BIO305 Final Study Guide PDF

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1 FA20 BIO305 Final Exam Study Guide There will be 100 multiple choice questions for the final exam. Each question will be 2 points. Chapter 26 has 30 questions, and here are the textbook page numbers and the section titles that you need to study for Chapters 1-6, 18 and 20.Chapter 1 pp. 4-5 A Micro...

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1 FA20 BIO305 Final Exam Study Guide There will be 100 multiple choice questions for the final exam. Each question will be 2 points. Chapter 26 has 30 questions, and here are the textbook page numbers and the section titles that you need to study for Chapters 1-6, 18 and 20.

Chapter 1 1. pp. 4-5 A Microbe Is a Microscopic Organism a. Microbe: a living organism that requires a microscope to be seen i. Contradictions: 1. Super-size microbial cells a. Some species of protists (ex: giant amoebas) grow to sizes large enough to see with the unaided eye i. Thiomargarita nambiensis (AKA: sulfur pearl of Namibia) ii. Caulerpa taxifoliasingle cell “killer alga” 2. Microbial communities (both microbial and macroscopic species) a. Some multinuclear worms and arthropods require a microscope to be seen, but are NOT considered microbes, unlike mushrooms, kelps, and biofilms 3. Viruses a. Virus: a noncellular particle containing genetic material that takes over the metabolism of a cell to generate more virus particles b. Although viruses are not full functional cells, some viral genomes may have evolved from cells ii. Microbes include prokaryotes and certain classes of eukaryotes 1. Included eukaryotic classes are: algae, fungi, and protozoa 2. Bacteria, archaea, and eukaryotes (known as the three “domains”) evolved from a common ancestral cell. 2. pp. 5-6 Microbial Genomes Are Sequenced a. Genome: the total genetic info contained in an organism’s chromosomal DNA i. Genome & DNA sequences reveal hoe microbe grows and associates with other species ii. Fred Sanger devised the method of DNA sequence analysis use to sequence the first genomes (1980 Nobel Prize) iii. DNA sequencesGenesFunctions/Chemicals b. Metagenome: the collection of sequences taken directly from the environment i. Metagenomes are sequenced for microbial communities of medical interest, such as that of the human colon ii. Comparing genomes/metagenomes has revealed a set of core genes shared by all organisms 3. pp. 10-12 Microscopes Reveal the Microbial World a. Robert Hooke observes the microscopic world i. Hooke built a compound microscope (2+ lenses) (best: 30x magnification)

ii. Hooke was the first to observe distinct units of living material, which he called “cells” (no single cells) b. Antonie van Leeuwenhoek becomes the first person to observe individual microbes with a single lens i. Leeuwenhoek performed experiments, such as microbe populations in the mouth before and after hot coffee heat killed microbes c. Agostino Bassi de Lodi noted most microbes were harmless i. However, it was hard to distinguish microbes from single-celled human components (RBCs and sperm) 4. pp. 12-13 Spontaneous Generation: Do Microbes Have Parents? a. Spontaneous generation is the concept that living creatures (Ex: maggots) could arise spontaneously, without parental organisms i. Widely disputed by several experiments, suggesting fissure? b. Louis Pasteur reveals the biochemical basis of microbial growth i. Fermentation: a process by which microbes gain energy by converting sugars into alcohol (yeastsingle-celled) ii. Autoclave: a steam pressure device used to sterilize to study microbes 5. pp. 14-16 Growth of Microbes in Pure Culture a. Germ theory of disease: the theory that many diseases are caused by microbes b. Robert Koch devised techniques of pure culture to study a single species of microbe in isolation i. A key technique is culture on solid medium using agar, as developed by Angelina and Walther Hesse, in a double dish devised by Julius Petri (Agar: a polymer of the sugar galactose) ii. Chain of infection: transmission of a disease iii. Pure culture: a culture grown from a single “parental” cell iv. Colonies: distinct populations of bacteria, each grown from a single “parental” cell v. Petri dish: a round dish with vertical walls covered by an inverted dish of slightly larger diameter, invented by Julius Richard Petri c. Note that some kinds of microbes cannot be grown in pure culture without other organisms (Ex: human host tissue culture) i. Note: All viruses can be cultured only within their host cells 6. pp. 18-19 Antiseptics and Antibiotics a. Ignaz Semmelweis –Antiseptic i. Women were dying in childbirth from puerpal fever at an alarming rate, and Semmelweis guessed doctors were transmitting pathogens from uncleaned hands afterwards 1. Chlorine was used as an antiseptic agent (a chemical that kills microbes) and mortality rates fell b. Joseph Lister –Aseptic i. Amputee patients were dying from sepsis (from microbial contamination) so using antiseptic agents, Lister wanted cleaner environment for his surgeries

ii. Surgeons developed fully aseptic (completely free of microbes) environments for surgery 1. Only problem was that most antiseptic chemicals that killed microbes would also kill the patient if ingested c. Alexander Fleming i. Fleming accidentally discovered that the Penicillium mold generates a substance (its own antibiotics) that kills bacteria 1. When culturing Staphylococcus (infects wounds), one plate had been contaminated by Penicillium notatum, which cleared a region of Staphylococcus d. Howard Florey and Ernst Chain i. Purified the substance penicillin, the first commercial antibiotic to save human lives (Allied troops of WWII)

Chapter 2 pp. 39-40 Microbial Size and Shape 1. Microbial Size a. Microbes differ in size, over a range of a few orders of magnitude (powers of 10) b. Eukaryotic Microbes i. Protozoa, algae, fungi ii. 2 μm – 20cm iii. Structures can be seen under a light microscope c. Prokaryotic Microbes i. Bacteria, archaea ii. 0.4-10 μm iii. Subcellular structures are too small to resolve by light microscopy 2. Microbial Shape a. Prokaryotic cell structures are generally simpler than those of eukaryotes (less organelles) b. Certain shapes of bacteria are common to many taxonomic groups: i. Bacillirod ii. Coccispheres iii. Spiral Forms: 1. Spirochetes (singular:spirochete)tightly coiled 2. Spirilla (singular:spirillum—wider)curvy iv. Vibriocurved rods pp. 43-45 Light Interacts with an Object 1. Absorption means that the photon’s energy is acquired by the absorbing object 2. Reflection means that the wavefront bounces off the surface of an object 3. Refraction is the bending of light as it enters a substance that slows its speed

pp. 47-48 The Compound Microscope 1. A compound microscope is a system of multiple lenses designed to correct or compensate for aberration a. Ocular lens (10x) b. Objective lens c. Needs to be parfocal (focus the lower and then go higher) 2. Total magnification = magnification of the ocular multiplied by that of the objective pp. 63-66 Electron Microscopy 1. Electron Microscopy (EM): the foremost tool for observing the shapes of macromolecular structures a. Electrons behave like light waves i. Very high frequency ii. Allow very great resolution 1. A few nm b. Sample must absorb electrons i. Coated with heavy metal c. Electron beam and sample are in a vacuum i. Lenses are magnetic fields d. Two major types i. Transmission electron microscopy (TEM) (parallels the design of BF microscope) 1. Reveals internal structures ii. Scanning electron microscopy (SEM) 1. Electrons scan the specimen surface 2. Reveals external features in 3D 3. Arranged differently from the TEM e. Preparing a specimen for electron microscopy i. The specimens for EM can be prepared in several ways: 1. Embedded in a polymer for thin sections a. Microtome is used to cut slices 2. Sprayed onto a copper grid ii. The specimen is then treated with a heavy-metal salt such as uranyl acetate iii. Note: For SEM, the specimen is coated with heavy-metal and is NOT sliced. pp. 66-69 Cryo-Electron Microscopy and Tomography 1. Cryo-Electron Microscopy a. High strength electron beams now permit low-temperature cryo-election microscopy (or cryo-EM) i. In cryo-EM, the specimen does not require staining ii. The specimen must, however, be flash-frozen 1. Suspended in water and frozen rapidly in a refrigerant 2. Another innovation made possible by cryo-EM is tomography, the acquisition of projected images from different angles of a transparent specimen

a. Cryo-electron tomography, or electron cryotomography, avoids the need to physically slice the sample for thin-section TEM i. The images are combined digitally to visualize the entire object in 3D ii. Generates high-resolution models of virus particles iii. Can also be used to build a 3D model of rotary flagellar motors b. While cryo-EM models of a flagellar motor are impressive, even more so is the building of a 3D model of an entire cell Chapter 3 p. 78 Model of a Bacterial Cell 1. 2. 3. 4.

Cytoplasm: consists of a gel-like network Cell membrane: encloses the cytoplasm (AKA: plasma membrane) Cell wall: rigid structure external to the cell membrane Nucleoid: non-membrane-bound area of the cytoplasm that contains the chromosome in the form of looped coils 5. Flagellum: external helical filament whose rotary motor propels the cell 6. Glycocalyx: sugar encasing external to cell wall

pp. 84-85 Transport across the Cell Membrane 1. The cell membrane acts as a semipermeable barrier 2. Selective transport is essential for survival a. Small, uncharged molecules, such as O₂ and CO₂, easily permeate the membrane by passive diffusion b. Water diffuses across the membrane in a process called osmosis 3. A special case of movement across cell membranes is that of membrane-permeant weak acids and weak bases a. These exist in equilibrium between charged and uncharged forms: i. Weak Acid: HA ↔ H⁺+A⁻ ii. Weak Base: B + H₂O ↔ BH⁺ + OH⁻ b. In their uncharged state, they can diffuse across the membrane and increase/decrease, respectively, the H⁺ concentration of the cell 4. Polar molecules and charged molecules require transport through specific protein transporters a. Passive Transport: molecules move from an area of high concentration to an area of lower i. Uses concentration gradient b. Active transport: molecules move from an area of low concentration to an area of higher concentration i. Requires energy pp. 85-87 Membrane Lipid Diversity 1. Phospholipids vary with respect to their phosphoryl head groups and their fatty acid side chains a. Cardiolipin (diphosphatidylglycerol)

i. A double phospholipid linked by a glycerol ii. Concentration increases under conditions of cell stress iii. Localizes to the cell poles in wide, upside down V shape 1. Binds certain environmental stress proteins, such as a protein that transports osmoprotectants when the cell is under osmotic stress 2. Fatty acid chains may be saturated, unsaturated, or polyunsaturated a. May also contain cyclic structures 3. Membranes also include planar molecules that fill gaps between hydrocarbon chains a. In eukaryotic membranes, the reinforcing agents are sterols, such as cholesterol (recall LDL and HDL) b. In bacteria, the same function is served by hopanoids, or hopanes 4. Archaea have the most extreme variations in phospholipid side-chain structures a. Ether links between glycerol and fatty acids i. Diethers or tetraethers b. Hydrocarbon chains are branched terpenoids i. Can cyclize to form cyclopentane pp. 92-95 Proteobacterial Cell Envelope – Gram-Negative 1. The thin peptidoglycan layer consists of one or two sheets a. Covered by an outer membrane, which confers defensive abilities and toxigenic properties on many pathogens i. Inward-facing leaflet including lipoprotein ii. Outward-facing leaflet containing lipopolysaccharides iii. Contains transmembrane proteins called porins pp. 103-105 Bacterial Cell Differentiation 1. Some bacteria generate two kinds of daughter cells: one stationary and one mobile a. Example: the flagellum-to-stalk transition of the bacterium Caulobacter crescentus 2. The process has been studied via genetic analysis a. TipN is a landmark protein that correctly marks the site of a new cell pole and the polar placement of flagella 3. Cell Cycle of Caulobacter a. Cell development involves many such proteins working together 4. Growth Asymmetry and Polar Aging a. The actual process of cell division itself determines that the poles of each daughter cell differ chemically from each other i. Polar aging is increased by stress b. A major form of asymmetrical growth is endospore formation by Firmicutes such as Bacillus and Clostridium species i. Endospores can remain dormant but viable for thousands of years

Chapter 4

p. 120 Nutrient Supplies Limit Microbial Growth 1. Essential nutrients: are those that MUST be supplied from the environment a. Macronutrients i. Major elements in cell macromolecules 1. CHOPNS (carbon is the most important!) ii. Cations necessary for protein function (serve as cofactors) 1. Mg²⁺, Ca²⁺, Fe²⁺, K⁺ b. Micronutrients i. Trace elements necessary for enzyme function 1. Co, Cu, Mn, Zn pp. 120-121 Microbes Build Biomass through Autotrophy or Heterotrophy 1. All of earth’s life-forms are based on carbon, which they acquire in different ways a. Autotrophs fix CO₂ and assemble into organic molecules (mainly sugars) plants (producers) b. Heterotrophs use preformed organic molecules (consumers) 2. How Microbes Obtain Energy a. All organisms require an energy source i. Phototrophs obtain energy from chemical reactions triggered by light ii. Chemotrophs obtain energy from redox reactions iii. Lithotrophs use inorganic molecules as a source of electrons iv. Organotrophs use organic molecules b. In short, microbes are classified based on their carbon and energy acquisition as follows: i. Autotrophs 1. Photoautotrophs (energy from light, C from CO₂) 2. Chemolithotrophs (or lithotrophs) (inorganic, C from CO₂) ii. Heterotrophs 1. Photoheterotrophs (energy from light, C from consuming) 2. Chemoheterotrophs (or organotrophs) (energy and C from the same source) pp. 126-127 Active Transport Requires Energy 1. Coupled transport systems are those in which energy released by a driving ion moving down its gradient is used to move a solute up its gradient a. In symport, the two molecules travel in the same direction b. In antiport, the actively transported molecule moves in the direction opposite to the driving ion pp. 128-129 Siderophores Are Secreted to Scavenge Iron 1. Siderophores are specialized molecules secreted to bind ferric ion (Fe³⁺) and transport it into the cell a. The iron is released into the cytoplasm and reduced to more useful ferrous (Fe²⁺) form

2. Note: Neisseria gonorrhoeae employs receptors on its surface that bind human iron complexes and wrest iron from them p. 132 Complex versus Synthetic Media 1. Types of Media a. Complex media are nutrient rich but poorly defined b. Minimal defined media contain only those nutrients that are essential for growth of a given bacteria c. Enriched media are complex media to which specific blood components are added d. Selective media favor the growth of one organism over another e. Differential media exploit differences between two species that grow equally well f. Several media used in clinical microbiology are both selective and differential i. Example: MacConkey medium 1. Only grows gram-negative (selective) 2. Only grows species capable of fermenting lactose produces pink colonies (differential) pp. 141-143 Generation Time 1. Generation time is the time it takes for a population to double 2. For cells undergoing binary fission, a. Nt = No * 2^n i. Where Nt is the final cell number, ii. No is the original cell number, iii. N is the number of generations 3. Stages of Growth in a Batch Culture a. Exponential growth never lasts indefinitely b. The simples way to model the effects of a changing environment is to culture bacteria in a batch culture i. A liquid medium within a closed system c. The changing conditions in this system greatly affect bacterial physiology and growth i. This illustrates the remarkable ability of bacteria to adapt to their environment d. Bacterial Growth Curves i. Phases of bacterial growth in typical batch culture 1. Lag phase: bacteria are preparing their cell machinery for growth 2. Log phase: growth approximates an exponential curve (straight line, on a logarithmic scale) 3. Stationary phase: cells stop growing and shut down their growth machinery while turning on stress responses to help retain viability 4. Death phase: cells die with a “half-life” similar to that of radioactive decay, a negative exponential curve p. 151 Endospores Are Bacteria in Suspended Animation 2 1. Clostridium and Bacillus species can produce dormant spores that are heat resistant 2. Starvation initiates an elaborate 8-hour genetic program that involves:

a. An asymmetrical cell division process that produces a forespore and ultimately an endospore 3. Sporulation can be divided into discrete stages based primarily on morphological appearance 4. Endospore formation a. Stage 1: Septum forms near one pole. DNA replicates and extends into axial filament b. Stage 2: Septum separates forespore from mother cell. DNA is pumped through septum until each compartment gets a chromosome c. Stage 3: Mother cell engulfs forespore, surrounding it with a second membrane d. Stage 4: Chromosomes of mother cell disintegrate e. Stage 5: Forespore develops a cortex layer of peptidoglycan between original forespore membrane and the membrane from the mother cell. Coat proteins are deposited on outer membrane f. Stage 6: Dipicolinic acid is synthesized, and calcium is incorporated into the spore coat g. Stage 7: Mother cell releases spore

Chapter 5 pp. 161-162 Growth Rate and Temperature 1. Microbes that grow at higher temperatures typically can achieve higher rates of growth 2. Microbial growth rates roughly double for every 10° rise in temperature 3. Thermodynamic principles limit a cell’s growth to a narrow temperature range a. The typical temperature growth range usually spans the organism’s optimal growth temp by 30-40°C pp. 162-165 Microbial Classification by Growth Temperature 1. Microorganisms can be classified by their growth temperature a. Psychrophiles: ~0°-20°C b. Mesophiles: ~15°-45°C c. Thermophiles: ~40°-80°C d. Hyperthermophiles: ~65°C-121°C 2. All of these organisms have membranes and proteins best suited for their temperatures pp. 174-175 Aerobes versus Anaerobes 1. 2. 3. 4. 5.

Strict aerobes can only grow in oxygen Microaerophiles grow only at lower O₂ levels Strict anaerobes die in the least bit of oxygen Aerotolerant anaerobes grow in oxygen while retaining a fermentation-based metabolism Facultative anaerobes can live with or without oxygen a. They possess both the ability for fermentative metabolism and respiration (anaerobic and aerobic) 6. Growth Zones (top to bottom) a. Aerobesmicroaerophilicanaerobes i. Facultative or aerotolerant aerobes throughout

pp. 181-181 Cells Treated with Antimicrobials Die at a Logarithmic Rate 1. Microbes die according to a negative exponential curve, where the cell numbers are reduced in equal fractions at constant intervals 2. Decimal reduction time (D-value) is the length of time it takes an agent or a condition to kill 90% of a population pp. 182-185 Physical Agents That Kills Microbes 1. High temperature a. Moist heat is more effective than dry heat b. Boiling water (100°C) kills most cells c. Killing spores and thermophiles usually requires a combination of high pressure and temperature d. At high pressure, the boiling point of water rises to a temperature rarely experienced by microbes i. Even endospores quickly die under these conditions e. Steam autoclave i. 121°C (250°F) at 15 psi for 20 minutes ii. Similar conditions are produced in pressure cookers when canning vegetables 2. Pasteurization a. Three time and temperature combinations are approved by US Government for milke pasteurization: i. LTLT (low temp, long time) ii. HTST (high temp, short time) iii. UHT (ultra-high temperature) b. All three methods kill Coxiella burnetii, the causative agent of Q fever and the most heat-resistant non-spore-forming pathogen known. UHT yields nearly sterile milk with a 6-month shelf life 3. Cold a. Low temperatures slow growth and preserve strains b. Refrigeration temps are used for food preservation c. For long-term storage of cultures, bacteria are either suspended in a glycerol solution and stored at or below -70°...