Stephen R. Bolsover - Cell Biology

1 COVER

2 TITLE PAGE

3 COPYRIGHT PAGE

4 PREFACE

5 ACKNOWLEDGMENTS

6 ABOUT THE COMPANION WEBSITE

7 SECTION 1: THE STRUCTURE OF THE CELL 1 A LOOK AT CELLS AND TISSUES ONLY TWO TYPES OF CELL VIRUSES ORIGIN OF EUKARYOTIC CELLS CELL SPECIALIZATION IN ANIMALS STEM CELLS AND TISSUE REPLACEMENT THE CELL WALL MICROSCOPES REVEAL CELL STRUCTURE FLUORESCENCE MICROSCOPY FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION 2 MEMBRANES AND ORGANELLES BASIC PROPERTIES OF CELL MEMBRANES ORGANELLES BOUNDED BY DOUBLE‐MEMBRANE ENVELOPES ORGANELLES BOUNDED BY SINGLE MEMBRANES THE CONNECTED CELL FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION

8 SECTION 2: THE MOLECULAR BIOLOGY OF THE CELL 3 DNA STRUCTURE AND THE GENETIC CODE THE STRUCTURE OF DNA DNA AS THE GENETIC MATERIAL PACKAGING OF DNA MOLECULES INTO CHROMOSOMES THE GENETIC CODE FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION 4 DNA AS A DATA STORAGE MEDIUM DNA REPLICATION PROTEINS OPEN UP THE DNA DOUBLE HELIX DURING REPLICATION BIOCHEMISTRY OF DNA REPLICATION DNA REPAIR AFTER REPLICATION GENE STRUCTURE AND ORGANIZATION IN EUKARYOTES GENE NOMENCLATURE FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION 5 TRANSCRIPTION AND THE CONTROLOF GENE EXPRESSION STRUCTURE OF RNA RNA POLYMERASE GENE NOTATION BACTERIAL RNA SYNTHESIS CONTROL OF BACTERIAL GENE EXPRESSION EUKARYOTIC RNA SYNTHESIS CONTROL OF EUKARYOTIC GENE EXPRESSION NONCODING RNAs AND THE CONTROL OF EUKARYOTIC GENE EXPRESSION FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION 6 MANUFACTURING PROTEIN ATTACHMENT OF AN AMINO ACID TO ITS tRNA THE RIBOSOME BACTERIAL PROTEIN SYNTHESIS EUKARYOTIC PROTEIN SYNTHESIS IS A LITTLE MORE COMPLEX ANTIBIOTICS AND PROTEIN SYNTHESIS PROTEIN DESTRUCTION FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION 7 PROTEIN STRUCTURE NAMING PROTEINS POLYMERS OF AMINO ACIDS OTHER AMINO ACIDS ARE FOUND IN NATURE THE THREE‐DIMENSIONAL STRUCTURES OF PROTEINS LEVELS OF COMPLEXITY PROSTHETIC GROUPS THE PRIMARY STRUCTURE CONTAINS ALL THE INFORMATION NECESSARY TO SPECIFY HIGHER‐LEVEL STRUCTURES PROTEIN–PROTEIN INTERACTIONS UNDERLIE ALL OF CELL BIOLOGY FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION 8 RECOMBINANT DNA TECHNOLOGYAND GENETIC ENGINEERING DNA CLONING CREATING THE CLONE USES OF DNA CLONES “OMICS” IDENTIFYING THE GENE RESPONSIBLE FOR A DISEASE REVERSE GENETICS TRANSGENIC AND KNOCKOUT MICE RNA INTERFERENCE (RNAi) CRISPR/CAS9 ETHICS OF DNA TESTING FOR INHERITED DISEASE FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION

9 SECTION 3: CELL COMMUNICATION 9 CARRIERS, CHANNELS, AND VOLTAGES CARRIERS THE POTASSIUM GRADIENT AND THE RESTING VOLTAGE THE ACTION POTENTIAL FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION 10 SIGNALING THROUGH IONS CALCIUM AS A SIGNALING ION PROPAGATING THE SIGNAL RAPID COMMUNICATION: FROM NEURONS TO THEIR TARGETS REVIEW QUESTIONS THOUGHT QUESTION 11 SIGNALING THROUGH ENZYMES G PROTEIN‐COUPLED RECEPTORS AND SECOND MESSENGERS RECEPTOR TYROSINE KINASES AND THE MAP KINASE CASCADE CYTOKINE RECEPTORS SIGNALING THROUGH PROTEOLYSIS INTRACELLULAR RECEPTORS CROSSTALK – SIGNALING PATHWAYS OR SIGNALING WEBS? SIGNALING IN THE CONTROL OF MUSCLE BLOOD SUPPLY FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION

10 SECTION 4: THE MECHANICS OF THE CELL 12 INTRACELLULAR TRAFFICKING PRINCIPLES OF PROTEIN TRANSPORT TRAFFICKING TO THE ENDOPLASMIC RETICULUM AND PLASMA MEMBRANE TRAFFICKING TO THE LYSOSOME TRAFFICKING TO AND FROM THE NUCLEUS TRAFFICKING TO OTHER ORGANELLES FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION 13 CELLULAR SCAFFOLDING MICROTUBULES FUNCTIONS OF MICROTUBULES MICROFILAMENTS FUNCTIONS OF MICROFILAMENTS INTERMEDIATE FILAMENTS FUNCTIONS OF INTERMEDIATE FILAMENTS FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION 14 CONTROLLING CELL NUMBER M‐PHASE CONTROL OF THE CELL CYCLE MEIOSIS AND FERTILIZATION CELL DEATH FURTHER READING REVIEW QUESTIONS THOUGHT QUESTION

11 SECTION 5: CASE STUDY 15 CASE STUDY CYSTIC FIBROSIS IS A SEVERE GENETIC DISEASE THE FUNDAMENTAL LESION IN CYSTIC FIBROSIS LIES IN CHLORIDE TRANSPORT CLONING THE CFTR GENE THE CFTR GENE CODES FOR A CHLORIDE ION CHANNEL REPLACING OR REPAIRING THE GENE TAILORING TREATMENT TO THE PATIENT'S LESION NEW TREATMENTS FOR CF DIAGNOSTIC TESTS FOR CF CONCLUSION FURTHER READING REVIEW QUESTIONS THOUGHT QUESTIONS

12 ANSWERS TO REVIEW QUESTIONSANSWERS TO REVIEW QUESTIONS

13 GLOSSARY

14 INDEX

15 END USER LICENSE AGREEMENT

1 Chapter 1 TABLE 1.1. Differences between prokaryotic and eukaryotic cells.

2 Chapter 3 TABLE 3.1. Numbers of predicted protein‐coding genes in various organisms.

3 Chapter 6TABLE 6.1. Allowed combinations at the wobble base.

4 Chapter 8TABLE 8.1. Vectors Used for Cloning Genomic DNATABLE 8.2. Blotting Techniques

5 Chapter 9TABLE 9.1. Typical concentrations for five important ions in mammalian cyt...

1 Chapter 1 Figure 1.1. Dimensions of some example cells. 1 mm = 10 −3m; 1 μm = 1... Figure 1.2. Organization of prokaryotic and eukaryotic cells. Figure 1.3. The tree of life. The diagram shows the currently accepted view... Figure 1.4. Transmission electron micrograph of a capillary blood vessel ru... Figure 1.5. Different types of animal cells. Figure 1.6. Tissues and structures of the intestine wall. Figure 1.7. Scanning electron micrograph of airway epithelium. Figure 1.8. Basic design of a light microscope. Figure 1.9. A simple upright light microscope. Figure 1.10. Cultured human cells on a hemocytometer grid under bright‐fiel... Figure 1.11. Cell structure as seen through light and transmission electron... Figure 1.12. Preparation of tissue for electron microscopy. Figure 1.13. (a) Basic design of a fluorescence light microscope. (b–d) Cul... Figure 1.14. Super‐resolution microscopy. Fluorescence image of the surface... Figure 1.15. (a) Fluorescence microscope image of two‐cell mouse embryo exp...

2 Chapter 2 Figure 2.1. Membranes comprise a lipid bilayer plus integral and peripheral... Figure 2.2. Small uncharged molecules can pass through membranes by simple ... Figure 2.3. The nucleus and the relationship of its membranes to those of t... Figure 2.4. The mitochondrion. Figure 2.5. Electron micrographs showing contact sites between the endoplas... Figure 2.6. Gap junctions allow solute and electrical current to pass from ... Figure 2.7. Not all connexins are compatible. A √ indicates a working gap j...

3 Chapter 3 Figure 3.1. Adenine nucleotides. (a) Deoxyadenosine triphosphate. The H on ... Figure 3.2. The four bases found in DNA. Figure 3.3. The phosphodiester bond and the sugar‐phosphate backbone of DNA... Figure 3.4. The DNA double helix is held together by hydrogen bonds. Figure 3.5. How DNA is packaged into chromosomes. Figure 3.6. A spread of human chromosomes (at metaphase – see page 236). Th... Figure 3.7. Amino acids and the peptide bond. Figure 3.8. DNA makes RNA makes protein: the central dogma of molecular bio... Figure 3.9. The genetic code. Amino acid side chains are shown in alphabeti... Figure 3.10. Reading frames. The genetic code is read in blocks of three. Figure 3.11. Mutations that alter the sequence of bases.

4 Chapter 4 Figure 4.1. DNA replication. The helicases, and the replication fork, are m... Figure 4.2. DNA polymerase III can correct its own mistakes. Figure 4.3. Mismatch repair of DNA. Figure 4.4. Spontaneous reactions corrupt the DNA database. Figure 4.5. Formation of a thymine dimer in DNA. Figure 4.6. Base excision repair. Figure 4.7. The human α‐and β‐globin gene family clusters. ψ indicates a ps...

5 Chapter 5 Figure 5.1. RNA contains the sugar ribose and the base uracil in place of ... Figure 5.2. Synthesis of an RNA strand. Figure 5.3. Numbering on a DNA sequence. Figure 5.4. (a) RNA polymerase binds to the promoter to form the closed pro... Figure 5.5. Rho‐independent transcription termination in Escherichia coli .... Figure 5.6. A bacterial operon is transcribed into a polycistronic mRNA.Figure 5.7. Reactions catalyzed by β‐galactosidase.Figure 5.8. Transcription of the lac operon requires the presence of an ind...Figure 5.9. Cyclic adenosine monophosphate, also called cyclic AMP or just ...Figure 5.10. For efficient transcription of the lac operon, both cAMP and a...Figure 5.11. Isopropylthio‐β‐D‐galactoside (IPTG), which can bind to the la...Figure 5.12. Transcription of the trp operon is controlled by the concentra...Figure 5.13. mRNA processing in eukaryotes.Figure 5.14. In eukaryotes, RNA polymerase II is guided to the promoter by ...Figure 5.15. Tissue‐specific transcription. The myosin IIa gene is not tran...Figure 5.16. The glucocorticoid hormone receptor acts to increase gene tran...Figure 5.17. The dimerized glucocorticoid hormone receptor binds to a palin...Figure 5.18. Noncoding RNAs such as microRNA (miRNA), long noncoding RNA (l...