BIO 117: Cell and Molecular Biology - Module 1 PDF

BIO 117: CELL AND MOLECULAR BIOLOGY Anabelle Dece A. Espadero, Ph.D. Department of Marine Biology and Environmental Science College of Science and Environment MSU at Naawan MODULE 1: The Fundamental units of life Module Outline: History of cell bio...

BIO 117: CELL AND MOLECULAR BIOLOGY Anabelle Dece A. Espadero, Ph.D. Department of Marine Biology and Environmental Science College of Science and Environment MSU at Naawan MODULE 1: The Fundamental units of life Module Outline: History of cell biology Cell theory The formal practice of science Domains of life Vital tools in cell biology This module introduces the fundamentals of cell and molecular biology, and students should be able to: Compare and contrast hypotheses and theories. Compare and contrast structures common to and that distinguish the domains of life. Understand the function of different cellular substructures. Distinguished different tools used in cell biology studies The Fundamental Units of Life Timeline 1595 - Hans and Zacharias Janssen, developed the first light microscope 1655 – Robert Hooke, described cells in cork 1674 – Anton van Leeuwenhoek, first man to witness a live cell under a microscope 1833 – Robert Brown, first person to name and describe in detail the cell nucleus. 1839 – Theodor Schwann and Matthias Jakob Schleiden, propose that cells are the basic building blocks of all living things. 1858 – Rudolf Virchow, proposed that living cells arise only from other living cells through cell division. Omnis cellula e cellula 1874 – Walther Flemming, described chromosome behavior during cell division 1894 – Robert Altmann, first describe the mitochondria 1898 – Camillo Golgi, discovered golgi apparatus 1925 – Evert Gorter and François Grendel, described the basic structure of the plasma membrane. 1945 – Keith Porter et al., pioneers of the field of electron microscopy, first to identify endoplasmic reticulum and other elements in the cytoskeleton. And so on... The Fundamental Units of Life Formulation of cell theory: The cell is the unit of structure, physiology, and organization in living things. The cell retains a dual existence as a distinct entity and a building block in the construction of organisms. Cells form by free-cell formation, similar to the formation of crystals (spontaneous generation). Modern Cell Theory 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 Fundamental Units of Life Scientific Method – The Formal Practice of Science Scientific method – a standardized protocol for observing, asking questions about, and investigating natural phenomena. Key elements of the scientific method: Scientific theory a theory is a statement well supported by Observe natural phenomena (includes reading the science of others). experimental evidence and widely Infer and propose an hypothesis (explanation) based on objectivity and accepted by the scientific community reason. Hypotheses are declarative sentences that sound like a fact, but aren’t! Good hypotheses are testable, easily turned into if/then Scientific Law is thought of as universal (predictive) yes-or-no questions. and even closer to ‘fact’ than a theory! Design an experiment to test the hypothesis: results must be measurable most common in math and physics. evidence for or against the hypothesis. Laws are not facts! Like Theories, Laws Perform the experiment and then observe, measure, collect data and are always subject to experimental test test for statistical validity (where applicable). Then, repeat the experiment. Consider how your data supports or does not support your hypothesis Science is a way of knowing the world and then integrate your experimental results with earlier hypotheses and around us through constant test, prior knowledge. confirmation, and rejection that ultimately reveals new knowledge, integrating that knowledge into our worldview The Fundamental Units of Life Domains of Life Three domains of life 1. Prokaryotes (Eubacteria) are among the first descendants of that common ancestral cell. They lack nuclei (pro - before and karyon - kernel, or nucleus). bacteria and cyanobacteria (blue-green algae) 2. Eukaryotes (Eukarya) include all higher life forms, characterized by cells with true nuclei (Eu - true; karyon - nucleus). 3. Archaebacteria (Archaea), (meaning “old” bacteria) include many extremophile bacteria (‘lovers’ of life at extreme temperatures, salinity, etc.). Originally classified as ancient prokaryotes, Archaebacteria were shown by Carl Woese compared the DNA 1990 to be separate from prokaryotes and eukaryotes, a third domain of life. sequences of genes for ribosomal RNAs Found in inhospitable environments as boiling hot springs or arctic ice, in normal bacteria and extremophiles. Based on sequence similarities and differences, he concluded that the Five Kingdoms latter are in fact a domain separate from the rest of the bacteria as well as from eukaryotes. Monera (prokaryotes), Protista, Fungi, Plants, and Animals (all eukaryotes). Chapter 1 Cells: The Fundamental Units of Life Domains of Life The Fundamental Units of Life Domains of Life: Viruses What about viruses? Viruses that infect bacteria are called bacteriophage (phage – eaters) Hence, bacteria eaters! Eukaryotic viruses include many that cause diseases in plants and animals. In humans, the corona viruses that cause influenza, the common cold, SARS Viruses were not identified as agents of and COVID-19 are retroviruses, with an RNA genome. disease until late in the 19th century. In 1892, Dmitri Ivanofsky, a Russian botanist, Familiar retroviral diseases also include HIV (AIDS), Ebola, Zika, yellow fever was studying plant diseases. and some cancers. One that damaged tobacco (and was thus of agricultural significance) was the mosaic On the other hand, Small pox, Hepatitis B, Herpes, chicken pox/shingles, disease. adenovirus and more are caused by DNA viruses. Tobacco Mosaic Virus, or TMV The Fundamental Units of Life Domains of Life: Viruses Viruses are invisible by light microscopy, since they are sub- microscopic non-cellular bits of life- chemistry that only become reproductive (come alive) when they parasitize a host cell. Virology – study of viruses As eventually seen in the electron microscope, viruses (called virions or viral particles) are typically 150 nm or less in diameter. Viruses cause disease. However, in 2002, a particle inside an amoeba, Most were identified precisely because they are harmful originally believed to be a bacterium, was also shown by to life. electron microscopy to be a virus…, albeit a giant virus! Several more giant, or Megavirales were discovered which COVID-19, is caused by the SARS-CoV-2 (Retrovirus). falls into two groups, pandoraviruses and mimiviruses. At 1000nm (1 µm) Megavirus chilensis (a pandoravirus) may Vector vaccines - a modified version of virus that gives be the largest, compared with bacterium (Escherichia coli) cells instruction to build anti-bodied to fight the virus. and the AIDS virus. The Fundamental Units of Life Domains of Life: The Prokaryotes (Eubacteria = Bacteria and Cyanobacteria) Prokaryotic cells are cells without a nucleus. The DNA in prokaryotic cells is in the cytoplasm rather than enclosed within a nuclear membrane. Prokaryotic cells are found in single-celled organisms. Organisms with prokaryotic cells are called prokaryotes. The first type of organisms to evolve and are still the most common organisms today. Cell Structure Description Long projection(s) outside of the cell in some bacteria; aids in Flagellum the motility Pili Small projections outside of the cell; aid in attachment Capsule A thick protective layer outside the cell wall of some bacteria Outer layer of bacterial cells; more chemically complex than Cell wall eukaryotic cell walls Plasma Membrane Phospholipid bilayer marking the outside of the cytoplasm Cytoplasm The fluid portion of the cell Ribosome Involved in protein synthesis Nucleoid Circular DNA found in the cytoplasm Plasmid Small loops of DNA found in some bacteria The Fundamental Units of Life Domains of Life: The Prokaryotes Bacterial Reproduction Bacterial DNA is a circular double helix that duplicates as the cell grows. It is concentrated in a region of the cell called the nucleoid. When not crowded at high density, bacteria replicate their DNA throughout the life of the cell, dividing by binary fission which results in the equal partition of duplicated bacterial “chromosomes” into new cells. The bacterial chromosome is essentially naked DNA, unassociated with proteins. Cell Motility Movement of bacteria is typically by chemotaxis, a response to environmental chemicals. Phototaxy respond to light (phototaxy). Example, many move using flagella made up largely of the protein flagellin. Prokaryotes were long thought to lack these or similar cytoskeletal components. The Fundamental Units of Life Domains of Life: The Prokaryotes D. Bacterial Ribosomes Do the Same Thing as Eukaryotic Ribosomes… Ribosomes are the protein-synthesizing machines of life. Ribosomes of prokaryotes are smaller than those of eukaryotes but are able to translate eukaryotic messenger RNA (mRNA) in vitro. Common basic function - ribosomal RNAs of all species share base sequence and structural similarities indicating a long and conserved evolutionary relationship. The prokarya (eubacteria) are a diverse group of organisms, occupying almost every wet, dry, hot or cold place in earth Despite this diversity, all prokaryotic cells share many structural and functional metabolic properties with each other… and with the archaea and eukaryotes! As we have seen with ribosomes, shared structural and functional properties support the common ancestry of all life. We do not only share common ancestry with prokaryotes, we even share living arrangements with them. Our gut bacteria represent up to 10X more cells than our own! The Fundamental Units of Life Domains of Life: The Archaebacteria (Archaea) 1776 - Allessandro Volta, discovered methane producing bacteria (methanogens) living in the extreme environment at the bottom of Lago Maggiore, a lake shared by Italy and Switzerland. These unusual bacteria are cheomoautotrophs that get energy from H2 and CO2 and also generate methane gas in the process. 1960s - Thomas Brock discovered thermophilic bacteria living at temperatures approaching 100oC in Yellowstone National Park in Wyoming. Organisms living in any extreme environment were called extremophiles. One of the thermophilic bacteria, now called Thermus aquaticus, became the source of Taq polymerase, the heat-stable DNA polymerase that made the polymerase chain reaction (PCR) a household name in labs around the world! Here are some examples of extremophiles: Acidophiles: grow at acidic (low) pH. Alkaliphiles: grow at high pH. Halophiles: require high salt concentrations; see Halobacterium salinarium Methanogens: produce methane; Barophiles: grow best at high hydrostatic pressure. Psychrophiles: grow best at temperature 15 °C or lower. Xerophiles: growth at very low water activity (drought or near drought conditions). Thermophiles and hyperthermophiles: organisms that grow best at 40°C or higher, or 80°C or higher Toxicolerants: grow in the presence of high levels of damaging elements (e.g., pools of benzene, nuclear waste) The Fundamental Units of Life Domains of Life: The Eukaryotes Eukaryotic cells are cells that contain a nucleus. Eukaryotic cells are usually larger than prokaryotic cells. They are found in some single-celled and all multicellular organisms. Organisms with eukaryotic cells are called eukaryotes, and they range from fungi to people. Besides a nucleus, eukaryotic cells also contain other organelles. An organelle is a structure within the cytoplasm that performs a specific job in the cell. Organelles called mitochondria, for example, provide energy to the cell, and organelles called vacuoles store substances in the cell. Organelles allow eukaryotic cells to carry out more functions than prokaryotic cells can. The Fundamental Units of Life Domains of Life: The Eukaryotes Structure Location Description A projection used for locomotion in some Flagellum Outside the cell eukaryotic cells Plasma Phospholipid bilayer Outer layer of cell Membrane enclosing the cytoplasm Entire region between the plasma Bound by membrane and the nuclear envelope, Cytoplasm the plasma consisting of organelles suspended in membrane the gel-like cytosol, the cytoskeleton, and various chemicals A series of stacked membranes that sorts, Golgi Vesicles Cytoplasm tags, and packages lipids and proteins for (Golgi Apparatus) distribution free-floating or on Ribosomes Involved in protein synthesis rough ER The Fundamental Units of Life Domains of Life: The Eukaryotes Structure Location Description Interconnected membranous structures that Rough are studded with ribosomes and engage Endoplasmic Cytoplasm in protein modification and phospholipid Reticulum synthesis Interconnected membranous structures that have few or no ribosomes on its cytoplasmic Smooth surface and synthesize carbohydrates, lipids, Endoplasmic Cytoplasm and steroid hormones; detoxifies certain Reticulum chemicals (like pesticides, preservatives, medications, and environmental pollutants), and stores calcium ions (singular = mitochondrion) cellular organelles responsible for carrying Mitochondria Cytoplasm out cellular respiration, resulting in producing ATP, the cell’s main energy -carrying molecule The small, round organelle Peroxisome Cytoplasm that contains hydrogen peroxide, and detoxifies many poisons Chapter 1 Cells: The Fundamental Units of Life Domains of Life: The Eukaryotes Structure Location Description Organelle in an animal cell that functions as the cell’s digestive component; it breaks Lysosome Cytoplasm down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles Small, membrane-bound sac that functions in cellular storage and transport; its Secretory membrane is capable of fusing with Cytoplasm Vesicle the plasma membrane and the membranes of the endoplasmic reticulum and Golgi apparatus Centrosome Region in animal cells made of two centrioles (with 2 Cytoplasm that serve as an organizing center for centrioles) microtubules The Fundamental Units of Life Domains of Life: The Eukaryotes Structure Location Description The cytoskeleton's narrowest element; it Actin Cytoskeleton provides rigidity and shape to the cell Filaments and enables cellular movements Cytoskeletal component, comprised of several fibrous protein intertwined strands, Intermediate Cytoskeleton that bears tension, supports cell-cell Filaments junctions, and anchors cells to extracellular structures The cytoskeleton’s widest element; provides a track along which vesicles move through Microtubules Cytoskeleton the cell, pulls replicated chromosomes to opposite ends of a dividing cell, and is the structural element of centrioles Protein fiber network that collectively maintains the cell’s shape, secures some Cytoskeleton Throughout cell organelles in specific positions and allows cytoplasm and vesicles to move within the cell The Fundamental Units of Life Domains of Life: The Eukaryotes Structure Location Description Cell organelle that houses the cell’s DNA and Nucleus Cytoplasm directs ribosome and protein synthesis Pores in the nuclear envelope allow Nuclear Pore Nucleus substances to enter and exit the nucleus. Nuclear Double-membrane structure that Nucleus Envelope constitutes the nucleus’ outermost portion Protein-DNA complex that serves as the Chromatin Nucleus chromosomes’ building material Darkly staining body within the nucleus that Nucleolus Nucleus is responsible for assembling ribosome subunits The Fundamental Units of Life Vital tools in cell biology Fluorescence microscope Fluorescent dyes used for Light microscope staining cells use visible light to illuminate specimens dyes absorb light at one viewed using optical glass lenses wavelength and emit it at allows us to magnify cells up to 1000 times another, longer wavelength and to resolve details as small as 0.2 μm. Some dyes bind specifically to used to observed live specimens particular molecules in cells and can reveal their location. Thiel et al., 2019 The Fundamental Units of Life Vital tools in cell biology Electron microscope generates an image by passing electrons through, or reflecting electrons from a specimen, and capturing the electron image on a screen Transmission electron microscopy (TEM) Similar principle with light microscope, except uses a beam of electrons and magnetic coils to focus higher magnification (up to 106X) and resolution (2.0 nm) magnify cells up to a million-fold and resolve details as small as about 1 nm Scanning Electron Microscopy (SEM) creates striking images of three-dimensional objects can magnify up to 105X with a resolution of 3.0-20.0 nm resolve details between 3 nm and 20 nm The Fundamental Units of Life Vital tools in cell biology Transmission electron microscope image shows SARS-CoV-2, the virus that causes COVID-19, isolated from a patient in the This image shows a collection of particles (coloured pink) of the new coronavirus, SARS-CoV-2, emerging U.S. Virus particles are emerging from the surface of cells from an infected cell in a scanning-electron- cultured in the lab. The spikes on the outer edge of the virus particles give coronaviruses their name, crown-like.NIAID- microscope image. NIAID-RML/de Wit/Fischer RML References: Alberts, B., Bray, D., Hopkin, K., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P. 2014. Essential Cell Biology. Fourth edition. Garland Science, Taylor & Francis Group, LLC Bergtrom, G. 2021. Basic Cell and Molecular Biology. Open Education Resource (OER) LibreTexts Project