Chapter 3. Cell Structure and Taxonomy PDF

Burton's Microbiology for the Health Sciences Section II. Introduction to Microbes and Cellular Biology Chapter 3. Cell Structure and Taxonomy Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Introduction The cell is the fundamental unit of any living organism because it exhibi...

Burton's Microbiology for the Health Sciences Section II. Introduction to Microbes and Cellular Biology Chapter 3. Cell Structure and Taxonomy Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Introduction The cell is the fundamental unit of any living organism because it exhibits the basic characteristics of life (obtains nutrients, metabolism, mutant) Cytology: study of structure and function of the cell There are two categories of cells: eucaryotic and procaryotic. Some microbes are procaryotes (bacteria and archaea), some are eucaryotes (algae, protozoa, fungi), and some are not composed of cells (viruses, prions, viroids) regressive evolution (genes+protein) use energy and metabolism of the cell. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Acellular and Cellular Microbes Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Introduction, cont. Eucaryotic cells contain a “true” (eu) nucleus (caryo), whereas procaryotic cells do not. A true nucleus consists of nucleoplasm, chromosomes, and a nuclear membrane. Eucaryotic cells (10-30 µm) possess a complex system of membranes and membrane-bound organelles, whereas procaryotic cells do not. Both eucaryotic and procaryotic cells possess a cell membrane. Cell membranes have selective permeability, allowing only certain substances to pass through them. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Eucaryotic Cell Structure cell membrane is composed of proteins and phospholipids seperate cell from outside Regulates passage of nutrient and waste Selective permeability Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins The Eucaryotic Nucleus The “command center” of the cell. Controls all cellular functions 3 components: nucleoplasm (gelatinous matrix), chromosomes, and nuclear membrane (containing holes). Chromosomes are embedded in the nucleoplasm. Eucaryotic chromosomes consist of linear DNA molecules and proteins (histones). Genes are located along chromosomes. An organism's complete collection of genes is referred to as its genotype or genome. Each gene contains the information to produce one or more gene products (usually proteins). Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins The Eucaryotic Nucleus, cont. Although most genes code for proteins, some code for 2 types of ribonucleic acid (RNA) – Ribosomal ribonucleic acid (rRNA) – Transfer ribonucleic acid (tRNA) The number and composition of chromosomes and the number of genes on each chromosome are characteristic of the particular species of organism. Human diploid cells have 46 chromosomes (23 pairs). It has been estimated that the human genome consists of between 20,000 and 30,000 genes. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Other Eucaryotic Cell Structures Cytoplasm Endoplasmic Reticulum (ER) – A semi-fluid, gelatinous, nutrient matrix – Contains storage granules and a variety of organelles – Each organelle has a specific function – The cytoplasm is where most metabolic reactions occur, (cytosol) – A highly convoluted system of membranes arranged to form a transport network in the cytoplasm – Rough ER has ribosomes attached to it; smooth ER does not Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Other Eucaryotic Cell Structures Ribosomes (18-22 nm) – Consist of ribosomal RNA and protein – The sites of protein synthesis – Polyribosomes, polysomes= clusters of ribosomes with mRNA – Composed of two subunits, in eucaryotes 80S, 40S and 60S (S=Svedberg, sedimentation coefficient) – Subunits are produced in nucleus, then transported to cytoplasm, and only gathered with mRNA to start protein synthesis. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Other Eucaryotic Cell Structures, cont. Lysosomes and Peroxisomes Golgi Complex – Also called the Golgi apparatus or Golgi body – Connects or communicates with ER – Completes the transformation of newly synthesized proteins and packages them for storage or export exocytosis or secretion (“packaging plants”) – Originate in the Golgi complex – Lysosomes contain lysozyme and other digestive enzymes breakdown foreign material and worn out parts of cell and autolysis – Peroxisomes are membrane-bound vesicles where H2O2 is generated and broken down, in mammalian liver Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Other Eucaryotic Cell Structures, cont. Mitochondria (0,5-1 µm and 7 µm in depth) – “Power plants,” “powerhouses,” or “energy factories” – ATP molecules are produced within mitochondria by cellular respiration – Number of mitochondria varies depending on activities of the cell Plastids, in plant cells – Membrane-bound structures containing photosynthetic pigments – They are sites of photosynthesis CO2 to O2 and carbohydrates – Chloroplasts are a type of plastid; they contain chlorophyll Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Other Eucaryotic Cell Structures, cont. Cytoskeleton Cell wall – A system of fibers throughout the cytoplasm – 3 types of fibers: microtubules, microfilaments and intermediate filaments – Microtubules and microfilaments are essential for a variety of activities, division, contraction, motility strengthen and support cell – Some eucaryotic cells contain cell walls – an external structure to provide shape, protection, and rigidity – Simpler in structure than procaryotic cell walls – Polysaccharides (Cellulose, pectin, chitin) and mineral salts – Chitin found in cell walls of fungi; cellulose in cell walls of algae and plants Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Other Eucaryotic Cell Structures, cont. Flagella and Cilia (contain microtubules) – Some eucaryotic cells (e.g., spermatozoa and certain protozoa) possess long, thin, whiplike organelles of locomotion called flagella. – Flagellated cells may possess one or more flagella. – Some cells move by means of cilia, which are shorter, thinner, and more numerous than flagella; described as being “hair-like.” – Cilia can be found on some species of protozoa and certain types of cells in our bodies (e.g., ciliated epithelial cells in the respiratory tract). Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Cilia Cross sections of cilia showing the 9 + 2 arrangement of microtubules. Beat in rhythm and coordination Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Procaryotic Cell Structure Procaryotic cells are about 10 times smaller than eucaryotic cells. E. coli : 1µm wide, 2-3 µm long Procaryotic cells are simple compared to eucaryotic cells. Procaryotic cells reproduce by binary fission. All bacteria are procaryotes, as are archaea. Unlike eucaryotic cells, the cytoplasm of procaryotic cells is not filled with internal membranes. (chromosomes, particles, ribosomes) The cytoplasm of procaryotic cells is surrounded by a cell membrane, a cell wall (usually), and sometimes a capsule or slime layer. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Procaryotic Cell Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Procaryotic Cell Structure, cont. Cell membrane – Similar in structure and function to the eucaryotic cell membrane – Selectively permeable – Flexible and thin, (TEM) – Many enzymes are attached to the cell membrane and metabolic reactions take place there (mesosomes): cell. Resp. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Procaryotic Cell Structure, cont. Chromosome – Procaryotic chromosome usually consists of a single, long, supercoiled, circular DNA molecule – serves as the control center of the cell – Embedded in the cytoplasm, no nucleus, but nucleoid – Contains between 450 -8000 genes – Plasmids are small circular molecules of DNA that are not part of the chromosome (extra-chromosomal), many types, many copies (yeast) – Plasmids code for 10 to several hundreds of genes. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Procaryotic Cell Structure, cont. Cytoplasm – Semi-liquid that consists of water, enzymes, waste products, nutrients, proteins, carbohydrates and lipids – materials required for metabolic functions Cytoplasmic particles – Most are ribosomes, some of which occur in clusters – Procaryotic ribosomes are smaller than eucaryotic ribosomes, but their function is the same – they are the sites of protein synthesis 70S: 50S, 30S. – Cytoplasmic granules in certain bact., consist of starch iron lipid sulfer… Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Procaryotic Cell Structure, cont. Bacterial Cell Wall – A rigid exterior that defines the shape of bacterial cells – chemically complex – Main constituent of most bacterial cell walls is peptidoglycan (murein) (only found in bacteria), polyssacharide chaines liked by proteins chains. – Gram-positive bacteria have a thick layer of peptidoglycan; Gram-negative bacteria have a much thinner layer – L forms or CWD (cell wall deficient) difficult to culture – Mycoplasma spp. do not have a cell wall; they are pleomorphic Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Gram-negative and Gram-positive Cell Walls Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Bacterial Cell Walls A. Gram-positive bacterium B. Gram-negative bacterium Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Procaryotic Cell Structure, cont. Bacterial Glycocalyx (Slime Layers and Capsules) – Some bacteria possess glycocalyx, a slimy, gelatinous material produced by the cell membrane and secreted outside the cell wall – 2 types of glycocalyx – slime layer (loosely connected to the cell wall) and capsule (highly organized and firmly connected) Pseudomonas spp. produces a slime layer (sliding) K. pneumoniae, N. meningitidis and S. pneumoniae possess a capsule, which serves an antiphagocytic function (composed of polysaccharides, lipids and proteins) Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Capsule Stain (Example of a negative staining technique) R-colonies: dry rough S-colonies: mucoid glistening smooth Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Capsules and slime layers Attachment  Protection from phagocytic engulfment.  Resistance to drying.  Depot for waste products.  Reservoir for certain nutrients.   protection  These are structures surrounding the outside of the cell envelope. They usually consist of polysaccharide. They are not essential to cell viability and some strains within a species will produce a capsule, whilst others do not. Capsules are often lost during in vitro culture. Procaryotic Cell Structure, cont. Flagella – Motile bacteria possess flagella – whiplike appendages composed of threads of protein called flagellin (not microtubules), giving motility, – Number and arrangement of characteristic of a particular species: flagella are Peritrichous bacteria – flagella over entire surface Lophotrichous bacteria – flagella at one end Amphitrichous bacteria – flagella at both ends Monotrichous bacteria – single polar flagellum Axial filament: spiral movement Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Four Basic Types of Flagellar Arrangement on Bacteria Can’t be seen with compound microscope; gotta be stained Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins A Peritrichous Salmonella Cell Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Some bacterial species are mobile and possess locomotory organelles - flagella. Flagella consist of a number of proteins including flagellin The diameter of a flagellum is thin, 20 nm, and long with some having a length 10 times the diameter of cell. Due to their small diameter, flagella cannot be seen in the light microscope unless a special stain is applied. Bacteria can have one or more flagella arranged in clumps or spread all over the cell.     Flagella Identification of Bacteria Pathogenesis Pathogenicity Motility of bacteria Monotrichate/Amphitrichate/Lophotrichate/Perit richate Procaryotic Cell Structure (continued) Pili (also called fimbriae) – Hair-like structures, most often observed on Gramnegative bacteria – Composed of polymerized protein molecules called pilin – Pili are thinner than flagella, have a rigid structure and are not associated with motility: – Pili enable bacteria to anchor themselves to surfaces, causing disease. – Some bacteria possess a sex pilus for conjugation Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Proteus vulgaris cell, showing pili and several flagella Pili Flagella Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Pili Procaryotic Cell Structure, cont. Spores (Endospores) – A few genera (e.g., Bacillus and Clostridium) are capable of forming thick-walled spores as a means of survival – The process of spore formation is called sporulation – it is not reproduction – Spores have been shown to survive for many years and are resistant to heat, cold, drying, and most chemicals – Usually one spore is produced in a bacterial cell and generates into one vegetative bacterium (growing and dividing) – Endospores can be visualized using a spore stain, terminal , subterminal Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins A Bacillus Cell With a Well-Defined Endospore Endospore Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Endospores (spores) Dormant cell Resistant to adverse conditions - high temperatures - organic solvents  Identification of Bacteria  Pathogenesis.  Pathogenicity.  Resistance Produced when starved Bacillus and Clostridium Recap of Structural Differences Between Procaryotic and Eucaryotic Cells Eucaryotic cells contain a true nucleus; procaryotic cells do not. Eucaryotic cells are divided into plant and animal types – Animal cells do not have a cell wall, plant cells have a simple cell wall. Eucaryotic cells contain membranous structures and many membrane-bound organelles; procaryotic cells possess no membranes other than the cell membrane that encloses the cytoplasm Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Reproduction of Organisms and Their Cells Procaryotic Cell Reproduction – Procaryotic cells reproduce by a process known as binary fission – one cell splits in half to become two daughter cells. Before a procaryotic cell divides in half, the chromosome must be duplicated. – The time it takes for binary fission to occur is called the generation time. Generation time varies from one species to another and depends on growth conditions (under ideal conditions, E. coli has a generation time of about 20 minutes). Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Binary Fission of a Bacterial Cell Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Taxonomy Taxonomy is the science of classification of living organisms. Taxonomy consists of classification, nomenclature, and identification. Classification is the arrangement of organisms into taxonomic groups (known as taxa). Tool for remembering the sequence of Taxa – “King David Came Over for Good Spaghetti” KDCOFGS, K for Kingdom, D for Division, C for Class, O for Order, F for Family, G for Genus and S for species. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Microbial Classification The science of taxonomy was established based on the binomial system of nomenclature. In the binomial system, each organism is given 2 names – genus and the specific epithet. Taken together, both names constitute the species. – For example, Escherichia coli; Escherichia is the genus and coli is the specific epithet. – The genus is frequently abbreviated with just a single letter, (e.g., E for Escherichia). The abbreviation “sp.” is used to designate a single species and “spp.” for more than one species. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Microbial Classification Organisms are categorized into larger groups based on their similarities and differences. The Five-Kingdom System of Classification 1. Bacteria and archaea – Kingdom Procaryotae 2. Algae and protozoa – Kingdom Protista 3. Fungi – Kingdom Fungi 4. Plants – Kingdom Plantae 5. Animals – Kingdom Animalia Viruses are not included because they are acellular. Other systems of classification do exist. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Microbial Classification (continued) The Three-Domain System of Classification 1. Archaea (procaryotic) 2. Bacteria (procaryotic) 3. Eucarya (all eucaryotic organisms) The Three-Domain System is based on differences in the structure of certain ribosomal RNA (rRNA) molecules among organisms in the 3 domains. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Determining Relatedness Among Organisms The most widely used technique for gauging diversity or “relatedness” of organisms is called ribosomal RNA (rRNA) sequencing. Ribosomes are composed of two subunits; a small subunit and a large subunit. The small subunit is composed of only one rRNA molecule, which is coded for by a gene called the 16S rRNA gene in procaryotes and the 18S rRNA gene in eucaryotes. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Determining Relatedness Among Organisms, cont. To determine how closely related one procaryotic organism is to another, scientists compare the sequence of nucleotide base pairs in the 16S rRNA gene from one of the organisms to the sequence of base pairs in the 16S rRNA gene from the other organisms. The more similar the sequence of base pairs, the more closely related are the organisms. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins