduin M & Emr S (2001) Location, location,
location: Membrane targeting directed by PX
domains. Science 294:1881–1885.
Schramm VL (1998) Enzymatic transition states and
transition state analog design. Annu Rev Biochem
67:693–720.
Schultz PG & Lerner RA (1995) From molecular
diversity to catalysis: lessons from the immune
system. Science 269:1835–1842.
Vale RD & Milligan RA (2000) The way things move:
looking under the hood of molecular motor proteins.
Science 288:88–95.
Vocadlo DJ, Davies GJ, Laine R & Withers SG (2001)
Catalysis by hen egg‐white lysozyme proceeds via a
covalent intermediate. Nature 412:835–838.
Walsh C (2001) Enabling the chemistry of life. Nature
409:226–231.
Yang XJ (2005) Multisite protein modification and
intramolecular signaling. Oncogene 24:1653–1662.
Zhu H, Bilgin M & Snyder M (2003) Proteomics. Annu
Rev Biochem 72:783–812.
Purifying Proteins
de Duve C & Beaufay H (1981) A short history of tissue
fractionation. J Cell Biol 91:293s–299s.
Krogan NJ, Cagney G, Yu H et al (2006) Global
landscape of protein complexes in the yeast
Saccharomyces cerevisiae. Nature 440:637–43.
Laemmli UK (1970) Cleavage of structural proteins
during the assembly of the head of bacteriophage
T4. Nature 227:680–685.
Nirenberg MW & Matthaei JH (1961) The dependence
of cell‐free protein synthesis in E. coli on naturally
occurring or synthetic polyribonucleotides. Proc Natl
Acad Sci. USA 47:1588–1602.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
O’Farrell PH (1975) High‐resolution two‐dimensional
electrophoresis of proteins. J Biol Chem 250:4007–
4021.
Palade G (1975) Intracellular aspects of the process of
protein synthesis. Science 189:347–358.
Scopes RK & Cantor CR (1994) Protein Purification:
Principles and Practice, 3rd ed. New York: Springer‐
Verlag.
Analyzing Proteins
Branden C & Tooze J (1999) Introduction to Protein
Structure, 2nd ed. New York: Garland Science.
Fields S & Song O (1989) A novel genetic system to
detect protein–protein interactions. Nature
340:245–246.
Giepmans BN, Adams SR et al (2006) The fluorescent
toolbox for assessing protein location and function.
Science 312:217–24.
Kendrew JC (1961) The three‐dimensional structure of
a protein molecule. Sci Am 205:96–111.
Knight ZA & Shokat KM (2007) Chemical genetics:
Where genetics and pharmacology meet. Cell
128:425–30.
Rigaut G, Shevchenko A, Rutz B et al (1999) A generic
protein purification method for protein complex
characterization and proteome exploration. Nature
Biotechnol 17:1030–1032.
Washburn MP, Wolters D and Yates JR (2001) Largescale
analysis of the yeast proteome by
multidimensional protein identification technology.
Nature Biotechnol 19:242–7.
Wuthrich K (1989) Protein structure determination in
solution by nuclear magnetic resonance
spectroscopy. Science 243:45–50.
Chapter 5
The Structure and Function of DNA
Avery OT, MacLeod CM & McCarty M (1944) Studies on
the chemical nature of the substance inducing
transformation of pneumococcal types. J Exp Med
79:137–158.
Meselson M & Stahl FW (1958) The replication of DNA
in E. coli. Proc Natl Acad Sci USA 44:671–682.
Watson JD & Crick FHC (1953) Molecular structure of
nucleic acids. A structure for deoxyribose nucleic
acids. Nature 171:737–738.
Chromosomal DNA and Its Packaging in the
Chromatin Fiber
Jin J, Cai Y, Li B et al (2005) In and out: histone variant
exchange in chromatin. Trends Biochem Sci 30:680–
687.
Kornberg RD & Lorch Y (1999) Twenty‐five years of the
nucleosome, fundamental particle of the eukaryote
chromosome. Cell 98:285–294.
Li G, Levitus M, Bustamante C & Widom J (2005) Rapid
spontaneous accessibility of nucleosomal DNA.
Nature Struct Mol Biol 12:46–53.
Lorch Y, Maier‐Davis B & Kornberg RD (2006)
Chromatin remodeling by nucleosome disassembly
in vitro. Proc Natl Acad Sci USA 103:3090–3093.
Luger K, Mader AW, Richmond RK et al (1997) Crystal
structure of the nucleosome core particle at 2.8 Å
resolution. Nature 389:251–260.
Luger K & Richmond TJ (1998) The histone tails of the
nucleosome. Curr Opin Genet Dev 8:140–146.
Malik H S & Henikoff S (2003) Phylogenomics of the
nucleosome Nature Struct Biol 10:882‐891.
Ried T, Schrock E, Ning Y & Wienberg J (1998)
Chromosome painting: a useful art. Hum Mol Genet
7:1619–1626.
Robinson PJ & Rhodes R (2006) Structure of the 30 nm
chromatin fibre: A key role for the linker histone.
Curr Opin Struct Biol 16:1–8.
Saha A, Wittmeyer J & Cairns BR (2006) Chromatin
remodeling: the industrial revolution of DNA around
histones. Nature Rev Mol Cell Biol 7:437–446.
Woodcock CL (2006) Chromatin architecture. Curr Opin
Struct Biol 16:213–220.
The Regulation of Chromatin Structure
Egger G, Liang, G, Aparicio A & Jones PA (2004)
Epigenetics in human disease and prospects for
epigenetic therapy. Nature 429:457–463.
Henikoff S (1990) Position‐effect variegation after 60
years. Trends Genet 6:422–426.
Henikoff S & Ahmad K (2005) Assembly of variant
histones into chromatiin. Annu Rev Cell Dev Biol
21:133–153.
Gaszner M & Felsenfeld G (2006) Insulators: exploiting
transcriptional and epigenetic mechanisms. Nature
Rev Genet 7:703–713.
Hake SB & Allis CD (2006) Histone H3 variants and their
potential role in indexing mammalian genomes: the
“H3 barcode hypothesis.” Proc Natl Acad Sci USA
103:6428–6435.
Jenuwein T (2006) The epigenetic magic of histone
lysine methylation. FEBS J 273:3121–3135.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Martin C & Zhang Y (2005) The diverse functions of
histone lysine methylation. Nature Rev Mol Cell Biol
6:838–849.
Mellone B, Erhardt S & Karpen GH (2006) The ABCs of
centromeres. Nature Cell Biol 8:427–429.
Peterson CL & Laniel MA (2004) Histones and histone
modifications. Curr Biol 14:R546–R551.
Ruthenburg AJ, Allis CD & Wysocka J (2007)
Methylation of lysine 4 on histone H3: intricacy of
writing and reading a single epigenetic mark. Mol
Cell 25:15–30.
Shahbazian MD & Grunstein M (2007) Functions of
site‐specific histone acetylation and deacetylation.
Annu Rev Biochem 76:75–100.
The Global Structure of Chromosomes
Akhtar A & Gasser SM (2007) The nuclear envelope
and transcriptional control. Nature Rev Genet 8:507–
517.
Callan HG (1982) Lampbrush chromosomes. Proc Roy
Soc Lond Ser B 21:417–448.
Chakalova L, Debrand E, Mitchel JA et al (2005)
Replication and transcription: shaping the landscape
of the genome. Nature Rev Genet 6:669–678.
Cremer T, Cremer M, Dietzel S et al (2006)
Chromosome territories—a functional nuclear
landscape. Curr Opin Cell Biol 18:307–316.
Ebert A, Lein S, Schotta G & Reuter G (2006) Histone
modification and the control of heterochromatic
gene silencing in Drosophila. Chromosome Res
14:377–392.
Fraser P & Bickmore W (2007) Nuclear organization of
the genome and the potential for gene regulation.
Nature 447:413–417.
Handwerger KE & Gall JG (2006) Subnuclear organelles:
new insights into form and function. Trends Cell Biol
16:19–26.
Hirano T (2006) At the heart of the chromosome: SMC
proteins in action. Nature Rev Mol Cell Biol 7:311–
322.
Lamond AI & Spector DL (2003) Nuclear speckles: a
model for nuclear organelles. Nature Rev Mol Cell
Biol 4:605–612.
Maeshima K & Laemmli UK (2003) A two‐step
scaffolding model for mitotic chromosome assembly.
Dev Cell 4:467–480.
Sims JK, Houston SI, Magazinnik T & Rice JC (2006) A
trans‐tail histone code defined by monomethylated
H4 Lys‐20 and H3 Lys‐9 demarcates distinct regions
of silent chromatin. J Biol Chem 281:12760–12766.
Speicher MR & Carter NP (2005) The new cytogenetics:
blurring the boundaries with molecular biology.
Nature Rev Genet 6:782–792.
Zhimulev IF (1998) Morphology and structure of
polytene chromosomes. Adv Genet 37:1–566.
Chapter 6
The Maintenance of DNA Sequences
Cooper GM, Brudno M, Stone ES et al (2004)
Characterization of evolutionary rates and
constraints in three mammalian genomes. Genome
Res 14:539–548.
Crow JF (2000) The origins, patterns and implications
of human spontaneous mutation. Nature Rev Genet
1:40–47.
Hedges SB (2002) The origin and evolution of model
organisms. Nature Rev Genet 3:838–849.
King MC, Wilson AC (1965) Evolution at two levels in
humans and chimpanzees. Science 188:107–16.
DNA Replication Mechanisms
Alberts B (1998) The cell as a collection of protein
machines: preparing the next generation of
molecular biologists. Cell 92:291–294.
Dillingham MS (2006) Replicative helicases: a staircase
with a twist. Curr Biol 16:R844–R847.
Indiani C & O’Donnell M (2006) The replication clamploading
machine at work in the three domains of life.
Nature Rev Mol Cell Biol 7:751–761.
Kornberg A (1960) Biological synthesis of DNA. Science
131:1503–1508.
Li JJ & Kelly TJ (1984) SV40 DNA replication in vitro.
Proc Natl Acad Sci USA 81:6973.
Meselson M & Stahl FW (1958) The replication of DNA
in E. coli. Proc Natl Acad Sci USA 44:671–682.
Modrich P & Lahue R (1996) Mismatch repair in
replication fidelity, genetic recombination, and
cancer biology. Annu Rev Biochem 65:101–133.
Mott ML & Berger JM (2007) DNA replication initiation:
mechanisms and regulation in bacteria. Nature Rev
Microbiol 5:343–354.
O’Donnell M (2006) Replisome architecture and
dynamics in E. coli. J Biol Chem 281:10653–10656.
Okazaki R, Okazaki T, Sakabe K et al. (1968) Mechanism
of DNA chain growth. I. Possible discontinuity and
unusual secondary structure of newly synthesized
chains. Proc Natl Acad Sci USA 59:598–605.
Raghuraman MK, Winzeler EA, Collingwood D et al
(2001) Replication dynamics of the yeast genome.
Science 294:115–121.
Rao PN & Johnson RT (1970) Mammalian cell fusion:
studies on the regulation of DNA synthesis and
mitosis. Nature 225:159.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Wang JC (2002) Cellular roles of DNA topoisomerases:
a molecular perspective. Nature Rev Mol Cell Biol
3:430–440.
The Initiation and Completion of DNA Replication in
Chromosomes
Chan SR & Blackburn EH (2004) Telomeres and
telomerase. Philos Trans R Soc Lond B Bio Sci
359:109–121.
Costa S & Blow JJ (2007) The elusive determinants of
replication origins. EMBO Rep 8:332–334.
Groth A, Rocha W & Almouzni G (2007) Chromatin
challenges during DNA replication and repair. Cell
128:721–733.
Machida YJ, Hamlin JL & Dutta A (2005) Right place,
right time, and only once: replication initiation in
metazoans. Cell 123:13–24.
O’Donnell M & Kuriyan J (2005) Clamp loaders and
replication initiation. Curr Opin Struct Biol 16:35–41.
Robinson NP & Bell SD (2005) Origins of DNA
replication in the three domains of life. FEBS J
272:3757–3766.
Smogorzewska A & de Lange T (2004) Regulation of
telomerase by telomeric proteins. Annu Rev Biochem
73:177–208.
DNA Repair
Barnes DE, & Lindahl T (2004) Repair and genetic
consequences of endogenous DNA base damage in
mammalian cells. Annu Rev Genet 38:445–476.
Harrison JC & Haber JE (2006) Surviving the breakup:
the DNA damage checkpoint. Annu Rev Genet
40:209–235.
Heller RC & Marians KJ (2006) Replisome assembly and
the direct restart of stalled replication. Nature Rev
Mol Cell Biol 7:932–43.
Lieber M, Ma Y et al (2003) Mechanism and regulation
of human nonhomologous DNA end‐joining. Nature
Rev Mol Cell Biol 4:712–720.
Lindahl T (1993) Instability and decay of the primary
structure of DNA. Nature 362:709–715.
Prakash S & Prakash L (2002) Translesion DNA
synthesis in eukaryotes: a one‐ or two‐polymerase
affair. Genes Dev 16:1872–1883.
Sancar A, Lindsey‐Boltz LA et al. (2004) Molecular
mechanisms of mammalian DNA repair and the DNA
damage checkpoints. Annu Rev Biochem 73:39–85.
Svejstrup JQ (2002) Mechanisms of transcriptioncoupled
DNA repair. Nature Rev Mol Cell Biol 3:21–
29.
Wyman C & Kanaar R (2006) DNA double‐strand break
repair: all’s well that ends well. Annu Rev Genet
40:363–383.
Homologous Recombination
Adams MD, McVey M & Sekelsky JJ (2003) Drosophila
BLM in double‐strand break repair by synthesisdependent
strand annealing. Science 299:265–267.
Cox MM (2001) Historical overview: searching for
replication help in all of the rec places. Proc Natl
Acad Sci USA 98:8173–8180.
Holliday R (1990) The history of the DNA heteroduplex.
BioEssays 12:133–142.
Lisby M, Bartow JH et al (2004) Choreography of the
DNA damage response: spatiotemporal relationships
among checkpoint and repair proteins. Cell 118:699–
713.
McEachern MJ & Haber JE (2006) Break‐induced
replication and recombinational telomere elongation
in yeast. Annu Rev Biochem 75:111–135.
Michel B, Gromponee G et al (2004) Multiple pathways
process stalled replication forks. Proc Natl Acad Sci
USA 101:12783–12788.
Szostak JW, Orr‐Weaver TK, Rothstein RJ et al (1983)
The double‐strand break repair model for
recombination. Cell 33:25–35.
West SC (2003) Molecular views of recombination
proteins and their control. Nature Rev Mol Cell Biol
4:435–445.
Transposition and Site‐Specific Recombination
Campbell AM (1993) Thirty years ago in genetics:
prophage insertion into bacterial chromosomes.
Genetics 133:433–438.
Comfort NC (2001) From controlling elements to
transposons: Barbara McClintock and the Nobel
Prize. Trends Biochem Sci 26:454–457.
Craig NL (1996) Transposition, in Escherichia coli and
Salmonella, pp 2339–2362. Washington, DC: ASM
Press.
Gottesman M (1999) Bacteriophage lambda: the
untold story. J Mol Biol 293:177–180.
Grindley ND, Whiteson KL & Rice PA (2006)
Mechanisms of site‐specific recombination. Annu
Rev Biochem 75:567–605.
Varmus H (1988) Retroviruses. Science 240:1427–1435.
Zickler D & Kleckner N (1999) Meiotic chromosomes:
integrating structure and function. Annu Rev Genet
33:603–754.
Chapter 7
From DNA to RNA
Bentley DL (2005) Rules of engagement: cotranscriptional
recruitment of pre‐mRNA processing
factors. Curr Opin Cell Biol 17:251–256.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Berget SM, Moore C & Sharp PA (1977) Spliced
segments at the 5¢ terminus of adenovirus 2 late
mRNA. Proc Natl Acad Sci USA 74:3171–3175.
Black DL (2003). Mechanisms of alternative premessenger
RNA splicing. Annu Rev Biochem 72:291–
336.
Brenner S, Jacob F & Meselson M (1961) An unstable
intermediate carrying information from genes to
ribosomes for protein synthesis. Nature 190:576–
581.
Cate JH, Gooding AR, Podell E et al. (1996) Crystal
structure of a group I ribozyme domain: principles of
RNA packing. Science 273:1678–1685.
Chow LT, Gelinas RE, Broker TR et al (1977) An amazing
sequence arrangement at the 5¢ ends of adenovirus
2 messenger RNA. Cell 12:1–8.
Cramer P (2002) Multisubunit RNA polymerases. Curr
Opin Struct Biol 12:89–97.
Daneholt B (1997) A look at messenger RNP moving
through the nuclear pore. Cell 88:585–588.
Dreyfuss G, Kim VN, & Kataoka N (2002) Messenger‐
RNA‐binding proteins and the messages they carry.
Nature Rev Mol Cell Biol 3:195–205.
Houseley J, LaCava J & Tollervey D (2006) RNA‐quality
control by the exosome. Nature Rev Mol Cell Biol
7:529–539.
Izquierdo JM, & Valcárcel J (2006) A simple principle to
explain the evolution of pre‐mRNA splicing. Genes
Dev 20:1679–1684.
Kornberg RD (2005) Mediator and the mechanism of
transcriptional activation. Trends Biochem Sci
30:235–239.
Malik S & Roeder RG (2005) Dynamic regulation of pol
II transcription by the mammalian Mediator
complex. Trends Biochem Sci 30:256–263.
Matsui T, Segall J, Weil PA & Roeder RG (1980)
Multiple factors required for accurate initiation of
transcription by purified RNA polymerase II. J Biol
Chem 255:11992–11996.
Patel AA & Steitz JA (2003) Splicing double: insights
from the second spliceosome. Nature Rev Mol Cell
Biol 4|:960–970.
Phatnani HP & Greenleaf AL (2006) Phosphorylation
and functions of the RNA polymerase II CTD. Genes
Dev 20:2922–2936.
Query CC & Konarska MM (2006) Splicing fidelity
revisited. Nature Struct Mol Biol 13:472–474.
Ruskin B, Krainer AR, Maniatis T et al (1984) Excision of
an intact intron as a novel lariat structure during premRNA
splicing in vitro. Cell 38:317–331.
Spector DL (2003) The dynamics of chromosome
organization and gene regulation. Annu Rev Biochem
72:573–608.
Staley JP & Guthrie C (1998) Mechanical devices of the
spliceosome: motors, clocks, springs, and things. Cell
92:315–326.
Thomas MC & Chiang CM (2006) The general
transcription machinery and general cofactors.
Critical Rev Biochem Mol Biol 41:105–178.
Wang D, Bushnell DA, Westover KD et al (2006)
Structural basis of transcription: role of the trigger
loop in substrate specificity and catalysis. Cell
127:941–954.
From RNA to Protein
Allen GS & Frank J (2007) Structural insights on the
translation initiation complex: ghosts of a universal
initiation complex. Mol Microbiol 63:941–950.
Anfinsen CB (1973) Principles that govern the folding
of protein chains. Science 181:223–230.
Brunelle JL, Youngman EM, Sharma D et al (2006) The
interaction between C75 of tRNA and the A loop of
the ribosome stimulates peptidyl transferase
activity. RNA 12:33–39.
Chien P, Weissman JS, & DePace AH (2004). Emerging
principles of conformation‐based prion inheritance.
Annu Rev Biochem 73:617–656.
Crick FHC (1966) The genetic code: III. Sci Am 215:55–
62.
Hershko A, Ciechanover A & Varshavsky A (2000) The
ubiquitin system. Nature Med 6:1073–1081.
Ibba M & Soll D (2000) Aminoacyl‐tRNA synthesis.
Annu Rev Biochem 69:617–650.
Kozak M (1992) Regulation of translation in eukaryotic
systems. Annu Rev Cell Biol 8:197–225.
Kuzmiak HA, & Maquat LE (2006) Applying nonsensemediated
mRNA decay research to the clinic:
progress and challenges. Trends Mol Med 12:306–
316.
Moore PB & Steitz TA (2005) The ribosome revealed.
Trends Biochem Sci 30:281–283.
Noller HF (2005) RNA structure: reading the ribosome.
Science 309:1508–1514.
Ogle JM, Carter AP & Ramakrishnan V (2003) Insights
into the decoding mechanism from recent ribosome
structures. Trends Biochem Sci 28:259–266.
Prusiner SB (1998) Nobel lecture. Prions. Proc Natl
Acad Sci USA 95:13363–13383.
Rehwinkel J, Raes J & Izaurralde E (2006) Nonsensemediated
mRNA decay: Target genes and functional
diversification of effectors. Trends Biochem Sci
31:639–646.
Sauer RT, Bolon DN, Burton BM et al (2004) Sculpting
the proteome with AAA(+) proteases and
disassembly machines. Cell 119:9–18.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Shorter J & Lindquist S (2005) Prions as adaptive
conduits of memory and inheritance. Nature Rev
Genet 6:435–450.
Varshavsky A (2005) Regulated protein degradation.
Trends in Biochem Sci 30:283–286.
Voges D, Zwickl P & Baumeister W (1999) The 26S
proteasome: a molecular machine designed for
controlled proteolysis. Annu Rev Biochem 68:1015–
1068.
Weissmann C (2005) Birth of a prion: spontaneous
generation revisited. Cell 122:165–168.
Young JC, Agashe VR, Siegers K et al (2004) Pathways
of chaperone‐mediated protein folding in the
cytosol. Nature Rev Mol Cell Biol 5:781–791.
The RNA World and the Origins of Life
Joyce GF (1992) Directed molecular evolution. Sci Am
267:90–97.
Orgel L (2000) Origin of life. A simpler nucleic acid.
Science 290:1306–1307.
Kruger K, Grabowski P, Zaug P et al (1982) Self‐splicing
RNA: Autoexcision and autocyclization of the
ribosomal RNA intervening seuence of Tetrahymena.
Cell 31:147–157.
Silverman SK (2003) Rube Goldberg goes (ribo)nuclear?
Molecular switches and sensors made from RNA.
RNA 9:377–383.
Szostak JW, Bartel DP & Luisi PL (2001) Synthesizing
life. Nature 409:387–390.
Chapter 8
An Overview of Gene Control
Campbell KH, McWhir J, Ritchie WA & Wilmut I (1996)
Sheep cloned by nuclear transfer from a cultured cell
line. Nature 380:64–66.
Davidson EH (2006) The Regulatory Genome: Gene
Regulatory Networks in Development and Evolution.
Burlington, MA: Elsevier.
Gurdon JB (1992) The generation of diversity and
pattern in animal development. Cell 68:185–199.
Levine M & Tjian R (2003) Transcription regulation and
animal diversity. Nature 424:147–151.
Ross DT, Scherf U, Eisen MB et al (2000) Systematic
variation in gene expression patterns in human
cancer cell lines. Nature Genet 24:227–235.
DNA‐binding Motifs in Gene Regulatory Proteins
Gehring WJ, Affolter M & Burglin T (1994)
Homeodomain proteins. Annu Rev Biochem 63:487–
526.
Harbison CT, Gordon DB, Lee TI et al (2004)
Transcriptional regulatory code of a eukaryotic
genome. Nature 431:99–104.
Luscombe NM, Austin SE, Berman HM, et al (2000) An
overview of the structures of protein–DNA
complexes. Gen Biol 1:reviews 001.1–001.37.
McKnight SL (1991) Molecular zippers in gene
regulation. Sci Am 264:54–64.
Pabo CO & Sauer RT (1992) Transcription factors:
structural families and principles of DNA recognition.
Annu Rev Biochem 61:1053–1095.
Rhodes D & Klug A (1993) Zinc fingers. Sci Am 268:56–
65.
Seeman NC, Rosenberg JM & Rich A (1976) Sequencespecific
recognition of double helical nucleic acids by
proteins. Proc Natl Acad Sci USA 73:804–808.
How Genetic Switches Work
Becker PB & Hörz W (2002) ATP‐dependent
nucleosome remodeling. Annu Rev Biochem 71:247–
273.
Beckwith J (1987) The operon: an historical account. In
Escherichia coli and Salmonella typhimurium:
Cellular and Molecular Biology (Neidhart FC,
Ingraham JL, Low KB et al eds), vol 2, pp 1439–1443.
Washington, DC: ASM Press.
Gaszner M & Felsenfeld G (2006) Insulators: exploiting
transcriptional and epigenetic mechanisms. Nature
Rev Genet 7:703–713.
Gilbert W and Müller‐Hill B (1967) The lac operator is
DNA. Proc Natl Acad Sci USA 58:2415.
Green MR (2005) Eukaryotic transcription activation:
right on target. Mol Cell 18:399–402.
Jacob F & Monod J (1961) Genetic regulatory
mechanisms in the synthesis of proteins. J Mol Biol
3:318–356.
Lawson CL, Swigon D, Murakami KS et al (2004)
Catabolite activator protein: DNA binding and
transcription activation. Curr Opin Struct Biol 14:10–
20.
Millar CB, & Grunstein M (2006) Genome‐wide
patterns of histone modifications in yeast. Nature
Rev Mol Cell Biol 7:657–666.
Narlikar GJ, Fan HY & Kingston RE (2002) Cooperation
between complexes that regulate chromatin
structure and transcription. Cell 108:475–487.
Oehler S, Eismann ER, Krämer H et al (1990) The three
operators of the lac operon cooperate in repression.
EMBO J 9:973–979.
Ptashne M (2004) A Genetic Switch: Phage and
Lambda Revisited, 3rd ed. Cold Spring Harbor, NY:
Cold Spring Harbor Laboratory Press.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Ptashne M (1967) Specific binding of the lambda phage
repressor to lambda DNA. Nature 214:232–234.
St Johnston D & Nusslein‐Volhard C (1992) The origin
of pattern and polarity in the Drosophila embryo.
Cell 68:201–219.
Strahl BD & Allis CD (2000) The language of covalent
histone modifications. Nature 403:41–45.
The Molecular Genetic Mechanisms that Create
Specialized Cell Types
Alon, U (2006) An Introduction to Systems Biology:
Design Principles of Biological Circuits (Chapman &
Hall/Crc Mathematical and Computational Biology
Series) TF Chapman.
Bell‐Pedersen D, Cassone VM, Earnest DJ et al (2005)
Circadian rhythms from multiple oscillators: lessons
from diverse organisms. Nature Rev Genet 6:544–
556.
Bernstein BE, Meissner A & Lander ES (2007) The
mammalian epigenome. Cell 128:669–681.
Herskowitz I (1989) A regulatory hierarchy for cell
specialization in yeast. Nature 342:749–757.
Klose RJ & Bird AP (2006) Genomic DNA methylation:
the mark and its mediators. Trends Biochem Sci
31:89–97.
Meyer BJ (2000) Sex in the worm: counting and
compensating X‐chromosome dose. Trends Genet
16:247–253.
Surani MA (2001) Reprogramming of genome function
through epigenetic inheritance. Nature 414:122–
128.
Tapscott SJ (2005) The circuitry of a master switch:
MyoD and the regulation of skeletal muscle gene
transcription. Development 132:2685–2695.
Post‐transcriptional Controls
Bass BL (2002) RNA editing by adenosine deaminases
that act on RNA. Annu Rev Biochem 71:817–846.
Blencowe BJ (2006) Alternative splicing: new insights
from global analyses. Cell 126:37–47.
Brennecke J, Stark A, Russell RB et al (2005) Principles
of microRNAtarget recognition. PLoS Biology 3.
Fire A, Xu S, Montgomery MK et al (1998) Potent and
specific genetic interference by double‐stranded
RNA in Caenorhabditis elegans. Nature 391:806–811.
Frankel AD & Young JAT (1998) HIV‐1: fifteen proteins
and an RNA. Annu Rev Biochem 67:1–25.
Gottesman S (2004) The small RNA regulators of
Escherichia coli: roles and mechanisms. Annu Rev
Microbiol 58:303–328.
Mello CC & Conte D (2004) Revealing the world of RNA
interference. Nature 431:338–342.
Parker R & Sheth U (2007) P bodies and the control of
mRNA translation and degradation. Mol Cell 25:635–
646.
Stuart KD, Schnaufer A, Ernst NL et al (2005) Complex
management: RNA editing in trypanosomes. Trends
Biochem Sci 30:97–105.
Tolia NH & Joshua‐Tor L (2007) Slicer and the
argonautes. Nature Chem Biol 3:36–43.
Tomari Y & Zamore PD (2005) Perspective: machines
for RNAi. Genes Dev 19:517–529.
Valencia‐Sanchez MA, Liu J, Hannon GJ et al (2006)
Control of translation and mRNA degradation by
miRNAs and siRNAs. Genes Dev 20:515–524.
Verdel A & Moazed D (2005) RNAi‐directed assembly
of heterochromatin in fission yeast. FEBS Letters
579:5872–5878.
Wilhelm JE & Smibert, CA (2005) Mechanisms of
translational regulation in Drosophila. Biol Cell
97:235–252.
Winkler WC & Breaker RR (2005) Regulation of
bacterial gene expression by riboswitches. Annu Rev
Microbiol 59:487–517.
Chapter 9
How Genomes Evolve
Batzer MA & Deininger PL (2002) ALU repeats and
human genomic diversity. Nature Rev Genet 3:370–
379.
Blanchette M, Green ED, Miller W, & Haussler D
(2004) Reconstructing large regions of an ancestral
mammalian genome in silico. Genome Res 14:2412–
2423.
Cheng Z, Ventura M, She X et al (2005) A genome‐wide
comparison of recent chimpanzee and human
segmental duplications. Nature 437:88–93.
Feuk L, Carson AR & Scherer S (2006) Structural
variation in the human genome. Nature Rev Genet
7:85–97.
International Human Genome Sequencing Consortium
(2001) Initial sequencing and analysis of the human
genome. Nature 409:860–921.
International Human Genome Consortium (2004)
Finishing the euchromatic sequence of the human
genome. Nature 431:931–945.
Koszul R, Caburet S, Dujon B & Fischer G (2004)
Eucaryotic genome evolution through the
spontaneous duplication of large chromosomal
segments. EMBO J 23:234–243.
Margulies EH, NISC Comparative Sequencing Program
& Green ED (2003) Detecting highly conserved
regions of the human genome by multispecies
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
sequence comparisons. Cold Spring Harbor Symp
Quant Biol 68:255–263.
Mouse Genome Sequencing Consortium (2002) Initial
sequencing and comparative analysis of the mouse
genome. Nature 420:520–562.
Pollard KS, Salama SR, Lambert N et al (2006) An RNA
gene expressed during cortical development evolved
rapidly in humans. Nature 443:167–172.
Sharp AJ, Cheng Z & Eichler EE (2007) Structural
variation of the human genome. Annu Rev Genomics
Hum Genet 7:407–442.
Siepel A, Bejerano G, Pedersen JS et al (2005)
Evolutionarily conserved elements in vertebrate,
insect, worm, and yeast genomes. Genome Res
15:1034–1050.
The International HapMap Consortium (2005) A
haplotype map of the human genome. Nature
437:1299–1320.
The ENCODE Project Consortium (2007) Identification
and analysis of functional elements in 1% of the
human genome by the ENCODE pilot project. Nature
447:799–816.
The Diversity of Genomes and the Tree of Life
Blattner FR, Plunkett G, Bloch CA et al (1997) The
complete genome sequence of Escherichia coli K‐12.
Science 277:1453–1474.
Boucher Y, Douady CJ, Papke RT et al (2003) Lateral
gene transfer and the origins of prokaryotic groups.
Annu Rev Genet 37:283–328.
Cole ST, Brosch R, Parkhill J et al (1998) Deciphering
the biology of Mycobacterium tuberculosis from the
complete genome sequence. Nature 393:537–544.
Dixon B (1994) Power Unseen: How Microbes Rule the
World. Oxford: Freeman.
Kerr RA (1997) Life goes to extremes in the deep
earth—and elsewhere? Science 276:703–704.
Lee TI, Rinaldi NJ, Robert F et al (2002) Transcriptional
regulatory networks in Saccharomyces cerevisiae.
Science 298:799–804.
Olsen GJ & Woese CR (1997) Archaeal genomics: an
overview. Cell 89:991–994.
Pace NR (1997) A molecular view of microbial diversity
and the biosphere. Science 276:734–740.
Woese C (1998) The universal ancestor. Proc Natl Acad
Sci USA 95:6854–6859.
Genetic Information in Eucaryotes
Adams MD, Celniker SE, Holt RA et al (2000) The
genome sequence of Drosophila melanogaster.
Science 287:2185–2195.
Andersson SG, Zomorodipour A, Andersson JO et al
(1998) The genome sequence of Rickettsia
prowazekii and the origin of mitochondria. Nature
396:133–140.
The Arabidopsis Initiative (2000) Analysis of the
genome sequence of the flowering plant Arabidopsis
thaliana. Nature 408:796–815.
Carroll SB, Grenier JK & Weatherbee SD (2005) From
DNA to Diversity: Molecular Genetics and the
Evolution of Animal Design, 2nd ed. Maldon, MA:
Blackwell Science.
de Duve C (2007) The origin of eukaryotes: a
reappraisal. Nature Rev Genet 8:395‐403.
Delsuc F, Brinkmann H & Philippe H (2005)
Phylogenomics and the reconstruction of the tree of
life. Nature Rev Genet 6:361–375.
DeRisi JL, Iyer VR & Brown PO (1997) Exploring the
metabolic and genetic control of gene expression on
a genomic scale. Science 278:680–686.
Gabriel SB, Schaffner SF, Nguyen H et al (2002) The
structure of haplotype blocks in the human genome.
Science 296:2225–2229.
Goffeau A, Barrell BG, Bussey H et al (1996) Life with
6000 genes. Science 274:546–567.
International Human Genome Sequencing Consortium
(2001) Initial sequencing and analysis of the human
genome. Nature 409:860–921.
Kellis M, Birren BW & Lander ES (2004) Proof and
evolutionary analysis of ancient genome duplication
in the yeast Saccharomyces cerevisiae. Nature
428:617–624.
Lynch M & Conery JS (2000) The evolutionary fate and
consequences of duplicate genes. Science 290:1151–
1155.
Mulley J & Holland P (2004) Comparative genomics:
Small genome, big insights. Nature 431:916–917.
National Center for Biotechnology Information.
http://www.ncbi.nlm.nih.gov/ Owens K & King MC
(1999) Genomic views of human history. Science
286:451–453.
Palmer JD & Delwiche CF (1996) Second‐hand
chloroplasts and the case of the disappearing
nucleus. Proc Natl Acad Sci USA 93:7432–7435.
Pennisi E (2004) The birth of the nucleus. Science
305:766–768.
Plasterk RH (1999) The year of the worm. BioEssays
21:105–109.
Reed FA & Tishkoff SA (2006) African human diversity,
origins and migrations. Curr Opin Genet Dev 16:597–
605.
Rubin GM, Yandell MD, Wortman JR et al (2000)
Comparative genomics of the eukaryotes. Science
287:2204–2215.
Stillman B & Stewart D (2003) The genome of Homo
sapiens. (Cold Spring Harbor Symp. Quant. Biol.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
LXVIII). Cold Spring Harbor, NY: Cold Spring Harbor
Laboratory Press.
The C. elegans Sequencing Consortium (1998) Genome
sequence of the nematode C. elegans: a platform for
investigating biology. Science 282:2012–2018.
Tinsley RC & Kobel HR (eds) (1996) The Biology of
Xenopus. Oxford: Clarendon Press.
Tyson JJ, Chen KC & Novak B (2003) Sniffers, buzzers,
toggles and blinkers: dynamics of regulatory and
signaling pathways in the cell. Curr Opin Cell Biol
15:221–231.
Venter JC, Adams MD, Myers EW et al (2001) The
sequence of the human genome. Science 291:1304–
1351.
Studying Gene Expression and Function
Boone C, Bussey H & Andrews BJ (2007) Exploring
genetic interactions and networks with yeast. Nature
Rev Genet 8:437–449.
Botstein D, White RL, Skolnick M & Davis RW (1980)
Construction of a genetic linkage map in man using
restriction fragment length polymorphisms. Am J
Hum Genet 32:314–331.
DeRisi JL, Iyer VR & Brown PO (1997) Exploring the
metabolic and genetic control of gene expression on
a genomic scale. Science 278:680–686.
International HapMap Consortium (2005) A haplotype
map of the human genome. Nature 437:1299–320.
Lockhart DJ & Winzeler EA (2000) Genomics, gene
expression and DNA arrays. Nature 405:827–836.
Mello CC & Conte D (2004) Revealing the world of RNA
interference. Nature 431:338–342.
Nusslein‐Volhard C & Weischaus E (1980) Mutations
affecting segment number and polarity in
Drosophila. Nature 287:795–801.
Palmiter RD & Brinster RL (1985) Transgenic mice. Cell
41:343–345.
Rubin GM & Sprading AC (1982) Genetic
transformation of Drosophila with transposable
element vectors. Science 218:348–353.
Sabeti PC, Schaffner SF, Fry B et al (2006) Positive
natural selection in the human lineage. Science
312:1614–1620.
Weigel D & Glazebrook J (2001) Arabidopsis: A
Laboratory Manual. Cold Spring Harbor, NY: Cold
Spring Harbor Laboratory Press.
Chapter 10
Isolating Cells and Growing Them in Culture
Emmert‐Buck MR, Bonner RF, Smith PD et al (1996)
Laser capture microdissection. Science 274:998–
1001.
Ham RG (1965) Clonal growth of mammalian cells in a
chemically defined, synthetic medium. Proc Natl
Acad Sci USA 53:288–293.
Harlow E & Lane D (1999) Using Antibodies: A
Laboratory Manual. Cold Spring Harbor, NY: Cold
Spring Harbor Laboratory Press.
Herzenberg LA, Sweet RG & Herzenberg LA (1976)
Fluorescence‐activated cell sorting. Sci Am 234:108–
116.
Levi‐Montalcini R (1987) The nerve growth factor
thirty‐five years later. Science 237:1154–1162.
Lerou PH & Daley GQ (2005) Therapeutic potential of
embryonic stem cells. Blood Rev 19:321–31.
Milstein C (1980) Monoclonal antibodies. Sci Am
243:66–74.
Isolating, Cloning, and Sequencing DNA
Adams MD, Celniker SE, Holt RA et al (2000) The
genome sequence of Drosophila melanogaster.
Science 287:2185–2195.
Alwine JC, Kemp DJ & Stark GR (1977) Method for
detection of specific RNAs in agarose gels by transfer
to diabenzyloxymethyl
paper and hybridization with DNA probes. Proc Natl
Acad Sci USA 74:5350–5354.
Blattner FR, Plunkett G, Bloch CA et al (1997) The
complete genome sequence of Escherichia coli K‐12.
Science 277:1453–1474.
Cohen S, Chang A, Boyer H & Helling R (1973)
Construction of biologically functional bacterial
plasmids in vitro. Proc Natl Acad Sci USA 70:3240–
3244.
International Human Genome Sequencing Consortium
(2000) Initial sequencing and analysis of the human
genome. Nature 409:860–921.
International Human Genome Sequencing Consortium
(2006) The DNA sequence, annotation and analysis
of human chromosome 3. Nature 440:1194–1198.
Jackson D, Symons R & Berg P (1972) Biochemical
method for inserting new genetic information into
DNA of simian virus 40: circular SV40 DNA molecules
containing lambda phage genes and the galactose
operon of Escherichia coli. Proc Natl Acad Sci USA
69:2904–2909.
Maniatis T et al (1978) The isolation of structural genes
from libraries of eukaryotic DNA. Cell 15:687–701.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Mullis KB (1990). The unusual origin of the polymerase
chain reaction. Sci Am 262:56–61.
Nathans D & Smith HO (1975) Restriction
endonucleases in the analysis and restructuring of
dna molecules. Annu Rev Biochem 44:273–93.
Saiki RK, Gelfand DH, Stoffel S et al (1988) Primerdirected
enzymatic amplification of DNA with a
thermostable DNA polymerase. Science 239:487–
491.
Sambrook J, Russell D (2001) Molecular Cloning: A
Laboratory Manual, 3rd ed. Cold Spring Harbor, NY:
Cold Spring Harbor Laboratory Press.
Sanger F, Nicklen S & Coulson AR (1977) DNA
sequencing with chain‐terminating inhibitors. Proc
Natl Acad Sci USA 74:5463–5467.
Smith M (1994) Nobel lecture. Synthetic DNA and
biology. Biosci Rep 14:51–66.
Southern EM (1975) Detection of specific sequences
among DNA fragments separated by gel
electrophoresis. J Mol Biol 98:503–517.
The Arabidopsis Genome Initiative (2000) Analysis of
the genome sequence of the flowering plant
Arabidopsis thaliana. Nature 408:796–815.
The C. elegans Sequencing Consortium (1998) Genome
sequence of the nematode C. elegans: a platform for
investigating biology. Science 282:2012–2018.
Venter JC, Adams MA, Myers EW et al (2000) The
sequence of the human genome. Science 291:1304–
1351.
Chapter 11
The Lipid Bilayer
Bevers EM, Comfurius P & Zwaal RF (1999) Lipid
translocation across the plasma membrane of
mammalian cells. Biochim Biophys Acta 1439:317–
330.
Devaux PF (1993) Lipid transmembrane asymmetry
and flip‐flop in biological membranes and in lipid
bilayers. Curr Opin Struct Biol 3:489–494.
Dowhan W (1997) Molecular basis for membrane
phospholipid diversity:why are there so many lipids?
Annu Rev Biochem 66:199–232.
Hakomori Si SI (2002) Inaugural Article:The
glycosynapse. Proc Natl Acad Sci USA 99:225–232.
Harder T & Simons K (1997) Caveolae, DIGs, and the
dynamics of sphingolipid‐cholesterol microdomains.
Curr Opin Cell Biol 9:534–542.
Hazel JR (1995) Thermal adaptation in biological
membranes:is homeoviscous adaptation the
explanation? Annu Rev Physiol 57:19–42.
Ichikawa S & Hirabayashi Y (1998) Glucosylceramide
synthase and glycosphingolipid synthesis. Trends Cell
Biol 8:198–202.
Kornberg RD & McConnell HM (1971) Lateral diffusion
of phospholipids in a vesicle membrane. Proc Natl
Acad Sci USA 68:2564–2568.
Mansilla MC, Cybulski LE & de Mendoza D (2004)
Control of membrane lipid fluidity by molecular
thermosensors. J Bacteriol 186:6681–6688.
McConnell HM & Radhakrishnan A (2003) Condensed
complexes of cholesterol and phospholipids. Biochim
Biophys Acta 1610:159–73.
Pomorski T & Menon AK (2006) Lipid flippases and
their biological functions. Cell Mol Life Sci 63:2908–
2921.
Rothman JE & Lenard J (1977) Membrane asymmetry.
Science 195:743–53.
Simons K & Vaz WL (2004) Model systems, lipid rafts,
and cell membranes. Annu Rev Biophys Biomol Struct
33:269–95.
Tanford C (1980) The Hydrophobic Effect: Formation of
Micelles and Biological Membranes. New York:
Wiley.
van Meer G (2005) Cellular lipidomics. EMBO J
24:3159–3165.
Membrane Proteins
Bennett V & Baines AJ (2001) Spectrin and ankyrinbased
pathways: metazoan inventions for
integrating cells into tissues. Physiol Rev 81:1353–
1392.
Bijlmakers MJ & Marsh M (2003) The on‐off story of
protein palmitoylation. Trends Cell Biol 13:32–42.
Branden C & Tooze J (1999) Introduction to Protein
Structure, 2nd ed. New York: Garland Science.
Bretscher MS & Raff MC (1975) Mammalian plasma
membranes. Nature 258:43–49.
Buchanan SK (1999) Beta‐barrel proteins from bacterial
outer membranes:structure, function and refolding.
Curr Opin Struct Biol 9:455–461.
Chen Y, Lagerholm BC & Jacobson K (2006) Methods to
measure the lateral diffusion of membrane lipids
and proteins. Methods 39:147–153.
Curranb AR & Engelman DM (2003) Sequence motifs,
polar interactions and conformational changes in
helical membrane proteins. Curr Opin Struct Biol
13:412
Deisenhofer J & Michel H (1991) Structures of bacterial
photosynthetic reaction centers. Annu Rev Cell Biol
7:1–23.
Drickamer K & Taylor ME (1993) Biology of animal
lectins. Annu Rev Cell Biol 9:237–64.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Drickamer K & Taylor ME (1998) Evolving views of
protein glycosylation. Trends Biochem Sci 23:321–
324.
Frye LD & Edidin M (1970) The rapid intermixing of cell
surface antigens after formation of mouse‐human
heterokaryons. J Cell Sci 7:319–335.
Helenius A and Simons K (1975) Solubilization of
membranes by detergents. Biochim Biophys Acta
415:29–79.
Henderson R & Unwin PN (1975) Three‐dimensional
model of purple membrane obtained by electron
microscopy. Nature 257:28–32.
Kyte J & Doolittle RF (1982) A simple method for
displaying the hydropathic character of a protein. J
Mol Biol 157:105–132.
le Maire M, Champeil P et al (2000) Interaction of
membrane proteins and lipids with solubilizing
detergents. Biochim Biophys Acta 1508:86–111.
Lee AG (2003) Lipid‐protein interactions in biological
membranes:a structural perspective. Biochim
Biophys Acta 1612:1–40.
Marchesi VT, Furthmayr H et al (1976) The red cell
membrane. Annu Rev Biochem 45:667–698.
Nakada C, Ritchie K & Kusumi A (2003) Accumulation of
anchored proteins forms membrane diffusion
barriers during neuronal polarization. Nat Cell Biol
5:626–632.
Oesterhelt D (1998) The structure and mechanism of
the family of retinal proteins from halophilic
archaea. Curr Opin Struct Biol 8:489–500.
Reig N & van der Goot FG (2006) About lipids and
toxins. FEBS Lett 580:5572–5579.
Reithmeier RAF (1993) The erythrocyte anion
transporter (band 3) Curr Opin Cell Biol 7:707–714.
Rodgers W & Glaser M (1993) Distributions of proteins
and lipids in the erythrocyte membrane.
Biochemistry 32:12591–12598.
Sharon N & Lis H (2004) History of lectins:from
hemagglutinins to biological recognition molecules.
Glycobiology 14:53R–62R.
Sheetz MP (2001) Cell control by membranecytoskeleton
adhesion. Nat Rev Mol Cell Biol 2:392–
396.
Silvius JR (1992) Solubilization and functional
reconstitution of biomembrane components. Annu
Rev Biophys Biomol Struct 21:323–348.
Steck TL (1974) The organization of proteins in the
human red blood cell membrane. A review. J Cell Biol
62:1–19.
Subramaniam S (1999) The structure of
bacteriorhodopsin:an emerging consensus. Curr Opin
Struct Biol 9:462–468.
Viel A & Branton D (1996) Spectrin:on the path from
structure to function. Curr Opin Cell Biol 8:49–55.
Wallin E & von Heijne G (1998) Genome‐wide analysis
of integral membrane proteins from eubacterial,
archaean, and eukaryotic organisms. Protein Sci
7:1029–1038.
White SH & Wimley WC (1999) Membrane protein
folding and stability:physical principles. Annu Rev
Biophys Biomol Struct 28:319–365.
Chapter 12
Principles of Membrane Transport
Al‐Awqati Q (1999) One hundred years of membrane
permeability: does Overton still rule? Nature Cell Biol
1: E201–E202.
Forrest LR & Sansom MS (2000) Membrane
simulations: bigger and better? Curr Opin Struct Biol
10:174–181.
Gouaux E and MacKinnon R (2005) Principles of
selective ion transport in channels and pumps.
Science 310:1461–1465.
Mitchell P (1977) Vectorial chemiosmotic processes.
Annu Rev Biochem 46:996–1005.
Tanford C (1983) Mechanism of free energy coupling in
active transport. Annu Rev Biochem 52:379–409.
Carrier Proteins and Active Membrane Transport
Almers W & Stirling C (1984) Distribution of transport
proteins over animal cell membranes. J Membr Biol
77:169–186.
Baldwin SA & Henderson PJ (1989) Homologies
between sugar transporters from eukaryotes and
prokaryotes. Annu Rev Physiol 51:459–471.
Borst P & Elferink RO (2002) Mammalian ABC
transporters in health and disease. Annu Rev
Biochem 71:537–592.
Carafoli E & Brini M (2000) Calcium pumps: structural
basis for and mechanism of calcium transmembrane
transport. Curr Opin Chem Biol 4:152–161.
Dean M, Rzhetsky A et al (2001) The human ATPbinding
cassette (ABC) transporter superfamily.
Genome Res 11:1156–1166.
Doige CA & Ames GF (1993) ATP‐dependent transport
systems in bacteria and humans: relevance to cystic
fibrosis and multidrug resistance. Annu Rev
Microbiol 47:291–319.
Gadsby DC, Vergani P & Csanady L (2006) The ABC
protein turned chloride channel whose failure causes
cystic fibrosis. Nature 440:477–83.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Higgins CF (2007) Multiple molecular mechanisms for
multidrug resistance transporters. Nature 446:749–
57.
Kaback HR, Sahin‐Toth M et al (2001) The kamikaze
approach to membrane transport. Nature Rev Mol
Cell Biol 2:610–620.
Kühlbrandt W (2004) Biology, structure and
mechanism of P‐type ATPases. Nature Rev Mol Cell
Biol 5:282–295.
Lodish HF (1986) Anion‐exchange and glucose
transport proteins: structure, function, and
distribution. Harvey Lect 82:19–46.
Pedersen PL & Carafoli E (1987) Ion motive ATPases. 1.
Ubiquity, properties, and significance to cell
function. Trends Biochem Sci 12:146–150.
Romero MF & Boron WF (1999) Electrogenic Na+/HCO3
cotransporters: cloning and physiology. Annu Rev
Physiol 61:699–723.
Saier MH, Jr (2000) Vectorial metabolism and the
evolution of transport systems. J Bacteriol 182:5029–
5035.
Scarborough GA (2003) Rethinking the P‐type ATPase
problem. Trends Biochem Sci 28:581–584.
Stein WD (2002) Cell volume homeostasis: ionic and
nonionic mechanisms. The sodium pump in the
emergence of animal cells. Int Rev Cytol 215:231–
258.
Ion Channels and the Electrical Properties of
Membranes
Armstrong C (1998) The vision of the pore. Science
280:56–57.
Choe S (2002) Potassium channel structures. Nature
Rev Neurosci 3:115–21.
Choe S, Kreusch A & Pfaffinger PJ (1999) Towards the
three‐dimensional structure of voltage‐gated
potassium channels. Trends Biochem Sci 24:345–349.
Franks NP & Lieb WR (1994) Molecular and cellular
mechanisms of general anaesthesia. Nature
367:607–614.
Greengard P (2001) The neurobiology of slow synaptic
transmission. Science 294:1024–30.
Hille B (2001) Ionic Channels of Excitable Membranes,
3rd ed. Sunderland, MA: Sinauer.
Hucho F, Tsetlin VI & Machold J (1996) The emerging
three‐dimensional structure of a receptor. The
nicotinic acetylcholine receptor. Eur J Biochem
239:539–557.
Hodgkin AL & Huxley AF (1952) A quantitative
description of membrane current and its application
to conduction and excitation in nerve. J Physiol
117:500–544.
Hodgkin AL & Huxley AF (1952) Currents carried by
sodium and potassium ions through the membrane
of the giant axon of Loligo. J Physiol 116:449–472.
Jessell TM & Kandel ER (1993) Synaptic transmission: a
bidirectional and self‐modifiable form of cell–cell
communication. Cell 72[Suppl]:1–30.
Kandel ER, Schwartz JH & Jessell TM (2000) Principles
of Neural Science, 4th ed. New York: McGraw‐Hill.
Karlin A (2002) Emerging structure of the nicotinic
acetylcholine receptors. Nature Rev Neurosci 3:102–
114.
Katz B (1966) Nerve, Muscle and Synapse. New York:
McGraw‐Hill.
King LS, Kozono D & Agre P (2004) From structure to
disease: the evolving tale of aquaporin biology.
Nature Rev Mol Cell Biol 5:687–698.
MacKinnon R (2003) Potassium channels. FEBS Lett
555:62–65.
Malenka RC & Nicoll RA (1999) Long‐term
potentiation—a decade of progress? Science
285:1870–1874.
Moss SJ & Smart TG (2001) Constructing inhibitory
synapses. Nature Rev Neurosci 2:240–250.
Neher E and Sakmann B (1992) The patch clamp
technique. Sci Am 266:44–51.
Nicholls JG, Fuchs PA, Martin AR & Wallace BG (2000)
From Neuron to Brain, 4th ed. Sunderland, MA:
Sinauer.
Numa S (1987) A molecular view of neurotransmitter
receptors and ionic channels. Harvey Lect 83:121–
165.
Scannevin RH & Huganir RL (2000) Postsynaptic
organization and regulation of excitatory synapses.
Nature Rev Neurosci 1:133–141.
Seeburg PH (1993) The molecular biology of
mammalian glutamate receptor channels. Trends
Neurosci 16:359–365.
Snyder SH (1996) Drugs and the Brain. New York: WH
Freeman/ Scientific American Books.
Stevens CF (2004) Presynaptic function. Curr Opin
Neurobiol 14:341–345.
Tsien RW, Lipscombe D, Madison DV et al (1988)
Multiple types of neuronal calcium channels and
their selective modulation. Trends Neurosci 11:431–
438.
Unwin N (2003) Structure and action of the nicotinic
acetylcholine receptor explored by electron
microscopy. FEBS Lett 555:91–95.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Chapter 13
How Cells Obtain Energy from Food
Cramer WA & Knaff DB (1990) Energy Transduction in
Biological Membranes. New York: Springer‐Verlag.
Dismukes GC, Klimov VV, Baranov SV et al (2001) The
origin of atmospheric oxygen on Earth: The
innovation of oxygenic photosyntheis. Proc Nat Acad
Sci USA 98:2170–2175.
Fell D (1997) Understanding the Control of
Metabolism. London: Portland Press.
Flatt JP (1995) Use and storage of carbohydrate and
fat. Am J Clin Nutr 61, 952S–959S.
Friedmann HC (2004) From Butybacterium to E. coli:
An essay on unity in biochemistry. Perspect Biol Med
47:47–66.
Fothergill‐Gilmore LA (1986) The evolution of the
glycolytic pathway. Trends Biochem Sci 11:47–51.
Heinrich R, Melendez‐Hevia E, Montero F et al (1999)
The structural design of glycolysis: An evolutionary
approach. Biochem Soc Trans 27:294–298.
Huynen MA, Dandekar T & Bork P (1999) Variation and
evolution of the citric‐acid cycle: a genomic
perspective. Trends Microbiol 7:281–291.
Kornberg HL (2000) Krebs and his trinity of cycles.
Nature Rev Mol Cell Biol 1:225–228.
Krebs HA & Martin A (1981) Reminiscences and
Reflections. Oxford/New York: Clarendon
Press/Oxford University Press.
Krebs HA (1970) The history of the tricarboxylic acid
cycle. Perspect Biol Med 14:154–170.
Martin BR (1987) Metabolic Regulation: A Molecular
Approach. Oxford: Blackwell Scientific.
McGilvery RW (1983) Biochemistry: A Functional
Approach, 3rd ed. Philadelphia: Saunders.
Morowitz HJ (1993) Beginnings of Cellular Life:
Metabolism Recapitulates Biogenesis. New Haven:
Yale University Press
Newsholme EA & Stark C (1973) Regulation of
Metabolism. New York: Wiley.
Chapter 14
The Mitochondrion
Abrahams JP, Leslie AG, Lutter R & Walker JE (1994)
Structure at 2.8Å resolution of F1‐ATPase from
bovine heart mitochondria. Nature 370:621–628.
Berg HC (2003) The rotary motor of bacterial flagella.
Annu Rev Biochem 72:19‐54.
Boyer PD (1997) The ATP synthase—a splendid
molecular machine. Annu Rev Biochem 66:717–749.
Ernster L & Schatz G (1981) Mitochondria: a historical
review. J Cell Biol 91:227s–255s.
Frey TG, Renken CW & Perkins GA (2002) Insight into
mitochondrial structure and function from electron
tomography. Biochim Biophys Acta 1555:196–203.
Pebay‐Peyroula E & Brandolin G (2004) Nucleotide
exchange in mitochondria: insight at a molecular
level. Curr Opin Struct Biol 14:420–425.
Meier T, Polzer P, Diederichs K et al (2005) Structure of
the rotor ring of F‐type Na+‐ATPase from Ilyobacter
tartaricus. Science 308:659–662.
Mitchell P (1961) Coupling of phosphorylation to
electron and hydrogen transfer by a chemi‐osmotic
type of mechanism. Nature 191:144–148.
Nicholls DG (2006) The physiological regulation of
uncoupling proteins. Biochim Biophys Acta
1757:459–466.
Racker E & Stoeckenius W (1974) Reconstitution of
purple membrane vesicles catalyzing light‐driven
proton uptake and adenosine triphosphate
formation. J Biol Chem 249:662–663.
Saraste M (1999) Oxidative phosphorylation at the fin
de siecle. Science 283:1488–1493.
Scheffler IE (1999) Mitochondria. New
York/Chichester: Wiley‐Liss.
Stock D, Gibbons C, Arechaga I et al. (2000) The rotary
mechanism of ATP synthase. Curr Opin Struct Biol
10:672–679.
Weber J (2007) ATP synthase—the structure of the
stator stalk. Trends Biochem Sci 32:53–56.
Electron‐Transport Chains and Their Proton Pumps
Beinert H, Holm RH & Munck E (1997) Iron‐sulfur
clusters: nature’s modular, multipurpose structures.
Science 277:653–659.
Berry EA, Guergova‐Kuras M, Huang LS & Crofts AR
(2000) Structure and function of cytochrome bc
complexes. Annu Rev Biochem 69:1005–1075.
Brand MD (2005) The efficiency and plasticity of
mitochondrial energy transduction. Biochem Soc
Trans 33:897–904.
Brandt U (2006) Energy converting NADH:quinone
oxidoreductase (complex I). Annu Rev Biochem
75:69–92.
Chance B & Williams GR (1955) A method for the
localization of sites for oxidative phosphorylation.
Nature 176:250–254.
Gottschalk G (1997) Bacterial Metabolism, 2nd ed.
New York: Springer.
Gray HB & Winkler JR (1996) Electron transfer in
proteins. Annu Rev Biochem 65:537–556.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Keilin D (1966) The History of Cell Respiration and
Cytochromes. Cambridge: Cambridge University
Press.
Sazanov LA (2007) Respiratory complex I: mechanistic
and structural insights provided by the crystal
structure of the hydrophilic domain. Biochemistry
46:2275–2288.
Subramaniam S & Henderson R (2000) Molecular
mechanism of vectorial proton translocation by
bacteriorhodopsin. Nature 406:653–657.
Tsukihara T, Aoyama H, Yamashita E et al (1996) The
whole structure of the 13‐subunit oxidized
cytochrome c oxidase at 2.8Å. Science 272:1136–
1144.
Wikstrom M & Verkhovsky MI (2006) Towards the
mechanism of proton pumping by the haem‐copper
oxidases. Biochim Biophys Acta 1757:1047–1051.
Chloroplasts and Photosynthesis
Blankenship RE (2002) Molecular Mechanisms of
Photosynthesis. Oxford, UK:Blackwell Scientific.
Bassham JA (1962) The path of carbon in
photosynthesis. Sci Am 206:88–100.
Deisenhofer J & Michel H (1989) Nobel lecture. The
photosynthetic reaction centre from the purple
bacterium Rhodopseudomonas viridis. EMBO J
8:2149–2170.
Edwards GE, Furbank RT, Hatch MD & Osmond CB
(2001) What does it take to be c(4)?—lessons from
the evolution of c(4) photosynthesis. Plant Physiol
125:46–49.
Ferreira KN, Iverson TM, Maghlaoui K et al (2004)
Architecture of the photosynthetic oxygen‐evolving
center. Science 303:1831–1838.
Iwata S & Barber J (2004) Structure of photosystem II
and molecular architecture of the oxygen‐evolving
centre. Curr Opin Struct Biol 14:447–453.
Jordan P, Fromme P, Witt HT et al (2001) Threedimensional
structure of cyanobacterial
photosystem I at 2.5Å resolution. Nature 411:909–
917.
Merchant S & Sawaya MR (2005) The light reactions: A
guide to recent acquisitions for the picture gallery.
The Plant Cell 17:648–663.
Nelson N & Ben‐Shem A (2004) The complex
architecture of oxygenic photosynthesis. Nature Rev
Mol Cell Biol 5:971–982.
The Evolution of Electron‐Transport Chains
Blankenship RE & Bauer CE (eds) (1995) Anoxygenic
Photosynthetic Bacteria. Dordrecht: Kluwer.
de Las Rivas J, Balsera M & Barber J (2004) Evolution of
oxygenic photosynthesis: genome‐wide analysis of
the OEC extrinsic proteins. Trends Plant Sci 9:18–25.
Orgel LE (1998) The origin of life—a review of facts and
speculations. Trends Biochem Sci. 23:491–495.
Schafer G, Purschke W & Schmidt CL (1996) On the
origin of respiration: electron transport proteins
from archaea to man. FEMS Microbiol Rev 18:173–
188.
Skulachev VP (1994) Bioenergetics: the evolution of
molecular mechanisms and the development of
bioenergetic concepts. Antonie Van Leeuwenhoek
65:271–284.
Chapter 15
The Compartmentalization of Cells
Blobel G (1980) Intracellular protein topogenesis. Proc
Natl Acad Sci USA 77:1496–1500.
De Duve C (2007) The origin of eukaryotes: a
reappraisal. Nature Rev Genet 8:395–403.
Schatz G & Dobberstein B (1996) Common principles of
protein translocation across membranes. Science
271:1519–1526.
Warren G & Wickner W (1996) Organelle inheritance.
Cell 84:395–400.
The Transport of Molecules Between the Nucleus and
the Cytosol
Adam SA & Gerace L (1991) Cytosolic proteins that
specifically bind nuclear location signals are
receptors for nuclear import. Cell 66:837–847.
Bednenko J, Cingolani G & Gerace L (2003)
Nucleocytoplasmic transport: navigating the
channel. Traffic 4:127–135.
Chook YM & Blobel G (2001) Karyopherins and nuclear
import. Curr Opin Struct Biol 11:703–715.
Cole CN & Scarcelli JJ (2006) Transport of messenger
RNA from the nucleus to the cytoplasm. Curr Opin
Cell Biol 18:299–306.
Fahrenkrog B, Koser J & Aebi U (2004) The nuclear
pore complex: a jack of all trades? Trends Biochem
Sci 29:175–182.
Görlich D & Kutay U (1999) Transport between the cell
nucleus and the cytoplasm. Annu Rev Cell Dev Biol
15:607–660.
Hetzer MW, Walther TC & Mattaj IW (2005) Pushing
the envelope: structure, function, and dynamics of
the nuclear periphery. Annu Rev Cell Dev Biol
21:347–380.
Komeili A & O’Shea EK (2000) Nuclear transport and
transcription. Curr Opin Cell Biol 12:355–360.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Kuersten S, Ohno M & Mattaj IW (2001)
Nucleocytoplasmic transport: Ran, beta and beyond.
Trends Cell Biol 11:497–503.
Tran EJ & Wente SR (2006) Dynamic nuclear pore
complexes: life on the edge. Cell 125:1041–1053.
Weis K (2002) Nucleocytoplasmic transport: cargo
trafficking across the border. Curr Opin Cell Biol
14:328–335.
The Transport of Proteins Into Mitochondria and
Chloroplasts
Jarvis P & Robinson C (2004) Mechanisms of protein
import and routing in chloroplasts. Curr Biol
14:R1064–R1077.
Kessler F & Schnell DJ (2004) Chloroplast protein
import: solve the GTPase riddle for entry. Trends Cell
Biol 14:334–338.
Koehler CM, Merchant S & Schatz G (1999) How
membrane proteins travel across the mitochondrial
intermembrane space. Trends Biochem Sci 24:428–
432.
Mokranjac D & Neupert W (2005) Protein import into
mitochondria. Biochem Soc Trans 33:1019–1023.
Prakash S & Matouschek A (2004) Protein unfolding in
the cell. Trends Biochem Sci 29:593–600.
Soll J & Schleiff E (2004) Protein import into
chloroplasts. Nature Rev Mol Cell Biol 5:198–208.
Truscott KN, Brandner K & Pfanner N (2003)
Mechanisms of protein import into mitochondria.
Curr Biol 13:R326–R337.
The Endoplasmic Reticulum
Adelman MR, Sabatini DD et al (1973) Ribosomemembrane
interaction. Nondestructive disassembly
of rat liver rough microsomes into ribosomal and
membranous components. J Cell Biol 56:206–229.
Bernales S, Papa FR & Walter P (2006) Intracellular
signaling by the unfolded protein response. Annu
Rev Cell Dev Biol 22:487–508.
Bishop WR & Bell RM (1988) Assembly of
phospholipids into cellular membranes: biosynthesis,
transmembrane movement and intracellular
translocation. Annu Rev Cell Biol 4:579–610.
Blobel G & Dobberstein B (1975) Transfer of proteins
across membranes. I. Presence of proteolytically
processed and unprocessed nascent immunoglobulin
light chains on membrane‐bound ribosomes of
murine myeloma. J Cell Biol 67:835–851.
Borgese N, Mok W & Sabatini DD (1974) Ribosomalmembrane
interaction: in vitro binding of ribosomes
to microsomal membranes. J Mol Biol 88:559–580.
Daleke DL (2003) Regulation of transbilayer plasma
membrane phospholipid asymmetry. J Lipid Res
44:233–242.
Deshaies RJ, Sanders SL & Schekman R (1991)
Assembly of yeast Sec proteins involved in
translocation into the endoplasmic reticulum into a
membrane‐bound multisubunit complex. Nature
349:806–808.
Ellgaard L & Helenius A (2003) Quality control in the
endoplasmic reticulum. Nature Rev Mol Cell Biol
4:181–191.
Ferguson MA (1999) The structure, biosynthesis and
functions of glycosylphosphatidylinositol anchors,
and the contributions of trypanosome research. J
Cell Sci 112:2799–2809.
Gething MJ (1999) Role and regulation of the ER
chaperone BiP. Semin Cell Dev Biol 10:465–472.
Görlich D, Prehn S et al (1992) A mammalian homolog
of SEC61p and SECYp is associated with ribosomes
and nascent polypeptides during translocation. Cell
71:489–503.
Helenius J & Aebi M (2002) Transmembrane
movement of dolichol linked carbohydrates during
N‐glycoprotein biosynthesis in the endoplasmic
reticulum. Semin Cell Dev Biol 13:171–178.
Johnson AE & van Waes MA (1999) The translocon: a
dynamic gateway at the ER membrane. Annu Rev
Cell Dev Biol 15:799–842.
Keenan RJ, Freymann DM & Walter P (2001) The signal
recognition particle. Annu Rev Biochem 70:755–775.
Kostova Z & Wolf DH (2003) For whom the bell tolls:
protein quality control of the endoplasmic reticulum
and the ubiquitin‐proteasome connection. EMBO J
22:2309–2317.
Levine T & Loewen C (2006) Inter‐organelle membrane
contact sites: through a glass, darkly. Curr Opin Cell
Biol 18:371–378.
Marciniak SJ & Ron D (2006) Endoplasmic reticulum
stress signaling in disease. Physiol Rev 86:1133–
1149.
Milstein C, Brownlee GG et al (1972) A possible
precursor of immunoglobulin light chains. Nature
New Biol 239:117–120.
Römisch K (2005) Endoplasmic reticulum‐associated
degradation. Annu Rev Cell Dev Biol 21:435–456.
Simon SM & Blobel G (1991) A protein‐conducting
channel in the endoplasmic reticulum. Cell 65:371–
380.
Staehelin LA (1997) The plant ER: a dynamic organelle
composed of a large number of discrete functional
domains. Plant J 11:1151–1165.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Trombetta ES & Parodi AJ (2003) Quality control and
protein folding in the secretory pathway. Annu Rev
Cell Dev Biol 19:649–676.
Tsai B, Ye Y & Rapoport TA (2002) Retro‐translocation
of proteins from the endoplasmic reticulum into the
cytosol. Nature Rev Mol Cell Biol 3:246–255.
Shibata Y, Voeltz GK & Rapoport TA (2006) Rough
sheets and smooth tubules. Cell 126:435–439
White SH & von Heijne G (2004) The machinery of
membrane protein assembly. Curr Opin Struct Biol
14:397–404.
Yan A & Lennarz WJ (2005) Unraveling the mechanism
of protein N‐glycosylation. J Biol Chem 280:3121–
3124.
Chapter 16
General Principles of Cell Communication
Ben‐Shlomo I, Yu Hsu S, Rauch R et al (2003) Signaling
receptome: a genomic and evolutionary perspective
of plasma membrane receptors involved in signal
transduction. Sci STKE 187:RE9.
Bourne HR (1995) GTPases: a family of molecular
switches and clocks. Philos Trans R Soc Lond B Biol
Sci 349:283–289.
Ferrell JE Jr (2002) Self‐perpetuating states in signal
transduction: positive feedback, double‐negative
feedback and bistability. Curr Opin Cell Biol 14:140–
148.
Mangelsdorf DJ, Thummel C, Beato M et al (1995) The
nuclear receptor superfamily: the second decade.
Cell 83:835–839.
Murad F (2006) Shattuck Lecture. Nitric oxide and
cyclic GMP in cell signaling and drug development. N
Engl J Med 355:2003–2011.
Papin JA, Hunter T, Palsson BO & Subramaniam S
(2005) Reconstruction of cellular signalling networks
and analysis of their properties. Nature Rev Mol Cell
Biol 6:99–111.
Pawson T & Scott JD (2005) Protein phosphorylation in
signaling—50 years and counting. Trends Biochem
Sci 30:286–290.
Pires‐daSilva A & Sommer RJ (2003) The evolution of
signalling pathways in animal development. Nature
Rev Genet 4:39–49.
Robinson‐Rechavi M, Escriva Garcia H & Laudet V
(2003) The nuclear receptor superfamily. J Cell Sci
116:585–586.
Seet BT, Dikic I, Zhou MM & Pawson T (2006) Reading
protein modifications with interaction domains.
Nature Rev Mol Cell Biol 7:473–483.
Singla V & Reiter JF (2006) The primary cilium as the
cell’s antenna: signaling at a sensory organelle.
Science 313:629–633.
Signaling Through G‐protein‐coupled Cell‐surface
Receptors and Small Intracellular Mediators
Berridge MJ (2005) Unlocking the secrets of cell
signaling. Annu Rev Physiol 67:1–21.
Berridge MJ, Bootman MD & Roderick HL (2003)
Calcium signalling: dynamics, homeostasis and
remodelling. Nature Rev Mol Cell Biol 4:517–529.
Breer H (2003) Sense of smell: recognition and
transduction of olfactory signals. Biochem Soc Trans
31:113–116.
Burns ME & Baylor DA (2001) Activation, deactivation,
and adaptation in vertebrate photoreceptor cells.
Annu Rev Neurosci 24:779–805.
Cooper DM (2005) Compartmentalization of adenylate
cyclase and cAMP signalling. Biochem Soc Trans
33:1319–1322.
Hoeflich KP & Ikura M (2002) Calmodulin in action:
diversity in target recognition and activation
mechanisms. Cell 108:739–742.
Hudmon A & Schulman H (2002) Structure‐function of
the multifunctional Ca2+/calmodulin‐dependent
protein kinase II. Biochem J 364:593–611.
Kamenetsky M, Middelhaufe S, Bank EM et al (2006)
Molecular details of cAMP generation in mammalian
cells: a tale of two systems. J Mol Biol 362:623–639.
Luttrell LM (2006) Transmembrane signaling by G
protein‐coupled receptors. Methods Mol Biol 332:3–
49.
McConnachie G, Langeberg LK & Scott JD (2006) AKAP
signaling complexes: getting to the heart of the
matter. Trends Mol Med 12:317–323.
Parker PJ (2004) The ubiquitous phosphoinositides.
Biochem Soc Trans 32:893–898.
Pierce KL, Premont RT & Lefkowitz RJ (2002) Seventransmembrane
receptors. Nature Rev Mol Cell Biol
3:639–650.
Reiter E & Lefkowitz RJ (2006) GRKs and beta‐arrestins:
roles in receptor silencing, trafficking and signaling.
Trends Endocrinol Metab 17:159–165.
Rhee SG (2001) Regulation of phosphoinositide‐specific
phospholipase
C. Annu Rev Biochem 70:281–312. Robishaw JD &
Berlot CH (2004) Translating G protein subunit
diversity into functional specificity. Curr Opin Cell
Biol 16:206–209.
Shaywitz AJ & Greenberg ME (1999) CREB: a stimulusinduced
transcription factor activated by a diverse
array of extracellular signals. Annu Rev Biochem
68:821–861.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Signaling Through Enzyme‐coupled Cell‐surface
Receptors
Baker MD, Wolanin PM & Stock JB (2006) Signal
transduction in bacterial chemotaxis. BioEssays
28:9–22.
Dard N & Peter M (2006) Scaffold proteins in MAP
kinase signaling: more than simple passive activating
platforms. BioEssays 28:146–156.
Darnell JE Jr, Kerr IM & Stark GR (1994) Jak‐STAT
pathways and transcriptional activation in response
to IFNs and other extracellular signaling proteins.
Science 264:1415–1421.
Downward J (2004) PI 3‐kinase, Akt and cell survival.
Semin Cell Dev Biol 15:177–182.
Jaffe AB & Hall A (2005) Rho GTPases: biochemistry
and biology. Annu Rev Cell Dev Biol 21:247–269.
Massague J & Gomis RR (2006) The logic of TGFb
signaling. FEBS Lett 580:2811–2820.
Mitin N, Rossman KL & Der CJ (2005) Signaling
interplay in Ras superfamily function. Curr Biol
15:R563–574.
Murai KK & Pasquale EB (2003) Eph’ective signaling:
forward, reverse and crosstalk. J Cell Sci 116:2823–
2832.
Pawson T (2004) Specificity in signal transduction: from
phosphotyrosine‐SH2 domain interactions to
complex cellular systems. Cell 116:191–203.
Qi M & Elion EA (2005) MAP kinase pathways. J Cell Sci
118:3569–3572.
Rawlings JS, Rosler KM & Harrison DA (2004) The
JAK/STAT signaling pathway. J Cell Sci 117:1281–
1283.
Roskoski R Jr (2004) Src protein‐tyrosine kinase
structure and regulation. Biochem Biophys Res
Commun 324:1155–1164.
Schlessinger J (2000) Cell signaling by receptor tyrosine
kinases. Cell 103:211–225.
Sahin M, Greer PL, Lin MZ et al (2005) Eph‐dependent
tyrosine phosphorylation of ephexin1 modulates
growth cone collapse. Neuron 46:191–204.
Schwartz MA & Madhani HD (2004) Principles of MAP
kinase signaling specificity in Saccharomyces
cerevisiae. Annu Rev Genet 38:725–748.
Shaw RJ & Cantley LC (2006) Ras, PI(3)K and mTOR
signalling controls tumour cell growth. Nature
44:424–430.
Wassarman DA, Therrien M & Rubin GM (1995) The
Ras signaling pathway in Drosophila. Curr Opin Genet
Dev 5:44–50.
Wullschleger S, Loewith R & Hall MN (2006) TOR
signaling in growth and metabolism. Cell 124:471–
484.
Chapter 17
The Self‐Assembly and Dynamic Structure of
Cytoskeletal Filaments
Dogterom M & Yurke B (1997) Measurement of the
force‐velocity relation for growing microtubules.
Science 278:856–860.
Garner EC, Campbell CS & Mullins RD (2004) Dynamic
instability in a DNA‐segregating prokaryotic actin
homolog. Science 306:1021–1025.
Helfand BT, Chang L & Goldman RD (2003) The
dynamic and motile properties of intermediate
filaments. Annu Rev Cell Dev Biol 19:445–467.
Hill TL & Kirschner MW (1982) Bioenergetics and
kinetics of microtubule and actin filament assemblydisassembly.
Int Rev Cytol 78:1–125.
Hotani H & Horio T (1988) Dynamics of microtubules
visualized by darkfield microscopy: treadmilling and
dynamic instability. Cell Motil Cytoskeleton 10:229–
236.
Jones LJ, Carballido‐Lopez R & Errington J (2001)
Control of cell shape in bacteria: helical, actin‐like
filaments in Bacillus subtilis. Cell 104:913–922.
Kerssemakers JW, Munteanu EL, Laan L et al (2006)
Assembly dynamics of microtubules at molecular
resolution. Nature 442:709–712.
Luby‐Phelps K (2000) Cytoarchitecture and physical
properties of cytoplasm: volume, viscosity, diffusion,
intracellular surface area. Int Rev Cytol 192:189–221.
Mitchison T & Kirschner M (1984) Dynamic instability
of microtubule growth. Nature 312:237–242.
Mitchison TJ (1995) Evolution of a dynamic
cytoskeleton. Philos Trans R Soc Lond B Biol Sci
349:299–304.
Mukherjee A & Lutkenhaus J (1994) Guanine
nucleotide‐dependent assembly of FtsZ into
filaments. J Bacteriol 176:2754–2758.
Oosawa F & Asakura S (1975) Thermodynamics of the
polymerization of protein. New York: Academic
Press, pp 41–55, pp 90–108.
Pauling L (1953) Aggregation of Globular Proteins.
Discuss Faraday Soc 13:170–176
Rodionov VI & Borisy GG (1997) Microtubule
treadmilling in vivo. Science. 275:215–218.
Shih YL & Rothfield L (2006) The bacterial cytoskeleton.
Microbiol Mol Biol Rev 70:729–754.
Theriot JA (2000) The polymerization motor. Traffic
1:19–28.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
How Cells Regulate Their Cytoskeletal Filaments
Aldaz H, Rice LM, Stearns T & Agard DA (2005) Insights
into microtubule nucleation from the crystal
structure of human gamma‐tubulin. Nature
435:523–527
Bretscher A, Chambers D, Nguyen R & Reczek D (2000)
ERM‐Merlin and EBP50 protein families in plasma
membrane organization and function. Annu Rev Cell
Dev Biol 16:113–143.
Doxsey S, McCollum D & Theurkauf W (2005)
Centrosomes in cellular regulation. Annu Rev Cell
Dev Biol 21:411–434.
Garcia ML & Cleveland DW (2001) Going new places
using an old MAP: tau, microtubules and human
neurodegenerative disease. Curr Opin Cell Biol
13:41–48.
Holy TE, Dogterom M, Yurke B & Leibler S (1997)
Assembly and positioning of microtubule asters in
microfabricated chambers. Proc Natl Acad Sci USA
94:6228–6231.
Mullins RD, Heuser JA & Pollard TD (1998) The
interaction of Arp2/3 complex with actin: nucleation,
high affinity pointed end capping, and formation of
branching networks of filaments. Proc Natl Acad Sci
USA 95:6181–6186.
Robinson RC, Turbedsky K, Kaiser DA et al (2001)
Crystal structure of Arp2/3 complex. Science
294:1679–1684.
Quarmby L (2000) Cellular Samurai: katanin and the
severing of microtubules. J Cell Sci 113:2821–2827.
Stearns T & Kirschner M (1994) In vitro reconstitution
of centrosome assembly and function: the central
role of gamma‐tubulin. Cell 76:623–637.
Wiese C & Zheng Y (2006) Microtubule nucleation:
gamma‐tubulin and beyond. J Cell Sci 119:4143–
4153.
Zheng Y, Wong ML, Alberts B & Mitchison T (1995)
Nucleation of microtubule assembly by a gammatubulin‐
containing ring complex. Nature 378:578–
583.
Zigmond SH (2004) Formin‐induced nucleation of actin
filaments. Curr Opin Cell Biol 16:99–105.
Molecular Motors
Burgess SA, Walker ML, Sakakibara H et al (2003)
Dynein structure and power stroke. Nature 421:715–
718.
Hirokawa N (1998) Kinesin and dynein superfamily
proteins and the mechanism of organelle transport.
Science 279:519–526.
Howard J, Hudspeth AJ & Vale RD (1989) Movement of
microtubules by single kinesin molecules. Nature
342:154–158.
Howard J (1997) Molecular motors: structural
adaptations to cellular functions. Nature 389:561–
567.
Rayment I, Rypniewski WR, Schmidt‐Base K et al (1993)
Three‐dimensional structure of myosin subfragment‐
1: a molecular motor. Science 261:50–58.
Reck‐Peterson SL, Yildiz A, Carter AP et al (2006) Singlemolecule
analysis of dynein processivity and
stepping behavior. Cell 126:335–348.
Rice S, Lin AW, Safer D et al (1999) A structural change
in the kinesin motor protein that drives motility.
Nature 402:778–784.
Richards TA & Cavalier‐Smith T (2005) Myosin domain
evolution and the primary divergence of eukaryotes.
Nature 436:1113–1118.
Svoboda K, Schmidt CF, Schnapp BJ & Block SM (1993)
Direct observation of kinesin stepping by optical
trapping interferometry. Nature 365:721–727.
Vikstrom KL & Leinwand LA (1996) Contractile protein
mutations and heart disease. Curr Opin Cell Biol
8:97–105.
Wells AL, Lin AW, Chen LQ et al (1999) Myosin VI is an
actin‐based motor that moves backwards. Nature
401:505–508.
Yildiz A, Forkey JN, McKinney SA et al (2003) Myosin V
walks hand‐overhand: single fluorophore imaging
with 1.5‐nm localization. Science 300:2061–2065.
Yildiz A & Selvin PR (2005) Kinesin: walking, crawling or
sliding along? Trends Cell Biol 15:112–120.
The Cytoskeleton and Cell Behavior
Abercrombie M (1980) The crawling movement of
metazoan cells. Proc Roy Soc B 207:129–147.
Cooke R (2004) The sliding filament model: 1972–2004.
J Gen Physiol 123:643–656.
Dent EW & Gertler FB (2003) Cytoskeletal dynamics
and transport in growth cone motility and axon
guidance. Neuron 40:209–227.
Lauffenburger DA & Horwitz AF (1996) Cell migration: a
physically integrated molecular process. Cell 84:359–
369.
Lo CM, Wang HB, Dembo M & Wang YL (2000) Cell
movement is guided by the rigidity of the substrate.
Biophys J 79:144–152.
Madden K & Snyder M (1998) Cell polarity and
morphogenesis in budding yeast. Annu Rev Microbiol
52:687–744.
Ridley AJ, Schwartz MA, Burridge K et al (2003) Cell
migration: integrating signals from front to back.
Science 302:1704–1709.
Rafelski SM & Theriot JA (2004) Crawling toward a
unified model of cell motility: spatial and temporal
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
regulation of actin dynamics. Annu Rev Biochem
73:209–239.
Parent CA & Devreotes PN (1999) A cell’s sense of
direction. Science 284:765–770.
Pollard TD & Borisy GG (2003) Cellular motility driven
by assembly and disassembly of actin filaments. Cell
112:453–465.
Purcell EM (1977) Life at low Reynolds’ number. Am J
Phys 45:3–11.
Wittmann T, Hyman A & Desai A (2001) The spindle: a
dynamic assembly of microtubules and motors.
Nature Cell Biol 3:E28–E34.
Chapter 18
Overview of the Cell Cycle
Forsburg SL & Nurse P (1991) Cell cycle regulation in
the yeasts Saccharomyces cerevisiae and
Schizosaccharomyces pombe. Annu Rev Cell Biol
7:227–256.
Hartwell LH, Culotti J, Pringle JR et al (1974) Genetic
control of the cell division cycle in yeast. Science
183:46–51.
Kirschner M, Newport J & Gerhart J (1985) The timing
of early developmental events in Xenopus. Trends
Genet 1:41–47.
Nurse P, Thuriaux P & Nasmyth K (1976) Genetic
control of the cell division cycle in the fission yeast
Schizosaccharomyces pombe. Mol Gen Genet
146:167–178.
The Cell‐Cycle Control System
Evans T, Rosenthal ET, Youngblom J et al (1983) Cyclin:
a protein specified by maternal mRNA in sea urchin
eggs that is destroyed at each cleavage division. Cell
33:389–396.
Lohka MJ, Hayes MK & Maller JL (1988) Purification of
maturation‐promoting factor, an intracellular
regulator of early mitotic events. Proc Natl Acad Sci
USA 85:3009–3013.
Masui Y and Markert CL (1971) Cytoplasmic control of
nuclear behavior during meiotic maturation of frog
oocytes. J Exp Zool 177:129–146.
Morgan DO (1997) Cyclin‐dependent kinases: engines,
clocks, and microprocessors. Annu Rev Cell Dev Biol
13:261–291.
Murray AW & Kirschner MW (1989) Cyclin synthesis
drives the early embryonic cell cycle. Nature
339:275–280.
Pavletich NP (1999) Mechanisms of cyclin‐dependent
kinase regulation: structures of Cdks, their cyclin
activators, and CIP and Ink4 inhibitors. J Mol Biol
287:821–828.
Peters JM (2006) The anaphase promoting
complex/cyclosome: a machine designed to destroy.
Nature Rev Mol Cell Biol 7:644–656.
Petroski MD & Deshaies RJ (2005) Function and
regulation of cullin‐RING ubiquitin ligases. Nature
Rev Mol Cell Biol 6:9–20.
Wittenberg C & Reed SI (2005) Cell cycle‐dependent
transcription in yeast: promoters, transcription
factors, and transcriptomes. Oncogene 24:2746–
2755.
S Phase
Arias EE & Walter JC (2007) Strength in numbers:
preventing rereplication via multiple mechanisms in
eukaryotic cells. Genes Dev 21:497–518.
Bell SP & Dutta A (2002) DNA replication in eukaryotic
cells. Annu Rev Biochem 71:333–374.
Bell SP & Stillman B (1992) ATP‐dependent recognition
of eukaryotic origins of DNA replication by a
multiprotein complex. Nature 357:128–134.
Diffley JF (2004) Regulation of early events in
chromosome replication. Curr Biol 14:R778–R786.
Groth A, Rocha W, Verreault A et al (2007) Chromatin
challenges during DNA replication and repair. Cell
128:721–733.
Tanaka S, Umemori T, Hirai K et al (2007) CDKdependent
phosphorylation of Sld2 and Sld3 initiates
DNA replication in budding yeast. Nature 445:328–
332.
Zegerman P & Diffley JF (2007) Phosphorylation of Sld2
and Sld3 by cyclin‐dependent kinases promotes DNA
replication in budding yeast. Nature 445:281–285.
Mitosis
Cheeseman IM, Chappie JS, Wilson‐Kubalek EM et al
(2006) The conserved KMN network constitutes the
core microtubule‐binding site of the kinetochore.
Cell 127:983–997.
Dong Y, Vanden Beldt KJ, Meng X et al (2007) The outer
plate in vertebrate kinetochores is a flexible network
with multiple microtubule interactions. Nature Cell
Biol 9:516–522.
Heald R, Tournebize R, Blank T et al (1996) Selforganization
of microtubules into bipolar spindles
around artificial chromosomes in Xenopus egg
extracts. Nature 382:420–425.
Hirano T (2005) Condensins: organizing and
segregating the genome. Curr Biol 15:R265–R275.
Kapoor TM, Lampson MA, Hergert P et al (2006)
Chromosomes can congress to the metaphase plate
before biorientation. Science 311:388–391.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Mitchison T & Kirschner M (1984) Dynamic instability
of microtubule growth. Nature 312:237–242.
Mitchison TJ (1989) Polewards microtubule flux in the
mitotic spindle: evidence from photoactivation of
fluorescence. J Cell Biol 109:637–652.
Mitchison TJ & Salmon ED (2001) Mitosis: a history of
division. Nature Cell Biol 3:E17–E21.
Musacchio A & Salmon ED (2007) The spindle‐assembly
checkpoint in space and time. Nature Rev Mol Cell
Biol 8:379–393.
Nasmyth K (2002) Segregating sister genomes: the
molecular biology of chromosome separation.
Science 297:559–565.
Nigg EA (2007) Centrosome duplication: of rules and
licenses. Trends Cell Biol 17:215–221.
Nurse P (1990) Universal control mechanism regulating
onset of M‐phase. Nature 344:503–508.
Page SL & Hawley RS (2003) Chromosome
choreography: the meiotic ballet. Science 301:785–
789.
Petronczki M, Siomos MF & Nasmyth K (2003) Un
ménage à quatre: the molecular biology of
chromosome segregation in meiosis. Cell 112:423–
440.
Salmon ED (2005) Microtubules: a ring for the
depolymerization motor. Curr Biol 15:R299–R302.
Tanaka TU, Stark MJ & Tanaka K (2005) Kinetochore
capture and biorientation on the mitotic spindle.
Nature Rev Mol Cell Biol 6:929–942.
Uhlmann F, Lottspeich F & Nasmyth K (1999) Sisterchromatid
separation at anaphase onset is promoted
by cleavage of the cohesin subunit Scc1. Nature
400:37–42.
Wadsworth P & Khodjakov A (2004) E pluribus unum:
towards a universal mechanism for spindle
assembly. Trends Cell Biol 14:413–419.
Cytokinesis
Albertson R, Riggs B & Sullivan W (2005) Membrane
traffic: a driving force in cytokinesis. Trends Cell Biol
15:92–101.
Burgess DR & Chang F (2005) Site selection for the
cleavage furrow at cytokinesis. Trends Cell Biol.
15:156–162.
Dechant R & Glotzer M (2003) Centrosome separation
and central spindle assembly act in redundant
pathways that regulate microtubule density and
trigger cleavage furrow formation. Dev Cell 4:333–
344.
Eggert US, Mitchison TJ & Field CM (2006) Animal
cytokinesis: from parts list to mechanisms. Annu Rev
Biochem 75:543–566.
Glotzer M (2005) The molecular requirements for
cytokinesis. Science 307:1735–1739.
Grill SW, Gonczy P, Stelzer EH et al (2001) Polarity
controls forces governing asymmetric spindle
positioning in the Caenorhabditis elegans embryo.
Nature 409:630–633.
Jurgens G (2005) Plant cytokinesis: fission by fusion.
Trends Cell Biol 15:277–283.
Rappaport R (1986) Establishment of the mechanism of
cytokinesis in animal cells. Int Rev Cytol 105:245–
281.
Control of Cell Division and Cell Growth
Adhikary S & Eilers M (2005) Transcriptional regulation
and transformation by Myc proteins. Nature Rev Mol
Cell Biol 6:635–645.
Campisi J (2005) Senescent cells, tumor suppression,
and organismal aging: good citizens, bad neighbors.
Cell 120:513–522.
Conlon I & Raff M (1999) Size control in animal
development. Cell 96:235–244.
Frolov MV, Huen DS, Stevaux O et al (2001) Functional
antagonism between E2F family members. Genes
Dev 15:2146–2160.
Harrison JC & Haber JE (2006) Surviving the breakup:
the DNA damage checkpoint. Annu Rev Genet
40:209–235.
Jorgensen P & Tyers M (2004) How cells coordinate
growth and division. Curr Biol 14:R1014–R1027.
Levine AJ (1997) p53, the cellular gatekeeper for
growth and division. Cell 88:323–331.
Raff MC (1992) Social controls on cell survival and cell
death. Nature 356:397–400.
Sherr CJ & DePinho RA (2000) Cellular senescence:
mitotic clock or culture shock? Cell 102:407–410.
Sherr CJ & Roberts JM (1999) CDK inhibitors: positive
and negative regulators of G1‐phase progression.
Genes Dev 13:1501–1512.
Trimarchi JM & Lees JA (2002) Sibling rivalry in the E2F
family. Nature Rev Mol Cell Biol 3:11–20.
Vousden KH & Lu X (2002) Live or let die: the cell’s
response to p53. Nature Rev Cancer 2:594–604.
Zetterberg A & Larsson O (1985) Kinetic analysis of
regulatory events in G1 leading to proliferation or
quiescence of Swiss 3T3 cells. Proc Natl Acad Sci USA
82:5365–5369.
Apoptosis
Adams JM, Huang DC, Strasser A et al (2005)
Subversion of the Bcl‐2 life/death switch in cancer
development and therapy. Cold Spring Harb Symp
Quant Biol 70:469–77.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Boatright KM & Salvesen GS (2003) Mechanisms of
caspase activation. Curr Opin Cell Biol 15:725–731.
Danial NN & Korsmeyer SJ (2004) Cell death: critical
control points. Cell 116:205–219.
Ellis RE, Yuan JY & Horvitz RA (1991) Mechanisms and
functions of cell death. Annu Rev Cell Biol 7:663–698.
Fadok VA & Henson PM (2003) Apoptosis: giving
phosphatidylserine recognition an assist—with a
twist. Curr Biol 13:R655–R657.
Galonek HL & Hardwick JM (2006) Upgrading the BCL‐2
network. Nature Cell Biol 8:1317–1319.
Green DR (2005) Apoptotic pathways: ten minutes to
dead. Cell 121:671–674.
Horvitz HR (2003) Worms, life, and death (Nobel
lecture). Chembiochem 4:697–711.
Hyun‐Eui K, Fenghe D, Fang M & Wang X (2005)
Formation of apoptosome is initiated by cytochrome
c‐induced dATP hydrolysis and subsequent
nucleotide exchange on Apaf‐1. Proc Natl Acad Sci
USA 102:17545–17550.
Jacobson MD, Weil M & Raff MC (1997) Programmed
cell death in animal development. Cell 88:347–354.
Jiang X & Wang X (2004) Cytochrome C‐mediated
apoptosis. Annu Rev Biochem 73:87–106.
Kerr JF, Wyllie AH & Currie AR (1972) Apoptosis: a basic
biological phenomenon with wide‐ranging
implications in tissue kinetics. B J Cancer 26:239–
257.
Kumar S (2007) Caspase function in programmed cell
death. Cell Death Differ 14:32–43.
Lavrik I, Golks A & Krammer PH (2005) Death receptor
signaling. J Cell Sci 118:265–267.
Lowe SW, Cepero E & Evan G (2004) Intrinsic tumour
suppression. Nature 432:307–315.
Lum JJ, Bauer DE, Kong M et al (2005) Growth factor
regulation of autophagy and cell survival in the
absence of apoptosis. Cell 120:237–48.
McCall K & Steller H (1997) Facing death in the fly:
genetic analysis of apoptosis in Drosophila. Trends
Genet 13:222–226.
Nagata S (1999) Fas ligand‐induced apoptosis. Annu
Rev Genet 33:29–55.
Nagata S (2005) DNA degradation in development and
programmed cell death. Annu Rev Immunol 23:853–
875.
Pop C, Timmer J, Sperandio S & Salvesen GS (2006) The
apoptosome activates caspase‐9 by dimerization.
Mol Cell 22:269–275.
Raff MC (1999) Cell suicide for beginners. Nature
396:119–122.
Rathmell JC & Thompson CB (2002) Pathways of
apoptosis in lymphocyte development, homeostasis,
and disease. Cell 109:S97–107.
Tittel JN & Steller H (2000) A comparison of
programmed cell death between species. Genome
Biol 1.
Verhagen AM, Coulson EJ & Vaux DL (2001) Inhibitor of
apoptosis proteins and their relatives: IAPs and other
BIRPs. Genome Biol 2:3009.1–3009.10.
Vousden KH (2005) Apoptosis. p53 and PUMA: a
deadly duo. Science 309:1685–1686.
Willis SN & Adams JM (2005) Life in the balance: how
BH3‐only proteins induce apoptosis. Curr Opin Cell
Biol 17:617–625.
Chapter 19
Overview of Sexual Reproduction
Cavalier‐Smith T (2002) Origins of the machinery of
recombination and sex. Heredity 88:125–41.
Charlesworth B (2006) The evolutionary biology of sex.
Curr Biol 16:R693–R695.
Hoekstra RF (2005) Evolutionary biology: why sex is
good. Nature 434:571–573.
Maynard Smith J (1978) Evolution of Sex. Cambridge,
UK: Cambridge University Press.
Meiosis
Blat Y, Protacio RU, Hunter N and Kleckner N (2002)
Physical and functional interactions among basic
chromosome organizational features govern early
steps of meiotic chiasma formation. Cell 111:791–
802.
Börner GV, Kleckner N and Hunter N (2004)
Crossover/noncrossover differentiation,
synaptonemal complex formation and regulatory
surveillance at the leptotene/zygotene transition of
meiosis. Cell 117:29–45.
De Massy B (2003) Distribution of meiotic
recombination sites. Trends Genet 19:514–522.
Gerton JL, and Hawley RS (2005) Homologous
chromosome interactions in meiosis: diversity
amidst conservation. Nature Rev Genet 6:477–487.
Hall H, Hunt P and Hassold T (2006) Meiosis and sex
chromosome aneuploidy: how meiotic errors cause
aneuploidy; how aneuploidy causes meiotic errors.
Curr Opin Genet Dev 16:323–329.
Hauf S and Watanabe Y (2004) Kinetochore orientation
in mitosis and meiosis. Cell 119:317–327.
Hunt PA and Hassold TJ (2002) Sex matters in meiosis.
Science 296:2181–2183.
Jordan P (2006) Initiation of homologous chromosome
pairing during meiosis. Biochem Soc Trans 34:545–
549.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Nasmyth K (2001) Disseminating the genome: joining,
resolving, and separating sister chromatids during
mitosis and meiosis. Annu Rev Genet 35:673–745.
Page SL and Hawley RS (2004) The genetics and
molecular biology of the synaptonemal complex.
Annu Rev Cell Dev Biol 20:525–558.
Petronczki M, Siomos MF and Nasmyth K (2003) Un
menage a quatre: the molecular biology of
chromosome segregation in meiosis. Cell 112:423–
440.
Fertilization
De Jonge C (2005) Biological basis for human
capacitation. Hum Reprod Update 11:205–214.
Hafez ES, Goff L and Hafez B (2004) Mammalian
fertilization, IVF, ICSI:physiological/molecular
parameters, clinical application. Arch Androl 50:69–
88.
Jaenisch R (2004) Human Cloning—The Science and
Ethics of Nuclear Transplantation. N Eng J Med
351:2787–2791.
Shur BD, Rodeheffer C and Ensslin MA (2004)
Mammalian fertilization. Curr Biol 14:R691–692.
Stein KK, Primakoff P and Myles D (2004) Sperm‐egg
fusion: events at the plasma membrane. J Cell Sci
117:6269–6274.
Takahashi K and Yamanaka S (2006) Induction of
pluripotent stem cells from mouse embryonic and
adult fibroblast cultures by defined factors. Cell
126:663–676.
Tsaadon A, Eliyahu E, Shtraizent N and Shalgi R (2006)
When a sperm meets an egg: block to polyspermy.
Mol Cell Endocrinol 252:107–114.
Wassarman PM (2005) Contribution of mouse egg zona
pellucida glycoproteins to gamete recognition during
fertilization. J Cell Physiol 204:388–391.
Whitaker M (2006) Calcium at fertilization and in early
development. Physiol Rev 86:25–88.
Chapter 20
Tight Junctions and the Organization of Epithelia
Furuse M, Hata M, Furuse K et al (2002) Claudin‐based
tight junctions are crucial for the mammalian
epidermal barrier: a lesson from claudin‐1‐deficient
mice. J Cell Biol 156:1099–1111.
Ikenouchi J, Furuse M, Furuse K et al (2005) Tricellulin
constitutes a novel barrier at tricellular contacts of
epithelial cells. J Cell Biol 171:939–945.
Henrique D & Schweisguth F (2003) Cell polarity: the
ups and downs of the Par6/aPKC complex. Curr Opin
Genet Dev 13:341–350.
Nelson WJ (2003) Adaptation of core mechanisms to
generate cell polarity. Nature 422:766–774.
O’Brien LE, Jou TS, Pollack AL et al (2001) Rac1
orientates epithelial apical polarity through effects
on basolateral laminin assembly. Nature Cell Biol
3:831–838.
Seifert JR & Mlodzik M (2007) Frizzled/PCP signalling: a
conserved mechanism regulating cell polarity and
directed motility. Nature Rev Genet 8:126–138.
Shin K, Fogg VC & Margolis B (2006) Tight junctions and
cell polarity. Annu Rev Cell Dev Biol 22:207–236.
Passageways from Cell to Cell: Gap Junctions and
Plasmodesmata
Cilia ML & Jackson D (2004) Plasmodesmata form and
function. Curr Opin Cell Biol 16:500–506.
Gaietta G, Deerinck TJ, Adams SR et al (2002)
Multicolor and electron microscopic imaging of
connexin trafficking. Science 296:503–507.
Goodenough DA & Paul DL (2003) Beyond the gap:
functions of unpaired connexon channels. Nature
Rev Mol Cell Biol 4:285–294.
Segretain D & Falk MM (2004) Regulation of connexin
biosynthesis, assembly, gap junction formation, and
removal. Biochim Biophys Acta 1662:3–21.
Wei CJ, Xu X & Lo CW (2004) Connexins and cell
signaling in development and disease. Annu Rev Cell
Dev Biol 20:811–838.
The Basal Lamina
Miner JH & Yurchenco PD (2004) Laminin functions in
tissue morphogenesis. Annu Rev Cell Dev Biol
20:255–284.
Sanes JR. (2003) The basement membrane/basal
lamina of skeletal muscle. J Biol Chem 278:12601–
12604.
Sasaki T, Fassler R & Hohenester E (2004) Laminin: the
crux of basement membrane assembly. J Cell Biol
164:959–963.
Yurchenco PD, Amenta PS & Patton BL (2004)
Basement membrane assembly, stability and
activities observed through a developmental lens.
Matrix Biol 22:521–538.
The Extracellular Matrix of Animal Connective Tissues
Aszodi A, Legate KR, Nakchbandi I & Fassler R (2006)
What mouse mutants teach us about extracellular
matrix function. Annu Rev Cell Dev Biol 22:591–621.
Bulow HE & Hobert O (2006) The molecular diversity of
glycosaminoglycans shapes animal development.
Annu Rev Cell Dev Biol 22:375–407.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Couchman JR (2003) Syndecans: proteoglycan
regulators of cell‐surface microdomains? Nature Rev
Mol Cell Biol 4:926–937.
Hotary KB, Allen ED, Brooks PC et al (2003) Membrane
type I matrix metalloproteinase usurps tumor
growth control imposed by the three‐dimensional
extracellular matrix. Cell 114:33–45.
Kielty CM, Sherratt MJ & Shuttleworth CA (2002)
Elastic fibres. J Cell Sci 115:2817–2828.
Larsen M, Artym VV, Green JA & Yamada KM (2006)
The matrix reorganized: extracellular matrix
remodeling and integrin signaling. Curr Opin Cell Biol
18:463–471.
Lin X (2004) Functions of heparan sulfate
proteoglycans in cell signaling during development.
Development 131:6009–6021.
Mott JD & Werb Z (2004) Regulation of matrix biology
by matrix metalloproteases. Curr Opin Cell Biol
16:558–564.
Prockop DJ & Kivirikko KI (1995) Collagens: molecular
biology, diseases, and potentials for therapy. Annu
Rev Biochem 64:403–434.
Toole BP (2001) Hyaluronan in morphogenesis. Semin
Cell Dev Biol 12:79–87.
The Plant Cell Wall
Carpita NC & McCann M (2000) The Cell Wall. In
Biochemistry and Molecular Biology of Plants
(Buchanan BB,Gruissem W & Jones RL eds), pp 52–
108. Rockville, MD: ASPB.
Carpita NC, Campbell M & Tierney M (eds) (2001) Plant
cell walls. Plant Mol Biol 47:1–340. (special issue)
Dhugga KS (2001) Building the wall: genes and enzyme
complexes for polysaccharide synthases. Curr Opin
Plant Biol 4:488–493.
McCann MC & Roberts K (1991) Architecture of the
primary cell wall. In The Cytoskeletal Basis of Plant
Growth and Form (Lloyd CW ed), pp 109–129.
London: Academic Press.
Smith LG & Oppenheimer DG (2005) Spatial control of
cell expansion by the plant cytoskeleton. Annu Rev
Cell Dev Biol 21:271–295.
Somerville C (2006) Cellulose synthesis in higher
plants. Annu Rev Cell Dev Biol 22:53–78.
Epidermis and Its Renewal by Stem Cells
Fuchs E (2007) Scratching the surface of skin
development. Nature 445:834–842.
Imagawa W, Yang J, Guzman R & Nandi S (1994)
Control of mammary gland development. In The
Physiology of Reproduction (Knobil E & Neill JD eds),
2nd ed, pp 1033–1063. New York: Raven Press.
Ito M, Yang Z, Andl T et al (2007) Wnt‐dependent de
novo hair follicle regeneration in adult mouse skin
after wounding. Nature 447:316–320.
Jacinto A, Martinez‐Arias A & Martin P (2001)
Mechanisms of epithelial fusion and repair. Nature
Cell Biol 3:E117–123.
Jensen UB, Lowell S & Watt FM (1999) The spatial
relationship between stem cells and their progeny in
the basal layer of human epidermis: a new view
based on whole‐mount labelling and lineage
analysis. Development 126:2409–2418.
Prince JM, Klinowska TC, Marshman E et al (2002) Cellmatrix
interactions during development and
apoptosis of the mouse mammary gland in vivo. Dev
Dyn 223:497–516.
Shackleton M, Vaillant F, Simpson KJ et al (2006)
Generation of a functional mammary gland from a
single stem cell. Nature 439:84–88.
Shinin V, Gayraud‐Morel B, Gomes D & Tajbakhsh S
(2006) Asymmetric division and cosegregation of
template DNA strands in adult muscle satellite cells.
Nature Cell Biol 8:677–687.
Stanger BZ, Tanaka AJ & Melton DA (2007) Organ size
is limited by the number of embryonic progenitor
cells in the pancreas but not the liver. Nature
445:886–891.
Steinert PM (2000) The complexity and redundancy of
epithelial barrier function. J Cell Biol 151:F5–F8.
Watt FM, Lo Celso C & Silva‐Vargas V (2006) Epidermal
stem cells: an update. Curr Opin Genet Dev 16:518–
524.
Renewal by Multipotent Stem Cells: Blood Cell
Formation
Allsopp RC, Morin GB, DePinho R, Harley CB &
Weissman IL (2003) Telomerase is required to slow
telomere shortening and extend replicative lifespan
of HSCs during serial transplantation. Blood
102:517–520.
Calvi LM, Adams GB, Weibrecht KW et al (2003)
Osteoblastic cells regulate the haematopoietic stem
cell niche. Nature 425:841–846.
Hock H, Hamblen MJ, Rooke HM et al (2004) Gfi‐1
restricts proliferation and preserves functional
integrity of haematopoietic stem cells. Nature
431:1002–1007.
Metcalf D (1980) Clonal analysis of proliferation and
differentiation of paired daughter cells: action of
granulocyte‐macrophage colony‐stimulating factor
on granulocyte‐macrophage precursors. Proc Natl
Acad Sci USA 77:5327–5330.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Metcalf D (1999) Stem cells, pre‐progenitor cells and
lineage‐committed cells: are our dogmas correct?
Annu NY Acad Sci 872:289–303.
Orkin SH (2000) Diversification of haematopoietic stem
cells to specific lineages. Nature Rev Genet 1:57–64.
Reya T, Duncan AW, Ailles L et al (2003) A role for Wnt
signalling in self‐renewal of haematopoietic stem
cells. Nature 423:409–414.
Shizuru JA, Negrin RS & Weissman IL (2005)
Hematopoietic stem and progenitor cells: clinical
and preclinical regeneration of the hematolymphoid
system. Annu Rev Med 56:509–538.
Wintrobe MM (1980) Blood, Pure and Eloquent. New
York: McGraw‐Hill.
Stem‐cell Engineering
Brockes JP & Kumar A (2005) Appendage regeneration
in adult vertebrates and implications for
regenerative medicine. Science 310:1919–1923.
Brustle O, Jones KN, Learish RD et al (1999) Embryonic
stem cell‐derived glial precursors: a source of
myelinating transplants. Science 285:754–756.
Conti L, Pollard SM, Gorba T et al (2005) Nicheindependent
symmetrical self‐renewal of a
mammalian tissue stem cell. PLoS Biol 3:e283.
Eggan K, Baldwin K, Tackett M et al (2004) Mice cloned
from olfactory sensory neurons. Nature 428:44–49.
Lee TI, Jenner RG, Boyer LA et al (2006) Control of
developmental regulators by Polycomb in human
embryonic stem cells. Cell 125:301–313.
Ming GL & Song H (2005) Adult neurogenesis in the
mammalian central nervous system. Annu Rev
Neurosci 28:223–250.
Okita K, Ichisaka T & Yamanaka S (2007) Generation of
germlinecompetent induced pluripotent stem cells.
Nature in press.
Raff M (2003) Adult stem cell plasticity: fact or artifact?
Annu Rev Cell Dev Biol 19:1–22.
Schulz JT, 3rd,Tompkins RG & Burke JF (2000) Artificial
skin. Annu Rev Med 51:231–244.
Suhonen JO, Peterson DA, Ray J & Gage FH (1996)
Differentiation of adult hippocampus‐derived
progenitors into olfactory neurons in vivo. Nature
383:624–627.
Wagers AJ & Weissman IL (2004) Plasticity of adult
stem cells. Cell 116:639–648.
Cancer as a Microevolutionary Process
Al‐Hajj M, Becker MW, Wicha M et al (2004)
Therapeutic implications of cancer stem cells. Curr
Opin Genet Dev 14:43–47.
Bielas JH, Loeb KR, Rubin BP et al (2006) Human
cancers express a mutator phenotype. Proc Natl
Acad Sci USA 103:18238–18242.
Cairns J (1975) Mutation, selection and the natural
history of cancer. Nature 255:197–200.
Campesi J (2005) Senescent cells, tumor supression,
and organismal aging: good citizens, bad neighbors.
Cell 120:513–522.
Evan GI & Vousden KH (2001) Proliferation, cell cycle
and apoptosis in cancer. Nature 411:342–348.
Fialkow PJ (1976) Clonal origin of human tumors.
Biochim Biophys Acta 458:283–321.
Fidler IJ (2003) The pathogenesis of cancer metastasis:
the ‘seed and soil’ hypothesis revisited. Nature Rev
Cancer 3:453–458.
Jones PA & Baylin SB (2002) The fundamental role of
epigenetic events in cancer. Nature Rev Genet
3:415–428.
Loeb LA, Loeb KR & Anderson JP (2003) Multiple
mutations and cancer. Proc Natl Acad Sci USA
100:776–781.
Lowe SW, Cepero E & Evan G (2004) Intrinsic tumour
suppression. Nature 432:307–315.
Nowell PC (1976) The clonal evolution of tumor cell
populations. Science 194:23–28.
Pardal R, Clarke MF & Morrison SJ (2003) Applying the
principles of stem‐cell biology to cancer. Nature Rev
Cancer 3:895–902.
Sjoblom T, Jones S, Wood LD et al (2006) The
consensus coding sequences of human breast and
colorectal cancers. Science 314:268–274.
Thiery JP (2002) Epithelial‐mesenchymal transitions in
tumour progression. Nature Rev Cancer 2:442–454.
Tlsty TD & Coussens LM (2006) Tumor Stroma and
Regulation of Cancer Development. Annu Rev Pathol
Mech Dis 1:119–150.
Ward RJ & Dirks PB (2007) Cancer stem cells: at the
headwaters of tumor development. Annu Rev Pathol
Mech Dis 2:175–189.
The Preventable Causes of Cancer
Ames B, Durston WE, Yamasaki E & Lee FD (1973)
Carcinogens are mutagens: a simple test system
combining liver homogenates for activation and
bacteria for detection. Proc Natl Acad Sci USA
70:2281–2285.
Berenblum I (1954) A speculative review: the probable
nature of promoting action and its significance in the
understanding of the mechanism of carcinogenesis.
Cancer Res 14:471–477.
Cairns J (1985) The treatment of diseases and the war
against cancer. Sci Am 253:51–59.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Doll R (1977) Strategy for detection of cancer hazards
to man. Nature 265:589–597.
Doll R & Peto R (1981) The causes of cancer:
quantitative estimates of avoidable risks of cancer in
the United States today. J Natl Cancer Inst 66:1191–
1308.
Hsu IC, Metcalf RA, Sun T et al (1991) Mutational
hotspot in the p53 gene in human hepatocellular
carcinomas. Nature 350:427–428.
Newton R, Beral V & Weiss RA (eds) (1999) Infections
and Human Cancer. Cold Spring Harbor Laboratory
Press: Cold Spring Harbor.
Peto J (2001) Cancer epidemiology in the last century
and the next decade. Nature 411:390–395.
Finding the Cancer‐Critical Genes
Davies H, Bignell GR, Cox C et al (2002) Mutations of
the BRAF gene in human cancer. Nature 417:949–
954.
Easton DF, Pooley KA, Dunning AM et al (2007)
Genome‐wide association study identifies novel
breast cancer susceptibility loci. Nature 447:1087–
1095.
Feinberg AP (2007) Phenotypic plasticity and the
epigenetics of human disease. Nature 447:433–440.
Herman JG & Baylin SB (2003) Gene silencing in cancer
in association with promoter hypermethylation. N
Engl J Med 349:2042–2054.
Lowe SW, Cepero E & Evan G (2004) Intrinsic tumour
suppression. Nature 432:307–315.
Mitelman F, Johansson B & Mertens F (2007) The
impact of translocations and gene fusions on cancer
causation. Nature Rev Cancer 7:233‐245.
Pinkel D & Albertson DG (2005). Comparative genomic
hybridization. Annu Rev Genomics Hum Genet
6:331–354.
Rowley JD (2001) Chromosome translocations:
dangerous liasisons revisited. Nature Rev Cancer
1:245–250.
The Wellcome Trust Case Control Consortium (2007)
Genome‐wide association study of 14,000 cases of
seven common diseases and 3,000 shared controls.
Nature 447:661–683.
Westbrook TF, Stegmeier F & Elledge SJ (2005)
Dissecting cancer pathways and vulnerabilities with
RNAi. Cold Spring Harb Symp Quant Biol 70:435–444.
The Molecular Basis of Cancer Cell Behavior
Artandi SE & DePinho RA (2000) Mice without
telomerase: what can they teach us about human
cancer? Nature Med 6:852–855.
Brown JM & Attardi LD (2005) The role of apoptosis in
cancer development and treatment response.
Nature Rev Cancer 5:231–237.
Chambers AF, Naumov GN, Vantyghem S & Tuck AB
(2000) Molecular biology of breast cancer
metastasis: clinical implications of experimental
studies on metastatic inefficiency. Breast Cancer Res
2:400–407.
Edwards PAW (1999) The impact of developmental
biology on cancer research: an overview. Cancer
Metastasis Rev 18:175–180.
Futreal PA, Coin L, Marshall M et al (2004) A census of
human cancer genes. Nature Rev Cancer 4:177–183.
Hanahan D & Weinberg RA (2000) The hallmarks of
cancer. Cell 100:57–70.
Hoffman RM (2005) The multiple uses of fluorescent
proteins to visualize cancer in vivo. Nature Rev
Cancer 5:796–806.
Kinzler KW & Vogelstein B (1996) Lessons from
hereditary colorectal cancer. Cell 87:159–170.
Levine AJ, Hu W & Feng Z (2006) The P53 pathway:
what questions remain to be explored? Cell Death
Differ 13:1027–1036.
Macleod KF & Jacks T (1999) Insights into cancer from
transgenic mouse models. J Pathol 187:43–60.
Mani SA, Yang J, Brooks M et al (2007) Mesenchyme
Forkhead 1 (FOXC2) plays a key role in metastasis
and is associated with aggressive basal‐like breast
cancers. Proc Natl Acad Sci USA 104:10069–10074.
Mueller MM & Fusenig NE (2004) Friends or foes—
bipolar effects of the tumour stroma in cancer.
Nature Rev Cancer 4:839–849.
Plas DR & Thompson CB (2005) Akt‐dependent
transformation: there is more to growth than just
surviving. Oncogene 24:7435–7442.
Ridley A (2000) Molecular switches in metastasis.
Nature 406:466–467.
Shaw RJ & Cantley LC (2006) Ras, PI(3)K and mTOR
signalling controls tumour cell growth. Nature
441:424–430.
Sherr CJ (2006) Divorcing ARF and p53: an unsettled
case. Nature Rev Cancer 6:663–673.
Vogelstein B & Kinzler KW (2004) Cancer genes and the
pathways they control. Nature Med 10:789–799.
Weinberg RA (1995) The retinoblastoma protein and
cell‐cycle control. Cell 81:323–330.
Cancer Treatment: Present and Future
Alizadeh AA, Eisen MB, Davis RE et al (2000). Distinct
types of diffuse large B‐cell lymphoma identified by
gene expression profiling. Nature 403:503–511.
Essential Cell Biology, 3/e
REFERENCES adapted from Molecular Biology of the Cell, 5/e
Baselga J & Albanell J (2001) Mechanism of action of
anti‐HER2 monoclonal antibodies. Annu Oncol
12:S35–S41.
Druker BJ & Lydon NB (2000) Lessons learned from the
development of an abl tyrosine kinase inhibitor for
chronic myelogenous leukemia. J Clin Invest 105:3–
7.
Folkman J (1996) Fighting cancer by attacking its blood
supply. Sci Am 275:150–154.
Golub TR, Slonim DK, Tamayo P et al (1999) Molecular
classification of cancer: class discovery and class
prediction by gene expression monitoring. Science
286:531–537.
Huang P & Oliff A (2001) Signaling pathways in
apoptosis as potential targets for cancer therapy.
Trends Cell Biol 11:343–348.
Garraway LA & Sellers WR (2006) Lineage dependency
and lineage‐survival oncogenes in human cancer.
Nature Rev Cancer 6:593–602.
Jonkers J & Berns A (2004) Oncogene addiction:
sometimes a temporary slavery. Cancer Cell 6:535–
538.
Jain RK (2005) Normalization of tumor vasculature: an
emerging concept in antiangiogenic therapy. Science
307:58–62.
Kim R, Emi M & Tanabe K (2007) Cancer
immunoediting from immune surveillance to
immune escape. Immunology 121:1–14.
Madhusudan S & Middleton MR (2005) The emerging
role of DNA repair proteins as predictive, prognostic
and therapeutic targets in cancer. Cancer Treat Rev
31:603–617.
Roninson IB, Abelson HT, Housman DE et al (1984)
Amplification of specific DNA sequences correlates
with multi‐drug resistance in Chinese hamster cells.
Nature 309:626–628.
Sarkadi B, Homolya L, Szakács G & Váradi A (2006)
Human multidrug resistance ABCB and ABCG
transporters: participation in a chemoimmunity
defense system. Physiol Rev 86:1179–236.
Sawyers C (2004) Targeted cancer therapy. Nature
432:294–297.
van ‘t Veer LJ, Dai H, van de Vijver MJ et al (2002) Gene
expression profiling predicts clinical outcome of
breast cancer. Nature 415:530–536.
Varmus H, Pao W, Politi K et al (2005) Oncogenes come
of age. Cold Spring Harb Symp Quant Biol 70:1–9.
Ventura A, Kirsch DG, McLaughlin ME et al (2007)
Restoration of p53 function leads to tumour
regression in vivo. Nature 445:661–665.