Cell and Molecular Biology Ninth Edition PDF

Cell and Molecular Biology Ninth Edition Gerald Karp, Janet Iwasa, Wallace Marshall Chapter 1 Introduction to the Study of Cell and Molecular Biology 1.1 | The Discovery of Cells (1 of 3) ▪ Cells are the topic of intense study. ▪ The study of cells...

Cell and Molecular Biology Ninth Edition Gerald Karp, Janet Iwasa, Wallace Marshall Chapter 1 Introduction to the Study of Cell and Molecular Biology 1.1 | The Discovery of Cells (1 of 3) ▪ Cells are the topic of intense study. ▪ The study of cells requires creative instruments and techniques. ▪ Cell biology is reductionist, based on the premise that studying the parts of the whole can explain the character of the whole. Copyright © 2020 John Wiley & Sons, Inc. 1.1 | The Discovery of Cells (2 of 3) Microscopy ▪ Microscopes allowed cell visualization: ▪ Robert Hooke Termed pores inside cork cells because they reminded him of the cells inhabited by monastery monks ▪ Antonie van Leeuwenhoek Examine a drop of pond water and observed teeming microscopic “animalcules” Saw bacteria from peppercorn water and dental plaque Fig. 1.1 The discovery of cells Copyright © 2020 John Wiley & Sons, Inc. 1.1 | The Discovery of Cells (3 of 3) Cell Theory ▪ The cell theory was articulated in the mid-1800s by Matthias Schleiden, Theodor Schwann and Rudolf Virchow. All organisms are composed or one or more cells. The cell is the structural unit of life. Cells arise only by division from a pre-existing cell. ▪ Added since: Cells contain genetic information (DNA) passed to next cell generation Copyright © 2020 John Wiley & Sons, Inc. 1.2 | Basic Properties of Cells (1 of 11) Cells are Highly Complex and Organized ▪ Life is the most basic property of cells. ▪ Cells can grow and reproduce in culture for extended periods. ▪ HeLa cells are cultured tumor cells isolated from a cancer patient (Henrietta Lacks) ▪ Cultured cells are an essential tool for cell biologists. Fig. 1.2 HeLa cells Copyright © 2020 John Wiley & Sons, Inc. 1.2 | Basic Properties of Cells (2 of 11) Cells are Highly Complex and Organized ▪ Cellular processes are highly regulated. ▪ Cells from different species share similar structure, composition, and metabolic features. Fig. 1.3 Levels of cellular and molecular organization Copyright © 2020 John Wiley & Sons, Inc. 1.2 | Basic Properties of Cells (3 of 11) Cells Possess a Genetic Program and the Means to Use It ▪ Information for building an organism is encoded in genes (constructed from DNA) and packaged into a set of chromosomes within the cell nucleus. ▪ Genes store information and instructions for: ▪ Constructing cellular structures, the directions for ▪ Running cellular activities, and the program for ▪ Making more of themselves. ▪ Genetic information can be haploid or diploid in cells Copyright © 2020 John Wiley & Sons, Inc. 1.2 | Basic Properties of Cells (4 of 11) Cells Are Capable of Producing More of Themselves ▪ Cells reproduce by division, a process in which the contents of a “mother” cell are distributed into two “daughter” cells. Fig. 1.4 Cell Reproduction Copyright © 2020 John Wiley & Sons, Inc. 1.2 | Basic Properties of Cells (5 of 11) Cells Acquire and Utilize Energy ▪ Photosynthesis provides fuel for all living organisms. ▪ Animal cells derive energy from the products of photosynthesis, mainly in the form of glucose. ▪ Cells can store glucose bond energy in ATP—a molecule with readily Fig. 1.5 Acquiring energy available energy. Copyright © 2020 John Wiley & Sons, Inc. 1.2 | Basic Properties of Cells (6 of 11) Cells Carry Out a Variety of Chemical Reactions ▪ Cells function like miniaturized chemical plants. ▪ A bacterial cell is capable of hundreds of different chemical transformations. ▪ Virtually all chemical changes that take place in cells require enzymes to increase the rate at which a chemical reaction occurs. ▪ The sum total of the chemical reactions in a cell represents that cell’s metabolism. Copyright © 2020 John Wiley & Sons, Inc. 1.2 | Basic Properties of Cells (7 of 11) Cells Engage in Mechanical Activities ▪ Cells are very active, they can: transport materials, assemble and disassemble structures, and sometimes move itself from one site to another. ▪ Activities are based on dynamic, mechanical changes within cells, many of which are initiated by changes in the shape of “motor” proteins. Copyright © 2020 John Wiley & Sons, Inc. 1.2 | Basic Properties of Cells (8 of 11) Cells Are Able to Respond to Stimuli ▪ A single-celled protest can move away from an object in its path or toward nutrients. ▪ Cells in plants or animals are covered with receptors that interact with substances in the environment. ▪ Hormones, growth factors, extracellular materials, and substances on the surfaces of other cells can interact with these receptors. ▪ Cells may respond to stimuli by altering their metabolism, moving from one place to another, or even committing suicide. Copyright © 2020 John Wiley & Sons, Inc. 1.2 | Basic Properties of Cells (9 of 11) Cells Are Capable of Self-Regulation ▪ Cells are robust and are protected from dangerous fluctuations in composition and behavior. ▪ Feedback circuits serve to return the cell to the appropriate state. ▪ Maintaining a complex, ordered state requires constant regulation. Fig. 1.6 Self-regulation Copyright © 2020 John Wiley & Sons, Inc. 1.2 | Basic Properties of Cells (10 of 11) Cells Are Capable of Self-Regulation ▪ Information for product design resides in the nucleic acids, and the construction workers are primarily proteins. ▪ Each step of a process must occur spontaneously so that the next step is automatically triggered. Fig. 1.7 Cellular activities Copyright © 2020 John Wiley & Sons, Inc. 1.2 | Basic Properties of Cells (11 of 11) Cells Evolve ▪ Whereas the origin of cells is shrouded in near-total mystery, the evolution of cells can be studied by examining organisms that are alive today. ▪ Cells share many features, including a common genetic code, a plasma membrane, and ribosomes. ▪ According to a tenet of modern biology, all living organisms evolved from a single, common ancestral cell that lived more than three billion years ago. ▪ This ancient cell is often referred to as the last universal common ancestor (or LUCA). Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (1 of 19) ▪ Two basic classes of cells, Prokaryotic – bacteria Eukaryotic – plants, animals, protists, fungi ▪ These different classes are distinguished by their size and the types of organelles they contain. ▪ Both types of cells share an identical genetic language, a common set of metabolic Fig. 1.8a The structure of cells pathways, and many common structural features. Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (2 of 19) Characteristics That Distinguish Prokaryotic and Eukaryotic Cells ▪ Both bounded by plasma membranes of similar construction, serving as a selectively permeable barrier. ▪ Both may be surrounded by a rigid cell wall that protects the cell. ▪ Genetic material is membrane- bound in eukaryotes (nucleus), in nuclear area of cytosol in Fig. 1.8b The structure of cells prokaryotes Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (3 of 19) Characteristics That Distinguish Prokaryotic and Eukaryotic Cells ▪ Eukaryotic cells are much more complex, both structurally and functionally, than prokaryotic cells. Fig. 1.8c The structure of cells Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (4 of 19) Characteristics That Distinguish Prokaryotic and Eukaryotic Cells ▪ Prokaryotes – relatively small amounts of DNA; 600-8,000 Mb ▪ Eukaryotes – simple yeast cells have 12 Mb DNA, most eukaryotic cells possess more ▪ Complex multicellular animals appear rather suddenly in the fossil record approximately 600 million years ago. Fig. 1.9 Earth’s biogeologic clock Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (5 of 19) Characteristics That Distinguish Prokaryotic and Eukaryotic Cells ▪ Cytoplasm: Eukaryotes have membrane- bound organelles and complex cytoskeletal proteins. Both have ribosomes but they differ in size. ▪ Cellular reproduction: Eukaryotes divide by mitosis; prokaryotes divide by simple fission. ▪ Locomotion: Eukaryotes use both cytoplasmic movement, and cilia and flagella; prokaryotes have flagella, but they differ in both form and mechanism. Fig. 1.10 The structure of a eukaryotic cell Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (6 of 19) Characteristics That Distinguish Prokaryotic and Eukaryotic Cells ▪ The cytoplasm of a eukaryotic cell is extremely crowded: Near the cell membrane is a region where membrane-bound organelles tend to be absent. The cytoskeleton and other large macromolecular complexes, mostly ribosomes, are found throughout the cytoplasm. Fig. 1.11 The cytoplasm of a eukaryotic cell is a crowded compartment Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (7 of 19) Characteristics That Distinguish Prokaryotic and Eukaryotic Cells ▪ Eukaryotic cells divide by a complex process of mitosis. ▪ Duplicated chromosomes condense into compact structures that are segregated by an elaborate microtubule-containing apparatus. ▪ This apparatus, the mitotic spindle, allows each daughter cell to receive an equivalent array of Fig. 1.12 Cell division in eukaryotes genetic material. Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (8 of 19) Characteristics That Distinguish Prokaryotic and Eukaryotic Cells ▪ Prokaryotes contain one copy of their single chromosome and have no processes comparable to meiosis, gamete formation, or true fertilization. ▪ Some are capable of conjugation, in which a piece of DNA is passed to another cell. ▪ Prokaryotes are more adept at picking up and incorporating foreign DNA from their environment, which has had considerable impact on microbial evolution Fig. 1.13 Bacterial conjugation Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (9 of 19) Characteristics That Distinguish Prokaryotic and Eukaryotic Cells ▪ Locomotion in prokaryotes is relatively simple. ▪ Can be accomplished by a thin protein filament, called a flagellum, which protrudes from the cell and rotates. ▪ The rotations exert pressure against the surrounding fluid, propelling the cell through the medium. Fig. 1.14 The different between prokaryotic and eukaryotic flagella Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (10 of 19) Characteristics That Distinguish Prokaryotic and Eukaryotic Cells ▪ Certain eukaryotic cells, including many protists and sperm cells, also possess flagella. ▪ Eukaryotic versions are much more complex than the simple protein filaments of bacteria, and they generate movement by a different mechanism. Fig. 1.14 The difference between prokaryotic and eukaryotic flagella Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (11 of 19) Types of Prokaryotic Cells: Domain Archaea and Domain Bacteria ▪ Archaea are evolutionarlity related species that live in extremely inhospitable environments, often referred to as “extremophiles.” Methanogens: Convert CO2 and H2 gases into methane Halophiles: Live in extremely salty environments, like the Dead Sea or deep sea brine pools with salinity equivalent to 5M MgCl2. Acidophiles: Acid-loving prokaryotes that thrive at a pH as low as 0. Thermophiles: Live at very high temperatures. Hyperthermophiles: Live in the hydrothermal vents of the ocean floor up to a temperature of 121˚C, the temperature used to sterilize surgical instruments in an autoclave. Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (12 of 19) Types of Prokaryotic Cells: Domain Archaea and Domain Bacteria ▪ Bacteria are present in every conceivable habitat on Earth, even found in rock layers kilometers beneath the Earth’s surface. ▪ Cyanobacteria contain arrays of cytoplasmic membranes that serve as sites of photosynthesis. ▪ Cyanobacteria gave rise to green plants and an oxygen-rich atmosphere, and some are capable of nitrogen fixation. Fig. 1.15 Cyanobacteria Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (13 of 19) Types of Prokaryotic Cells: Prokaryotic Diversity ▪ 6000 species of prokaryotes have been identified, less than one-tenth of 1 percent of the millions of prokaryotic species thought to exist. ▪ DNA sequencing is so rapid and cost-efficient that virtually all of the genes present in the microbes of a given habitat can be sequenced, generating a collective genome, or metagenome. ▪ These same molecular strategies are being used to explore the collection of microbes living on us, known as the human microbiome. Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (14 of 19) Types of Prokaryotic Cells: Domain Archaea and Domain Bacteria Environment No. of prokaryotic Pg of C in Environment cells, x 1028 prokaryotes* Aquatic habitats 12 2.2 Oceanic subsurface 355 303 Soil 26 26 Terrestrial subsurface 25–250 22–215 Total 415–640 353–546 *1 petagram (Pg) = 1015g. Source: W. B. Whitman et al., Proc. Nat’l. Acad. Sci. U.S.A. 95: 6578, 1998 Copyright (1998) National Academy of Sciences, U.S.A. Reproduced with permission of National Academy of Sciences. Number and Biomass of Prokaryotes in the World Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (15 of 19) Types of Eukaryotic Cells ▪ The most complex eukaryotic cells are found among the single-celled Protists. ▪ The machinery needed for sensing the environment, trapping food, expelling excess fluid, and evading predators is found in a single cell. ▪ Vorticella have a contractile ribbon in the stalk and a large macronucleus that contains multiple copies of its genes. Fig. 1.16 Vorticella, a complex ciliated protist Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (16 of 19) Types of Eukaryotic Cells: Cell Differentiation ▪ Multicellular eukaryotes have different cell types for different functions. ▪ Differentiation – the formation of specialized cells ▪ The numbers and arrangements of organelles relate to the function and activity of the cell. ▪ Despite differentiation, cells have many features in common most being composed of the same organelles. Fig. 1.17 Pathways of cell differentiation Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (17 of 19) Types of Eukaryotic Cells: Model Organisms Fig. 1.18 Six model organisms Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (18 of 19) The Sizes of Cells and Their Components ▪ Cells are commonly measured in units of micrometers (1 μm = 10–6 meter) and nanometers (1 nm = 10–9 meter). ▪ The cell size is limited by: Volume of cytoplasm that can be supported by the genes in the nucleus. Volume of cytoplasm that can be supported by exchange of nutrients. Distance over which substances can efficiently travel through the cytoplasm via diffusion. Fig. 1.19 Relative sizes of cells and cell components Copyright © 2020 John Wiley & Sons, Inc. 1.3 | Two Fundamentally Different Classes of Cells (19 of 19) Types of Eukaryotic Cells: Model Organisms ▪ Synthetic Biology is a field oriented to create a living cell in the laboratory. ▪ A more modest goal is to develop novel life forms, beginning with existing organisms. ▪ Possible applications to medicine, industry, or the environment. ▪ Prospect is good after replacing the genome of one bacterium with that Fig. 1.20 The synthetic biologist toolkit of of a closely related species. the future? Copyright © 2020 John Wiley & Sons, Inc. 1.4 | Viruses and Viroids (1 of 3) ▪ Viruses are pathogens and intracellular obligate parasites. ▪ A virion is a virus particle outside the host cell. Contains genetic material plus protein subunits (capsids). Some virions are also encased by a lipid membrane- derived envelope ▪ Viruses that infect bacteria are bacteriophages – complex infection cycles and medicinal potential ▪ Viroids are pathogens, each consisting of a small, naked RNA molecule, which can cause disease by interfering with gene expression in host cells. Fig. 1.21 Tobacco mosaic virus (TMV) Copyright © 2020 John Wiley & Sons, Inc. 1.4 | Viruses and Viroids (2 of 3) ▪ Viral capsids are generally made up of subunits from only one or a few proteins to conserve genome size. ▪ Viral specificity for a certain host is determined by the virus’ surface proteins, since infection requires those proteins to bind surface proteins of the host cell. Insert Fig. 1.22 Virus Diversity Copyright © 2020 John Wiley & Sons, Inc. 1.4 | Viruses and Viroids (3 of 3) ▪ Viral infection types: 1. Lytic infection: the virus redirects the host into making more virus particles, the host cell lyses and releases the viruses. 2. Integration: the virus integrates its DNA (called a provirus) into the host cell’s chromosomes. Fig. 1.23 A virus infection Copyright © 2020 John Wiley & Sons, Inc. 1.5 | Green Cells: Volvox, an Experiment in Multicellularity ▪ Multicellularity has arisen from a single-celled organism. ▪ An example is the Volvox which takes the form of a spherical group of thousands of cells embedded in a gelatinous matrix. ▪ Volvox and its relatives evolved from unicellular green algae. Fig. 1.24 Evolutionary experiments in multicelluarity Copyright © 2020 John Wiley & Sons, Inc. 1.6 | Engineering Linkage: Tissue Engineering ▪ Biocompatibility is the major challenge in artificial organ development. ▪ To increase biocompatibility we need to find a way to build an organ or tissue from living cells. ▪ Major strategies: 1. Tissue engineering - enhanced cell culture, where cells are grown on a 3D patterned Fig. 1.25 Replacement blood vessel that substrate (scaffold) incorporates living cells, created using 2. Making replacement organs - tissue engineering models relies on the ability of cells to self-assemble into 3D aggregates known as organoids Copyright © 2020 John Wiley & Sons, Inc. Copyright Copyright 2020 John Wiley & Sons, Inc. All rights reserved. Reproduction or translation of this work beyond that permitted in section 117 of the 1976 United States Copyright Act without express permission of the copyright owner is unlawful. Request for further information should be addressed to the Permissions Department, John Wiley & Sons, Inc. The purchaser may make back-up copies for his/her own use only and not for distribution or resale. The Publisher assumes no responsibility for errors, omissions, or damages caused by the use of these programs or from the use of the information herein. 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