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Chapter 1. Introduction to cell biology 2 nd Edition 11

Contents 1. 1. What is cell biology? 1. 2. The cell theory 1. 3. Cell is the basic unit of life 1. 4. Diversity of cells 1. 5. The prokaryotic cell 1. 6. The eukaryotic cell 1. 7. Modern cell biology 1. 8. The technology of cell biology 1. 9. Training the scientists of tomorrow 2021/12/28 12

1. 1. What is cell biology? l. The application of molecular biological approaches to an understanding of life at the cellular level. l. The molecular basis of cell structure, cell function and cell interactions l. Understanding of whole organisms composed with cells 2021/12/28 13

The Basis of Modern Biology Study the molecules within cells Ø macromolecules and reactions, investigated by biochemists Ø the functional processes described by cell biologists Ø the gene control pathways identified by molecular biologists and geneticists. 2021/12/28 14

Cell Biology Is in Progress Two gathering forces will reshape cell biology: The genomics, the complete DNA sequence of many organisms, DNA m. RNA Protein The proteomics, the knowledge of all the possible shapes and functions that proteins employ. 2021/12/28 15

The Study the molecular similarities and differences between cell types uthe molecular composition of cells uhow cells work due to molecular similarities and differences uclosely related to genetics, biochemistry, molecular biology and developmental biology. 2021/12/28 16

1. 2. The cell theory Three indispensable theories upon which the science of biology is built. n The theory of evolution n The cell theory n The theory of equilibrium thermodynamics 2021/12/28 17

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2021/12/28 He gave the first complete descriptions of the bacteria, the protozoans原生动物 (which he called animalcules), spermatozoa, and striped muscle. He also observed the red blood cells in his detailed study of capillary circulation. 19

Matthias Jakob, Schleiden, (1804 -1881) He worked under Johannes Müller and studied primarily cells in plants. He observed that all plants seemed to be composed of cells, and is thus considered the co-founder of cell theory together with Schwann. Theodor Schwann (1810 -1882), German physiologist and histologist He identified the cell as the basic structure of plant and animal tissue in 1938 -1839. Together with Matthias Schleiden he formulated the cell theory of life. 2021/12/28 20

The Cell Theory (1938) Schleiden and Schwann proposed the cell theory in 1838. The cell theory states that: The cell is the unit of structure, physiology, and organization in living things. p The cell retains a dual existence as a distinct entity and a building block in the construction of organisms. p Cells form by free-cell formation, similar to the formation of crystals (spontaneous generation). p 2021/12/28 21

The modern tenets of the Cell Theory p p p All known living things are made up of cells. The cell is structural & functional unit of all living things. All cells come from pre-existing cells by division. (Spontaneous Generation does not occur). Cells contains hereditary information which is passed from cell to cell during cell division. All cells are basically the same in chemical composition. All energy flow (metabolism & biochemistry) of life occurs within cells. The cell theory also provides us with an operational definition of "life". 2021/12/28 22

1. 3. Cell is the basic unit of life All cells have some recognizable similarities • Plasma membrane • Nucleus • Organelles Ribosomes mitochondrion lysosomes 2021/12/28 23

All living things are composed of one or more cells. n Cell has the special features of living thing. n Movement Respiration Sensitivity to environment Growth Reproduction Metabolism 2021/12/28 Even plants move, such as opening and closing petals, and turning to face the sun. Breathing. Animals breathe in oxygen, and breathe out carbon dioxide. Plants breathe in carbon dioxide, and breathe out oxygen. Plants are sensitive to light and gravity (stems grow up and roots grow down). Animals are sensitive to many things such as noise and light. Do I need to explain this? Babies! Plants and animals can make more of themselves with similarly inherited features. All living things need to eat food and give off waste, such as moisture (eg. sweat) or going to the toilet! 24

Differences between Plant Cell and Animal Cell Plant Cell Prokaryotic cells and plant cells both have a rigid cell wall made up of polysaccharides. Animal Cell 2021/12/28 Plant cells have the chloroplast which is the site of photosynthesis. While animal cells have the mitochondrion which is the site of aerobic respiration. The vacuoles, large empty appearing areas in the cytoplasm, are usually found in plant cells where they store waste. Vesicles are much smaller than vacuoles in animal cells. 25

Origin of the Cell The earliest cells might be as much as 3. 8 billion years old. Where did life originate and how ? Inorganic Extra-terrestrial or Organic Chemical Evolution Organic Amino acids Pre-cellular Single cell Multicellular organisms Stanley Miller (b. 1930) was a doctoral student working with Urey at the University of Chicago, researching possible environments of early Earth. In 1953 he combined the ideas of Urey and Oparin in a short, simple experiment. 2021/12/28 26

The interactions of these molecules would have increased as their concentrations increased. Reactions would have led to the building of larger, more complex molecules. A pre-cellular life would have began with the formation of nucleic acids. Chemicals made by these nucleic acids would have remained in proximity to the nucleic acids. Eventually the pre-cells would have been enclosed in a lipid-protein membrane, which would have resulted in the first cells. 2021/12/28 27

Origins of Life and the RNA World Which came first in the origin of life, DNA, RNA or protein? RNA has the ability to act as both genes and enzymes. This property could offer a way around the "chicken-and-egg" problem. (Genes require enzymes; enzymes require genes. ) RNA can be transcribed into DNA. From RNA to life and the RNA world could be the original pathway to cells. Sidney Altman and Thomas Cech were awarded the Nobel Prize for Biochemistry in 1989 2021/12/28 DNA RNA Protein 28

Three Things Make Cell Different from Non-cell system 1. The presence of enzymes and other complex molecules essential to the processes needed by living systems. Miller's experiment showed how these could possibly form. 2. The capacity for replication from one generation to another. Most organisms today use DNA as the hereditary material, although recent evidence (ribozymes) suggests that RNA may have been the first nucleic acid system to have formed, referred to the RNA world. 3. A membrane that separates the internal chemicals from the external chemical environment. This also delimits the cell from not-cell areas. The work of Sidney W. Fox has produced proteinoid spheres , which while not cells, suggest a possible route from chemical to cellular life. 2021/12/28 29

Microscope Is Needed to Visualize Cells 2021/12/28 30

1. 4. Diversity of cells Prokaryotes have no nucleus or other membrane-bounded compartments. They lack distinct organelles, although some do have invaginated membrane structures. Eukaryotes have a membranebounded nucleus and usually have other membrane-bounded compartments or organelles as well. 2021/12/28 31

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Differences between Prokaryotes and Eukaryotes Prokaryotes Eukaryotes Size 1 -10 microns 10 -100 microns Complexity Nucleus Unicellular, rarely small clusters or filaments None (mesosome is infolding of cytoplasmic membrane) no Sometimes unicellular more often multicellular nuclei, mitochondria, chloroplasts, lysosomes, endoplasmic reticulum, golgi, vacuoles yes Chromosome Single and circular Usually several and linear Introns & Exons occasionally frequent Histones no yes Ploidy haploid Diploid Mitosis & meiosis absent present Membrane bound organelles (To be continued) 2021/12/28 33

Sexual reproduction Ribosomes None or unidirectional from donor to recipient 70 s(50 s + 30 s subunits) Cytoskeleton absent Cell wall Usually present Motility Simple, prokaryotic flagella, gliding motion Usually absent Usually, involves fusion of haploid gametes 80 s(60 s + 40 s) in cytoplasm (mitochondria & chloroplasts have prokaryotic ribosomes) Microtubules and microfilamemts Many divers pathways in various bacteria absent Absent in animals, present in fungi {chitin) and plants (cellulose) Complex “ 9+2” flagella or cilia with centrioles Cells differentiae to form tissue & organs Glycolysis in cytoplasm, krebs cycle and ETC in mitochondria present Oxygen Aerobic and / or anaerobic Usually aerobic Sterols甾酮 Usually absent Used as hormones and in plasma membrane Differentiation Energy metabolism Endocytosis & cytoplasmic streaming 2021/12/28 34

Prokaryotes Two kingdoms of prokaryotes – Eubacteria 真细菌 (细菌) Archaebacteria 原始细菌(古细菌) Three different types of bacteria Bacilli 杆菌 Cocci 球菌 Spiral 螺旋菌 Philip Hugenholtz : Exploring prokaryotic diversity in the genomic era, Genome Biol. 2002; 3(2): reviews 2021/12/28 35

Bacteria Morphological Diversity 2021/12/28 From http: //ag. arizona. edu/plp/courses/plp 329/micdivintro. ppt 36

Prokaryotic cell structure Scale Bacteria vs. Eucaryotes 2021/12/28 37

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Eukaryotes Algae Protista Fungi Plantae Animalia Jessica L. Green, et al: Spatial scaling of microbial eukaryote diversity Nature 432, 747– 750 (2004); 2021/12/28 40

Plant cell structure 2021/12/28 41

Animal cell structure 2021/12/28 42

Genetic Control of Cell Diversity The diversity derives from both variety in gene expression and from the patterns of cellular control for gene product behavior. Cell diversity derives from both evolution and development of living things, Evolution Development 2021/12/28 genome difference same genome with different gene expression Different cells 43

One cell, one cell type 2021/12/28 Trillions of cells, 200+ cell types 44

Metazoan Phenotypic Complexity from selective gene expression 2021/12/28 45

1. 7. Modern cell biology Contemporary cell biology, often referred to as Molecular Cell Biology Genetic control in cells ● Three flows within cells 1) flow of information; 2) flow of mass 3) flow of energy. ● Systems Biology of the Cell 1) Molecular cytomics 2) Cellular genomics 3) Cellular proteomics 4) Cellular epigenomics 5) In silico cell ● 2021/12/28 46

Genetic control in cells The molecular basis of genetic control in cells, particularly in eukaryotic cells is one of the most basic active areas of molecular cell biology. ▪Each cell has whole genetic information ▪ Different cell has different genes expression pattern ▪ There are interactions among genes ▪ Phenotype is a result of the interaction between genes and environment. 2021/12/28 47

Three flows within cells Flow of inherit information Flow of energy Material flows within cells None of these three flows operates in isolation from the other two. The flow of mass and flow of energy are extremely closely linked, as biological molecules are broken apart to make other biological molecules or to harvest energy. 2021/12/28 48

Flow of inherit information ØGenetic information Central dogma (中心法则) ØEpigenetic information Chromatin based gene regulation Chromatin remodeling （染色质重塑） Histone acetylation (组蛋白乙酰化) Histone methylation (组蛋白的甲基化 ) Histon phosphorylation (组蛋白的磷酸化 ) DNA methylation (Cp. G岛甲基化) 2021/12/28 49

Flow of energy- metabolism — Some processes (anabolic) are energy consuming. Other processes are energy producing (catabolic). — Energy intermediates are the molecules, adenosine triphosphate (ATP) and adenosine diphosphate (ADP), which are used to allow endergonic reactions to occur in cells. — Energy transduction happens in mitochondria and chloroplasts. 2021/12/28 50

Material flows within cells Simple molecules absorbed by cells are incorporated into larger molecules and/or used to make other molecules, called material transformation. Metabolic pathway networks in a cell include: l Carbohydrate metabolism l Amino acid metabolism l Lipids metabolism l Nucleotide metabolism 2021/12/28 51

Systems Biology of the Cell Currently, biologists tend to study the cell structure and behaviors as the ultimate objective to systemically understand the effect of — the molecules on the whole cell, and — the effect of the individual cell on the whole organism as well. cytomics 2021/12/28 52

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E-cell The computational model of living cell, reflecting the molecular networks within a cell. E-Cell A concept of constructing virtual cells on computers. E-Cell Project An international research project aiming at developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation. E-Cell System An object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells http: //www. e-cell. org/software/e-cell-system 2021/12/28 54

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Cell Models for Research of Life Sciences 1. Cell is the basic unit of life 2. Cell has all the features of living things 3. Cell has whole inherit material 4. Cell has whole regulation on gene expression 5. The developments of modern techniques in researches 2021/12/28 56

1. 8. The technology of cell biology ØCell Culture ØFlow Cytometry ØFunctional Bio-imaging of Cell Modern light microscopy Confocal microscopy Two-photon microscopy Live cell Image analysis ØRNA Interference Technology ØAntisense Technique ØGene Microarray ØProtein Chips 2021/12/28 57

Flow Cytometry 2021/12/28 58

Fluorescence Microscopy 2021/12/28 59

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Tracing molecule in living cells 2021/12/28 61

Exogenous and Endogenous RNAi Liposome-mediated Transfection 2021/12/28 62

Gene Microarray (Biochips) 2021/12/28 63

1. 9. Training the scientists of tomorrow What we know about the cell — The main content of the molecular cell biology course includes: • The structure and function of the cell • The organelles of the cell; • The mechanisms of important activities of the cell • The regulation of the activities. • The advance in cellular research. 2021/12/28 64

How we know what we know about the cell It is critical to present to students the experimental basis of our understanding to show them how we know what we know. Hopefully this will demonstrate the dynamic nature of science and prepare them not only to engage actively in scientific research and teaching but also to become educated members. 2021/12/28 65

Why we do what we do about the cell Of course, we want students to learn not only how we know what we know, but why we do what we do. As in other cell biology books, our coverage of basic cell biology, medical topics, biotechnology, human biology is integrated throughout. We know that these topics may be of particular interest to students. 2021/12/28 66

Who Is a Cell Biologist What do they work on All aspects of cells, from their interactions with each other and their environments to their cellular and atomic composition. What are they interested in Very concerned with investigating both the processes and structures that occur and exist within cells. 2021/12/28 67

Questions 1. What does cell biology concern? 2. Why we say the cell is a complex system? 3. What is cell theory? 4. What are the contemporary views on cell biology? 5. What cause cell diversity? 6. How many modern techniques are employed in cell biology research? 2021/12/28 68