Cell Biology — Textbook Reader

Chapter 1 Evolution: Molecules, Genes, Cells, and Organisms Tardigrades are tiny -long invertebrates that have evolved to survive exposures to extreme conditions that kill other life forms; they are the only metazoan organisms known to survive exposure to the deadly combination of low pressure and intense radiation in outer space. [Schokraie E., Warnken U., Hotz-Wagenblatt A., Grohme M. A., Hengherr S., et al. 2012. Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus

Chapter 2 Chemical Foundations Model of sodium chloride (NaCl) crystal. This photograph shows the largest (3.1 m tall) balland-stick physical model of a crystalline salt ever constructed, built from 40,110 balls by Robert Krickl.

Chapter 3 Protein Structure and Function Computationally designed, hypothetical four-stranded fiber protein viewed down the fiber axis. Using advanced methods for protein design, the amino acid sequence of the

staphylococcal nuclease protein was modified so that the individual, folded protein chains (shown in different colors) would stack into long strands. The design predicts that four long strands would assemble into a four-stranded fiber held together by the binding of hydrophobic helices located in the center of the fiber. [Data from H. Shen et al., 2018, Science 362:705–709.]

Chapter 4 Culturing and Visualizing Cells Fluorescence microscopy showing the locations of DNA (green), microtubules (yellow), and microfilaments (purple) in two cultured cells. The cells were chemically fixed and then rendered permeable to antibodies using a gentle detergent. Microtubules were stained with an antibody to tubulin; microfilaments were stained with a labeled toxin, phalloidin, that binds selectively to F-actin; and DNA was visualized with a DNA-binding dye.

Chapter 5 Fundamental Molecular Genetic Mechanisms Model of DNA Polymerase I from Escherichia coli in the process of replicating DNA. The universal mechanism for copying information in DNA is replication by DNA polymerase, a remarkable copying and proofreading machine. The E. coli DNA polymerase I shown here can synthesize a complementary copy of the template strand at a rate of about 500 bases per second, making a mistake only once in every bases.

Genetic modifications make it possible to locate a specific cell type within the body of a living mouse. Scientists can label cells of the immune system by generating a transgenic mouse carrying the gene for insect luciferase expressed from the CD2 promoter, which is specifically expressed in T cells. After injection of the bioluminescent substrate for

luciferase, the light emitted through the skin is imaged for 30 seconds. T cells can be seen located in the lymph nodes (LNs), the thymus (thy), and the spleen (spl). [From J. W. Kleinovink et al., 2019. A dual-color bioluminescence reporter mouse for simultaneous in vivo imaging of T cell localization and function. Frontiers in Immunology 9:3097. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333049]

Chapter 7 Genes, Chromatin, and Chromosomes These brightly colored FISH-painted chromosomes are not only beautiful, but also useful in revealing chromosome anomalies and in comparing karyotypes of different species.

Chapter 8 Transcriptional Control of Gene Expression Drosophila polytene chromosomes stained with antibodies against a chromatin-remodeling ATPase called Kismet (blue), RNA polymerase II with low CTD phosphorylation (red), and RNA polymerase II with high CTD phosphorylation (green). [Reproduced with permission from The Company of Biologists, from S. Srinivasan et. al., 2005, “The Drosophila Trithorax Group Protein Kismet Facilitates an Early Step in

Chapter 9 Post-Transcriptional Gene Control Portion of a “lampbrush chromosome” from an oocyte of the newt Nophthalmus viridescens. The hnRNP protein associated with nascent RNA transcripts fluoresces red after staining with a monoclonal antibody.

Chapter 10 Biomembrane Structure Molecular model of a lipid bilayer with embedded membrane proteins. Integral membrane proteins have distinct exoplasmic, cytosolic, and membrane-spanning domains. Shown here are portions of the insulin receptor, which regulates cell metabolism.

Chapter 11 Transmembrane Transport of Ions and Small Molecules Transmembrane, side view of the human glucose transporter GLUT1. Like other glucose transporters, GLUT1 transports glucose across the cell’s plasma membrane by alternating between an outward-facing and an inward-facing state. In the outward-facing state, a molecule of glucose binds to GLUT1. Glucose binding changes the conformation of the transporter such that it is now open to the inside of the cell, releasing glucose into the cytoplasm. [Data from D. Deng et al., 2014 Nature 510:121–125, PDB ID 4PYP.]

Chapter 12 Cellular Energetics Computer generated image of chromatophores in the photosynthetic purple bacterium Rhodobacter sphaeroides. Each chromatophore contains membrane proteins that use light to drive the synthesis of ATP. Energy is absorbed by pigments in two types of light-harvesting complexes (green and red) and transferred to reaction centers (light blue) where high-energy electrons are generated. Their energy is used by pumps (purple) to move protons into the chromatophores, generating a proton gradient. This powers ATP synthase (orange) to convert ADP + P to ATP. i

A three-dimensional reconstruction of the internal membranes of a yeast cell using scanning electron microscopy. The cell wall has been removed and the organelles highlighted with false color to reveal the endoplasmic reticulum (yellow), mitochondria (red), and nucleus (blue). Cell diameter is . [From D. Wei et al., 2012, “High-Resolution Three-Dimensional Reconstruction of a Whole Yeast Cell Using Focused-Ion Beam Scanning Electron Microscopy,” Biotechniques 53(1):41–48.]

Chapter 14 Vesicular Traffic, Secretion, and Endocytosis Structural models of the coat protein complexes for three types of transport vesicles. The coat complexes are responsible for sculpting the curvature of the vesicle membrane and for selecting the types of cargo proteins incorporated into the vesicle. [Data from A. J. Noble and S. M. Stagg, 2015, Science 349(6244):142–143; https://doi.org/10.1126/science.aac6537.]

Chapter 15 Receptors, Hormones, and Cell Signaling Structure of a cell surface G protein–coupled receptor (green) bound to β-arrestin (purple). G protein–coupled receptors that are in the active state for a long period of time become phosphorylated, triggering binding of an arrestin and inhibition of further signaling by the receptor. [Data from Y. Kang et al., 2015, Nature 523:561–567, PDB ID 4zwj, and custom PDB.]

Chapter 16 Growth Factor and Cytokine Signaling Pathways That Control Gene Expression A planarian with multiple heads. Several hormones and their receptors regulate the regeneration of complex body parts in wounded planaria; the extracellular signaling protein Wnt promotes tail regeneration and inhibits head regeneration. In an experiment, the gene encoding beta-catenin-1, an essential protein in the Wnt signal transduction pathway, was inhibited by feeding animals an inhibitory double-stranded RNA. During the subsequent month, normal uninjured animals developed heads around their periphery in…

Chapter 17 Cell Organization and Movement I: Microfilaments A section of mouse intestine stained for actin (red), the extracellular matrix protein laminin (green), and DNA (blue). Each blue dot of DNA indicates the presence of a cell. Actin in the microvilli on the apical end of the epithelial cells can be seen lining the surface facing the lumen (top). Actin can also be seen prominently in the smooth muscle that surrounds the intestine (bottom).

17.7 Cell Migration: Mechanism, Signaling, and Chemotaxis When we look through a microscope at the diversity of cells in nature, the variety of cell shapes and movements we see is astonishing. We may notice that some cells, such as vertebrate sperm, ciliates such as Tetrahymena, or flagellates such as Chlamydomonas, swim rapidly, propelled by cilia and flagella. Other cells, such as amoebae and human macrophages, move more sedately, propelled not by external appendages, but by coordinated movement of the cell itself. If we examine tissues under the microscope, we might notice that some cells c…

Chapter 18 Cell Organization and Movement II: Microtubules and Intermediate Filaments Newt lung cell in mitosis stained for centrosomes (magenta), microtubules (green), chromosomes (blue), and keratin intermediate filaments (red).

[Reprinted by permission of Nature Publishing Group, from A. Khodjakov, “Olympus/Nature competition: A 1, 2, 3 in Light Microscopy,” Nature, 2000, 408:423–424; permission conveyed through Copyright Clearance Center, Inc.]

Chapter 19 The Eukaryotic Cell Cycle Micrograph on the left shows a human epithelial cell in metaphase. Following DNA replication, cells undergo mitosis to segregate their replicated chromosomes. The cell has aligned its chromosomes (blue) in the center of the mitotic spindle apparatus (green), prior to pulling them to opposite poles of the spindle, which will occur during anaphase. Thereafter, the cytoplasm of the cell is divided to produce two identical daughter cells. The micrograph on the right is the same cell without imaging the spindle apparatus in order to show the location of the cent…

Chapter 20 Integrating Cells into Tissues Antibody staining of mouse small intestinal villi, fingerlike projections of cell layers (see Figures 20-13 through 20-15). NPC1L1, a protein located primarily on the plasma membrane involved with cholesterol metabolism, is green. Villin, which binds to actin bundles in microvilli (very small membrane projections on the apical surfaces of absorptive cells that

take up digested nutrients), is red. Nuclei (DNA) are blue. The image shows all colors merged together (colocalization of green and red appears yellow). The yellow lines show how the apical surfaces of the cells face the lumen of the small intestine (black) from which nutrients are absorbed.

Chapter 21 Responding to the Cellular Environment Rapamycin (in black), a clinically important antifungal drug and inhibitor of the mTORC kinase complex, was isolated from the bacterium Streptomyces hygroscopicus found on Easter Island. It was named after the native name of the island, Rapa Nui.

Chapter 22 Stem Cells, Cell Asymmetry, and Regulated Cell Death Pluripotent stem cells called neoblasts provide the cellular basis for regeneration in planarian flatworms. Shown is a colony of neoblasts (yellow, orange, and red), all derived from a single neoblast 14 days after regeneration of the tail was initiated by amputation; differentiating cells (blue), also derived from the single neoblast, are shown as well.

Chapter 23 Cells of the Nervous System Coronal slice of CLARITY-treated adult mouse brain expressing green fluorescent protein (GFP) in a subset of neurons (Thy1-GFP). CLARITY renders tissue optically transparent, permitting deep and complete imaging of tissues. Each section was stained with antibodies to GFP and color coded by depth to facilitate individual neuron visualization. This approach provides unprecedented opportunity to image intact brains at cellular resolution, paving the way to a comprehensive understanding of how the brain is wired.

Chapter 25 Cancer Cells of the immune system often interact with cancer cells within the tumor microenvironment. This section of a lung adenocarcinoma shows all cell nuclei (blue), tumor cells (green) and T cells (magenta). Note the tendency of the T cells to be in contact with tumor cells.