Microbiology Master

Microbiology Master Cheat Sheet O1: Introduction to Microbiology

· Environmental Microbiology: The study of microorganisms and their interaction with both living and non-living components of the environment. · Germ Theory: The theory that diseases are caused by microorganisms. · Microbiology: The study of microorganisms, viruses and some multicellular parasites. · Microorganisms: Organisms that must be viewed with the aid of a microscope. · Spontaneous generation: The theory that living things arose form spontaneously from non-living components. · Viruses: Non-living infectious molecules, consisting of protein and genetic material. They are so small that they must be viewed with an electron microscope.

02: Techniques in Microbiology

· Brightfield Microscopy: Image seen is from the light passing directly through the specimen. Field without specimen is “brighter” that that with it. · Gram Stain: Gram positive and negative referrers to a characteristic of cells to retain a specific stain typically crystal violet or methylene blue. · Aseptic Method: A method to ensure that a sample remain pure. It does not contaminate the environment nor become contaminated from the environment. · Wet Mount Slide: A thin specimen immobilized on a slide with water or stain added. The sample is overlaid with a cover slip and excess stain removed.

Microbe Identification & Characterization

Koch’s Postulates

· A microorganism that causes a disease must be found in all cases. · The microorganism must be isolated and purified. · The isolated culture should cause the same disease in a test subject. · The microorganism should be recoverable from the test subject.

Hershey-Chase Experiment

· Label one group of bacteriophages with radioactive sulfur (S35). Sulfur is only found in proteins. · Label another group of bacteriophages with radioactive Phosphorous (P32). Phosphorous is only found in nucleic acids, such as DNA. · Allow bacteriophages to attach to bacteria. · At the early stages of the infection detach bacteriophages from bacteria by blending. · Only P32 is found inside the bacterial cell demonstrating that DNA and not protein was the genetic material.

How to study microbiology

· Read the textbook! · Memorize your vocabulary – Make flash cards · Construct a chart classifying all microorganisms you encounter through out the semester. · Make connections between the microorganisms you encounter and the disease(s) they cause, their use in industry, role in the environment and relation to other organisms.

A culture can be identified and characterized using: Molecular methods for DNA, RNA and protein I.D. and sequencing. Microscopy: optical methods as in light microscopy, atomic methods with electrons bombarding a sample and fluorescence methods in which the sample is stained using dyes that fluoresce when excited and emit a photon. Cell culture is used to get a pure sample and characterize the microbe physiology.

Pure Culture

Microbe (unknown or mixed sample) · Using a sterile transfer or inoculation loop touch tip of sample. · Streak 3 quadrants of a Petri dish having selective media. · Each quadrant touching just one point on the previous quadrant (creating a dilution effect on the plate). Correctly Streaked Plate Note how each quadrant the bacteria colonies become more distinctive. The last streak (by the end of the inoculation loop shows individual colonies)

Microscopy – Slide Preparation

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03: Chemical Basis of Life

· Chemical bonds store energy. · For covalent bonds, the more electrons pairs shared, the more energy is stored and the shorter the bond length. · Ionic bond: forms when atoms lose or gain electrons · Covalent bond: forms when atoms share electrons; very strong bonds · Atoms: o electrons: – charge, orbit nucleus o neutrons: uncharged, in nucleus o protons: + charge, in nucleus · Molecules: o formed from atoms o joined by chemical bonds (shared electrons) o molecular formula and structural formula · Organic Molecules/macromolecules: o amino acids --> proteins o monosaccharides --> polysaccharides o fatty acids --> lipid components o nucleotides --> nucleic acids

Organic Chemicals

· Classified by the functional groups: n Alcohols, R-OH n Aldehydes, R-CHO n Ketones, R-CO-R n Carboxylic Acids, R-COOH n Amines, R-NH2 n Thiols, R-SH n Esters, R-COO-R’ n Ethers, R-O-R’ n Amides, R-CONH2 n Organic Phosphates, R-OPO32· ·

· · · · · · ·

Law of Thermodynamics

First Law: The total energy of the universe is always conserved. Energy can neither be created nor destroyed. Second Law: The universe tends towards maximum disorder; the direction of all spontaneous processes serves to increase the entropy of a system plus its surroundings. DG: Change of free energy in a system. (DG=DH-TDS) DG <0: spontaneous reaction/exergonic DG >0: non-spontaneous reaction/endergonic DG =0: reaction at equilibrium DH: enthalpy, <0=exothermic, >0=endothermic T: the temperature in Kelvin DS: the net change in entropy

04: Prokaryotic and Eukaryotic Cells Structure and Function

Cell membrane: A lipid bilayer that surrounds the cells of prokaryotes and eukaryotes. Typically it has proteins embedded in or associated with the membrane. The membrane acts a semi permeable barrier. Cell Wall: Most prokaryotes have a cell wall and some eukaryotes. It serves as a ridged barrier to protect and give form to the cell. Ribosome: Is a protein complex that reads mRNA to make proteins. The ribosome in prokaryotes is smaller and less complex then that of eukaryotes. Prokaryote: Made up of two Kingdoms: eubacteria and archaebacteria. It lacks a membrane bound organelles and no nucleus. They reproduce by binary fission and do not undergo meiosis. Eukaryote: They posses membrane bound organelles and have a complex DNA structure. They reproduce via mitosis or meiosis. Organelle: A organelle is a structure within a eukaryotic cell. It is differentiated and membrane bound, e.g. mitochondria. Histone: A protein with a basic charge that binds to chromosomes of eukaryotes.

Eukaryote Cell Structure

Membrane bound organelles. The nucleus contains the cells chromosomes. Eukaryote cell division: two type mitosis and meiosis. Mitosis: involves the replication of the DNA and the cell splitting. This occurs in somatic cells. With the exception of mutations the two cells are identical. Meiosis occurs in sexual reproduction (never in prokaryotes). The DNA reduces from diploid (2N) to haploid (1N). The haploid cells (sperm, egg, germ cells) combine between parents to create a new and unique diploid cell (2N). Energy production is (predominantly) done in the mitochondria. Has cytoplasmic structures referred to as a cytoskeleton.

Chemical Reactions

· Coupled reactions: ATP hydrolysis can provide energy for many biosynthesis reactions (i.e., the overall reaction will have DG<0). The energy offered by ATP is stored in its phosphate bonds. ATP hydrolysis breaks ATP into ADP and inorganic phosphate (Pi). · Enzyme-catalyzed reactions: lower the free energy of activation (Ea) but do not change DG.

Prokaryote Cell Structure

Has a cell membrane and (usually) a cell wall.

Important Biochemical Molecules

· Organic molecules/macromolecules: n Polysaccharides o Monomer unit: monosaccharide o store energy, structural function (plants=cellulose) n Lipids o Monomer unit (triglyceride): 3 fatty acids + glycerol o Store energy, cellular membranes, steroid hormones n Proteins: o Monomer unit: amino acids o Structural proteins, enzymes n Nucleic Acids: o Monomer unit: nucleotides o Genetic material (RNA and DNA)

Typically single circular chromosome made up of DNA. Lipid bilayer membrane. No membrane bound organelles. Flagella used for motion, like a propeller. Replication by cell fission. Two Kingdoms of prokaryotes: Eubacteria and Archaebacteria. Genome is haploid having only one of each chromosome. Reparatory enzymes located in the cytoplasmic membrane.


05: Microbial Metabolism

· Aerobic Respiration: chemical process were oxygen is used to make energy from carbohydrates (sugars). · Anabolism:In metabolism were simple biomolecules are synthesized into the complex ones. · ATP: Adenosine tri-phosphate. A high energy phosphate molecule used to for energy for cellular processes. · Catabolism: Metabolic breakdown of large biomolecules to simpler molecules used by a living cell. · Glycolysis: The process in which glucose (sugar) is broken down to pyruvate acid. Glycolysis is one method that cells use to produce energy. · Kreb’s Cycle: Uses Acetyl-CoA to generate ATP, NADH and FADH2. Water and CO2 are biproducts. · Oxidative phosphorylation: The process in cell metabolism by which respiratory enzymes synthesize ATP from ADP . · REDOX: Refers to oxidation reduction reactions. Reduction is the acquisition of electrons and oxidation is the loss or donation of electrons.

Kreb’s Cycle

06: Microbial Growth and Control

Autotroph: A microbe that uses only inorganic carbon sources CO2 for nutrition. Chemoautotroph: Uses chemical compounds as energy source and inorganic carbon for nutrition. Chemotroph: Acquires energy from REDOX reactions with aerobic or anaerobic respiration or fermentation. Heterotroph: A microbe that catabolizes (reduces) carbon compounds from other organisms for nutrition e.g. protein, amino acids, carbohydrates or fatty acids. Obligate aerobes: Requires oxygen to be viable. Obligate anaerobes: Requires an oxygen free environment to be viable. Photoautotroph: Are organisms such as plants, algae and cyanobacteria that use water to reduce carbon dioxide and produce oxygen. They use light for energy and inorganic carbon. Photoheterotroph: Uses light and organic carbon for energy and nutrition. Phototroph: Acquires energy from light. Pure Cultures: Having cells that are only from one species and derived from a CFU (colony forming unit) composed of a single cell. Quorum sensing: The process that bacteria use to respond to changes in microbial density and use signal molecules and receptors to communicate with the population. Vitamins: organic molecules that used in small amount for metabolism and are considered growth factors.

Types of Selective Media

· Defined media: has an exact amount of nutrients. · Complex media: contains a variety of growth factors. · Selective media: functions to either inhibit or favor the growth of a particular microbe. · Differential media: designed to distinguish different groups of bacteria. · Reducing media: used to culture anaerobes. · Transport media: designed to transport specimens while keeping them viable and uncontaminated.

Growth of Microbial Population

Electron Transport System The successive passage of electrons from one electron carrier to another in a series of oxidation-reduction reactions in the presence of oxygen for the production of ATP. The electrons are donated to oxygen in the final step. The oxidation-reduction reactions generate the energy required for the production of ATP.

· Bacteria growth: logarithmic or exponential growth. · The time it takes bacteria to go through an entire cycle of binary fission is referred to as “doubling time”. · A growth curve of bacteria in culture can be characterized by four phases: Lag, Log, Stationary, and Death.

Glycolysis

Glycolysis pathway and energy production.

Lag Phase: microbes adjusting to new environment, activating metabolism. Log Phase: population actively growing. Stationary Phase: microbe reproduction and death are equal or balanced. Death Phase: the rate of microbes dying is greater then new cell production.


07: Microbial Genetics and Biotechnology

· Chromosomes: Prokaryote chromosomes are usually circular DNA strands associated with histone-like proteins and RNA. They are localized in an area of the cell cytosol referred to as the nucleoid. Some bacteria may also have extrachromosomal DNA molecules called plasmids. Plasmids have genes that confer non essential traits such as antibiotic resistance or ability to conjugation. · Eukaryotic chromosomes have histones associated with them arranged in nucleosomes (beads of DNA). Mitochondria and chloroplasts have DNA as well. · Genetics: The study of genes and heredity. How traits are transmitted from parents to offspring. · Genome: The sum of all the genetic material in a cell (or virus). Prokaryotes and eukaryotes use DNA as their genetic material. Viruses use DNA or RNA as the carrier of their genetic information. · mRNA: Messenger RNA carries the genetic information from the DNA to the ribosome where it is translated and t by tRNA into chemical compounds as energy source and inorganic carbon for nutrition. · Restriction enzyme: Enzymes from bacteria that cleave DNA at specific sequences. The ends of the DNA are either sticky (they have a 4 nucleotide lip) or blunt ends. · Semi conservative Replication: when DNA is copied each newly synthesized strand remains associated with one of the parental strands. The DNA is unwound by helicase and the parental DNA copied in opposite directions in the 5’ to 3’ direction. · · · · · · · · · · · ·

DNA Replication

DNA replication is semiconservative process. DNA is copied from the 5’ to the 3’ direction. The process starts at the Origin (of replication) Chromosomal proteins are released exposing the DNA. DNA helicase unwinds or unzips a local regeion of DNA breaking hydrogen bonds and exposing the two separate strands. This opening is called the replication fork (think of a fork in the road). DNA polymerase (an enzyme that matches a complementary base to the one exposed) binds to the open strand. Primase synthesizes a short complementary RNA molecule. The RNA primer provides a 3’hydroxyl group for the DNA polymerase to bind. The polymerase moves along the strand in the 5’ to 3’ direction. Because there are two strands that are antiparellel cells synthesize new strand in two ways. The leading strand is synthesized continuously in a single long chain of nucleotides. Lagging strand is synthesized in short segments that are later joined.

08: Classification of Microorganisms

· Binomial nomenclature: a Latin based two word organism naming system often referred to as the “scientific name”. The first word identifies the genus; the second often describes a characteristic of the organisms. · Cladistics: a branch of biology that determines the evolutionary relationship between organisms. The basis is “shared derived traits”. · Cladogram: graphical representation of the information compiled by cladistics. These are drawn to show different hypotheses of relationships. · Horizontal gene transfer: transfer of genes to an organism that is not its offspring. Genetic engineering would be an example of horizontal gene transfer. · Molecular systematics: A branch of systematics that uses molecular biology to group and classify organisms. · mRNA: Messenger RNA carries the genetic information from the DNA to the ribosome where it is translated. · Phenotype: Refers to how an organism appears its morphology. · Phylogeny: The study of how organisms are genetically related to each other. · Ribosomal RNA: (rRNA) is a type of RNA that is main component of the ribosome. rRNA is the most conserved (least variable) gene known. The genes that encode rRNA are refereed to as rDNA. · Ribosome: is an organelle in cells that translates the mRNA into proteins. Ribosomes are made up of: rRNA, ribosomal proteins (RNP). · Specific epithet: Is the second word in the scientific name of an organism. · Taxonomy: means to classify. Taxonomic units are known as taxa and are a hierarchical structure. · Vertical gene transfer: transfer of genes to an organism’s offspring. Taxonomic ranks: Domain, Kingdom, Phylum (plural, phyla), Class, Order, Family, Genus and Species.

Double stranded DNA unwinds

Transcription Into mRNA

Ribosome Translates mRNA

www.genome.gov


09: The Prokaryotes Domains Bacteria and Archaea

· Mycoplasmas: Are Gram-negative, pleomorphic, facultative anaerobes and obligate anaerobes. They do not have cell walls and can cause pneumonia and urinary tract infections. · Nitrifying bacteria: oxidize NH2 to NO3 by a process called nitrification. Alphaproteobacteria have nitrifying bacteria. · Vegetative Cell: Any cell except the reproductive cells. · %G+C: the percentage of guanine plus cytosine that an organism’s genome contains. Low G+C is a percentage less then 50%. High G+C containing organisms are > then 50%. · Halophiles: Microbe that requires a high saline concentration to live >9% NaCl. · Methanogens: Obligate anaerobes that make methane gas. · Actinomycetes: Resemble fungi in that they make spores and filaments. However they are bacteria. · Nitrogen fixation: In cyanobacteria it is the reduction of atmospheric N2 to NH3. · Saprothophic: organism that obtains its nutrients from non-living organic matter, usually dead and decaying plant or animal matter. · Archae: domain which includes all prokaryotic cells having archaea rRNA sequences. · Thermophiles: Microbes that require temperatures about 45°C to live.

Endospore Formation

The growth of microbes can be characterized by these parameters:

10: The Eukaryotes Fungi, Algae, Protozoa and Helminths

· Coenocytes: Multinucleate cells created by a delay in cytokinesis, as can occur in some algae and fungi, following mitosis. · Schizogony: Asexual reproduction (protozoan Plasmodium). Multiple mitoses form a multinucleate schizont. This is followed by cytokinesis. · Algae: typically reproduce ban an alternation of generations in which a haploid thallus alternates with a diploid thallus. · Chemoautotroph: Obtain nutrients by phagocytizing bacteria and organic matter in decay and tissues of hosts.

Fungi, Protozoa, Algae, Water & Slime Molds Major Characteristics

· Fungi: chemoheterotrophic eukaryotes that have cell walls typically composed of chitin. Saprophytic and parasitic organisms that lack chlorophyll and include molds, rusts, mildews, smuts, mushrooms and yeast. · Protozoa: Single-celled, eucaryotic microorganisms without cell walls. Most protozoa are free-living although many are parasitic. The majority of protozoa are aerobic or facultatively anaerobic heterotrophs. · Algae: Have cell walls with a diverse type of polysaccharides. Most are unicellular or filamentous. Phototrophic typically contain chlorophyll a and may have accessory pigments. Most algae are aquatic and live in the photic zone. Use sugar and starch as food reserves. 18S rRNA sequences are similar to plants and so are considered progenitors of plants. · Water Mold: Have tubular cristae in their mitochondria. Cell walls of cellulose. Spores have two flagella – one whip like the other like tinsel. True diploid thalli. Example: Phytophthora caused the great Irish potato famine of 1845. · Slime Mold: Feed by phagocytizing organic debris and bacteria. The thallus also called a plasmodium can have millions of diploid nuclei. Cytoplasmic streaming distributes the cells nutrients. When food or water is limiting the plasmodium will divides into cytoplasmic units which make a stalked sporangium. Meiosis occurs in the sporangia to make haploid spores. If water is not limiting myxamoebae make flagella a swim. Myxamoebae of opposite mating type fuse to form a diploid zygote.

Review of Mitosis & Meiosis

Shapes of Bacteria

Shown are the different shapes that cocci and bacilli can take. Shapes are function of replication mechanism. · Meiosis: nuclear division that results in four nuclei with half the number of chromosomes. · Mitosis involves the nuclear replication that results in an exact copy of the parent cell. · There are typically four phases in mitosis: prophase, metaphase, anaphase and telophase.

Modern Classification


11: Viruses and Other Non-Living Infectious Agents

· Virus: A small acellular infectious agent. It has one or several pieces of nucleic acid, DNA or RNA. Viruses have no cytoplasmic membrane but may have a envelope around its capsid.ltinucleate cells created by a delay in cytokinesis, as can occur in some algae and fungi, following mitosis. · Capsid: The capsid is the protein coat that surrounds the nucleic acid core of a virus. Capsids are composed of capsomeres that bind together. · Virion: A virus that in the extracellular state. · Viroid: A small infectous particle composed only of RNA. It causes diseases in plants. · Bacteriophage: Are viruses that only infect bacteria. · Viral Shapes: Three kinds, helical, polyhedral and complex. Capsid of polyhedral virus is spherical. Capsid of a helical virus is made up of capsomeres bonded in a spiral to form a tube. Complex shapes include icosahedral heads, helical tails and tail fibers. · Viral Envelope: Some viruses have a membrane (different from a cell’s membrane). A virion that has a membrane is said to have an envelope. · Naked virion: A virion without an envelope or nonenveloped virus. · Nucleocapsid: Viral nucleic acid surrounded by its capsid.

Lytic & Lysogenic Replication

· Attachment: virion binds to the host cell. · Entry: the virion or its genome enters the host cell. · Synthesis: nucleic acids and viral proteins are replicated by the host cell’s enzymes and ribosomes. · Assembly: new virions are put together within the host cell. · Release: The newly assembled virions are released from the host cell either by lysis or budding.

12: Principles of Disease and Epidemiology

· Epidemiology: Epidemiology is the study of the determinants, distribution, and frequency of disease · Epidemic : An epidemic occurs when there are significantly more cases of the same disease than past experience would have predicted. · Sporadic Disease :When a disease occurs occasionally , at irregular intervals, in a human population. · Endemic Disease: When a disease occurs at a steady , low level frequency at a moderately regular interval. · Out Break : It is the sudden unexpected occurrence of a disease, usually focally or in al limited segment of a population. · Pandemic: It is an increase in disease occurrence within a large population over the entire world. E.g. AIDS. · Symbiosis: symbiosis is the living together in close association of two or more dissimilar organisms. · Commensalism: It is the relationship in which one organism, the commensal, benefits while the host is neither harmed nor helped. It is like “eating on the same table”. · Mutualism: It is the relationship in which both the partners mutually benefit each other. They are metabolizing dependant on each other. · Pathogen: An organism capable of infecting a host, multiplying and impairing the normal physiological activities of the host , to such an extent that the individual suffers abnormal changes in its body or dies. · Infection: The manifestation caused by a pathogen in the host is called infection.

Koch’s Postulates

· Same pathogen present in every case of disease · Pathogen must be grown in pure culture · Pathogen isolated from pure culture must cause disease in a healthy host. · Pathogen must be re-isolated from the inoculated animal, who developed the disease.

Types of Carriers/Reservoirs

· Active carrier- An individual who has an overt clinical case of the disease. · Convalescent carrier-An individual who has recovered from the disease but continues to harbor the disease causing pathogen. · Healthy carrier; An individual who harbors the infectious organism but is not ill. · Incubatory Carrier- an individual who is incubating the organism in large numbers but not yet ill.

Mode of Transmission of infectious agent

· Airborne transmission· Contact transmission – a) direct contact & b) indirect contact. · Vehicle transmission. Vector borne

Major classification of symbiosis & examples

· Commensalism: (Latin com-together & Mensa, table) – e. A relationship where one organism, the commensal benefits, while host is neither harmed nor helped. E.g. E.coli lives in the human colon & derives nutrients, warmth, & shelter, but usually causes no disease to humans. · Mutualism: Latin mutus-to lend. In this relationship, the mutualist and host are metabolically dependant on each other eg. Lichens are the association between fungi and green algae. The fungus obtains its organic carbon from the alga and in turn provides water and minerals to the alga. · Parasitism: Relationship, when a symbiont either harms or lives at the expense of another organism. Vibrio cholera causing cholera in humans.

· Normal healthy state is a balance between host & pathogen, with environment as the fulcrum, akin to a see saw. When the pathogen wins, disease occurs. Biology24.com © Rapid Learning Inc. All Rights Reserved

13: Innate Immunity

· Innate immunity or native immunity: It is the resistance to infections which an individual possesses by virtue of his genetic and constitutional make-up. · Species immunity: refers to the total refractoriness to a pathogen, shown by all the members of a species obtained as their birthright. · Racial immunity: Within a species, different races may show differences in susceptibility to infections. This is known as racial immunity, it is genetic in origin. · Individual immunity: The difference in innate immunity exhibited by different individuals in a race is known as individual immunity. It is genetic in origin. · Endocytosis: Process by which macromolecules contained within the extracellular tissue fluid are internalized by cells. · Pinocytosis: Cells take up fluid from the surrounding medium it involves nonspecific cell invagination.

Innate Immune System

· The immune system comprises of two parallel but interrelated systems, which work in harmony with each other making them both more effective. These are Innate immunity and Adaptive immunity. · Innate immunity may be considered at the level of the species, race or individual. · Age, Hormonal levels & Nutrition are some factors which influence the level of innate immunity in an individual. · Various organs (eyes, nose, mouth, stomach, skin, intestine, lungs, & reproductive organs) involved in innate immunity protect the body from invading pathogens. · Innate immune response shows following characteristics : · Responses are Broad-Spectrum (non-specific). · There is no memory or lasting protective immunity. · There is a limited repertoire of recognition molecules. · The responses are phylogenetically ancient.

Phagocytic Barriers

· Various cells internalize (endocytose) and break down foreign macromolecules. Specialized cells such as blood monocytes, neutrophils, and tissue macrophages internalize i.e. phagocytose, kill and digest whole microorganisms. · Steps involved in phagocytosis are: 1. Chemotaxis & adherence of microbe to phagocyte. 2. Microbe is ingested by phagocyte. 3. Phagosomes are formed. 4. Phagolysosome is formed. 5. Microbe is ingested & digested with the help of enzymes. 6. Residual body is formed which contains indigestible materials. 7. Discharge of waste materials.

14: Adaptive Immunity

· Adaptive immunity or acquired immunity: The resistance that an individual acquires during life is known as adaptive or acquired immunity. It is capable of recognizing and selectively eliminating specific foreign microorganisms and molecules. · Active immunity: Active immunity is the resistance developed by an individual as a result of an antigenic stimulus. This involves the active functioning of person’s immune system leading to the synthesis of antibodies and/or the production of immunologically active cells. · Passive immunity: The resistant that is transferred to a recipient in a readymade form is known as passive immunity. Here the recipient’s immune system plays no active role. There is no antigenic stimulus; instead, preformed antibodies are administered. · Humoral immune response: Host defenses that are mediated by antibody present in the plasma, lymph, and tissue fluids. It protects against extracellular bacteria and foreign molecules. · Cell-mediated immune response: Host defenses that are mediated by antigen-specific T cells and various non-specific cells of the immune system. It protects against intracellular bacteria, viruses, cancer & is responsible for graft rejection.

Maturation & Development of B-cells

1. B-lymphocytes mature within the bone marrow. Pluripotent stem cell develops into progenitor B-cells. Pro-B cells proliferate and differentiate into precursor B-cells. Precursor B-cells develops into immature B-cells. 2. Inactive B cells before encountering the antigen are called as naïve B-cells. Naïve B-cells after encountering antigen become active B-cells. 3. T-helper cells primed by dendritic cells can interact with B cells and stimulate antigen-specific antibody production. 4. Active B- cells express a unique antigen binding receptor on its membrane i.e. antibody molecules. Binding of the antigen to the antibody causes the cell to divide rapidly. Its progeny differentiate into memory B cells and effector B-cells called plasma B- cells. 5. Plasma B-cells secrete antigen specific antibodies that destroy the pathogen. 6. Memory B cells have longer life span and continue to express the same antibody as their parent naïve B cells.

Clonal Selection

§Clonal selection occurs when an antigen binds with a B-cell whose membrane bound antibody molecules are specific for epitopes on that antigen. §Clonal selection of an antigen activated B-cell leads to a clone of effector B-cells (plasma cells) and memory B-cells. §Maturation & Clonal selection of T-cells takes place in similar fashion as that of the B-cells.

Humoral & Cell-Mediated Immunity

Mechanism of Innate Immunity

· Potential pathogens are encountered routinely, but only rarely cause disease. The vast majority of microorganisms are destroyed within minutes or hours by innate defenses. · Innate immune response includes four barriers anatomical, Physiological, Pagocytic & inflammatory barriers.

§The responses carried out by B-lymphocytes are termed as Humoral immune responses. And those carried out by Tlymphocytes are termed as cell-mediated immune responses. §Humoral immune responses are best suited for the elimination of exogenous antigens; whereas cell mediated immune response is best suited for the elimination of endogenous antigens.


15: Immunologic Disorders

· Hypersensitivity: an exaggerated immune response that results in tissue damage and is manifested in the individual on second exposure to the same antigen. · Inflammation: -a localized protective response to tissue injury or destruction. Acute inflammation is characterization by pain, heat, swelling and redness in the injured area. · Anaphylaxis: a sudden, severe, potentially fatal, systemic allergic reaction that can involve various areas of the body (such as the skin, respiratory tract, gastrointestinal tract, and cardiovascular system). · Autoimmune disease -When our immune system doesn't work the way it is supposed to. · Asthma: a chronic disease of the respiratory system in which theairwayoccasionally constricts, becomes inflamed, and is lined with excessive amounts of mucus, often in response to one or more triggers · Rheumatoid arthritis: a chronic, inflammatory auto immune disorder that causes the immune system to attack the .joints .It is a disabling and painful inflammatorycondition, which can lead to substantial loss of mobility due to pain and joint destruction. · Mast cells: a resident cell of areolar connective tissuethat contains many granules rich in histamine and heparin and play an important protective role indefense against pathogens · Antibodies: Group of proteins which bind to antigen and destroy it. · Cytokines: a group of proteins that are used extensively for inter-cell communication.

Types of Hypersensitivity

· Type-1is an allergic reaction provoked by reexposure to a specific antigen and is mediated by IgE antibodies and produced by immediate release of histamine,tryptase, arachidonate and derivatives by basophils and mast cells · Type-2: IgG and IgM antibodies bind to these antigens to form complexes that activate the classical pathway of complement of activation for eliminating cells · Type-3: soluble immune complexes (aggregations of antigens and IgG and IgM antibodies) form in the blood. and are deposited in various tissues (typically the skin, kidney and joints where they may trigger an immune response. · Type-4 It is a type of cell-mediated response and takes days to develop.

16: Antibiotics

· Beta lactam- A beta-lactam ring or penam is a lactam with a heteroatomic ring structure consisting of three carbon atoms and one Nitrogen atom. · Beta-lactam antibiotics- antibiotics having beta lactam rings e.g. penicillin, cephalosporin. · Penicillin- works by interfering with the synthesis of the bacterial cell wall — a structure that is not found in eukaryotes (see diagram below). · Glycopeptides- Another group of proteins which work by interfering with the synthesis of the protective cell wall in microbes. · Polymyxins- Polymyxin acts as an antibiotic by damaging the cytoplasmic membrane of bacteria. · · · ·

Categories of Antibiotics

Bactericidal Usually antibiotic of choice Bacteriostatic Duration of treatment sufficient for host defenses

Cell Components that are Targets for Antibiotics

· Cell walls-A rigid, protective structure which gives microbial and plant cells their shape and limits the total amount of liquid that can enter these cells. · Cell membrane-All cells have these membranes. They control what enters and exits the cells. · Cellular Proteins: These are composed of a variety of amino acids and play a variety of important roles in microbial cells. · Cellular Nucleic Acids: These are the building blocks of RNA and DNA molecules. They are found in the nucleus of microbial cells. · Penicillin The walls of bacteria are made of a complex polymeric material called peptidoglycan. It contains both amino acids and amino sugars Penicillin binds to and inhibits enzymes needed for the synthesis of the peptidoglycan wall.

Large scale production of antibiotics

· Most antibiotics are produced by staged fermentations in which strains of microorganisms producing high yields are grown under optimum conditions in nutrient media in fermentation tanks. · The mold is strained out of the fermentation broth. · The antibiotic is removed from the broth by filtration, precipitation, and other separation methods. · Most antibiotics are produced by staged fermentations in which strains of microorganisms producing high yields are grown under optimum conditions in nutrient media in fermentation tanks. · The mold is strained out of the fermentation broth. · The antibiotic is removed from the broth by filtration, precipitation, and other separation methods.

Immunological Disorders

· When one or more of its components is missing in the immune system the result is an immunodeficiency disorder. · They can be inherited, acquired through infection or produced unintentionally by drugs such as those used to treat people with cancer or those who have received transplants

Examples of Immunological Disorders

SLE-antibodies made against self antigens. Diabetes-antibodies are made against pancreatic cells. Rheumatoid arthritis AIDS (HIV) that infects immune cells, namely the T cells and disables the immune system. · Latent AIDS infection the T cells and makes the person susceptible to serious life threatening disease like cancer, TB etc. · · · ·


17: Skin and Eye Infections

· Epidermis: The epidermis is the outermost region of the skin that is indirect contact with the outside world. It consists of 5 distinct layers of cells, each with its own structural characteristics. · Dermis: The dermis region of the skin occurs immediately deep to the epidermis and contains two layers. The papillary region has ridges called papillae that are the origns of finger prints. The reticular layer is under the papillary layer. · Hypodermis: The hypodermis lays deep to the dermis and is not part of the skin. · Layers of the Epidermis: The five layers of the epidermis are: Stratum Corneum, Stratum Lucidum, Stratum Granulosum, Stratum Spinosum, Stratum Basale · Sebacceous Gland: The sebaceous glands are clustered at around the stalk of the hair and secrete sebum that waterproofs and protects the skin and hair. · Sweat Gland: The sweat glands secrete sweat that cools the body when it evaporates. · Eye compartments: The eye has an anterior and posterior segment. The anterior segmet is divided into anterior and posterior compartments by the lens. Aqueous humor flows from the posterior compartment to the anterior compartment. · Cornea: The outermost clear layer of the eye that provides a significant portion of the optical power. · Retina: A thin layer of cells lining the deep surface of the globe that absorb photons and generate neural signals. · Canal of Schleme: The very important opening in the anterior chamber that drains aqueous humor produced in the posterior chamber. Closure of this canal cause blindness. (Glaucoma is very serious !!!) · Iris: Segement of visible colored tissue containing muscles that control the amount of light entering the eye. · Pupil: Open space of the iris through which light passes. · Lens: Biconcave structure that works with the cornea to focus light on the retina.

Skin Structure

Eye Structure

18: Nervous System Infections

· CNS: Central Nervous System includes the brain and spinal cord surrounded by three layers of meninges: dura mater (outermost), arachnoid mater and pia mater. · PNS: The Peripheral nervous system is composed of cranial nerves and spinal nerves. A plexus is a bundle of branching nerves. · Subarachnoid space: Is filled with cerebrospinal fluid (CSF) which functions as a shock absorber and supplies nutrients, oxygen and removes wastes. · Petechiae: Small hemorrhages of blood vessels in the skin. · Meningitis: Can be caused by a variety of organisms. And involves the inflammation and cell death of the meninges. Symptoms include fever, headache, sleepiness, disorientation sometimes confusion and neuromuscular complications. · Neurons: one of two basic types of cells in the nervous system. Neuron transmits electrical information from the CNS to the body or from the body to the CNS. Information is transmitted via the use of neurotransmitters. · Neuroglia: One of two basic types of cells in the nervous system. It acts as a supportive cell acts to insulate, give nutrition and phagocytize microbes. · Virulence Factors: Enzymes, toxins, cell structures that affect the relative ability of a pathogen to infect, evade destruction or detection and cause disease. · Pathogenicity: A microbe’s ability to cause disease. · Epidemiology: Study of the occurrence, distribution and spread of diseases. · Arboviruses: Enveloped, positive ssRNA viruses that are transmitted by arthropods. · Encephalitis: Is an inflammation of the brain. · Zoonosis: Diseases spread from an animal host to humans.

Meninges Structure & Function

Meninges: is a system of membranes that cover and surround the central nervous system.

· Meninges are made up of three layers: dura mater, arachnoid mater and the pia mater. · Dura mater: is the strong and inflexible outermost layer of the meninges tissue system. It is most close to the bone of the skull and spinal column. · Arachnoid mater: is between the two other meninges. · Subarachnoid space: is a spider web like area between the arachnoid and the pia mater. It is attached to the inside of the dura and extends down to the pia mater. Cerebrospinal fluid flows within the subarachnoid space. · Pia mater: is a delicate innermost layer of the meninges. It covers the brain all the way into the fissures.

Central Nervous System Structure

CNS includes the Brain and spinal Cord.

Entire nervous system is made up of two basic types of cells: neuroglia which are supportive cells and neurons which carry signals as electrical signals to and from the CNS.


19: Cardiovascular, Lymphatic and Systemic Infections

20: Respiratory System infections Structures of the Respiratory System

Pneumococcal Pneumonia

· Main arteries are vessels that carry blood away from the heart. · Pulmonary arteries carry it to the lungs and the aorta to the body. Arteries connect to veins via capillaries. Veins carry blood back to the heart. The major veins are: pulmonary veins which carry blood from the lungs to the heart, superior vena cava head neck and arms to heart and inferior vena cava from the rest of the body to the heart. · Blood is made up of serum, which is the liquid, and erythrocytes and platelets. When clotting proteins are taken out from serum the plasma remains. · The atria and ventricles of heart are separated by valves which prevent backflow of blood. · The wall of the heart is made up of an outer, fibrous pericardium, muscular myocardium and inner endocardium. · Blood flows in this sequence: venae cavae, right atrium, atrioventricular valve, right ventricle, pulmonary semilunar valve, pulmonary arteries, lungs, pulmonary veins, left atrium, left atrioventricular valve, left ventricle, aortic semilunar valve, aorta, arteries, capillaries, veins, venae cavae.

Bacterial Cardiovascular and Systemic Disease

· Pneumococci sometimes inhaled into the lungs from the pharynx. · Phosphorylcholine triggers endocytosis the bacterium is protected by its unique capsule. · This allows the bacteria to live in the lung cells eventually killing them. · The bacteria multiply in the alveoli damaging them and allowing erythrocytes and leukocytes and blood plasma to enter. · With this added fluid in the alveoli the lung is losses ability to transfer oxygen to the blood this causes the pneumonia.

Tuberculosis

· Septicemia is the presence of pathogens in the blood. Lymphangitis is when lymphatic vessels become inflamed due to septicemia. Bacterial septicemia or bacteremia is the presence of relatively harmless bacteria in the blood. Sometimes physicians use bacteremia and septicemia interchangeably. · Toxemia or blood poisoning is when bacteria at a specific location releases toxins and can have systemic effects. Living microbes release exotoxins which can disrupt or kill cells of living tissue. Endotoxin is the lipid A part of lipopolysaccharides, and is released from dying Gram negative bacteria. It can trigger disseminated intravascular Tubercles: Small, hard lumps that are formed by the immune coagulation, shock, inflammation, diarrhea, hemorrhaging system encasing the diseased cells. Collagen fibers enclose and other advanced signs of septic shock. the lung cells. Infected cells in the center of the tubercle die · Bacterial septicemia can trigger Petechiae and and release more bacteria. This results in caseous necrosis osteomyelitis. which gives the lung a cheese like consistency. Biology24.com © Rapid Learning Inc. All Rights Reserved Normal microbiota can become pathogenic opportunists

21: Digestive system Infections

· Gastrointestinal tract: A mucus lined tube extending from the mouth to the anus. Includes the: mouth, esophagus, stomach, small intestine, large intestine, rectum and anus. · Accessory digestive organs: Grind food or inject digestive secretions. Include the: tongue, teeth, liver, gallbladder and pancreas. · Peritoneum: The membrane that covers and surrounds most of the organs of the GI tract. · Intestinal peristalsis: Is a series of coordinated contractions by the smooth muscles of the intestine that move undigested material into the large intestine. · Gingivitis: inflammation of the gums it is a form of periodontal disease. · Caries: Second only to the common cold in the frequency of this bacteria caused affliction. They usually look like holes or pits in the teeth. · Microbial antagonism: Microbiota that whose presence prevents other bacteria from growing in the same place. An example is in the intestine where the presence of normal microbes protects the body from pathogens by out competing them. · Prophage: A virus that infects bacteria and can insert its genome into the host’s chromosome or exist as a plasmid. The prophage can upon proper stimulus begin replication and production of virions. · Shigatoxin: A toxin that binds specific target cells and destroys the ability of ribosomes to synthesize proteins. · Enteropathic bacteria: “Entero” refers to the intestine (or gut). In naming bacteria that inhabit or cause disease of the gut the naming conventions: enterohemorrhagic bacteria cause bleeding in or of the intestine. · Dysentery: infectious disease of the colon. Symptoms include bloody, mucus-filled diarrhea and loss of fluids from the body.

Digestive System

22: Urogenital and Sexually Transmitted Disease

· Kidney: The renal arteries and veins supply and drain blood from the kidney respectively. The urine is produced in the cortex, medulla, renal column, and pyramid. The functional unit of the kidney that produces urine is called the nephron. · Nephron: Within the Glomerular capsule the cellular compnents of the blood are separated from the non-cellular components of the blood, most of which are returned to the blood. Besides removing waste, the nephrons help regulate blood pressure and ion concentrations within the blood. · Ureter: The ureter is a tube that drains the urine from the kidney to the bladder. · Bladder: Urine collects in the until 300 ml accumulates. Upon mitriculation, the sphincters relax, the detrusor muscle contracts, and urine streams through the internal urethral orifice, prostate gland, through the external urethral orifice and to ultimately out of the penile urethra. · Prostate: Trouble with the prostate gland often involves swelling. Swelling causes small amounts of urine to be retained, which leads to further inflammation. · Urethra: Only the upper portion of the urinary tract is sterile; the urethra has a normal complement of microbiota that prevent the colonization by harmful organisms. (Lactobacillus, Staphylococcus, Streptococcus) · Vagina: The vagina leads from outside the body to the cervix. At times other than ovulation the vagina has an acidic pH created by resident lactobacilli that feed on glycogen secreted by the walls of the vagina. This discourages infections. · Cervix: The cervix leads from the vagina to the uterus, and at times other than ovulation, is occluded by a plug of mucus that prevent infections from entering the body cavity. · Uterus: The uterus is the site of implantation of the fertilized egg. · Uterine Tubes: The fallopian tubes lead from ovaries to the uterus. Note that the fallopian tubes are NOT connected to the ovaries but rather are open to the entire body cavity. It is therefore possible for an infection to enter abdomen cavity directly from the vagina.

Reproductive System Structure

· · The digestive system is divided into two segments. Gastrointestinal Tract (GI) and Accessory Digestive Organs. In this schematic the GI organs are in the blue the other in green. GI tract is lined with a peritoneum. The Accessory Organs are primary defined by function which is to grind nutrients or inject digestive secretions like bile, salivary amylase and others to help in the breakdown of food.

Bacterial Diseases of the Mouth


23: Microbiology and the Environment

· Ecosystems: community of organisms and their physical & chemical environment that functions as an ecological unit. · Primary producers: The organisms which can accumulate organic matter. · Consumers: organisms that depend upon the organic matter synthesized by the primary producers · Mineralization: the process of organic matter decomposition that releases simpler, inorganic compounds. · Food web: a network of interlinked food chains · Biogeochemical cycling: the recycling of essential elements on earth by both biological and chemical processes. · Nitrification: the aerobic process of ammonium ion oxidation to nitrite and subsequent nitrite oxidation to nitrate · Denitrification:the process in which nitrate is used as an oxidant by certain heterotrophs producing nitrogen gas and nitrous oxide

Carbon Cycle

24: Microbiology and Industry

· Industry: An industry is generally any grouping of businesses that share a common method of generating profits. · Food microbiology: The field of science which deals with microbes useful to man in the production of food or bewerages.e.g.yeast is use din the leavening of bread. · Biopesticides: microbes (viruses bacteria, and fungi) which can be used for management of insect and nematodal pests · Mycorhiza: The symbiotic association of the mycelium of a fungus with the roots of certain plants such as conifers, beeches or orchids · Probiotics: live microorganisms administered in adequate amounts which confer a beneficial health effect on the host". Most probiotics are bacteria, which are small, single-celled organisms. One yeast - Saccharomyces boulardii - also has been evaluated as a probiotic. · Bioremediation: to use biological organisms to solve an environmental problem such as contaminated soil or groundwater.

Microbes in Food

· In the home and in industry, microbes are used in the production of fermented foods. · Yeasts are used in the manufacture of beer and wine and for the leavening of breads, · Lactic acid bacteria are used to make yogurt, cheese, sour cream, buttermilk and other fermented milk products. · Vinegars are acetic acid fermentation. · Other fermented foods include soy sauce, sauerkraut, dill pickles, olives, salami, cocoa and black teas.

Nitrogen Cycle Vaccines

· Vaccines are substances derived from microorganisms used to immunize against disease. · The microbes that are the cause of infectious disease are usually the ultimate source of vaccines. Thus, a version of the diphtheria toxin (called toxoid) is used to immunize against diphtheria, and parts of B. pertussis cells are used to vaccinate against pertussis (whooping cough). · The use of vaccines such as smallpox, polio, diphtheria, tetanus and whooping cough has led to virtual elimination of these diseases in regions of the world where the vaccines have been deployed.

Bioremediation

Phosphorus Cycle

· Micro organisms are responsible for getting rid of the waste generated by industry and households. They detoxify acid mine drainage and other toxins that we dump into the soil and water · Micro organisms help in waste water treatment

Microbes in Medicine

· Antibiotics are substances produced by microorganisms that kill or inhibit other microbes which are used in the treatment of infectious disease. · Antibiotics are produced in nature by molds such as Penicillium and bacteria such as Streptomyces and Bacillus

Microbes in Recovery of Oils

· Microbes like pseudomonas have been manipulated to harbour plasmids containing genes which can degrade hydrocarbons. · Some microbes have the inherent capacity to degrade hydrocarbons. · Such organisms can degrade wide variety of aromatic, polycyclic and aliphatic compounds in most petroleums.Thus oil spill degradations work better. Biology24.com © Rapid Learning Inc. All Rights Reserved


Microbiology Master

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