BIOL2380 Microbiology Final Exam Study Guide PDF

# BIOL2380 Microbiology ## Final Exam study guide ### Ch1 (Introduction to Microbiology) - Microbiology is the study of small organisms (microbes) which include bacteria, viruses, protozoan, algae, fungi, and helminths. - Microbial nomenclature is based on Latin and each microbe has a two-part nam...

# BIOL2380 Microbiology ## Final Exam study guide ### Ch1 (Introduction to Microbiology) - Microbiology is the study of small organisms (microbes) which include bacteria, viruses, protozoan, algae, fungi, and helminths. - Microbial nomenclature is based on Latin and each microbe has a two-part name, genus and specific epithet. - Many microbial discoveries occurred during the Golden Age of microbiology and made significant contributions to other sciences. - Microbiology can be divided into bacteriology, virology, parasitology, mycology, and immunology. - Most microbes are harmless and actually helpful for our life and used for production of goods. ### Ch3 (Microscopy) - Microbes are often measured in µm and nm (e.g., 10 μm = 10000 nm). - Microscopes used in microbiology are either light or electron microscopes with the electron microscopes giving the highest magnification and resolution. - Staining is used for light microscopy to increase contrast as most microbes are translucent. - Common microbial stains include Gram stain, negative stain, capsule stain, endospore stain, Acid-Fast stain, flagella stain. ### Ch4 (Cell Biology) - Eukaryotic cells contain multiple linear chromosomes, various organelles, nucleus, and histones, whereas prokaryotic cells do not have these structures. - Prokaryotic cells typically divide by binary fission whereas eukaryotic cells typically divide by mitosis. - Prokaryotic cells contain structures such as cell wall, pilus, fimbriae, and plasmids. - Gram negative cells have a thin peptidoglycan but have an outer membrane with LPS whereas Gram positive cells have a thick peptidoglycan with teichoic acids. - Plasma membrane is the semi-permeable barrier separating outside from inside the cell. - Molecules can move through plasma membrane via passive or active (require ATP) processes. - Endospores are hardy bacterial survival structures formed by Bacillus and Clostridium species in response to harsh environment. - Eukaryotic cells have many organelles, including rough ER, smooth ER, Golgi, mitochondria, peroxisomes, lysosomes. - Endosymbiotic theory explains the origin of eukaryotic cells. ### Ch5 (Metabolism) - Metabolism includes catabolism and anabolism. - Enzymes are proteins that catalyze specific reactions as substrate binds to the active site. - Competitive inhibitors compete with the substrate for the active site whereas noncompetitive inhibitors bind to the allosteric site. - ATP can be generated via substrate level phosphorylation, oxidative phosphorylation, photophosphorylation. - Glycolysis is the breakdown of six-carbons sugars into two three-carbon pyruvates and in the process ATP and NADH are generated. - Transition step is the breakdown of pyruvate into two-carbon acetyl-CoA and NADH is produced. - Krebs cycle is the breakdown of acetyl-CoA into CO2 and ATP, NADH and FADH2 are produced. - Electron transport chain accepts electrons from NADH and FADH2 and transfers them to the final electron acceptor and in the process generates proton movie force that helps to create ATP. - Fermentation is the giving of electrons from NADH back to pyruvate so glycolysis can continue and formation of fermentation end products. - Photosynthesis utilizes light to generate ATP and NADH which can then be used in the Calvin Benson cycle together with carbon fixation to generate organic molecules. - Proteins are broken down into amino acids which are deaminated and further broken down primarily in the Krebs cycle. - Lipids are broken down into glycerol, that can enter in the middle of glycolysis, and fatty acids which will be further broken down in beta oxidation into acetyl-CoA that can enter Krebs cycle. - Organisms are either chemoheterotrophs, chemoautotrophs, photoheterotrophs, or photoautotrophs based on their source of energy and carbon. - Biochemical tests are enzymatic reactions that can be used to identify microbes. ### Ch6 (Microbial Growth) - Microbes require specific physical and chemical conditions for growth. - Microbes cab be classified into psychrophiles, psychrotrophs, mesophiles, thermophiles, and extreme thermophiles based on their temperature preferences. - Biofilms are formed when bacteria secrete sticky material and stay attached to it forming resistant structures. - Microbes can be grown in complex or chemically defined media. - Pure cultures can be obtained by isolation streak plate or pour plate methods. - Microbial populations grow exponentially as each microbe results in two daughter cells. - Microbial growth can be measured directly or indirectly. ### Ch7 (Microbial Growth Control) - Microbial growth can be controlled by physical and chemical methods which affect either the plasma membrane, enzymes, or nucleic acids. - Heat is a common physical method of controlling microbes while disinfectants and antiseptics are chemical control methods - Come microbes are harder to control because they can form endospores, have capsules, or are Gram negative. - Common microbial growth control measurements include disk diffusion test and use dilution test. ### Ch8 (Genetics) - DNA -> mRNA -> protein -> function. - DNA replication occurs before cell division by DNA polymerase putting DNA nucleotides in right order based on the existing DNA strand after the DNA strand has been relaxed and opened. - Transcription (gene expression) occurs as the RNA polymerase puts RNA nucleotides in right order based on the template DNA strand. - Translation occurs in the ribosome as the mRNA codons are read by tRNAs bringing the amino acids. - DNA replication and transcription happen in the nucleus of eukaryotic cells whereas the translation happens in the cytoplasm. - Operons are genetic elements used by bacteria to control gene expression (transcription) efficiently. - Inducible operon can be turned on by substrate binding to repressor inactivating it. - Repressible operon can be turned off by co-repressor binding to repressor activating it. - Mutations are caused by errors in DNA replication and can be increased by chemical or physical mutagens. - Mutations can be caused by base substitution or frameshift and result in either silent, missense, or nonsense mutations. - Bacterial mutants can be identified by replica plating using either direct or indirect selection. - Bacteria can gain extra genetic information via conjugation, transformation, or transduction. - As microbes gain extra genetic information or mutate, they evolve. ### Ch9 (Biotechnology) - Biotechnology is the use of microbes and genetics tools to generate products. - Biotechnology utilizes restriction enzymes to cut DNA and ligase to add genes of interest into the plasmid which will be then transfected into microbes for gene product generation. - Site directed mutagenesis can generate specific mutations while PCR can be used to amplify genetic material. - Prokaryotic cells are great for gene product generations as they are cheap and easy to manipulate and grow, however, the products might contain toxins or be improperly modified. - Eukaryotic cells are great for gene product generations as they produce products that are correctly modified, however, they are more difficult and expensive to grow. - DNA technology can be used to produce drugs and vaccines for humans. - Genome projects provide detailed information of the organisms aiding in the treatment of diseases. - Safety issues must be considered when using DNA technology as undesired mutations and products can be generated. ### Ch10 (Classification) - Organisms are classified to build a reference guide that can be used in the identification process. - Organisms are classified based on their characteristics. - Genetic techniques, FAMEs, hybridization, staining, and biochemical assays can be used in classification and identification. - Dichotomous keys can be used to identify unknown microbes through series of experiments. - Cladograms provide evolutionary relatedness between organisms. ### Ch11 (Classifying Prokaryotes) - Gram negative bacteria contain thin peptidoglycan and outer membrane with LPS whereas Gram positive bacteria have a thick peptidoglycan with teichoic acids embedded in it. - Many pathogenic Gram-negative bacteria exist, and they are often more difficult to treat than Gram positive bacterial infections. - Archaea live in extreme environments and are not pathogenic. ### Ch12 (Classifying Eukaryotes) - Fungi can be single celled (yeast) or multicellular (mold) and they contain chitin in their cell wall and ergosterol in their plasma membrane. - Fungi can withstand various conditions including low moisture and low pH while decomposing organic matter. - Lichens are symbiotic organisms containing the supportive structure of fungi and photosynthetic component of algae or cyanobacteria and serve as food for herbivores. - Algae live in aquatic environments, can photosynthesize, some store oil, and some produce toxins. - Protozoans are single celled eukaryotic organisms with animal like behaviors. - Helminths are parasitic or free-living worms either roundworms or flatworms causing various diseases. - Biological or mechanical animal vectors, such as mosquitos and flies, can spread some diseases. ### Ch13 (Viruses, Viroids, and Prions) - Viruses are acellular obligate intracellular parasites that need a host cell to replicate. - Viruses can be identified using genetic and antibody-based tests. - During the lytic viral replication, the virus destroys the host cell while in the lysogenic cycle the viral DNA is inserted into the host genome. - Animal viruses enter the host cells whole after which they need to be uncoated and then use the host cell machinery to generate more viruses. - DNA viruses replicate their DNA in the nucleus whereas RNA viruses generate more RNA and protein in the cytoplasm. - Chronic viral infection or infections with retroviruses can result in cancers. - Viruses utilize host cell receptors and the process of endocytosis to get into the host cells. - Prions are infectious proteins causing spongiform encephalopathies. ### Ch14 (Diseases and Epidemiology) - Humans have microbes living in and on them forming the microbiome which helps in food digestion, production of other important molecules, and wards of pathogens. - Diseases can be transmitted directly through contact and indirectly through fomites. - Endemic diseases are always present in low amounts whereas epidemics occur when there is a high incidence of a disease in a particular area. - Pandemics are worldwide epidemics. - Diseases progress through incubation, prodromal, illness, decline, and convalescence period. - Nosocomial infections are acquired during a hospital stay and include antibiotic resistant bacteria. - Epidemiology can be divided into descriptive, analytical, and experimental. - Epidemiological graphs describe the incidence and prevalence of diseases. ### Ch15 (Pathogenicity) - Pathogens can enter the host through mucosal membranes and skin. - Pathogens can penetrate host defenses by secreting various enzymes that destroy host tissues and cells. - LD50 refers to the toxicity of a toxin whereas ID50 refers to the virulence of a microbe. - Pathogens can damage the host through destroying cells, digesting extracellular structures, producing toxins, and taking away nutrients. - Bacteria damage the host by toxin production, viruses destroy host cells, fungi create toxins, protozoans destroy cells, helminths generate waste. - Endotoxins are lipids released by Gram-negative bacteria that can cause fever and hard to destroy. - Exotoxins are proteins secreted by Gram-positive and Gram-negative cells and are effective in low doses, however, they can be destroyed by heat. - Pathogens typically leave the host via the way the entered the host. ### Ch16 (Innate Immunity) - First line of defense includes physical and chemical factors such as skin and mucous membranes. - Second line of defense includes processes such as phagocytosis, inflammation, fever, and complement activation. - Phagocytosis is the process of neutrophil or macrophage eating a microbe and then digesting it. - Inflammation is caused by secretion of factors at the site of injury/infection leading into vascular leakage that results in pain, heat, redness, and swelling. - Fever is caused by release of pyrogens by resident macrophages and damaged cells that lead into prostaglandin release by hypothalamus and resetting of the body temperature. - Fever increases metabolism and slows down microbial growth. - Alternative complement pathway is activated by the presence of microbes. - Lectin complement pathway is activated by MBL binding to the microbial mannoses. - Classical complement pathway is activated by antigen-antibody binding. - Activation of complement results in opsonization, inflammation, and cytolysis. ### Ch17 (Adaptive Immunity) - Humoral immunity refers to antibody production whereas cellular immunity refers to T cells. - Antigens are molecular determinants of microbes that will elicit on immune response. - Cytokines are molecules the immune cells use to communicate. - Antibodies can be IgG, IgM, IgE, IgA, or IgD and they recognize specific antigens. - Antibodies are produced by plasma cells that came from B cells that were clonally selected and expanded with the help of helper T cells. - Antibodies work by opsonization, aggregation, ADCC, neutralization, and activation of complement. - Antigens are processed and presented to T cells by dendritic cells, macrophages, or B cells. - Helper T cells activate macrophages, neutrophils, B cells, and cytotoxic T cells and recognize antigens presented by MHC class II, whereas cytotoxic T cells destroy abnormal self-cells and recognize antigens presented by MHC class I. - Immunological memory is formed during primary infection and includes memory T and B cells. - Adaptive immunity can be either naturally acquired active, naturally acquired passive, artificially acquired active, or artificially acquired passive. ### Ch18 (Applications of Immunology) - Vaccination is based on introducing the antigen to the body so it develops memory cells that can then be activated during subsequent exposures. - Vaccines can be either live attenuated, killed inactivated, subunit, nucleic acid, or combination. - Vaccine development includes the understanding of the pathogen and using genetic or proteomic techniques for vaccine development. - Vaccines can have side effects; however, they are much milder than the disease they protect from and generally very effective. - Diagnostic immunology is the use of immunological methods to diagnose diseases. - Diagnostic test must be sensitive and specific to minimize false negatives and false positives. - Immunological tests detect either the microbe or the antibodies produced against the microbes. ### Ch19 (Immune System Disorders) - Hypersensitivities can be either type I, II, III, or IV, and out of these, only type IV is cell mediated whereas others are antibody mediated. - Autoimmune diseases are caused by immune reactions against one's own body and lack of Treg responses, and are difficult to treat and cure. - Transplants are rejected often due to differences between the recipient's and donor's MHC class I molecules. - Chronic infections and infections with retroviruses can lead into cancers. - NK cells and cytotoxic T cells are the main cancer cell fighting cells. - Immunodeficiencies can be either congenital or acquired. - AIDS is caused by HIV infection as the numbers of helper T cells go down over the years. - HIV infection can be managed often by anti-retroviral therapy that targets the viral replication at various stages. ### Ch20 (Antimicrobial Drugs) - Antibiotics are naturally produced antimicrobial drugs. - Antimicrobial drugs work by affecting the plasma membrane, cell wall, nucleic acids, translation, or essential metabolite biosynthesis. - Many antimicrobial agents target the bacterial peptidoglycan biosynthesis. - Both natural and semi-synthetic penicillins have the ẞ-lactam ring, but semi-synthetic penicillins are not as sensitive to penicillinase enzyme secreted by some microbes. - Bacterial 70S ribosomes can be targeted by anti-microbial agents affecting protein synthesis. - Some drugs affect the plasma membrane permeability whereas other target DNA replication or transcription. - Folic acid synthesis is essential for bacteria, but can be targeted by antimicrobial drugs. - Many anti-fungal drugs target the chitin cell wall or ergosterol in the plasma membrane. - Antiviral drugs target the viral replication at various stages. - Anti-helminthic drugs target their nervous system or nutrient absorption. - Antimicrobial drug sensitivity can be tested by the disk-diffusion test or broth dilution test. - Microbes can become resistant to drugs through mutations resulting in inhibiting drug entry, development of drug exit pump, inactivation of the drug, or alteration in the target molecule. - Some antimicrobial drugs cause allergic reactions and have more serious side effects. - New antimicrobial drugs are being searched in soil and developed in the lab as the resistance of microbes is becoming more common.