Table of Contents

Section 1: Introduction to Cell Biology

1 Introduction to Cells

2 Evolution of Life on Earth

Section 2: Chemical and Physical Background

3 Molecules: Structures and Dynamics

4 Biophysical Principles

5 Macromolecular Assembly

6 Research Strategies

Section 3: Chromatin, Chromosomes, and the Cell Nucleus

7 Chromosome Organization

8 DNA Packaging in Chromatin and Chromosomes

9 Nuclear Structure and Dynamics

Section 4: Central Dogma: From Gene to Protein

10 Gene Expression

11 Eukaryotic RNA Processing

12 Protein Synthesis and Folding

Section 5: Membrane Structure and Function

13 Membrane Structure and Dynamics

14 Membrane Pumps

15  Membrane Carriers

16 Membrane Channels

17 Membrane Physiology

Section 6: Cellular Organelles and Membrane Trafficking

18 Posttranslational Targeting of Proteins

19 Mitochondria, Chloroplasts, Peroxisomes

20 Endoplasmic Reticulum

21 Secretory Membrane System and Golgi Apparatus

22 Endocytosis and the Endosomal Membrane

23 Processing and Degradation of Cellular Components

Section 7: Signaling Mechanisms

24 Plasma Membrane Receptors

25 Protein Hardware for Signaling

26 Second Messengers

27 Integration of Signals

Section 8: Cellular Adhesion and the Extracellular Matrix

28 Cells of the Extracellular Matrix and Immune System

29 Extracellular Matrix Molecules

30 Cellular Adhesion

31 Intercellular Junctions

32 Connective Tissues

Section 9: Cytoskeleton and Cellular Motility

33 Actin and Actin-Binding Proteins

34 Microtubules and Centrosomes

35 Intermediate Filaments

36 Motor Proteins

37 Intracellular Motility

38 Cellular Motility

39 Muscles

Section 10: Cell Cycle

40 Introduction to the Cell Cycle

41 G1 Phase and Regulation of Cell Proliferation

42 S Phase and DNA Replication

43 G2 Phase and Control of Entry into Mitosis

44 Mitosis and Cytokinesis

45 Meiosis

46 Programmed Cell Death

Glossary

Appendix

About the Author

Thomas Dean Pollard is a prominent educator, cell biologist and biophysicist whose research focuses on understanding cell motility through the study of actin filaments and myosin motors. He is Sterling Professor of Molecular, Cellular & Developmental Biology and a Professor of Cell Biology and Molecular Biophysics & Biochemistry at Yale University. He was Dean of Yale's Graduate School of Arts and Sciences from 2010 to 2014, and President of the Salk Institute for Biological Studies from 1996 to 2001. Pollard is very active in promoting scientific education and research primarily through two major societies, both of which he is a past President: the American Society for Cell Biology and the Biophysical Society William Charles Earnshaw is Professor of Chromosome Dynamics at the University of Edinburgh where he has been a Wellcome Trust Principal Research Fellow since 1996. Earnshaw is an elected Fellow of the Royal Society since 2013 for his studies of mitotic chromosome structure and segregation. Before Edinburgh, he was Professor of Cell Biology and Anatomy at Johns Hopkins School of Medicine. Jennifer Lippincott-Swartz is Group Leader at the Howard Hughes Medical Institute Janelia Research Campus. Her lab uses live cell imaging approaches to analyze the spatio-temporal behaviour and dynamic interactions of molecules in cells with a special focus on neurobiology. Before Janelia, Lippincott-Swartz was a primary investigator and chief of the Section on Organelle Biology in the Cell Biology and Metabolism Branch. Her work there included a collaboration with physicists Eric Betzig and Harald Hess (now group leaders at Janelia), who proposed a new function for the photoactivatable protein. The scientists used the protein to generate photoactivatable fluorophores, or dyes, which enabled them to illuminate different sets of molecules sequentially, creating a microscope image far more detailed than previously possible. The method, called super-resolution microscopy, garnered Betzig the 2014 Nobel Prize in Chemistry. Graham Johnson is a computational biologist and Certified Medical Illustrator (CMI) with approx. 20 years of professional experience. He is Director of the Animated Cell at the Allen Institute. Before the Allen Institute, Johnson's lab in the California Institute for Quantitative Biosciences at the University of California, San Francisco worked to generate, simulate and visualize molecular models of cells. His lab's Mesoscope project and his team at Allen Institute continue this mission by uniting biologists, programmers and artists to interoperate the computational tools of science and art.