Microorganisms: Friend or Foe PDF

MICROORGANISMS : FRIEND OR FOE  What are Microorganisms? The organisms which are too small to be seen by our naked eyes are called Microorganisms. The study of microorganisms is called Microbiology. Antonie Van Lewenhoek was the first scientist who observed small moving org...

MICROORGANISMS : FRIEND OR FOE  What are Microorganisms? The organisms which are too small to be seen by our naked eyes are called Microorganisms. The study of microorganisms is called Microbiology. Antonie Van Lewenhoek was the first scientist who observed small moving organisms in a drop of lake water under his microscope. He named them “animalcules”.  Where do Microorganisms live? Microorganisms are omni present, i.e. Microorganisms are found everywhere in the air, water, soil and even inside the living organisms. They can survive extreme conditions like hot spring to polar region. Spiral bacteria Rod shaped bacteria They can survive too acidic and too alkaline environment. Under unfavorable condition of temperature and water, they form hard and tough covering called cysts. Chlamydomonas Spirogyra Algae  MICROORGANISMS microscopic organisms that cannot be seen by the naked eye can only be observed under the microscope Most are unicellular. can be divided into a few types; bacteria, protozoa, algae, fungi and viruses.  WHAT IS MICROORGANISM? Tiny living things that are not visible to the naked and can only be viewed under a microscope Classification of microorganism Bacteria Protozoa Algae Fungi Virus  Viruses Protozoa Bread mould Penicillium Aspergillus Fungi Feature Bacteria Virus Fungi Algae Protists Not a cell Cell Type Prokaryotic (acellular) Eukaryotic Eukaryotic Eukaryotic Single or Single or Single-celled, Genetic material multicellular, with multicellular, varied Highly varied, single-celled or Structure simple structure in a protein coat hyphae forms colonial Autotrophic or N/A (relies on Heterotrophic Autotrophic Nutrition heterotrophic host) (absorption) (photosynthesis) Autotrophic or heterotrophic Reproductio Asexual (binary Replicates within a Sexual and n fission) host cell asexual (spores) Sexual and asexual Varied, sexual and asexual N/A (relies on Varied, some with flagella, Motility Some have flagella host) Non-motile Some have flagella cilia, or pseudopods Yeasts, E. coli, Influenza, HIV, mushrooms, Seaweed, diatoms, Amoeba, Paramecium, Examples Streptococcus SARS-CoV-2 molds green algae Euglena, slime molds Decomposers, Decomposers, Primary producers some cause some cause in aquatic Varied, some are parasites, Role disease Cause disease disease, food ecosystems others beneficial  Classification of Microorganisms 1. Based on Characteristics : a) Bacteria : Unicellular, Prokaryotic, occurs in various sizes and shapes. Ex: Lactobacillus b) Fungi : saprophytic, can be unicellular or multicellular. Ex: Penicillium, Aspergillus c) Algae : photosynthetic micro- organisms. Ex: Spirogyra d) Protozoa : unicellular, prokaryotic. Ex: Amoeba e) Virus : neither living nor nonliving. Form the boundary between the living and the nonliving. Ex: Bactriophage, HIV  2. Based on the number of cells: a) Unicellular – most of the protozoans b) Multicellular – most fungi and some algae 3. Based on the significance: Micro- Bacteria Fungi Protozoa Algae Virus organisms Useful Lactobacillus Yeast Tetrahymena Red algae Lambda phage pyriformis Harmful Haemophilus Rhizopus Plasmodium Gymnodinium Picorna influenza Uses of Microorganisms Used in the Used to Used in Used in the preparation of increase soil cleaning up of preparation of curd, bread fertility by environment. medicines. and cake. fixing nitrogen.  What is a bacteria a member of a large group of unicellular microorganisms which have cell walls but lack organelles and an organized nucleus, including some that can cause disease.  Characteristics of Bacteria Bacteria are among the smallest living organisms. They usually band together in colonies. Bacteria can be autotrophic, make their own food heterotrophic, feed off of other organisms Size of bacteria rang between 0.5 to 5 micrometer Have a single chromosome as Genetic material Enclosed in a rigid cell wall made up of peptidoglycan The Main Characteristics BACTERIA Do not have nucleus due to the lack of nuclear membranes. Genetic materials exist in the form of chromosomal threads (DNA) free-floating inside the cytoplasm. Known as the nucleoid. Some bacteria have plasmid, which is small DNA molecules that carry extra genes. Size of Bacteria Evolution of Bacteria Bacteria are considered as the first life-form to arise on the Earth about 4 billion years ago. All other life-forms are evolved from the bacteria. A hyperthermophile of about 2.5 – 3.2 billion years ago was the ancestor of bacteria and archaea that are found in the present time. Endosymbiotic association between different bacteria around 1.6 – 2.0 billion years ago give rise to the first proto-eukaryotic cell, which gradually gives rise to eukaryotes. Ecology (Habitat) of Bacteria Structure of a Bacterial Cell  Structure of Bacteria All cells have 3 main components: – DNA (‘nucleoid”) genetic instructions – surrounding membrane (“cytoplasmic membrane”) limits access to the cell’s interior – cytoplasm, between the DNA and the membrane where all metabolic reactions occur especially protein synthesis, which occurs on the ribosomes Bacteria also often have these features: – cell wall resists osmotic pressure – Flagella-movement – Pili-attachment – Capsule- protection and biofilms Dr.T.V.Rao D 27 External Structure of a Bacteria Flagella Also known as “little whips” Delicate, hair-like process Composed of protein sub-units called flagellin Parts of flagella Responsible for motility Aids in chemotaxis Aids in bacterial pathogenicity and survival External Structure of a Bacteria Parts of Flagella 1. Basal or Granular Body found just beneath the c ell wall & attached to the c ytoplasmic membrane 2. Hook-like structures found attached to the basal body and provides the rotatory movement of the flagellum 3. Filament long, thin, untapered serves as an antennae  External Structure of a Bacteria Classified according to the Number and Location of Flagella 1. Atrichous – no flagellum 2. Monotrichous – one flagellum at one end e.g. Pseudomonas aeruginosa 3. Amphitrichous – flagellum at both ends 4.Lopotrichous – tuft / group of flagella at one end 5. Peritrichous – flagella all over the body e.g. E. coli, Proteus vulgaris External Structure of a Bacteria Pili/Fimbriae They are the short, hollow, non-helical filamentous structure of about 0.5 μm in length and 0.01 μm in diameter. They are exclusively found in Gram- Negative bacteria. They are composed of protein ‘pilin’ arranged non-helically. They are short, numerous, and straight than flagella. Functions of Pili/Fimbriae Aids in adherence to host cells Sex pili helps in bacterial DNA transfer during bacterial conjugation  External Structure of a Bacteria Capsule It is a viscous outermost layer surrounding the cell wall. It is composed of either polysaccharides or polypeptides of both (~2%) and water (~98%). They are present only in some species of bacteria. Functions of Capsule Aids in adherence Prevents from desiccation Confer resistance against phagocytosis The Slime layer protects from proteolytic enzymes  Sheath and Prosthecae Sheath hollow tube-like structure enclosing chain-forming bacteria, mostly aquatic bacteria. It provides mechanical strength to the chain. Prosthecae semi-rigid extension of the cell wall and plasma membrane. It increases nutrient absorption helps in adhesion.  CELL WALL Outermost layer, encloses cytoplasm 1. Confers shape and rigidity 2. 10 - 25 nm thick 1. Composed of complex polysaccharides (peptidoglycan/ mucopeptide) - formed by N acetyl glucosamine (NAG) & N acetyl muramic acid (NAM) alternating in chains, held by peptide chains.  Cell Wall Cell wall – 4. Carries bacterial antigens – important in virulence & immunity 5. Chemical nature of the cell wall helps to divide bacteria into two broad groups – Gram positive & Gram negative 6. Gram +ve bacteria have simpler chemical nature than Gram –ve bacteria. 7. Several antibiotics may interfere with cell wall synthesis e.g. Penicillin, Cephalosporins Dr.T.V.Rao MD 27 Classification of Bacteria Classification of Bacteria based on Oxygen Requirements Bacteria are classified into 3 types as; 1. Aerobic bacteria They respire aerobically and can’t survive in anoxic environments. E.g. Pseudomonas aeruginosa, Nocardia spp., Mycobacterium tuberculosis, etc. 2. Facultative aerobes They survive in very low oxygen levels and can survive in both oxygenic and anoxic environments. They are Microaerophiles. E.g. E. coli, Klebsiella pneumoniae, Lactobacillus spp., Staphylococcus spp., etc. 3. Anaerobic bacteria They respire anaerobically and can’t survive in an oxygen-rich environment. E.g. Clostridium perfinges, Campylobacter, Listeria, Bifidobacterium, Bacteroides, etc.  Classification of Bacteria based on Optimum Temperature 1. Psychrophiles They have optimum growth temperature at 150C or below. E.g. Chryseobacterium, Psychrobaceter, Polaromonas, Sphingomonas, Alteromonas, Hyphomonas, Listeria monocytogenes, etc. 2. Mesophiles They have optimum growth temperature at 15 – 450C. Pathogenic bacteria fall in this category. E.g. E. coli, Staphylococcus aureus, Salmonella Typhi, Streptococcus pyogenes, Klebsiella spp., Pseudomonas spp., etc. 3. Thermophiles They have optimum growth temperature at above 450C. E.g. Bacillus thermophilus, Methanothrix, Archaeglobus, Thermophilus aquaticus, Geogemma barosii (at 1220C), Pyrolobus fumarii (at 1130C), Pyrococcus spp., etc. According to disease causing ability of bacteria, Pathogenic bacteria - Those who cause disease in human Non-Pathogenic bacteria - Those who cannot cause disease in humans According to disease causing ability of bacteria, According to disease causing ability of bacteria, How do bacteria reproduce? Most bacteria reproduce by binary fission. In this process the bacterium, which is a single cell, divides into two identical daughter cells. Binary fission begins when the DNA of the bacterium divides into two (replicates). The bacterial cell then elongates and splits into two daughter cells each with identical DNA to the parent cell. Each daughter cell is a clone of the parent cell.  Reproduction When conditions are favourable such as the right temperature and nutrients are available, some bacteria like Escherichia coli can divide every 20 minutes. This means that in just seven hours one bacterium can generate 2,097,152 bacteria. After one more hour the number of bacteria will have risen to a colossal 16,777,216. That’s why we can quickly become ill when pathogenic microbes invade our bodies. Phases of the Bacterial Growth Cycle 1.) Lag Phase - where the organisms are "getting used to the medium and physical conditions" - that is they are inducing the necessary enzymes for growth. 2.) Logarithmic (Log) Growth Phase - This is the phase where the generation time is measured. The more ideal the conditions, the faster the growth - up to the maximum growth rate for the species. 3.) Stationary Phase - during this phase the number of new cells equals the number of dead cells so that there is no net increase in viable cells. Nutrient are becoming depleted, the pH is changing, toxic wastes are building up, oxygen levels are becoming depleted. 4.) Death Phase - Rate of cell death is faster than regeneration. Death may accelerate and become exponential. factors that grows bacteria  Benefits of Bacteria Makes cheese, yogurt, buttermilk and pickles Produces vitamins in your intestine Helps in digestion of insoluble fibers In industry, bacteria are important in sewage treatment and the breakdown of oil spills, the recovery of gold, copper and other metals in the mining sector Bacteria are also helpful in biotechnology, and the manufacture of antibiotics and other chemicals. Many act as decomposers recycling nutrients Harmful bacteria vs GOOD bacteria  Characteristic Protozoa Unicellular (5µm-250µm) Motile Modes of Nutrition Parasitism Cilium Saprophytism Macronucleus Autotroph Micronucleus Amoeba Oral Food groove vacuole Food vacuole Nucleus Contractile Contractile vacuole vacuole Paramecium  PROTOZOA Animal-like unicellular microorganisms Move around using pseudopodia (false feet), cilia or flagellum Usually found in aquatic habitats. Heterotrophs or autotrophs. Euglena sp. is an autotrophic protozoa with chloroplasts that can undergo photosynthesis. Can be free-living or parasitic  Algae Algae Bloom Accumulation in Characteristic the population of Size 1µm - 10000µm algae result in large Simple aquatic plant scale death of No proper root, stem, aquatic animal and leaves and vascular system plant. Contain chlorophyll Chlamydomonas Modes of Nutrition Autotroph – photosynthesis Have pigment  ALGAE Consist of unicellular microorganisms like Chlamydomonas sp. and multicellular organisms such as the brown algae, Fucus sp. Some algae have flagellum to move in water. Algae have chloroplasts and are therefore autotrophs. However, algae do not have leaves, stems, or roots like plants do. Algae live in ponds, lakes and ocean Kingdom Fungi Overview Fungus comes from the Greek word mykes “Mushrooms” Eukaryotic organism that digests food externally and absorbs nutrients directly through its cell walls Consist of about 100,000 spp. The science dealing with the study of fungi is called Mycology Kingdom Fungi Overview Constitute an enormous variety of living organisms collectively referred to as Eucomycota They include; yeasts, rusts, smuts, mildews, and mushrooms Include also fungus-like protist such as slime molds and water molds General Characteristics: Habitat Most fungi are inconspicuous Found in most habitat Woods and meadows are the best places to go hunting for fungi. Of the two, woods are by far the best place to look, as over 80% of fungi are associated with trees.  GENERAL CHARACTERISTICS OF FUNGI Fungi constitute an extremely diverse group They have a nuclei and of organisms and are They are eukaryotic They ate heterotrophs mitochondria generally classified as molds or yeasts. They do not They depend on other They cant move on their photosynthesis nor have They are multicellular organisms for food own chlorophyl Mildews Molds Mushrooms  Structure of Fungus: YEAST The simplest type of fungus is the unicellular yeast Yeast originated hundreds of millions of years ago 1500 species are currently identified Measure 3-4 microns in diameter Some yeasts grow up to 40u in diameter  Yeast Cryptococcus neoformans is an encapsulated yeast that can live in both plants and animals. Its teleomorph is Filobasidiella neoformans, a filamentous fungus belonging to the class Tremellomycetes. It is often found in pigeon excrement Cryptococcus neoformans  YEAST Saccharomyces — cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to winemaking, baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes.  Structure of Fungus: YEAST Yeast like fungi have Sexual & Asexual Reproductive cycles Most common mode of vegetative growth in yeast is asexual reproduction by budding A small bud or daughter cell is formed on the parent cell The nucleus of the daughter cell splits into a daughter nucleus & enters into daughter cell Bud continues to grow until it separates from mother cell ROLE OF YEASTS IN FOOD SPOILAGE: ▸ The large and diverse group of microscopic foodborne yeasts includes several hundreds species. The ability of yeasts to attack my foods is due to their relatively versatile environmental requirement. Yeasts tend to grow within the food and drink matrices in planktonic form and they tend to ferment sugar, growing well under anaerobic ROLE OF YEASTS IN FOOD SPOILAGE: Several species of yeasts may be hazardous to human health due to their ability to produce toxic metabolites known as mycotoxins. Certain foodborne yeasts can also cause allergic reaction and may cause infections. Characteristics of Fungi: Thallus Organization The plant body of true fungi is a thallus It may be Non-mycelial or mycelia Most fungi are multicellular and are composed of long filaments called hyphae All hyphae in a particular fungus from an interwoven mass called a Mycelium Mycelium may be aseptate or septate Hypha Elongation of the cell produces a tubular thread like structure called the hypha Hypha consists of one or more cells surrounded by a tubular wall In most fungi hypha are divided into cells by internal cross walls called septa Septate Vs. Aseptate identify which on is the Septate Septa are usually perforated by pores large enough for ribosome's, Mitochondria & sometimes nuclei two flow between cells.  Molds Fungi which form Mycelia are called Moulds or filamentous fungi or Fungus that grows in the form of multicellular filaments  Molds There are thousands of mold species Molds have diverse lifestyle – Saprotrophs – Mesophiles – Psychrophiles – Thermophiles – Very few are Opportunistic pathogens of humans These are requiring moisture for growth & some live in aquatic environment  Cladosporium Cladosporium is olive green and thrives on plants in particular, but can also grow on household surfaces like walls, cabinets, and carpets.  Aspergillus Aspergillus is the mold that typically grows on spoiled food like bread. It can also grow on nutrient-poor but moisture-rich environments like the basement.  Penicillium Penicillium is famous for its antibacterial properties and is usually bluish-green. However, it can also emit mycotoxins that are toxic to both people and pets. Penicillium prefers colder environments like soil, but some also form on wet items in the home. Trichophyton rubrum is a fungus that is the most common cause of athlete's Came foot, jock itch, and ringworm. The growth rate of Trichophyton colonies in the lab can be slow to rather quick.  Mycelium are of three kinds: 1. Vegetative mycelium are those that penetrates the surface of the medium and absorbs nutrients. 2. Aerial mycelium are those that grow above the agar surface 3. Fertile mycelium are aerial hyphae that bear reproductive structures such as conidia or sporangia. —  Molds: Those fungi that possess melanin pigments in their cell wall are called phaeoid or dematiaceous and their colonies are coloured grey, black or olive. Those hyphae that don't possess any pigment in their cell wall are called hyaline.  Moulds: Hyphae may have some specialized structure or appearance that aid in identification some of these are: a) Spiral hyphae: These are spirally coiled hyphae commonly seen in Trichophyton mentagrophytes. b) Pectinate body: These are short, unilateral projections from the hyphae that resemble a broken comb commonly seen in Microsporum audouinii.  Moulds: c) Favic chandelier: These are the group of hyphal tips that collectively resemble a chandelier or the antlers of the deer (antler hyphae). They occur in Trichophyton schoenleinii and Trichophyton violaceum. d) Nodular organ: This is an enlargement in the mycelium that consists of closely twisted hyphae. Often seen in Trichophyton mentagrophytes and Microsporum canis.  ROLE OF MOULDS IN FOOD SPOILAGE: ▸ Moulds are filamentous fungi which grow at a pH range of 3-8 and can grow at very low water activity levels (0.7-0.8) which makes them tolerant to many adverse conditions. Some moulds species are also able to grow in refrigerators. They have a diverse secondary metabolites producing no. of toxic and carcinogenic mycotoxins. ▸ They reproduce through spore formation and these spores can easily dispersed through air and cause spoilage on food substrate if conditions are favourable. Structure of Fungi: Mushrooms are fungi What you see are the hyphae On the cap the hyphae are really close together Underground the hyphae are spaced out more  Characteristics of Fungi: Thallus Organization In higher forms the mycelium gets organized into loosely woven structure which looks like a tissue called pletenchyma Pseudoparenchyma- In the fructifications of higher fungi, the hyphae become woven and intertwined into a compact mass. Prosenchyma -It is rather a loosely woven tissue of hyphae. The hyphae- composing it do not lose their identity. They run more or less parallel to one another and are composed of elongated cells. Characteristics of Fungi: Cell Organization Cell wall mainly made up of chitin and cellulose Precisely, the cell wall may be made up of Cellulose-glucan (oomycetes), Chitin chitosan (zygomycetes) Mannan-glucan (ascomycotina), Chitin-mannan (basidiomycotina) Chitin-glucan (some ascomycotina, basidiomycotina and deuteromycotina) General Characteristics: Reproduction Three methods of reproduction; Vegetative Asexual Sexual reproduction reproduction reproduction Reproduction Cont’d: Vegetative Reproduction Any form of asexual reproduction in which a new plant grows from a fragment of the parent plant or a specialized reproductive structure Several types; Fragmentation Budding Fission Example of Fragmentation in Hydra Fragmentation: Pieces of hyphae (the thread-like structures that make up the fungus body) can break off and grow into new individuals.  Example of Budding in Hydra Budding: A small outgrowth (bud) forms on the parent cell, grows, and eventually detaches to become a new individual. This is common in yeasts. Parent Hydra Developing Bud New Bud New Hydra Reproduction Cont’d: Asexual Reproduction Involve a single parent and results in the formation of daughter cells identical to parent cell Spore production: This is the most common method. Spores are tiny, lightweight reproductive units that can be dispersed by wind, water, or animals. They are produced in vast numbers and can survive harsh conditions. Sporangiospores: Formed within a sac-like structure called a sporangium. Conidia: Formed externally on a specialized hypha called a conidiophore. Reproduction Cont’d: Sexual Reproduction Sexual reproduction is found in all groups of fungi except one Deuteromycotina (Fungi imperfecti) Compatible nuclei show specific behavior responsible for the onset of three distinct mycelial phases during sexual reproduction The three phases of nuclear behavior are; Plasmogamy: Two haploid hyphae of compatible mating types fuse, bringing together two genetically different nuclei within the same cell. Karyogamy: The two nuclei fuse to form a diploid zygote. Meiosis: The zygote undergoes meiosis to produce haploid spores, which can then germinate and grow into new individuals. Classification of Fungi: according to nutrition Saprophytic – The fungi obtain their nutrition by feeding on dead organic substances. Examples: Rhizopus, Penicillium and Aspergillus. Parasitic – The fungi obtain their nutrition by living on other living organisms (plants or animals) and absorb nutrients from their host. Examples: Taphrina and Puccinia. Symbiotic – These fungi live by having an interdependent relationship with other species in which both are mutually benefited. Examples: Lichens and mycorrhiza  Classification of Fungi: Kingdom fungi into two Divisions. 1. Division: Myxomycota- Fungi with plasmodium 2. Divison: Eumycota- (mobile multinucleate Fungi with cell wall and mass of cytoplasm without filaments a cell wall  Classification of Fungi The morphology of the mycelium, mode of spore formation and fruiting bodies form the basis for the division of the kingdom into various divisions; Those species that have well-characterized life cycles are placed in one of four phyla, namely; Phylum Chytridiomycota Phylum Zygomycota Phylum Ascomycota Phylum Basidiomycota Phylum Deuteromycota** Chytridiomycota (Chytrids): The simplest and most primitive fungi. Have flagellated spores called zoospores that can swim in aquatic environments.Examples: Allomyces, Synchytrium endobioticum (potato wart)  Zygomycota (Zygomycetes): Common bread molds and other saprophytic fungi. Have coenocytic hyphae (lacking cross-walls) that form thick- walled zygospores for sexual reproduction. Examples: Rhizopus stolonifer (black bread mold), Mucor mucedo (common bread mold)  Ascomycota (Ascomycetes) Sac fungi, named for their sac-like structures called asci that produce spores. Includes yeasts, morels, truffles, and cup fungi. Examples: Saccharomyces cerevisiae (baker's yeast), Penicillium notatum (source of penicillin), Morchella esculenta (morel mushroom)  Basidiomycota (Basidiomycetes): Club fungi, named for their club- shaped structures called basidia that produce spores. Includes mushrooms, toadstools, puffballs, and bracket fungi.Examples: Agaricus bisporus (common white mushroom), Amanita muscaria (fly agaric), Ganoderma lucidum (reishi mushroom) Virus  VIRUS Not included in any of the kingdoms because they are not cellular organisms. Does not carry out any life process outside of a cell. Reproduce using living cells by injecting their genetic materials into host cells. Made up of nucleic acid (DNA or RNA) and capsids made from protein. WE BREATH AND LIVE WITH MILLIONS OF VIRUS EVERY SECOND OF OUR LIVES  Size of a virus is too small (20 nm to 400 nm), therefore virus cannot be seen using a light microscope but can only be seen using an electron microscope. Examples : tobacco mosaic virus, T4 bacteriophage and HIV  What is a virus A virus is an infectious microbe consisting of a segment of nucleic acid (either DNA or RNA) surrounded by a protein coat. A virus cannot replicate alone; instead, it must infect cells and use components of the host cell to make copies of itself.  Viruses Major cause of disease also, importance as a new source of therapy new viruses are emerging Important members of aquatic world move organic matter from particulate to dissolved Important in evolution transfer genes between bacteria, others Important model systems in molecular biology  Virus structure Complete virus particles are virions. Most viruses are from 10 to 300 nm in diameter ( it is smaller than bacteria) Made of DNA or RNA and surrounded by a capsid  Host Range Host range is determined by specific host attachment sites and cellular factors Viruses infect humans, animals, plants , fungi , protozoa, algae and bacterial cells Some viruses called oncogenic viruses or oncoviruses cause specific types of cancer  Viruses' vs Living Viruses have five properties that distinguish them living cells: 1. they possess only DNA or RNA – living cells possess both 2. They are unable to replicate on their own. 3. Unlike cells, they do not divide by binary fission, mitosis or meiosis. 4. they lack the genes and enzymes necessary for energy production 5. they depend on the ribosomes , enzymes and metabolites of the host cell for protein and nucleic acid production  Characteristics Of Viruses They cannot be They have no They contain either They are incapable observed using a internal cellular DNA or RNA, but not of metabolism light microscope structure both Viruses lack cellular Viruses are smaller They replicate only organelles, such as than bacteria inside living cells. mitochondria and ribosomes.  Classification of Viruses Type of genetic material Shape and size of capsid Number of capsomeres Presence or absence of an envelope Type of host it infects Disease it produces Target cell(s) immunologic/ antigenic properties Viruses Diversity General Properties of Viruses Virion complete virus particle consists of >1 molecule of DNA or RNA enclosed in coat of protein cannot reproduce independent of living cells nor carry out cell division but can exist extracellularly  Virions Infect All Cell Types Bacterial viruses called bacteriophages (phages) Few archaeal viruses Most are eukaryotic viruses plants, animals, protists, and fungi Classified into families based on genome structure, life cycle, morphology, genetic relatedness The Structure of Viruses Virion size range is ~10– 400 nm in diameter and most viruses must be viewed with an electron microscope Components of Viruses 1. 3. 4. 2. Capsid Nucleoid Envelope Enzymes. Structure of virus: Nucleoid The nucleoid (meaning nucleus-like) is an irregularly shaped region within the prokaryotic cell that contains all or most of the genetic material. It may be linear or circular with various degrees of coiling. The nucleic acid is either DNA or RNA but never both. Structure of virus: Capsids Large macromolecular structures which serve as protein coat of virus Protect viral genetic material and aids in its transfer between host cells All viruses have capsids nucleocapsid = nucleic acid + caspid Structure of virus: Virus envelopes surrounds the entire capsid. viruses also have an external lipid membrane contain proteins that are specified by the virus, which often help viral particles bind to host cells. Although envelopes are common, especially among animal viruses, they are not found in every virus In contrast to enveloped viruses, the viruses without an envelope are called naked. Common enveloped viruses are HIV, Herpes Virus, Vaccinia Virus, etc.  Structure of virus: Enzymes They are occasional. Enzyme lysozyme is present in the region that comes in contact with host cell in bacteriophages. Reproduction Viruses are obligate intracellular parasites that can reproduce only within a host cell. They do not have Enzymes for metabolism Do not have ribosomes Do not have the equipment to make proteins  Each type of virus can infect and parasitize only a limited range of host cells called its HOST RANGE Some are broad based while other are not. Swine flu virus can infect swine or humans Rabies can infect may mammals Some can parasitize only E. coli Eukaryote viruses are usually tissue specific Viruses use a lock and key fit to identify hosts What is a viral infection? Attachment (Adsorption) Specific receptor attachment Receptor determines host preference – may be specific tissue (tropism) – may be more than one host – may be more than one receptor – may be in lipid rafts providing entry of virus  Viral Entry and Uncoating Varies between naked or enveloped virus Three methods used – fusion of the viral envelope with host membrane; nucleocapsid enters – endocytosis in vesicle; endosome aids in viral uncoating – injection of nucleic acid  Synthesis Stage The key to understanding the genomic expression of viruses is noting the fact that viruses must use host cellular machinery to replicate and make functional and structural proteins. Strategies for genomic expression for different taxonomic groupings of viruses are described below  Assembly Late proteins are important in assembly Assembly is complicated but varies – bacteriophages –stages – some are assembled in nucleus – some are assembled in cytoplasm – may be seen as Para crystalline structures in cell  Virion Release Nonenveloped viruses Enveloped viruses lyse the host cell use budding viral proteins are placed into host viral proteins may attack membrane peptidoglycan or membrane nucleocapsid may bind to viral proteins envelope derived from host cell membrane, but maybe Golgi, ER, or other virus may use host actin tails to propel through host membrane  Bacteriophages Viruses that infect bacteria are known as bacteriophages or simply phages Can be categorized based on: Their shape ( icosahedron , filamentous and complex_ The type of nucleic acid they posses ( ssDNA, dsDNA , ssRNA, dsRNA) Events that occur after invasion of the bacterial cell ( virulent and temperate)  Bacteriophages Virulent bacteriophages –what is known as the lytic cycle, which ends with the destruction of the bacterial cells Temperate bacteriophages – do not immediately initiate the lytic cycle, their DNA can stay in the host cell’s chromosome for generation Lytic Cycle  Animal Viruses Viruses that infect humans and animals are referred to as animal viruses They can be DNA viruses or RNA viruses They may consist solely of nucleic acids surrounded by protein coats or they may be more complex  Antiviral agent Drugs used to treat viral infections are called antiviral agents. Antibiotics function by inhibiting certain metabolic activities within cellular pathogens and, viruses are not cells. Antibiotics may be prescribed to prevent secondary bacterial infections. Viruses and Complex, multistep process Often involves oncogenes Cancer cancer causing genes may come from the virus OR may be transformed host proto-oncogenes (involved in normal regulation of cell growth/differentiation) Possible Mechanisms by Which Viruses Cause Cancer Viral proteins bind host cell tumor suppressor proteins Carry oncogene into cell and insert it into host genome Altered cell regulation Insertion of promoter or enhancer next to cellular oncogene Human Immunodeficiency virus The causative agent of aids Enveloped, single –stranded , RNA virus Part of Retroviridae (retroviruses) Able to attach to and invade cell bearing receptors that the virus recognized like CD4 receptors seen on helper T-cells Mimivirus Extremely large dsDNA virus recovered from amoebas There is an increasing body of evidence that mimiviruses might cause pneumonia ] Extremely large dsDNA virus recovered from amoebas There is an increasing body of evidence that mimiviruses might cause pneumonia Plant Viruses Are obligate intracellular parasites that do not have the molecular machinery to replicate without a host Most are rod-shaped, with protein discs forming a tube surrounding the viral genome; isometric particles are another common structure They rarely have an envelope The great majority have an RNA genome which is usually small and single stranded (ss), but some viruses have double-stranded (ds) RNA, ssDNA or dsDNA genome  Viroid and Prions Viroid Prions Infectious RNA molecules that Infectious proteins molecules cause a variety of plant that cause a variety of animal diseases. and human diseases  Kuru is a very rare disease. It is caused by an infectious protein (prion) found in contaminated human brain tissue. Kuru is found among people from New Guinea who practiced a form of cannibalism in which they ate the brains of dead people as part of a funeral ritual. https://www.youtube.com/watch?v=ZyvrjFcfHwQ  Mnemonic to remember DNA virus Remember Three are enveloped HHAPPy Herpes , Pox , Hepadna Herpes Hepadna Three are naked Adeno Papova Adeno Parvo Papova Pox Why Do Bats Carry So Many Diseases? Bats have a high metabolic rate and body temperature due to flight. This may create an environment within the bat that is favorable for viral replication. https://www.youtube.com/watch?v=Ao0dqJvH4a0 What are vaccine Vaccine: A preparation that is used to stimulate the body's immune response against diseases. Vaccines are usually administered through needle injections IMPORTANCE OF VACCINATION Vaccines help your body create protective antibodies—proteins that help it fight off infections. By getting vaccinated, you can protect yourself and also avoid spreading preventable diseases to other people in your community. RABIES In the Philippines, it is considered a public health problem as it is one of the most acutely fatal infection, responsible for the deaths of at least 200 Filipinos each year. According to the World Health Organization (WHO), 99% of all rabies transmissions are from dogs. The Role of Microorganisms in the Nitrogen Cycle Plants require nitrogen to synthesise protein in plant tissues and this nitrogen is obtained from the soil in the form of ammonium ions (NH4 +) and nitrate ions (NO3 – ). Nitrogen gas from the atmosphere be converted into a form that can be used by plants by NITROGEN CYCLE  Microorganisms as producers Microorganisms as decomposers Microorganisms as parasites Microorganism as symbionts THE ROLE OF MICROORGANISMS 1. Microorganisms as producers Microorganisms like phytoplankton are usually found floating on the surface of the oceans, ponds or lakes. For instance, green algae, blue-green algae (cyanobacteria), dinoflagellates and diatoms As they have chlorophyll, phytoplankton can undergo photosynthesis. Important to aquatic ecosystem as producers in food chains.  2. Microorganisms as decomposers Saprophytic fungi and saprophytic bacteria are important microorganisms that decompose organic materials from dead organisms Saprophytic fungi and bacteria are known as decomposers. Decomposers break down complex organic materials such as animal wastes, carcasses and rotting trees into simple compounds such as ammonium  Decomposers secrete digestive enzymes into the decaying organic materials, then absorb the products of the digestive process. The products of this process contain important elements required by plants such as carbon, nitrogen and sulphur which are returned to the soil These materials are then absorbed by plants  Parasite benefits from the relationship while the host is harmed or sometimes die from the negative effects caused by the parasite. Continue to benefit for as long as this interaction continues. Hence, most parasites try not to kill their hosts 3. Microorganisms as parasites  Examples of parasitic microorganisms is Plasmodium sp. (Photograph 8.19). Lives inside the female Anopheles mosquito (Photograph 8.20) Transmits malaria to anyone who is bitten by the mosquito when the parasite is transferred into the blood circulation system of the person Microorganism as symbionts Organism which has a close relationship with another organism (known as the host). There are two types of symbionts, ectosymbionts and endosymbionts  Definition of Pathogens and Vector  1. Pathogens Can cause infectious disease such as virus, bacteria, protozoa and fungi. Infection is caused when a pathogen such as a enters the body, divides and multiplies The disease caused by pathogens will occur when the cells inside the body are damage. This is caused by the infection and the infected person shows the symptoms. 2. Vector Vectors are organisms which transmit pathogens and cause certain disease. Examples : Mosquito, flies and cockroch  The bacteria Vibrio cholerae is spread amongst humans through flies. When a person consumes food that has been contaminated by Vibrio cholerae, they might get cholera.  The dengue virus is transmitted to humans through Aedes aegypti mosquito bites.  Salmonella typhi bacteria are transmitted to humans through food and water that has been contaminated by cockroaches  Pathogens disrupt the immunity system in many ways. Viruses or bacteria cause sickness when they disturb cell functions or cause cell damage. Some pathogens release toxins that could lead to paralysis or destroy metabolic activities in the body THE EFFECTS OF PATHOGENS ON HUMAN HEALTH  pH Temperature Most prefer alkaline pH Inactive: low tem. 7.4 or neutral Active: 35oC-45oC High of acid can kill the Death: Temp. over 50oC microorganism FACTOR AFFECT GROWTH OF MICROORGANISM Light Intensity Nutrient Prefer dark environment Need nutrient for survive Some need light Exp. Parasite, Saprophyte Humidity Need water for survive Form spore in dry condition  Medicine Dead bacteria and Decay process virus produce vaccine Decompose the Exmp: Insulin, Food digestion dead living thing penicillin (fungi) Bacteria in an intestine help the digestion THE USE OF MICROORGANISM Industry Agriculture Produce the food product Nitrogen fixing bacteria: Fix (yogurt) nitrogen: Fertilizer Kill pest: Myxomatosis virus control the population of rabbit  THE HARMFUL EFFECT OF MICROORGANISM Virus, bacteria, protozoa and fungi considered to be PATHOGEN. PATHOGEN : Microorganism that can cause disease Attack and destroy host Produce poisonous cell or tissues Food poisoning Tooth decay Cause by eating The formation of plaque contaminated food. (bacteria+saliva+food) Bacteria release toxin  Disease cause by Tuberculosis Pathogen:Bacilli bacteria bacteria Place infection: Lung Transmitted: Air Symptoms: Dry cough, lost weight Cholera Effect: Respiratory failure Pathogen: Vibrios bacteria Place infection: Intestine Transmitted: Food or water Symptoms: Vomitting, diarrhoea Effect: Dehydration/death Syphilis Pathogen:Spiral bacteria Gonorrhea Place infection:Reproductive, Skin / Organ Pathogen:Coccus bacteria Transmitted:Sex Place infection:Reproductive Symptoms:Red pimple, fever, headache. Transmitted:Sex Effect:Deafness, hearth failure, paralysis Symptoms:Penis excrete pus, inflamation of urethra Effect: Testes swollen, fallopian tube block  Common cold (Influenza) Disease cause by virus Pathogen: Viral virus Place infection: nose and throat Transmitted: Air Symptoms: Fever, sneezing Dengue fever Effect: Pneumonia, bronchitis Pathogen: Dengue virus Place infection: blood vessel Transmitted: mosquitoes Symptoms: Fever 5-7 day, pain in Hepatitis joint, headache Place infection: Liver Effect: bleeding in mouth, nose & Transmitted: Touch death Symptoms: Fatigue, poor appetite, liver swollen AIDS Effect: Cirrhosis, cancer Pathogen: HIV 1 & 2 Place infection: Immune system Transmitted: Sex, blood transfer Symptoms: Fever, inflammation of lymph Effect: Pneumonia, Kaposi’s sarcoma  Ringworm Disease cause by fungi Placed infection: below the breast, gap between finger, toes Symptom: Infected area appear red, wound and bleeding Tinea Effect: Phatogen: Round fungi Place of infection: body, hand, legs, face Symptom: Skin appear bright with white spots  Disease cause by protozoa Malaria Pathogen: Plasmodium sp. Place infection: bloodstream Symptom: Fever, headache, nausea Effect: Anaemia  Air Water Food Droplet infection Contaminated food Contaminated water (sneezing, cough) Exp: Hepatisis, (faeces,urine) Exp: influenza, cholera Exp: cholera tuberculosis Way Microorganism Cause Infection Contact Vector Indirectly: touch the infected Animal carry thing (tinea) pathogen Directly: Having sex, touch Exp: malaria (gonorrhea)  THE IMPORTANCE OF IMMUNITY To help the To prevent an To prevent To prevent the infected outbreak and humans from disease from person spread of certain being infected by getting worse recovers fast disease certain disease THE IMMUNISATION PROGRAMME IN MALAYSIA  WAY TO PREVENT INFECTION BY MICROORGANISM Sterilisation Control of vector Immunisation Active Use heat : autoclave, (body produce antibody) boiling Use chemicals : antiseptic, disinfectants Passive Use radiation: ultraviolet (Body receives antibody) Natural From mother Natural milk Obtained after Artificial recovery Artificial Obtained through Antibody inject vaccination into the body  TREAT DESEASES CAUSED BY MICROORGANISM Antibiotic Antiserum Chemical product made from Blood serum which contain microorganism to kill off another antibodies for certain disease microorganism The effect Prevention cell wall Disruption of chemical formation process Disruption of the cell membrane