A Tour of the Cell PDF - Biology Foundation Programme 2024/2025

A tour of the cell Lívia Eiselleová, PhD. [email protected] Biology - Foundation programme 2024/2025 What we will talk about what is a CELL history of cell research cell theory chemical composit...

A tour of the cell Lívia Eiselleová, PhD. [email protected] Biology - Foundation programme 2024/2025 What we will talk about what is a CELL history of cell research cell theory chemical composition of cells macromolecules – sacchcarides, proteins, nucleic acids, lipids prokaryotic and eukaryotic cell: basic characteristics Bacteria, Archea medically important prokaryotic organisms What is a cell? The cell (from Latin cella, meaning "small room") basic structural, functional, and biological unit of all known living organisms the study of cells is called cell biology cells consist of cytoplasm enclosed within a membrane, which contains many biomolecules (proteins, nucleic acids, saccharides and lipids) organisms can be classified as: unicellular (consisting of a single cell; including bacteria) multicellular (including fungi, plants and animals) cells are of two types: eukaryotic ( with nucleus) prokaryotic (without nucleus) History of cell research 1595 Zacharias Jensen creates the first microscope 1655 Robert Hooke discovers cells in cork, then in living plant tissue using an early compound microscope. He coins the term cell (from Latin cella, meaning "small room") still used in biology today 1656 Antonie van Leeuwenhoek teaches himself to make lenses, constructs basic optical microscopes and draws protozoa from rain water, and bacteria from his own mouth 1839 Theodor Schwann and Matthias Jakob Schleiden elucidate the principle that plants and animals are made of cells, concluding that cells are a common unit of structure and development, and thus founding the cell theory Zacharias Jensen’s microscope Antonie van Leeuwenhoek and his microscope History of cell research 1855 Rudolf Virchow states that new cells come from pre-existing cells by cell division (omnis cellula ex cellula) 1859 The belief that life forms can occur spontaneously (generatio spontanea) is contradicted by Louis Pasteur 1931 Ernst Ruska builds the first transmission electron microscope (TEM) at the University of Berlin. By 1935, he has built an EM with twice the resolution of a light microscope, revealing previously unresolvable organelles 1953 Watson and Crick made their first announcement on the double helix structure of DNA on February 28 1981 Lynn Margulis published Symbiosis in Cell Evolution detailing the endosymbiotic theory Cell theory cell theory - unifying concept in biology that includes germ theory, genetics, and evolutionary theory: 1 All living organisms are composed of one or more cells. 2 The cell is the basic unit of structure and organization in organisms. 3 Cells come from pre-existing cells. The modern version of the cell theory: 1 Energy flow occurs within cells. 2 Heredity information (DNA) is passed on from cell to cell. 3 All cells have the same basic chemical composition. Chemical composition of cells of the 90 naturally occurring elements on Earth, only 12 (C, H, O, N, P, S, Na, K, Ca, Mg, Fe, Cl) are found in living systems in more than trace amounts (0.01% or higher) of these 12, the first 4 elements (carbon, hydrogen, oxygen, and nitrogen) constitute 96.3% of the weight of your body the majority of molecules that make up your body are compounds of carbon, which we call organic compounds a. In this representation, the frequency of elements that occur in the Earth’s crust is indicated by the height of the block. Elements shaded in green are found in living systems in more than trace amounts. b. Common elements found in living systems are shown in colors that will be used throughout the text. Carbon the framework of biological molecules consists predominantly of carbon atoms bonded to other carbon atoms or to atoms of oxygen, nitrogen, sulfur, phosphorus, or hydrogen carbon atoms can form up to four covalent bonds, molecules containing carbon can form different shapes: straight chains, branches, or even rings, balls, tubes, and coils carbon and its compounds are studied by organic chemistry Straight chain Branched chain Ring Macromolecules carbohydrates, nucleic acids, proteins, and lipids in many cases, these macromolecules are polymers Polymer - long molecule built by linking together a large number of small, similar chemical subunits called monomers Macromolecules in the cellular context carbohydrates, nucleic acids, and proteins, all form polymers - a long molecule built by linking together a large number of small, similar chemical subunits called monomers lipids do not fit this simple monomer–polymer relationship, however, because they are constructed from glycerol and fatty acids Sacharides carbohydrates - group of molecules that all contain carbon, hydrogen, and oxygen in the molar ratio 1:2:1 they contain many carbon–hydrogen (C—H) bonds, which release energy when oxidation occurs, thus carbohydrates are well suited for energy storage the simplest of the carbohydrates are the monosaccharides (Greek mono, “single,” and Latin saccharum, “sugar”) Monosaccharides, or simple sugars, can contain as few as three carbon atoms and are often used as building blocks to form larger molecules. The fi ve-carbon sugars ribose and deoxyribose are components of nucleic acids. The carbons are conventionally numbered from the more oxidized end. The most common disaccharides in living organisms disaccharides - transport molecules in plants and nutrition in animals transport forms of sugars are commonly made by linking two monosaccharides together to form a disaccharide (Greek di, “two”) disaccharides serve as effective reservoirs of glucose glucose + fructose = sucrose Sucrose is the form most plants use to transport glucose and is the sugar that most humans and other animals eat. glucose + galactose = lactose The most common polysaccharides in living organisms Glycogen is found in animal cells and is highly brancched, insoluble, forming glycogen granules Starch is found in plants, composed of amylose and amylopectin Cellulose unbranched and forms long fibers cellulose fibers can be very strong and are quite resistant to metabolic breakdown Chitin principal structural element in the external skeletons of many invertebrates (lobster) Nucleic acids – information molecules Two main varieties of nucleic acids deoxyribonucleic acid (DNA) ribonucleic acid (RNA) monomers: nucleotides Each nucleotide consists of three components: pentose, or five-carbon sugar (ribose in RNA and deoxyribose in DNA) phosphate (—PO4 ) group organic nitrogenous (nitrogen-containing) base Nucleic acids are able to produce precise copies of themselves – preservation of genetic information DNA – stores genetic information found predominantly in the nuclear region of cells (in the nucleus in eukaryotic cells) double stranded encodes the genetic information RNA – processes genetic information single stranded found in the nucleus and the cytoplasm as well Various types of RNA messenger RNA (mRNA) transcribes genetic information into single- stranded copies of DNA (transcription) other RNA (transfer RNA - tRNA and ribosomal RNA - rRNA) rewrite this information in to lenguage of proteins (translation) both processes are important for expression of genetic information Proteins – molecules with diverse structures and functions coded by DNA in the nucleus linear polymers made with 20 different amino acids the covalent bond that links two amino acids is called a peptide bond protein’s structure and function is determined by specific order of amino acid in polypepide chain Functions of proteins enzyme catalysis (enzymes) defense (cell surface antigens) transport (membrane transporters) regulation (hormones) motion (muscle) support (fibers) storage (ion-binding) Proteins have levels of structure Primary structure: amino acid sequence Secondary structure: hydrogen bonding patterns Tertiary structure: folds and links Quaternary structure: subunit arrangements Lipids – hydrophobic molecules fats - complex polymers of fatty acids (long-chain hydrocarbons with a carboxylic acid (COOH) at one end) attached to a glycerol (three-carbon polyalcohol (three —OH groups) insoluble in water Lipids - energy storage molecules the ratio of energy storing C—H bonds in fats is more than twice that of carbohydrates lipids may be broadly defined as hydrophobic or amphiphilic the amphiphilic nature of some lipids allows them to form structures such as liposomes, or membranes in an aqueous environment phospholipids are the main structural component of biological membranes Two types of cells – prokrayotic and eukaryotic cell Prokaryotes pro = „before“, karyon = „nucleus“ nucleoid (plural: “nucleoids“) = nucleus-like do not have a real nucleus (DNA freely floates in the cytoplasm Eukaryotes eu = „true“, karyon = „nucleus “ nucleus (plural: “nuclei“) - DNA enveloped with a membrane nucleolus (plural: “nucleoli“) - site of RNA synthesis they do contain nucleus Prokaryotic cell within the tree of life prokaryotic cells – bacteria and archea Major characteristics of the three domains Property Archaea Bacteria Eukarya Ether-linked Ester-linked Ester-linked lipids, various Cell Membrane lipids, pseudopeptidoglyca lipids, peptidoglycan structures n Multiple, linear Circular chromosomes, Circular chromosomes, chromosomes, similar Gene Structure similar translation and unique translation and translation and transcription to Eukarya transcription transcription to Archaea No membrane-bound No membrane-bound Membrane-bound Internal Cell Structure organelles or nucleus organelles or nucleus organelles and nucleus Various, including Various, photosynthesis, aerobic Photosynthesis and Metabolism with methanogenesis uniq and anaerobic respiration, cellular respiration ue to Archaea fermentation, and autotrophy Asexual reproduction, Asexual reproduction, Sexual and asexual Reproduction horizontal gene transfer horizontal gene transfer reproduction Prokaryotic cell – basic characteristics pro = „before“, karyon = „nucleus“ no nucleus within the cytoplasm no membrane-bound organelles DNA contains 1 circular chromosome cell membrane present ribosomes different from eukaryotes some may have flagella for movement same may have a capsulle – role in adhesion examples: bacteria, cyanobacteria, archea Eukaryotic cell – basic characteriscs eu = „real“ , karyon = „nucleus“ they contain a nucleus DNA within the nucleus in form of linear chromosomes cytoplasm present have many specialized membrane-bound organelles outer boundary is cell membrane except in plants and fungi (cell wall made of cellulose or chitin) some have flagella/cillia for active movement examples: protozoans, algae, fungi, plants, animals Prokaryotic and eukaryotic cell – basic differences Prokaryotic and eukaryotic cell – what they have in common Comparison of prokaryotic and eukaryotic cell Bacteria bacteria are unicellular (cyanobacteria multicellular) no membrane-bound organelles (no nucleus) basic cellular components: nucleoid (typically 1 „circular“ DNA molecule) cytoplasm cell membrane cell wall ribosomes (different from eukaryotic) in some species or individuals: plasmids flagella or pili (move, conjugation) glycocalyx (glycoprotein coat- protection) capsulle cytoplasmic inclusions - drops and crystals of various molecules, pigments Genetic information of bacteria always double-stranded (ds) DNA genomic DNA nucleoid, nucleus-like DNA, bacterial chromosome in all prokaryotes usually a circular molecule freely embedded in the cytoplasm plasmid DNA in some cells only (usually a small circular molecule) „advantageous“ genetic information (antibiotic resistance, proteins responsible for higher pathogenicity) important tool in molecular biology for production of GMO Diverse types of prokaryotic metabolism phototrophs - energy from the sun chemotrophs - energy from chemical compounds autotrophs - fixing carbon from CO​2​ heterotrophs - carbon from organic compounds of other organisms prokaryotes play key roles in the cycling of nutrients through ecosystems A key to prokaryotic metabolism Classification according to oxygen need Aerobic need source of oxygen for their metabolism and survival - Bordetella pertussis (whooping cough), Mycobacterium sp., Mycoplasma pneumoniae, Legionella sp., Neisseria sp.,... Anaerobic do not need oxygen (obligate vs. facultative vs. aero-tolerant) - Escherichia coli, Listeria sp., Salmonella sp. Shigella sp., Clostridium tetani (tetanus), Clostridium botulinum (food poisoning), Enterococcus sp., Borrelia burgdorferi... Classification according to the morphology Classification according to the cell wall composition – Gram’s staining differentiates bacteria by the properties of their cell walls by detecting peptidoglycan gram-positive (Staphylococcus sp., Streptococcus sp, Clostridium sp, Listeria sp.) gram-negative (Escherichia coli, Salmonella sp., Pseudomonas sp., Helicobacter pylori) valuable diagnostic tool - the Gram stain is the first step in the preliminary identification of a bacterial organism Cyanobacteria gram-negative form single cells or cluster colonies of differentiated cells obtain energy through photosynthesis probably progenitors of plant chloroplasts - endosymbiotic theory they can fix atmospheric nitrogen in anaerobic conditions they contain compounds that can cause allergies, some species can be toxic eutrophication of waters - negative environmental effects - hypoxia, the depletion of oxygen in the water - death to aquatic animals Archea single celled-prokaryotes, initialy classified as bacteria they have unique properties – similar to bacteria but they they possess genes and metabolical pathways that are more closely related to those of eukaryota they lack peptidoglycan in their cell walls extremophiles living in harsh environments Medically important prokaryotic organisms pathogenic bacteria are bacteria that can cause infection although most bacteria are harmless or often beneficial, several are pathogenic. Mycobacterium tuberculosis causes tuberculosis, which kills about 2 million people a year, highly aerobic and requires high levels of oxygen first discovered in 1882 by Robert Koch Staphylococcus aureus gram-positive coccal bacterium, frequently found in the nose, respiratory tract, and on the skin not always pathogenic, it is a common cause of skin infections such as abscesses, respiratory infections such as sinusitis, and food poisoning Medically important prokaryotic organisms Streptococcus pneumonie spherical Gram-positive bacteria significant human pathogenic bacterium, major cause of pneumonia in the late 19th century. Salmonella sp. genus of rod-shaped (bacillus) gram- negative bacterium strains of Salmonella cause illnesses such as typhoid fever, paratyphoid fever, and food poisoning (salmonellosis) many infections are due to ingestion of contaminated food Medically important prokaryotic organisms Clostridium tetani is a rod-shaped, anaerobic species of pathogenic bacteria C. tetani produces a potent biological toxin, tetanospasmin, and is the causative agent of tetanus, a disease characterized by painful muscular spasms that can lead to respiratory failure and, in up to 10% of cases, death Treponema pallidum is a spirochaete gram – negative bacterium with subspecies that cause treponemal diseases such as syphilis Treatment bacterial infections may be treated with antibiotics, they can be: bacteriocidal bacteriostatic in 1928, Alexander Fleming identified penicillin, the first chemical compound with antibiotic properties resistance of bacteria to antibiotics is a common phenomenon and is connected to their overuse antibiotics are not effective against viruses Symbiotic bacteria in our gut - microbiome the gut microbiota has the largest numbers of bacteria intestinal bacteria play a role in synthesizing vitamin B and vitamin K as well as metabolizing the side products of our metabolism dysregulation of the gut flora has been correlated with a host of inflammatory and autoimmune conditions over 99% of the bacteria in the gut are anaerobes Symbiotic bacteria in our gut Escherichia coli gram-negative, facultatively anaerobic, rod- shaped bacterium benefits their host by producing vitamin K, natural antibiotics thus preventing the establishment of pathogenic bacteria and decomposition of food residues important in research - prokaryotic model organism Lactobacillus gram-positive, facultative anaerobic, rod-shaped, bacterium convert lactose and other sugars to lactic acid  Thank you for your attention Lívia Eiselleová, PhD. [email protected] Assoc. Prof. MUDr. Iva Slaninová, Ph.D. [email protected] Biology - Foundation programme 2024/2025