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Microbiology 170 Final Exam Study Guide

by: Elayne Ingram

Microbiology 170 Final Exam Study Guide BIOL 170

Marketplace > Gonzaga University > Biology > BIOL 170 > Microbiology 170 Final Exam Study Guide
Elayne Ingram
Gonzaga University
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Okay, this is very long, but I think it provides a good description of exactly what you need to know without having to search through the textbook for it all. I wasn't able to finish the last few c...
Microbiology (BIOL 170)
Dr. Schwartz
Study Guide
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This 21 page Study Guide was uploaded by Elayne Ingram on Wednesday May 4, 2016. The Study Guide belongs to BIOL 170 at Gonzaga University taught by Dr. Schwartz in Spring 2016. Since its upload, it has received 62 views. For similar materials see Microbiology (BIOL 170) in Biology at Gonzaga University.

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Date Created: 05/04/16
Study Guide for Microbiology Final – Spring Term 2016 Wednesday 5/4, 1:00-3:00pm What to expect on the final: Questions will be pulled from  Exams 1, 2, 3  Chapter 15 Mastering HW (21 questions)  Chapter 16 Mastering HW (21 questions) 85 new questions to study in  Chapter 18 addition to previous exams Mastering HW (21 questions)  Chapter 26 Mastering HW (22 questions) The final will be worth 150 points. If you want to know what your current percentage estimate is, see Blackboard. Keep in mind that this is only an estimate! Chapter 1 – A Brief History of Microbiology This chapter gives an abbreviated history of the science of microbiology, outlining the major discoveries and contributors, as well as important ideas and terms. The Golden Age of Microbiology is characterized by the vast amount of research done on microbes. The question that largely stimulated these many discoveries was: What causes disease, and is spontaneous generation of microbes possible? Important concepts: Antoni van Leeuwenhoek: microscopes; discovered protozoa and bacteria, but did NOT observe viruses John Snow: infection control and epidemiology Locomotive structures of protozoa: cilia (the numerous, hair-like ones), flagella (the whip-like ones), and pseudopods (the ones that look like limbs) Carl Linnaeus: taxonomic system for naming and grouping plants and animals: Bacteria Found everywhere there is Archaea sufficient moisture, reproduce asexually Fungi Include molds and yeasts, obtain food from other organisms, reproduce sexually and asexually Protozoa Similar to animals in nutrient needs and cellular structure, most are capable of locomotion, live freely in water and sometimes animal hosts, most reproduce asexually Algae Photosynthetic, categorized on the basis of pigmentation and cell wall composition Microscopic organisms Include parasites and viruses Spontaneous generation Francesco Redi: fly larvae (meat in jar w/ and w/o cheesecloth, see pg. 8 in text) Louis Pasteur: microbes, industrial microbiology, Germ Theory, swan-necked flasks to disprove spontaneous generation, experiments did NOT involve sealing the flasks with corks Fleming: penicillin Industrial uses of microbes: see Table 1 on pg. 13 of text Buchner: biochemistry, fermentation does NOT require living/intact cells, enzymes produce chemical reactions Robert Koch: simple staining techniques, first photomicrograph of bacteria, use of Petri dishes, examined and differentiated among individual colonies of bacteria Koch’s Postulates: 1) Suspected causative agent must be found in every case of the disease and must be absent from a healthy host. 2) Agent must be isolated and grown outside the host. 3) When agent is introduced into a healthy, susceptible host, the host must get the disease. 4) Same agent must be found in the diseased experimental host. (You should know the order of these postulates.) Key terms Epidemic: a higher than normal occurrence of a disease in a population Epidemiology: the study of the occurrence, distribution, and spread of disease Pandemic: prevalent over a whole country or the world; the occurrence of an epidemic on more than one continent simultaneously Immunology: the study of the body’s defenses against pathogens Serology: study of the blood components that fight infection Antisepsis: (literally means “against putrefaction”) Prokaryotes: microorganisms characterized by the absence of a nucleus Useful tables and charts: Pictures of protozoan locomotive structures on pg. 5 Chart of the scientific method on pg. 10 – you should at least be familiar with it Table 2 on pg. 15 (outlines notable scientists of the time and the agents of disease they discovered) Figure 19 on pg. 18 (summarizes biologists from the chapter and the modern disciplines that apply to their work and discoveries)  YOU WILL WANT TO REVIEW THIS Chapter 2 – The Chemistry of Microbiology This chapter covers atoms, chemical bonds, chemical reactions, acids/bases/salts, and organic macromolecules (lipids, carbohydrates, proteins, nucleic acids). Important concepts: Valence – combining capacity of an atom  Positive if the atom has an electron to give up  Negative if the atom has spaces to fill  Stable when outer electron shells contain 8 electrons Covalent bond – sharing of a pair of electrons by 2 atoms  Nonpolar: equal sharing of electron  Polar: unequal sharing of electron Ionic bonds – occur when 2 atoms with vastly different electronegativities come together  Cation (+)  Anion (-) Hydrogen bonds: fairly weak, but vital because they bind the double helix of our DNA Carbon: backbone of life on earth, can form 4 covalent bonds simultaneously Water: polar molecule, neutral pH, universal solvent, transports all of life’s dissolved molecules, location of all of life’s chemical reactions Atomic structure, isotopes, electron configurations Chemical reactions  Synthesis (small + small  large): requires energy (endothermic)  Decomposition (large  small + small): releases energy (exothermic)  Exchange (A + BC  AB + C) Metabolism is a composite of these chemical reactions. Acids/Bases/pH  Acids = low pH, bases = high pH  strong acids and bases are highly reactive with other substances  antacids raise pH of stomach contents Lipids - hydrophobic  Fats, phospholipids, waxes, steroids  Phospholipid bilayer (saturated fatty acids and monounsaturated fatty acids)  Keep membranes flexible at low temperatures Carbohydrates  Long-term storage of chemical energy, ready energy source, part of backbones of nucleic acids, converted to amino acids, form cell wall, involved in intracellular interactions between animal cells  Monosaccharides (e.g. glucose), disaccharides (e.g. sucrose), polysaccharides (e.g. glycogen) Proteins  Structural components, catalysts (enzymes), regulators (hormones), transportation, defense and offense (antibodies)  Function is dependent on shape  Amino acids, peptide bonds, denaturation, structures - Primary structure: sequence of amino acids (polypeptide) - Secondary: coils (α-helices), accordions (β-pleated sheets) - Tertiary: unique and complicated shapes - Quaternary: 2+ polypeptide chains linked together  Nucleic acids: deoxyribonucleic acid (DNA), ribonucleic acid (RNA) - Each nucleotide is compose of a pentose sugar, phosphate, and nitrogenous base - Nucleosides differ from nucleotides in that nucleosides are missing a phosphate Key terms: Matter: anything that takes up space and has mass Element: chemically pure substance composed of a single type of atom Atom: smallest chemical unit of matter Organic molecule: has a carbon-based backbone and at least one H-C bond (e.g. glucose) Inorganic molecule: lacks carbon-based backbone and H-C bond (e.g. carbon dioxide) Stereoisomers: molecules that are mirror images of one another (e.g. L-Serine and D-Serine) Emerging disease: disease that appears in a population for the first time Acidophile: microorganism that thrives in acidic environments Useful tables and charts: Table 2 on pg. 36 (describes characteristics and relative strengths of the four types of bonds) Diagram of a phospholipid on pg. 44 – YOU NEED TO KNOW THIS Table 5 on pg. 53 (comparison of nucleic acids) Chapter 3 – Cell Structure and Function This chapter discusses the processes of life; gives an overview of prokaryotic and eukaryotic cells; and describes the respective external structures, cell walls, cytoplasmic membranes, and cytoplasm of bacteria, archaea, and eukaryotic cells. Important concepts: Processes of life: growth, responsiveness, metabolism (VIRUSES DO NOT HAVE THESE) Bacterial cells – external structure  Glycocalyces (capsule or slime layer)  Flagella (parts include filament, hook, basal body)  Fimbriae (allow for adherence to substances in the environment)  Pili Phospholipid bilayer  Hydrophilic head  Hydrophobic tail Active/Passive transport  Active transport: uniport, antiport, coupled transport (uniport and symport)  Active transport only found in eukaryotes  Passive transport: diffusion, facilitated diffusion, osmosis Hypertonic vs. Hypotonic Flagella/Cilia  Cilia are found only in eukaryotic cells  Ear/nose hair, fallopian tubes Archaea – external structure  Glycocalyces  Flagella  Fimbriae and hami (like fimbriae) Eukaryotic cells – external structure  Glycocalyces  Flagella  Cilia Eukaryotic organelles  Nonmembranous: ribosomes, cytoskeleton, centrosome  Membranous: nucleus, endoplasmic reticulum (ER), Golgi bodies, lysosomes, peroxisomes, vacuoles, vesicles, mitochondria, chloroplasts (These are outlined in Table 5, pg. 87.) Key terms: Gram-positive: thick cell wall, purple stain Gram-negative: thin cell wall, extra membrane, pink stain Taxis: movement in response to a stimulus Endospore: stage of some bacterial cells that is extremely durable and potentially pathogenic Useful tables and diagrams: Table 1 on pg. 60 outlines characteristics of life and their distribution in microbes Figure 2 on pg. 61 details the typical prokaryotic cell Figure 3 on pg. 62 details the typical eukaryotic cell Figure 14 on pg. 69 compares the cell walls of gram-positive and gram-negative bacteria (you should be able to draw these) Table 6 on pg. 91 compares archaeal, bacterial, and eukaryotic cells Chapter 5 – Microbial Metabolism This chapter discusses the basic chemical reactions underlying metabolism; enzyme activity; carbohydrate catabolism (glycolysis, cellular, respiration, and the Kreb’s cycle) and fermentation; lipid and protein catabolism; photosynthesis; biosynthesis of carbohydrates, lipids, amino acids, and nucleotides; and integration and regulation of metabolic functions. Important concepts: Ultimate goal of metabolism: to reproduce the organism Metabolic process are guided by 8 elementary statements: 1) Every cell requires nutrients 2) Metabolism requires energy from light or catabolism of nutrients 3) Energy is stored in ATP 4) Cells catabolize nutrients to form precursor metabolites 5) Precursor metabolites, energy from ATP, and enzymes are used in anabolic reactions 6) Enzymes plus ATP form macromolecules 7) Cells grow by assembling macromolecules 8) Cells reproduce once they have doubled in size Factors that influence rate of enzymatic reactions:  Temperature  pH  enzyme and substrate concentrations  presence of inhibitors (competitive, allosteric, feedback) 6 classes of enzymes  hydrolase  isomerase  ligase or polymerase  lyase Table 5.1  oxidoreductase  transferase Kreb’s Cycle  38 net ATP produced per 1 molecule of glucose  Part of respiration Fermentation  Produces 2 ATP  Provides cells with alternative source of NAD+  Starts with glucose  Does not require oxygen  Turns pyruvic acid into: lactic acid, ethanol, propionic acid + CO ,2or acetone + isopropanol Respiration: C H 6 1266  6H 2 + 6CO2+ energy 2photosynthesis is the reverse of this) Key terms: Catabolism: breakdown of larger molecules into smaller products Anabolism: synthesis of large molecules from the smaller products of catabolism Enzymes: protein catalysts Allosteric inhibition and activation Glycolysis: breakdown of glucose by enzymes, releasing energy and pyruvic acid Chemiosmosis: use of ion gradients to generate ATP Autotrophs: organisms such as plants, algae, and certain bacteria that capture the light of the sun to produce energy Heterotrophs: organisms that obtain energy by consuming other organisms Stromatolites: cyanobacteria that are basically the reason we have an oxygenated atmosphere Useful tables and diagrams: Table 1 on pg. 138 (enzyme classification based on reaction types) Figure 7 on pg. 141 shows the representative effects of temp, pH, and concentration on enzyme activity Figure 12 on pg. 144 (summary of glucose catabolism) Figure 16 on pg. 147 (Kreb’s cycle) Chapter 6 – Microbial Nutrition and Growth This chapter explains the nutrient and physical growth requirements of organisms, biofilms, and, to a small extent, culturing microorganisms and microbial population growth (we covered these last two mostly in lab, so there likely will not be many questions on these topics). Important concepts: Microbial growth:  Increase in a population of microbes  Due to reproduction of individual microbes  Requirements: carbon, oxygen, nitrogen, hydrogen Classification of organisms:  Source of carbon: autotrophs and heterotrophs  Source of energy: phototrophs and chemotrophs Grouping of organisms based on oxygen requirements  Obligate aerobes – oxygen is essential  Obligate anaerobes – oxygen is deadly  Facultative anaerobes – oxygen increases growth, but not necessary  Aerotolerant anaerobes – could go either way  Microaerophiles – prefer a small amount of oxygen Nitrogen requirements  Anabolism often ceases due to insufficient nitrogen  Nitrogen acquired from organic and inorganic nutrients  All cells recycle nitrogen from amino acids and nucleotides  Nitrogen fixation by certain bacteria is essential to earth life Other chemical requirements  Phosphorous  Sulfur  Trace elements (required in small amounts  Growth factors (necessary organic chemicals that cannot be synthesized in an organism) Physical requirements  Temperature (affects membranes, protein structure, growth rate) - Psychrophiles, mesophiles (these ones cause disease because they can survive and thrive in the body), thermophiles, hyperthermophiles  pH - neutrophils, acidophiles, alkalinophiles  water (normal cellular processes, metabolic reactions, pressure) - osmotic pressure, hydrostatic pressure, biofilms - most cells die in absence of water, but endospores and cysts cease all metabolic activity and hibernate Associations and Biofilms  Organisms live in association with different species - Antagonistic (Darth Vader) - Synergistic (2 > 1 + 1) - Symbiotic (interdependent)  Biofilms… - Complex relationships among numerous microorganisms - Form on surfaces, medical devices, mucous membranes, digestive systems as a result of quorum sensing Steps in the formation of a biofilm 1) Free-swimming microbes land on a surface (e.g. tooth) 2) Cells begin producing an intercellular matrix and secrete quorum-sensing molecules 3) Quorum-sensing triggers cells to change biochemistry and shape 4) New cells arrive, possibly including new species, water channels 5) Some microbes escape to resume free-living existence, may form new biofilm on another surface Bacterial growth curve:  Lag phase  Log phase  Stationary phase  Death phase Why don’t algae cause disease? - They are photoautotrophs (get their energy from the sun) and can’t access sunlight when in our bodies. Why don’t hyperthermophiles cause disease in humans? - They cannot survive at body temperature. How does canning kill bacteria and fungi so food doesn’t spoil? - The bacteria is placed in a hypertonic solution (of salt or sugar), which pulls out water and kills the organism. Alternatively, the bacteria is exposed to boiling temperatures and high pressure (pasteurization), which kills other kinds of bacteria. Note: some hyperthermophiles can survive this process. Key terms: Hydrostatic pressure: pressure exerted by water in proportion to its depth Plaque: sticky, colorless film of bacteria Tartar: calcified plaque Useful tables and diagrams: Figure 6.1 (autotrophs, heterotrophs, phototrophs, cheotrophs) Chapters 7 & 8 – Microbial Genetics and Recombinant DNA Technology These chapters address genetics, genes, and the genome; use of DNA versus RNA; replication of DNA; replication of DNA using PCR; and modification of genomes. We didn’t really go over these chapters in any depth, so I’m guessing there won’t be many questions on them. But you should know the difference between transcription and translation. Important concepts: Prokaryotic and eukaryotic cells use DNA Some viruses use DNA, some use RNA PCR CRISPR (new DNA-editing tool) Key terms: Genetics: study of inheritance and inheritable traits Genes Genome: sum of all genetic material Useful tables and diagrams: Table 7.1 IS YOUR FRIEND! Table 7.3 (replication, transcription [DNA  mRNA], translation [mRNA  amino acids  proteins]) Chapter 9 – Controlling Microbial Growth in the Environment This chapter covers the basic principles of microbial control, selection of microbial control methods, biosafety levels, and physical and chemical methods of microbial control. Important concepts: Key terms: Useful tables and diagrams: Table 1 on pg. 280 defines and gives examples of microbial control terminology  THIS TABLE IS YOUR FRIEND Table 4 on pg. 291 describes physical methods of microbial control Table 5 on pg. 297 describes chemical methods of microbial control Microbial Cloud Paper (Meadow et al.) - A microbial cloud is kind of like a fingerprint - Always changing, changing quickly - Drawbacks of use for identification at crime scenes: o We don’t have a database of “microbial fingerprints” o There are still a lot of unknowns Chapter 10 – Controlling Microbial Growth in the Body: Antimicrobial Drugs This chapter talks about the history of antimicrobial agents, methods of antimicrobial action, and clinical considerations in prescribing antimicrobial drugs. Do not let this short chapter fool you – it really packs a punch in terms of information! There are several charts regarding different types of drugs. You do not have to memorize them, but at least be familiar with them, in particular their modes of action! Important concepts: Mechanisms of antimicrobial action: 1) Inhibition of cell wall synthesis - Prevents cross-linkage of NAM subunits - Cell wall weakened, cell lyses 2) Inhibition of protein synthesis - Prokaryotic and eukaryotic ribosomes differ in size - Selectively target translation - Mitochondria have prokaryotic ribosomes o Drugs can be harmful! 3) Disruption of cytoplasmic membranes - Form a channel through membrane and damage its integrity - Humans somewhat susceptible (cholesterol) o Attacks fungal ergosterol o Bacteria not susceptible (lack sterols) 4) Inhibition of metabolic pathways - Effective only when pathogen and host metabolic processes differ - Heavy metals inactivate enzymes - Sulfonamides inhibit nucleic acid synthesis - Block activation of viruses 5) Inhibition of nucleic acid synthesis - Block DNA replication or RNA transcription - Both eukaryotic and prokaryotic affected - Not normally used to treat infections - Distort shapes of nucleic acid molecules - Effective against rapidly dividing cancer cells/viruses 6) Prevention of virus attachment - Block viral attachment or receptor proteins - New area of antimicrobial drug development Ideal antimicrobial agent:  Specific to pathogen, not host  Affects a wide range of pathogens  Fewest number of side effects  Inexpensive  Fewest interactions with other drugs  Readily available  Chemically stable (shelf life)  Easily administered  Monotoxic and nonallergenic Spectrum of Action (broad-spectrum/narrow-spectrum) Routes of Administration  Topical  Oral  Intramuscular  Intravenous Key terms: Semisynthetic antimicrobial agent: chemically altered in lab Synthetic antimicrobial agent: completely synthesized in lab Therapeutic Index (TI): ratio of the dose of a drug that can be tolerated to the drug’s effective use Useful tables and diagrams: Study Tables 2, 3, 4, 5, & 6: be familiar with names and modes of action (essentially why and how they work); YOU DO NOT NEED TO MEMORIZE THEM  if you remember, there were questions on previous exams that referenced information found in these tables Figure 13 (effect of route administration on blood levels of a chemotherapeutic agent)  this was on a previous test Chapter 11 –Characterizing and Classifying Prokaryotes This chapter covers general characteristics of prokaryotic organisms, including morphology, endospores, reproduction, and cell arrangement; modern prokaryotic classification; archaea as a distinct and separate domain; and bacteria. Important concepts: 2 domains of prokaryotic life:  Bacteria  Archaea Why is rRNA in the Tree of Life? - Ribosomes are ancient and essential components of cellular organisms, form and function is consistent - rRNA function is highly conserved (maintained by natural selection) between and among species - rRNA sequences differ among species due only to mutation Archaea  lack true peptidoglycan (bacteria have peptidoglycan)  all membrane lipids have branched hydrocarbon chains (bacteria’s are straight)  AUG codon codes for methionine (same as Eukaryotes)  Reproduce by binary fission, budding, or fragmentation  Not known to cause disease (most are extremophiles) 2 phyla of Archaea  Crenarchaeota  Euryarchaeota Key terms: Binary fission Budding Useful tables and diagrams: Figure 1 shows typical prokaryotic morphologies Figure 3 shows binary fission Figure 7 shows arrangements of cocci Figure 8 shows arrangements of bacilli Chapter 12 –Characterizing and Classifying Eukaryotes This chapter covers general characteristics of eukaryotic organisms, including reproduction through meiosis and mitosis and classification of eukaryotes; protozoa; fungi and lichens (both protozoan); algae; water molds; and parasitic helminths and vectors. Important concepts: Lichens  Partnerships between fungi and photosynthetic microbes (green algae or cyanobacteria)  2 microbes in 1!  Fungus provides nutrients, water, protection  Photosynthetic microbe provides carbohydrates and oxygen  Occur in 3 basic shapes - Foliose (petal-like) - Crustose (crusty or flaky) - Fruticose (e.g. witch’s hair)  Create soil from weathered rocks  Some provide nitrogen in nutrient-deficient environments Arthropod vectors  Arachnids - Ticks - Mites  Insects - Fleas - Lice - Flies - Mosquitos - Bugs Key terms: Mitosis: what you start with is what you end with Meiosis: 2N  1N Useful tables and diagrams: Figure 1 shows mitosis and meiosis (you don’t have to have these memorized, just know the difference) Chapter 13 – Characterizing and Classifying Viruses, Viroids, and Prions This chapter discusses characteristics and classifications of viruses, viral replication, culturing viruses in the lab, and viroids and prions. Important concepts: Lytic replication cycle in bacterial biophages (see Figure 8) Lysogenic replication cycle in bacteriophages (see Figure 11) Process of budding in enveloped viruses (see Figure 14) Key terms: Budding Useful tables and diagrams: See “Important concepts” Chapter 14 – Infection, Infectious Diseases, and Epidemiology This chapter discusses symbiotic relationships between microbes and their hosts, reservoirs of infectious diseases of humans, infection, the nature of infectious disease, etiology, virulence factors, portals of entry and exit, modes of transmission, classification of infectious diseases, epidemiology, and nosocomial infections. Important concepts: 3 major entry portals for pathogens:  Skin  Mucous membranes (main portal of entry)  Placenta Modes of disease transmission  Contact: direct, indirect, droplet  Vehicle: airborne, waterborne, foodborne  Vector: mechanical, biological (see Table 14.10) SIR Model of Disease  S = # susceptible people  I = # infected people  R = # recovered (i.e. immune) people Key terms: Symptom: sensed by the patient Sign: detected or measured by an observer Etiology: study of the cause of disease Nosocomial: disease acquired in health care setting Infectious: caused by an infectious agent Useful tables and diagrams: Table 14.5 lists some typical manifestations (symptoms and signs) of disease Table 14.10 lists mechanical and biological vectors Table 14.11 (modes of disease transmission)  KNOW THIS Table 14.12 lists terms used to classify infectious diseases  you don’t need to know all of them, but be familiar with them Chapter 15 – Innate Immunity This chapter provides an overview of the body’s defenses, outlining the first line of defense, the role of mucous membranes, the second line of defense, phagocytosis, and chemical defenses. Important concepts: First line of defense: skin and mucous membranes (external physical barriers)  outer layer of cells is constantly being shed Most irritants that enter through our eyes and nose go down to our stomachs and are digested and killed Second line of defense: blood (internal physical barrier) Mosquitos don’t transfer HIV because:  Only saliva is injected during a mosquito bite  HIV virus gets digested and is not in the saliva  HIV replicates in human T-cells  HIV circulates at low levels in human blood Key terms: Useful tables and diagrams: Table 15.1 provides a comparison of skin and mucous membranes, but the biggest different is that the outer layer of skin cells is dead, while the outer layer of mucous membrane cells is alive Chapter 16 – Adaptive Immunity This chapter provides an overview of adaptive immunity, the organs involved, antigens and antibodies, B and T cells, preparation for adaptive immunity responses, cell-mediated immune responses, antibody immune responses, and types of acquired immunity. Important concepts: 5 attributes of adaptive immunity 1) Specificity: precisely tailored reactions against specific attackers 2) Inducibility: activate only in response to specific pathogens 3) Clonality: proliferate to form many generations of nearly identical cells 4) Unresponsiveness to self: does not act against normal body cells 5) Memory: generates faster and more effective responses in subsequent encounters 2 types of lymphocytes  B lymphocytes (mature in bone marrow)  T lymphocytes (mature in thymus) Classes of antibodies 5 functions of antibodies Innate defenses: first-line defenses, phagocytosis, inflammation, complement system Adaptive defenses: humoral immunity, cell-mediated immunity (helper T- cells, cytotoxic T-cells) Key terms: Antigens Antibodies B cells T cells Useful tables and diagrams: Chapter 18 – Immune Disorders This chapter covers hypersensitivities, including allergies and autoimmune disorders. Important concepts: Key terms: Useful tables and diagrams: Chapter 26 – Applied and Environmental Science This chapter discusses applied microbiology, including food and industrial microbiology; environmental microbiology; and agents of foodborne illness. Important concepts: Key terms: Useful tables and diagrams:


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