Introduction to Microbes and Cellular Biology PDF

MICROBIOLOGY & PARASITOLOGY Introduction to Microbes and Cellular Biology Dennis Espineli Salcedo, PhD School of Medical Technology  CONTENTS 1. Introduction 2. Eukaryotic Cell Structure 3. Prokaryotic Cell Structure 4. Summary of Structural Differe...

MICROBIOLOGY & PARASITOLOGY Introduction to Microbes and Cellular Biology Dennis Espineli Salcedo, PhD School of Medical Technology  CONTENTS 1. Introduction 2. Eukaryotic Cell Structure 3. Prokaryotic Cell Structure 4. Summary of Structural Differences between Prokaryotic and Eukaryotic Cells 5. Reproduction of Organisms and Their Cells 6. Taxonomy 7. Evolution and the Tree of Life 8. Determining Relatedness among Organisms Introduction The cell is the fundamental unit of any living organism because it exhibits the basic characteristics of life. There are two categories of cells: eukaryotic and prokaryotic. Some microbes are prokaryotes (bacteria and archaea), some are eukaryotes (algae, protozoa, fungi), and some are not composed of cells (viruses, prions, viroids). Acellular and Cellular Microbes Introduction Eukaryotic cells contain a “true” nucleus, whereas prokaryotic cells do not. A true nucleus consists of nucleoplasm, chromosomes, and a nuclear membrane. Eukaryotic cells possess a complex system of membranes and membrane-bound organelles, whereas prokaryotic cells do not. Both eukaryotic and prokaryotic cells possess a cell membrane. Cell membranes have selective permeability, allowing only certain substances to pass through them. EUKARYOTIC CELL STRUCTURE Eukaryotic Cell Structure The Eukaryotic Nucleus It is the “command center” of the cell. It has three components: nucleoplasm, chromosomes, and a nuclear membrane. Chromosomes are embedded in the nucleoplasm. Eukaryotic chromosomes consist of linear DNA molecules and proteins. 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). The Eukaryotic Nucleus Although most genes code for proteins, some code for two 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 25,000 genes. Other Eukaryotic Cell Structures Cytoplasm A semifluid, 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 Endoplasmic reticulum (ER) 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 Ribosomes Consist of ribosomal RNA and protein The sites of protein synthesis Other Eukaryotic Cell Structures 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 (“packaging plants”) Lysosomes and peroxisomes Originate in the Golgi complex Lysosomes contain lysozyme and other digestive enzymes Peroxisomes are membrane-bound vesicles where H2O2 is generated and broken down Other Eukaryotic Cell Structures Mitochondria “Power plants,” “powerhouses,” or “energy factories” ATP molecules are produced within mitochondria by cellular respiration Number of mitochondria varies depending on the activities of the cell Plastids Membrane-bound structures containing photosynthetic pigments They are sites of photosynthesis Chloroplasts are a type of plastid; they contain chlorophyll Other Eukaryotic Cell Structures Cytoskeleton A system of fibers throughout the cytoplasm Three types of fibers: microtubules, microfilaments, and intermediate filaments Microtubules and microfilaments are essential for a variety of activities Cell wall Some eukaryotic cells contain cell walls--an external structure to provide shape, protection, and rigidity Simpler in structure than prokaryotic cell walls Chitin found in cell walls of fungi; cellulose in cell walls of algae and plants Other Eukaryotic Cell Structures Other Eukaryotic Cell Structures Flagella and cilia (contain microtubules) Cross sections of cilia showing Some eukaryotic cells (e.g., spermatozoa and the 9 + 2 arrangement of microtubules 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, and 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). PROKARYOTIC CELL STRUCTURE Prokaryotic Cell Structure Prokaryotic cells are about 10 times smaller than eukaryotic cells. Prokaryotic cells are simple compared to eukaryotic cells. Prokaryotic cells reproduce by binary fission. All bacteria are prokaryotes, as are archaea. Unlike eukaryotic cells, the cytoplasm of prokaryotic cells is not filled with internal membranes. The cytoplasm of prokaryotic cells is surrounded by a cell membrane, a cell wall (usually), and sometimes a capsule or slime layer. Prokaryotic Cell Structure Cell membrane Similar in structure and function to the eukaryotic cell membrane Selectively permeable Many enzymes are attached to the cell membrane where metabolic reactions take place Chromosome Prokaryotic chromosome usually consists of a single, long, supercoiled, circular DNA molecule and serves as the control center of the cell Plasmids are small, circular molecules of DNA that are not part of the chromosome (extra-chromosomal) Prokaryotic Cell Structure Cytoplasm It is a semiliquid 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. Prokaryotic ribosomes are smaller than eukaryotic ribosomes, but their function is the same--they are the sites of protein synthesis Prokaryotic Cell Structure Bacterial cell wall A rigid exterior that defines the shape of Structure of Peptidoglycan bacterial cells--chemically complex Main constituent of most bacterial cell walls is peptidoglycan (found only in bacteria) Gram-positive bacteria have a thick layer of peptidoglycan; Gram-negative bacteria have a much thinner layer. Mycoplasma spp. do not have a cell wall; they are pleomorphic. Gram-Negative and Gram-Positive Cell Walls Prokaryotic Cell Structure Glycocalyx (slime layers and capsules) Capsule Staining Some bacteria possess glycocalyx, a slimy, (Example of a Negative Staining Technique) gelatinous material produced by the cell membrane and secreted outside the cell wall. There are two types of glycocalyx--slime layer (loosely connected to the cell wall) and capsule (highly organized and firmly connected). Pseudomonas spp. produce a slime layer Klebsiella pneumoniae, Neisseria meningitidis, and Streptococcus pneumoniae possess a capsule, which serves an antiphagocytic function. Prokaryotic Cell Structure Four Basic Types of Flagellar Flagella Arrangement on Bacteria Motile bacteria possess flagella--whip-like appendages composed of threads of protein called flagellin. Number and arrangement of flagella are characteristic of a particular species: 1. Peritrichous bacteria--flagella over entire surface 2. Lophotrichous bacteria--tuft of flagella at one end 3. Amphitrichous bacteria--one or more flagella at both ends 4. Monotrichous bacteria--single polar flagellum A Peritrichous Salmonella Cell Prokaryotic Cell Structure Proteus vulgaris Cell, Showing Many Pili and Several Flagella Pili (also called fimbriae) They are hairlike structures, most often observed on Gram-negative bacteria. They are composed of polymerized protein molecules called pilin. Pili are thinner than flagella, have a rigid structure, and are not associated with motility. They enable bacteria to anchor themselves to surfaces. Some bacteria possess a sex pilus for conjugation.  Terminal and Subterminal Spores Prokaryotic Cell Structure 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, which generates into one vegetative bacterium. Endospores can be visualized using a spore stain. Recap of Structural Differences between Prokaryotic and Eukaryotic Cells Eukaryotic cells contain a true nucleus, prokaryotic cells do not. Eukaryotic cells are divided into plant and animal types. Animal cells do not have a cell wall, plant cells have a simple cell wall. Eukaryotic cells contain membranous structures and many membrane- bound organelles; prokaryotic cells possess no membranes other than the cell membrane that encloses the cytoplasm. Reproduction of Organisms and Their Cells Prokaryotic cell reproduction Prokaryotic cells reproduce by a process known as binary fission--one cell splits in half to become two daughter cells. Before a prokaryotic 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, Escherichia coli has a generation time of about 20 minutes). Binary Fission Taxonomy Taxonomy is the science of classification K for Kingdom of living organisms. D for Division Taxonomy consists of classification, C for Class nomenclature, and identification. O for Order Classification is the arrangement of F for Family organisms into taxonomic groups (known G for Genus as taxa). S for species Tool for remembering the sequence of taxa “King David Came Over for Good Spaghetti” KDCOFGS— Microbial Classification The science of taxonomy was established based on the binomial system of nomenclature. In the binomial system, each organism is given two 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. Microbial Classification (cont.) Organisms are categorized into larger groups based on their similarities and differences. The Five-Kingdom System of Classification 1. Bacteria and archaea--Kingdom Prokaryotae 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. Microbial Classification (cont.) The Three-Domain System of Classification 1. Archaea (prokaryotic) 2. Bacteria (prokaryotic) 3. Eucarya (all eukaryotic organisms) The Three-Domain System is based on differences in the structure of certain ribosomal RNA (rRNA) molecules among organisms in the three domains.  The Three Domains Organisms are categorized into each domain based on unique characteristics. What is the difference between Bacteria Archaea and Eukarya? Bacteria are prokaryotes, meaning they are microscopic unicellular organisms that do not have a nucleus or organelles. Bacteria species are very diverse and include many pathogens (disease-causing bacteria), probiotics (beneficial bacteria), and cyanobacteria. The Archaea are also prokaryotes but have a genome that is very different from bacteria. Many Archaea are extremophiles that live in harsh environments. Eukarya are organisms that can be unicellular or multicellular and have eukaryotic cells. These cells have a nucleus and membrane-bound organelles. Organisms in the domain Eukarya include animals, plants, fungi, and algae. The Three Domains (cont’d) Determining Relatedness among Organisms The most widely used technique for gauging diversity or “relatedness” of organisms is called 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 prokaryotes and the 18S rRNA gene in eukaryotes. To determine how closely related one prokaryotic organism is to another, scientists compare the sequence of nucleotide base pairs in the 16S rRNA gene from one of the organisms with the sequence of base pairs in the 16S rRNA gene from the other organism. The more similar the sequence of base pairs, the more closely related are the organisms. Charles Darwin Charles Darwin (1809–1882) An English naturalist whose scientific theory of evolution by natural selection became the foundation of modern evolutionary studies. Darwin proposed that species can change over time, that new species come from pre-existing species, and that all species share a common ancestor. In this model, each species has its own unique set of heritable (genetic) differences from the common ancestor, which have accumulated gradually over very long time periods. THANKS FOR LISTENING