Becker's World of the Cell Tenth Edition Chapter 1 PDF

Becker’s World of the Cell Tenth Edition Chapter 1 A Preview of Cell Biology Lectures by Anna Hegsted, Simon Fraser University Copyright © 2022 Pearson Education, Inc. All...

Becker’s World of the Cell Tenth Edition Chapter 1 A Preview of Cell Biology Lectures by Anna Hegsted, Simon Fraser University Copyright © 2022 Pearson Education, Inc. All Rights Reserved 1.1 The Cell Theory: A Brief History Robert Hooke (1665) observed compartments in cork, under a microscope, and first named them cells. He had observed the compartments formed by cell walls of dead plant tissue. His observations were limited by the low magnification power (30X enlargement) of his microscope Antonie van Leeuwenhoek, a few years later, produced better lenses that magnified up to 300X Copyright © 2022 Pearson Education, Inc. All Rights Reserved Figure 1.1 The Birth of Microscopy The pore-like compartments are cork cells from oak bark Copyright © 2022 Pearson Education, Inc. All Rights Reserved Copyright © 2022 Pearson Education, Inc. All Rights Reserved Advances in Microscopy Allowed Detailed Studies of Cells Two factors restricted progress in early cell biology – Microscopes had limited resolution, or resolving power (ability to see fine detail) – The descriptive nature of cell biology: the focus was on observation, with little emphasis on explanation Copyright © 2022 Pearson Education, Inc. All Rights Reserved Compound Microscopes By the 1830s, compound microscopes were used – These had two lenses – Both magnification and resolution were improved – Structures only 1 µm in size could be seen clearly Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Cell Theory Applies to All Organisms Using a compound microscope, Robert Brown identified the nucleus, a structure inside plant cells. Matthias Schleiden concluded that all plant tissues are composed of cells. Thomas Schwann made the same conclusion for animals. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Cell Theory In 1839, Schwann postulated the cell theory: 1. All organisms consist of one or more cells. 2. The cell is the basic unit of structure for all organisms. Later, Virchow (1855) added: 1. All cells arise only from preexisting cells. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Cells of the World Figure 1.2 The Cells of the World. Copyright © 2022 Pearson Education, Inc. All Rights Reserved  1.2 The Emergence of Modern Cell Biology Three strands of biological inquiry weave into modern cell biology: – Cytology focuses mainly on cellular structure and emphasizes optical techniques. – Biochemistry focuses on cellular structure and function. – Genetics focuses on information flow and heredity and includes sequencing of the entire genome (all of the D N A) in numerous organisms. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Cell Biology Timeline Figure 1.3 The Cell Biology Timeline. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Cytological Strand Deals with Cellular Structure Historically, cytology deals primarily with cell structure and observation using optical techniques. Microscopy has been invaluable in helping cell biologists deal with the problem of small size of cells and their components. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Cellular Dimensions The units used to measure cells and organelles may not be familiar. The micrometer (µm), also called the micron, is one millionth of a meter (10−6 m). Bacterial cells are a few micrometers in diameter, whereas the cells of plants and animals are 10– 20 times larger. Organelles are comparable to bacterial cells in size. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Worlds of Micrometer and Nanometer Figure 1.4 The Worlds of the Micrometer and Nanometer. Copyright © 2022 Pearson Education, Inc. All Rights Reserved  Measurements in Cell Biology The nanometer (nm) is used for molecules and subcellular structures that are too small to be seen using the light microscope. – The nanometer is one-billionth of a meter (10−9 m). The angstrom (Å), which is 0.1 nm, equals about the size of a hydrogen atom. – It is used in cell biology to measure dimensions within proteins and D N A molecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Light Microscope The light microscope was the earliest tool of cytologists. It allowed identification of nuclei, mitochondria, and chloroplasts within cells. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Improvements in Microscopy The microtome (mid-1800s) allowed preparation of very thin slices of samples A variety of dyes for staining cells began to be used around the same time These improved the limit of resolution (how far apart objects must be to appear as distinct) The smaller the microscope’s limit of resolution, the greater its resolving power (ability to see fine details) Copyright © 2022 Pearson Education, Inc. All Rights Reserved Copyright © 2022 Pearson Education, Inc. All Rights Reserved  The light spectrum Wavelength ---- Frequency Blue light 488 nm Photon as a short wavelength wave high frequency packet of high energy (2 times energy the red) Red light 650 nm long wavelength low frequency low energy Copyright © 2022 Pearson Education, Inc. All Rights Reserved Lenses focus light rays at a specific place called the focal point distance between center of lens and focal point is the focal length strength of lens related to focal length –short focal length more magnification Copyright © 2022 Pearson Education, Inc. All Rights Reserved Copyright © 2022 Pearson Education, Inc. All Rights Reserved Microscope Resolution Ability of a lens to separate or distinguish small objects that are close together Resolution is governed by three factors: – the wavelength of light used to illuminate the object – The angular aperture – The refractive index of the medium surrounding the specimen Copyright © 2022 Pearson Education, Inc. All Rights Reserved Microscope resolution: refractive index light is refracted (bent) when passing from one medium to another refractive index –a measure of how greatly a substance slows the velocity of light direction and magnitude of bending is determined by the refractive indexes of the two media forming the interface Copyright © 2022 Pearson Education, Inc. All Rights Reserved Microscope resolution Limit for smallest resolvable distance d d = 1.22l between 2 points is 2 NA (Rayleigh criterion): This definesaa“resel” Thisdefines “resel”oror“resolution “resolutionelement” element” NA = n sin  n = the refractive index between the object and first objective element  is the angular aperture of the objective Limit of resolution (how far apart objects must be to appear as distinct) Copyright © 2022 Pearson Education, Inc. All Rights Reserved  Microscope resolution The lower the limit of resolution (“d”) a microscope has, the greater its resolving power Shorter wavelength, better resolving power Higher NA, better resolving power The limit of resolution for a microscope that uses visible light is ~300nm in air and ~200nm in oil Copyright © 2022 Pearson Education, Inc. All Rights Reserved Relative Resolving Power of the Human Eye, the Light Microscope, and the Electron Microscope Figure 1.5 Relative Resolving Power of the Human Eye, the Light Microscope, and the Electron Microscope. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Bright-Field Microscope The most common configuration of the light microscopy is brightfield microscopy, so called because –produces a dark image against a brighter background has several objective lenses –parfocal microscopes remain in focus when objectives are changed also called compound microscope –image formed by action of ocular lenses and objective lenses –total magnification product of the magnifications of the ocular lens and the objective lens. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Copyright © 2022 Pearson Education, Inc. All Rights Reserved Specialized Light Microscopes A variety of special optical techniques have been developed for observing living cells directly. These include: – Phase-contrast microscopy – Differential interference contrast microscopy – Fluorescence microscopy – Confocal microscopy Copyright © 2022 Pearson Education, Inc. All Rights Reserved  To observe a specimen with light microscopy: –it must absorb particular wavelengths of light (which results in color) –or it must slow the light so that different paths of light are out of phase Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Phase-Contrast Microscope Improves contrast without sectioning and staining by exploiting differences in the thickness and the refractive index of various regions of the cells The phase of transmitted light changes as it passes through a structure with a different density from the surrounding medium. Converts phase differences of the light waves into alterations in brightness Copyright © 2022 Pearson Education, Inc. All Rights Reserved  Bright-field microscopy Bright-field microscopy is poor for viewing colorless samples such as most animal cells. It cannot detect phase shifts. Phase-contrast microscopy The optics of a phase- contrast microscope brings parallel paths of light together so that constructive and destructive interference occurs. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Differential Interference Contrast Microscope Resembles phase-contrast microscopy in principle, i.e. enhances and amplifies slight changes in light phase as it passes through a structure with a different density from the surrounding medium – but is more sensitive because is uses a special prism to split the illuminating light beam into two separated rays Because the largest phase changes occur at the cell edge, the outline of the cell gives a strong signal – The image appears three dimensional Both phase-contrast and DIC make it possible to see living cells clearly Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Fluorescence Microscope Can be used to localize specific molecules (proteins, DNA & RNA sequences) within the specimen shows a bright image of the object resulting from the fluorescent light emitted by the specimen specimens usually stained directly with fluorescent molecules (fluorochromes) or detected by binding of fluorescently labeled antibodies An antibody is a protein that binds a particular target molecule, called an antigen The antibody can be coupled to a fluorescent molecule, which emits fluorescence wherever the target molecule is bound by the antibodyCopyright © 2022 Pearson Education, Inc. All Rights Reserved  - A variety of fluorescent molecules are used to visualize cells. -The fluorescent molecules absorb light at specific wavelengths and emit light of longer wavelengths. -More than one molecule (proteins, DNA) protein can be visualized in a sample Copyright © 2022 Pearson Education, Inc. All Rights Reserved Often, a two-antibody method is used to detect the location of an “antigen” with fluorescence. The method is referred to as indirect immunofluorescence or indirect immunocytochemistry. Primary antibodies are produced by the investigator. Secondary antibodies are available from companies. These antibodies are produced by injecting one species of animal with antibodies from another species of animals. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Fluorescence Microscope (continue) Green fluorescent protein (GFP) can also be used to study the temporal and spatial distribution of proteins in a living cell Copyright © 2022 Pearson Education, Inc. All Rights Reserved  Indirect immunofluorescence Dead cells. Fixed and permeabilized. Primary antibody binds antigen. Secondary antibody contains fluorescent tag. GFP-tagged protein View live cells. GFP fusion needs to behave properly. 2 views of a protein in the ER. Copyright © 2022 Pearson Education, Inc. All Rights Reserved  Confocal scanning laser microscope uses a laser beam to illuminate a single plane of a fluorescently labeled specimen laser beam is scanned over the specimen in a precise pattern computer compiles images created from each point to generate a 3- dimensional image Optical sections Copyright © 2022 Pearson Education, Inc. All Rights Reserved Copyright © 2022 Pearson Education, Inc. All Rights Reserved  Electron Microscopy (1 of 2) The electron microscope, which uses a beam of electrons rather than light, was a major breakthrough for cell biology. Wavelength of electron beam is much shorter than light, resulting in much higher resolution – The limit of resolution of electron microscopes is about 100 times better than light microscopes. 0.1- 0.2 nm (theoretically), 2nm (practical limit) The magnification is much higher than light microscopes—up to 100,000×. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Electron Microscopy (2 of 2) In transmission electron microscopy (TEM), electrons are transmitted through the specimen. In scanning electron microscopy (SEM), the surface of a specimen is scanned by detecting electrons deflected from the outer surface. Specialized approaches in electron microscopy allow for visualization of specimens in three dimensions, and allow for the determination of protein macromolecular structures. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Electron Microscopy Figure 1.6 Electron Microscopy. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Transmission electron microscopy - TEM Specimen scatters electrons The transmitted electrons strike a fluorescent screen or photographic film (electron micrograph) Copyright © 2022 Pearson Education, Inc. All Rights Reserved Sample preparation for electron microscopy Electron microscopy requires the use of heavy metal atoms – samples are almost always stained with heavy metals such as uranium, lead, platinum, osmium or gold since these do scatter electrons. For TEM, the samples must be extremely thin, no more than ~50nm-100nm – Ultramicrotome Specimen preparation for SEM involves fixation but not sectioning Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Biochemical Strand Studies the Chemistry of Biological Structure and Function Around the same time cytologists were studying cells microscopically, others began to explore cellular function. These scientists began to try to understand the structure and function of biological molecules. Much of biochemistry dates from the work of Fredrich Wöhler (1828), who showed that a compound made in a living organism could be synthesized in the lab Prior to this work, it was thought that living organisms were unique and not governed by the laws of physics and chemistry. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Key Observations in Early Biochemistry Louis Pasteur (1860s) showed that yeasts could ferment sugar into alcohol. The Buchners (1897) showed that yeast extracts could do the same. This led to the discovery of enzymes, biological catalysts. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Early Biochemistry Steps of the pathways of fermentation and other cellular processes were elucidated in the 1920s,1930s, and 1940s. Gustav Embden, Otto Meyerhof, Otto Warburg, and Hans Krebs described the steps of glycolysis (the Embden–Meyerhof pathway) and the Krebs cycle. Fritz Lipmann showed that adenosine triphosphate (A T P) is the principal energy storage compound in most cells. Melvin Calvin and colleagues elucidated the Calvin cycle. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Biochemistry Methods Subcellular fractionation—uses centrifugation to separate/isolate different structures and macromolecules on the basis of size, shape, and/or density –Differential centrifugation. –Density gradient centrifugation. –Equilibrium density centrifugation. –Ultracentrifuges—are capable of very high speeds (over 100,000 revolutions per minute) Copyright © 2022 Pearson Education, Inc. All Rights Reserved Centrifuge Rotators Figure 12A-1 Copyright © 2022 Pearson Education, Inc. All Rights Reserved Differential Centrifugation Separates organelles on the basis of size and/or density The relative size of an organelle or macromolecule can be expressed in terms of its sedimentation coefficient – How rapidly the particle sediments – Expressed in Svedberg units (S) Copyright © 2022 Pearson Education, Inc. All Rights Reserved Sedimentation Coefficients and Densities of Organelles, Macromolecules, and Viruses Figure 12A-3 Copyright © 2022 Pearson Education, Inc. All Rights Reserved Differential Centrifugation and the Isolation of Organelles Supernatant: the clarified suspension of homogenate that remain after particles of a given size and density are removed as a pellet Fractions are enriched for the respective organelles, but is also likely contaminated with other organelles Figure 12A-4 Copyright © 2022 Pearson Education, Inc. All Rights Reserved Density Gradient Centrifugation A variation of differential centrifugation in which the sample for fractionation is placed as a thin layer on top of a gradient of solute Gradient is an increasing concentration of solute from top to bottom Commonly used for separating both organelles and macromolecules Copyright © 2022 Pearson Education, Inc. All Rights Reserved Density Gradient Centrifugation and the Isolation of Organelles Copyright © 2022 Pearson Education, Inc. All Rights Reserved Equilibrium Density Centrifugation (or buoyant density) and the Isolation of Organelles In this case the solute is concentrated so that the density gradient spans the range of densities of the organelles or macromolecules to be separated Copyright © 2022 Pearson Education, Inc. All Rights Reserved Biochemistry Methods (continued) Radioisotopes - Use to trace the metabolic fate of specific atoms and molecules (led to elucidation of the Calvin cycle, 1950s) Chromatography—techniques to separate molecules from a solution based on size, charge, or chemical affinity Electrophoresis—uses an electrical field to move proteins, DNA, or RNA molecules through a medium based on size/charge Mass spectrometry—is used to determine the size and composition of individual proteins Copyright © 2022 Pearson Education, Inc. All Rights Reserved Separation of Molecules by Chromatography and Electrophoresis Figure 1.7 Separation of Molecules by Chromatography and Electrophoresis. Copyright © 2022 Pearson Education, Inc. All Rights Reserved  The Genetic Strand Focuses on Information Flow The genetic strand is the study of the inheritance of characteristics from generation to generation. It was not until the nineteenth century that scientists discovered the nature of inherited physical entities, now called genes. Gregor Mendel’s experiments with peas (1866) laid the foundation for understanding the passage of “hereditary factors” from parents to offspring. The hereditary factors are now known to be genes. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Chromosomes Walther Flemming (1880) saw threadlike bodies in the nucleus called chromosomes. He called the process of cell division mitosis. Wilhelm Roux (1883) and August Weisman (shortly after) suggested that chromosomes carried the genetic material. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Chromosome Theory Three geneticists formulated the chromosome theory of heredity, proposing that Mendel’s hereditary factors are located on chromosomes. Morgan, Bridges, and Sturtevant (1920s) were able to connect specific traits to specific chromosomes in the model organism, Drosophila melanogaster (the common fruit fly). Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA Friedrich Miescher (1869) first isolated D N A, which he called “nuclein.” DNA: – Known to be a component of chromosomes by 1914 – Known to be composed of only four different nucleotides by the 1930s – Proteins, composed of 20 different amino acids, were thought more likely to be a genetic material. Copyright © 2022 Pearson Education, Inc. All Rights Reserved DNA is the Genetic Material Experiments with bacteria and viruses in the 1940s began to implicate D N A as the genetic material. Beadle and Tatum formulated the one gene–one enzyme concept (each gene is responsible for the production of a single protein). Copyright © 2022 Pearson Education, Inc. All Rights Reserved Molecular Genetics In 1953, Watson and Crick, with assistance from Rosalind Franklin, proposed the double helix model for DNA structure. In the 1960s, there were many advances toward understanding DNA replication, RNA production, and the genetic code Crick coined the central dogma of molecular biology, which can be summarized as: Copyright © 2022 Pearson Education, Inc. All Rights Reserved RNA Three important kinds of RNA molecules: – mRNAs (messenger RNAs)—translated to produce protein – rRNAs (ribosomal RNAs)—components of ribosomes – tRNAs (transfer RNAs)—bring the appropriate amino acid for protein synthesis Exceptions to the central dogma include viruses with RNA genomes Reverse transcriptase is an enzyme that uses viral RNA to synthesize complementary DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Central Dogma: The Flow of Genetic Material in the Cell Figure 1.8 Central Dogma: The Flow of Genetic Information in the Cell. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Important techniques in genetics ▪ Electrophoresis - Allows separation of DNA molecules and fragments ▪ Nucleic acid hybridization - Based on binding of two single-stranded nucleic acid molecules with complementary base sequences ▪ useful for the detection and isolation of specific DNA or RNA molecules ▪ 1970 - Recombinant DNA technology ▪ DNA sequencing ▪ Bioinformatics Copyright © 2022 Pearson Education, Inc. All Rights Reserved Working with DNA Recombinant D N A technology uses restriction enzymes to cut D N A at specific places, allowing scientists to create recombinant D N A molecules with D N A from different sources. D N A cloning is the generation of many copies of a specific D N A sequence. D N A transformation is the process of introducing D N A into cells. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Sequencing DNA D N A sequencing methods are used routinely for rapidly determining the base sequences of D N A molecules. It is now possible to sequence entire genomes (entire D N A content of a cell). Copyright © 2022 Pearson Education, Inc. All Rights Reserved Bioinformatics and “-Omics” Bioinformatics merges computer science with biology to organize and interpret enormous amounts of sequencing and other data. Genomics is the study of all the genes of an organism. Proteomics is the study of the functions and interactions of all the proteins present (or proteome) in a particular cell. Copyright © 2022 Pearson Education, Inc. All Rights Reserved  Bioinformatic Tools Numerous bioinformatic tools are publicly available through NCBI (National Center for Biotechnology Information). High-throughput methods allow for dramatic increases in the speed of molecular analysis. Expression levels of hundreds or thousands of genes can be monitored simultaneously. Copyright © 2022 Pearson Education, Inc. All Rights Reserved -Omics Transcriptomics—the study of all the genes transcribed in a cell Metabolomics—the analysis of all metabolic reactions happening at a given time in a cell Lipidomics—study of all the lipids in a cell Ionomics—study of all the ions in a cell There are likely more “-omics” to come. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 1.3 How Do We Know What We Know? What we think of as “facts” today, things known to be true, are ideas that replaced earlier “facts,” now know to be misconceptions. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Biological “Facts” May Turn Out to Be Incorrect In science, “facts” are provisional pieces of information. These are dynamic and subject to change. To a scientist, a “fact” is an attempt to state our best current understanding of the world, based on observations and experiments. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Experiments Test Specific Scientific Hypotheses Researchers first search the scientific literature, using peer-reviewed sources in scientific or medical journals. They formulate a hypothesis, a tentative explanation that can be tested experimentally. This may take the form of a model, which appears to be a reasonable explanation for the phenomenon. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Testing Hypotheses Experimenters then design a controlled experiment, collecting the data and interpreting the results. Scientists seek to prove the null hypothesis, which is opposite to their hypothesis. The certainty of a particular hypothesis is strengthened when multiple attempts fail to confirm the null hypothesis. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Model Organisms Play a Key Role in Modern Cell Biology Research Scientists have developed a number of model systems to study cellular processes directly in living cells and organisms. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Cell and Tissue Cultures Cell cultures are commonly used as model systems. Cell cultures are used to study cancer, viruses, proteins, and cellular differentiation. Some of what is learned from cultured cells may not reflect what happens within an intact organism. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Model Organisms A model organism is a species widely studied, well characterized, and easy to manipulate. Each has particular advantages, useful for experimental studies. Much of our knowledge is based on research using relatively few organisms. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Common Model Organisms Figure 1.10 Common Model Organisms. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Well-Designed Experiments Alter Only One Variable at a Time In a typical experiment, one condition is varied, called the independent variable. All other variables are kept constant. The outcome is called the dependent variable. In vivo experiments involve living organisms. In vitro experiments are done outside the living organisms, for example, in a test tube. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Copyright This work is protected by United States copyright laws and is provided solely for the use of instructors in teaching their courses and assessing student learning. Dissemination or sale of any part of this work (including on the World Wide Web) will destroy the integrity of the work and is not permitted. The work and materials from it should never be made available to students except by instructors using the accompanying text in their classes. All recipients of this work are expected to abide by these restrictions and to honor the intended pedagogical purposes and the needs of other instructors who rely on these materials. Copyright © 2022 Pearson Education, Inc. All Rights Reserved