Microbiology

How small are bacteria?

- 1/60 the width of a human hair - 1/60 the width of a page in the textbook

Arrangement of DNA in Microbial Cells: Prokaryotes: What is a genome? Prokaryotic cells generally have a chromosome, what is a chromosome? DNA aggregates to form what? What are plasmids?

- A cell's full complement of genes - It's a single, circular DNA molecule -- DNA aggregates to form the nucleoid region -- Prokaryotes sometimes have small amounts of extra-chromosomal DNA called plasmids

X Brief Survey of Eukaryotic Microbes: Algae: What do they contain and what process do they use? Describe main characteristics of fungi, protozoa, and slime molds.

- Algae are photosynthetic -- Contain chloroplasts -- Need only a few minerals, CO2, and light -- Major primary producers in nature - Fungi are major recyclers of organic matter -- Not photosynthetic -- Major groups are unicellular (yeasts) or multicellular (molds) - Protozoa lack cell walls (fungi and algae have walls) -- Most are motile -- Many different taxonomic groups -- Most free-living, some pathogenic - Slime molds are between protists and fungi -- Resemble protists in their unicellular phase -- Cells sometimes aggregate forming mold-like fruiting body

X The Domain Archaea: T/F all archaea are autotrophic? What are methanogens? T/F most are cultured.

- All Archaea are chemotrophic - Many are extremophiles: -- Temperature -- pH -- Salt -- Extreme heat and acid - Some are chemoorganotrophs, and many are chemolithotrophs - Methanogens are included in Archaea (convert organic matter to methane gas) - Most never cultured, and known only by molecular biology

Microbial Diversity: What are the 3 sources that cells need to obtain energy and how are the microorganisms classified according to the type of energy they need? Microbes are diverse in what 6 ways?

- All cells need energy: 3 sources for obtaining energy: -- Organic chemicals (chemoorganotrophs) -- Inorganic chemicals (chemolithotrophs) -- Light (phototrophs) - Morphology (cell size and shape) - Metabolism - Motility - Mechanisms of cell division - Developmental biology - Adaptation to environment

Archaeal Membranes vs. Bacterial Membrane: The biggest difference between the two is what? What type of linkages are there in phospholipids of Archaea? What type of linkages are there in phospholipids of Bacteria and Eukarya? What do archaeal lipids lack? What do they have instead? What are glycerol diethers and tetraethers? In what different ways can archaeal membranes exist?

- An outer membrane is typically lacking in Archaea - Ether linkages in phospholipids of Archaea - Bacteria and Eukarya that have ester linkages in phospholipids - Archaeal Membranes: -- Archaeal lipids lack fatty acids -- They have isoprenes instead -- Major lipids are glycerol diethers and tetraethers -- Can exist as lipid monolayers, bilayers, or mixture

What is the basic structure and functions of bacterial cell walls? How does the structure differ from archaea?

- Basic structure: bacteria have peptidoglycan and archaeal cell walls have pseudomurein - Basic function: To withstand pressures and prevent bursting (cell lysis). Cells walls also confer shape and rigidity.

The Cell Wall of Prokaryotes: Cell wall gives the cell what two things? Bacteria divided into what 2 major groups? Gram reaction indicates what?

- Cell wall gives the cell: -- Shape -- Rigidity - Bacteria divided into 2 major groups: --Gram positive --Gram negative - Gram reaction indicates structure of the cell wall

Evolve: What can mutate and evolve (hint: they are contained in cells)? What shows relationships and evolutionary history?

- Cells contain genes - Genes can mutate and evolve - Phylogenetic trees can show relationships and evolutionary history

Group Morphology: Arrangements of Prokaryotic Cells: Cells may stay together in characteristic arrangements give three examples?

- Cells may stay together in characteristic arrangements -- Chains of cocci or rods -- Thin sheets of cells -- Cubes or cube-like clusters

X Lower Limits of Cell Size: Cellular organisms less than how many μm in diameter are unlikely to exist? Why is there a limit to how small a cell can be? Where do small cells tend to be located?

- Cellular organisms < 0.15 μm in diameter are unlikely - Needs enough volume to house the essential components of a free-living cell -- Why viruses and parasites can be smaller - Open oceans tend to contain small cells (0.2-0.4 μm in diameter)

X Eukaryotic Microorganisms: Collectively known as what? Major groups include what? Are some protists (e.g. algae) phototrophic? T/F Protozoa have cell walls, Algae and fungi do not? Earlier branches of Eukarya (e.g. diplomonads like Giardia) lack what? Describe the metabolism of Diplomonads and what has happened as a result?

- Collectively known as protista - Major groups include algae, protozoa, fungi, and slime molds - Some protists (e.g. algae) phototrophic - False, Algae and fungi have cell walls, protozoa do not - Earlier branches of Eukarya (e.g. diplomonads like Giardia) lack mitochondria. -- Diplomonads are metabolically deficient -- Most diplomonads are thus pathogenic parasites

Why is microbial life important?

- Collectively they constitute the bulk of biomass on Earth and carry out many necessary chemical reactions for higher organisms. In the absence of microorganisms, higher life forms would have never evolved and could not now be sustained

X The Domains: What has defined three distinct lineages of cells called domains? What are the three domains? Are archaea and bacteria closely related?

- Comparative rRNA sequencing has defined three distinct lineages of cells called domains: -- Bacteria (prokaryotic) -- Archaea (prokaryotic) -- Eukarya (eukaryotic) - Archaea and Bacteria are NOT closely related (Archaea are more closely related to Eukarya than Bacteria)

X Simple Transport: Consists of only what type of protein?

- Consists of only membrane-spanning transport protein - Lac Permease of Escherichia coli -- Lactose is transported into E. coli by simple transporter lac permease, a symporter -- Activity of lac permease is energy driven -- Other symporters, uniporters, and antiporters

X ABC (ATP-Binding Cassette) Systems:

- Consists of three components, a substrate-binding protein, a membrane-integrated transporter, and an ATP-hydrolyzing protein - (>200) different systems identified in prokaryotes - Often involved in uptake of organic compounds (e.g., sugars, amino acids), inorganic nutrients (e.g., sulfate, phosphate), and trace metals - Typically display high substrate specificity - Contain periplasmic binding proteins

X Cytoplasmic Membrane Composition II:

- Contains Embedded proteins - Stabilized by hydrogen bonds and hydrophobic interactions - Mg2+ and Ca2+ help stabilize membrane by forming ionic bonds with negative charges on the phospholipids - Somewhat fluid

What are the 4 basic cell structures of microbial cells and what are their basic functions?

- Cytoplasmic (cell) membrane -- Barrier that separates the inside of the cell from the outside environment - Cytoplasm -- Fluid that fills cells - Ribosomes -- Protein synthesis - Cell wall -- Present in most bacteria, confers structural strength

Gram Stain: What type of stain is the gram stain? By using this type of stain bacteria can be divided into what two major groups? How does the gram stain work?

- Differential stain - Widely used in microbiology -- Bacteria can be divided into two major groups: gram-positive and gram-negative - Due to differences in the thickness of a peptidoglycan layer in the cell membrane between Gram positive and Gram negative bacteria, Gram positive bacteria (with a thicker peptidoglycan layer) retain crystal violet stain during the decolorization process, while Gram negative bacteria lose the crystal violet stain and are instead stained by the safranin in the final staining process.

Louis Pasteur (1822-1895): He disproved what? What is the basic idea behind what he disproved?

- Disproved spontaneous generation - Spontaneous generation: Food putrefied spontaneously because of nonliving materials - Supplemental info: Developed vaccines for chickenpox, anthrax, rabies - Demonstrated that all fermentations were due to the activities of specific yeasts and bacteria.

Differences Between Eukaryotes and Prokaryotes: In eukaryotes how is DNA stored? How do eukaryotic cells compare in size and complexity? How do organelles different in eukaryotes compared to prokaryotes? Do prokaryotes have a nucleus?

- Eukaryotes: -- DNA enclosed in a membrane-bound nucleus -- Cells are generally larger and more complex -- Contain organelles - Prokaryotes: -- No membrane-enclosed organelles, no nucleus -- Generally smaller than eukaryotic cells

Arrangement of DNA in Eukaryotes: How is it arranged and where is it found? Associated with what that help in folding the DNA? Is there only one chromosome? During cell division how does the nucleus divide? During sexual reproduction, the genome is halved by what process?

- Eukaryotic DNA: -- It's arranged linearly and found within the nucleus -- Associated with proteins that help in folding the DNA -- Usually there is more than one chromosome -- Typically two copies of each chromosome -- During cell division, the nucleus divides by mitosis -- During sexual reproduction, the genome is halved by meiosis

Eukaryotes and Multicellularity: Eukaryotic microorganisms were the ancestors of? What contain their own genomes (circular, like prokaryotes)? These organelles are related to specific lineages of what? What took up residence in Eukarya eons ago?

- Eukaryotic microorganisms were the ancestors of multicellular organisms - Mitochondria and chloroplasts also contain their own genomes (circular, like prokaryotes) - These organelles are related to specific lineages of Bacteria - Mitochondria and chloroplasts took up residence in Eukarya eons ago => endosymbiosis

What is the extent of microbial life: Where can they be found? About how many microbial cells are there on Earth? How are they related to biomass on earth? What are they comparable to? How many more bacterial cells are there in our bodies compared to human cells? Where do most bacteria live?

- Examination of natural materials such as soil and water invariably reveals microbial cells, but unusual habitats such as boiling hot springs and glacial ice are also teeming with microorganisms. - Estimates of total microbial cell numbers on Earth are on the order of 2.5 * 10^30 cells. - Microorganisms comprise more biomass than all animals - Comparable amount to plant life - 10X more bacteria cells than human cells in our bodies - Most bacteria live under Earth's surface in oceanic and terrestrial habitats

Autotrophs and Heterotrophs: T/F Only eukaryotic cells require carbon as a major nutrient? What are autotrophs sometimes referred to as and what do they use as their carbon source? T/F Heterotrophs require more than one organic molecule for their carbon source? What is a heterotrophs relationship to an autotroph?

- False: All cells require carbon as a major nutrient - Autotrophs -- Use carbon dioxide as their carbon source -- Sometimes referred to as primary producers - Heterotrophs -- False: They require one or more organic molecules for their carbon source -- They feed directly on autotrophs or live off products produced by autotrophs

Chemolithotrophs: T/F they obtain energy from oxidation of organic molecules? T/F they are found only in eukaryotes? T/F Each species of chemolithotroph will usually use 2 classes of inorganic molecules? Many compounds used by chemolithotrophs come from where?

- False: They obtain energy from oxidation of inorganic molecules - False: They are found only in prokaryotes - Many different types of inorganic molecules used by chemolithotrophs - False: Each species of chemolithotroph usually will use only one class of inorganic molecule - Many compounds used by chemolithotrophs are waste products of chemoorganotrophs

Antoni van Leeuwenhoek (1632-1723): He was the first person to see what? What did he term this?

- He was the first person to see bacteria - "Wee beasties"

Light Microscopy: In general, light microscopes are used for what? What do light microscopes use to illuminate cells? Name the four different types of light microscopy.

- In general, light microscopes are used to examine cells at relatively low magnification - Light microscopes use visible light to illuminate cells - Many different types of light microscopy: -- Bright-field -- Phase-contrast -- Dark-field -- Fluorescence -- Differential interference contrast (not mentioned on slide but mentioned in textbook)

Surface Area and Volume Relationships in Cells: What is the relationship?

- In general, the smaller the cell, the greater the surface to volume ratio.

X Group Translocation: The Phosphotransferase System:

- Involves a series of proteins in the transport event - Substance transported is chemically modified during transport across the membrane - Highly studied system - Moves glucose, fructose, and mannose - Five proteins required - Energy derived from phosphoenolpyruvate

State the germ theory of disease:

- It states that some diseases are caused by microorganisms. - Supplemental info: These small organisms, too small to see without magnification, invade humans, animals, and other living hosts. Their growth and reproduction within their hosts can cause a disease. "Germ" may refer to a virus, bacterium, protist, fungus, or prion. Microorganisms that cause disease are called pathogens, and the diseases they cause are called infectious diseases. Even when a pathogen is the principal cause of a disease, environmental and hereditary factors often influence the severity of the disease, and whether a particular host individual becomes infected when exposed to the pathogen.

Determining evolutionary relationships using RNA: Why use rRNA sequence to phylogenetically divide organisms into the three domains? How can relationships within the three domains be deduced with the use of phylogeny? rRNAs are highly conserved, what does that mean? How is degree of relatedness indicated? The more or less conserved regions allows for what?

- It's fundamental to all life meaning it can be used to study all life (e.g. prokaryotes and eukaryotes) - relationships can be deduced by comparing genetic information - Highly Conserved: -- Can compare all life to each other -- Amount of similarity indicates degree of relatedness - Has more and less conserved regions: -- Allows for PCR (polymerase chain reaction) and for informed differences

X Lichens

- Lichens are an example of a mutualistic relationship between two groups of protists -- Fungi and cyanobacteria -- Fungi and algae

Dark-Field microscopy: How does light reach the specimen? How is the light reaching the lens affected by the specimen? What makes the specimen appear light against a dark background?

- Light reaches specimen from the sides only - the only light reaching the lens is scattered by the specimen - Light bouncing off specimen makes it light against a dark background - Excellent for observing motility -- Resolution is high (eg. bundles of flagella are resolvable)

X Bacterial Diversity: All known bacteria are what type of cells? How many bacteria are there, relatively? what is the Proteobacteria and what does it include? what is the second largest phylum? Cyanobacteria are relatives of what type of bacteria?

- Many many many Bacteria - All known pathogenic prokaryotes - The Proteobacteria = largest phylum -- Gram-negative -- E.G., E. coli, Pseudomonas and Salmonella - Gram-Positive = Second largest phylum -- E.G. Clostridium, Bacillus, Streptomyces, Streptococcus, Lactobacillus - Cyanobacteria are relatives of Gram-positive bacteria -- oxygenated the atmosphere

X The 2 phyla of Archaea: Euryarchaeota: Define extreme halophiles and thermoacidophiles

- Methanogens: anaerobically degrade organic matter, produce methane (natural gas) - Extreme halophiles: require high salt concentrations for metabolism and reproduction - Thermoacidophiles: grow in moderately high temperatures and low pH environments

X Environmental Microbiology: Can microbes affect their environment?

- Microbes affect their environments

The characteristics of living systems: All cells are able to do what three things and only some cells do what three things?

- Microbes are Alive (Except for Viruses) - All cells: 1. Grow/Reproduce 2. Metabolize 3. Evolve - Some cells: 1. Communicate 2. Move 3. Differentiate

The Scope of Microbiology and the kinds of work Microbiologists do: Name some things microbiology has an impact on. Name some different types of microbiology.

- Microbiology has an impact on medicine, agriculture, food science, ecology, genetics, biochemistry, immunology, and many other fields. - Many microbiologists are primarily interested in the biology of microorganisms, while others focus on specific groups. - Virologists - viruses ; Bacteriologists - bacteria ; Phycologists - algae ; Mycologist -fungi - Protozoologists - protozoa - Medical Microbiology: deals with diseases of humans and animals; identify and plan measures to eliminate agents causing infectious diseases. - Immunology: study of the immune system that protects the body from pathogens. - Agricultural Microbiology: impact of microorganisms on agriculture; combat plant diseases that attack important food crops. - Food and Dairy Microbiology: prevent microbial spoilage of food & transmission of food-borne diseases (e.g. salmonellosis); use microorganisms to make food such as cheeses, yogurts, pickles, beer, etc. - Industrial Microbiology: using microorganisms to make products such as antibiotics, vaccines, steroids, alcohols & other solvents, vitamins, amino acids, enzymes, etc. - Genetic Engineering: Engineered microorganisms used to make hormones, antibiotics, vaccines and other products.

Microbiology as an applied science:

- Microbiology is at the center of many important aspects of human and veterinary medicine, agriculture, and industry. - Many large-scale industrial processes, such as the production of antibiotics and human proteins, rely heavily on microorganisms. - Microorganisms affect the everyday lives of humans in both detrimental and beneficial ways.

Cell Morphology: What is morphology? What are the three major cell morphologies and what basic shape do they relate to?

- Morphology = cell shape - Major cell morphologies -- Coccus (pl. cocci): spherical or ovoid -- Bacillus (pl. bacilli) Rod: cylindrical shape -- Spirillum (pl. Spirilla): spiral shape - Many variations on basic morphological types

X Cell Morphology Cont. : Does morphology typically predict physiology, ecology, phylogeny, etc? What are some selective forces involved in setting morphology?

- Morphology typically does not predict physiology, ecology, phylogeny, etc. - Some selective forces involved in setting morphology -- Optimization for nutrient uptake (small cells and those with high surface-to-volume ratio) -- Swimming motility in viscous environments or near surfaces (helical or spiral-shaped cells) -- Gliding motility (filamentous bacteria)

Cell Walls of Archaea: Do they have peptidoglycan? Do they have an outer membrane? They have Pseudomurein. What is it comparable to and what is it composed of? It's found in cells walls of a certain type of archaea?

- No peptidoglycan - Typically no outer membrane - Pseudomurein -- Polysaccharide similar to peptidoglycan -- Composed of Nacetylglucosamine and Nacetylalosaminuronic acid -- Found in cell walls of certain methanogenic Archaea

Viruses: How are viruses classified and what types of metabolic abilities do they have of their own? What do they completely rely on? What types of cells can they infect? How big is the smallest virus?

- Not considered cells - No metabolic abilities of their own - Rely completely on biosynthetic machinery of infected cell - Infect all types of cells - Smallest virus is 10 nm in diameter

Chemoorganotrophs: What are they? Do they use oxygen? T/F They can only break down organic compounds aerobically. What are they called if they use oxygen? What if they don't use oxygen? What type of bacteria are mostly chemoorganotrophs? T/F All archaea are chemoorganotrophs.

- Organisms that conserve energy from chemicals are called chemotrophs and those that use organic chemicals are Chemoorganotrophs. - False: Some can break down organic compounds either aerobically or anaerobically (facultative anaerobes) - Many use oxygen (aerobes) - Some do not use oxygen (anaerobes) - Most cultured bacteria are chemoorganotrophs - False: All animals are chemoorganotrophs

Diversity of Habitats: Organisms that inhabit extreme environments are called what? Habitats include what?

- Organisms that inhabit extreme environments are called extremophiles - Habitats include boiling hot springs, glaciers,extremely salty bodies of water, and high pH environments

X Cross-linking amino acids in peptidoglycan:

- Peptidoglycan is a sheet formed by joining the glycan tetrapeptides -- Glycosidic bonds in the glycan chains are very strong, but not rigid -- Peptide cross-links, the bonding of amino acids, make it more rigid

X 3 Functions of the Cytoplasmic Membrane

- Permeability Barrier -- Polar and charged molecules must be transported -- Transport proteins accumulate solutes against the concentration gradient - Protein Anchor -- Holds transport proteins in place - Energy Conservation

X Other groups within Bacteria: Describe: Planctomyces group, Spirochetes, Green Sulfur Bacteria, Green Nonsulfur Bacteria (Chloroflexus group), Deinococcus, Chlamydia

- Planctomyces group have distinct stalk structure on cells, allowing them to attach to solid substrate. - Spirochetes have helical shape, and include some pathogens (eg. syphilis, Lyme disease) - Green Sulfur Bacteria are phototrophs - Green Nonsulfur Bacteria (Chloroflexus group) -- Phototrophs that form filaments in hot springs and shallow marine bays. -- Filaments form basis for microbial mats containing a varied community of organisms. - Deinococcus are extremely resistant to radioactivity - Chlamydia are obligate intracelluar parasites

Define: Population ; Habitat ; Community ; Ecosystem ; Microbial Ecology

- Population: A group of organisms of one species that interbreed and live in the same place at the same time (e.g. deer population). - Habitat: The environment in which a microbial population resides - Community: An ecological unit composed of a group of organisms or a population of different species occupying a particular area, usually interacting with each other and their environment. -- microbial communities: Microorganisms exist in nature in populations of interacting assemblages - Ecosystem: refers to all living organisms plus physical and chemical constituents of their environment - Microbial Ecology: The study of microorganisms in their natural environments

What are the two major classifications of cells and what are they comprised of? What similarities do all cells share?

- Prokaryotic: Bacteria and archaea - Eukaryotic: Everything else (algae and protozoa collectively called protists, and the fungi and slime molds ; Also cells of plants and animals) - Cytoplasmic (cell) membrane, Cytoplasm, Ribosomes

X Peptidoglycan: What is it and what is it composed of?

- Rigid layer that provides strength to cell wall - Polysaccharide composed of: -- N-acetylglucosamine and Nacetylmuramic acid -- Amino acids -- Lysine or diaminopimelic acid (DAP) -- Cross-linked differently in gram-negative bacteria and gram-positive bacteria

Carrier-Mediated Transport Systems:

- Show saturation effect - Highly specific

Robert Koch (1843-1910): What did he show caused disease? He developed techniques for what purpose? In general what were Koch's postulates and what were they for?

- Showed bacteria cause disease - Developed techniques to obtain pure cultures - Koch's postulates: a set of rigorous criteria for definitively linking a specific microorganism to a specific disease. -- The postulates not only offered a means for linking the cause and effect of infectious disease, but also stressed the importance of laboratory culture of the putative infectious agent.

Simple vs. Differential Staining: What's the difference?

- Simple Staining: a method of staining microorganisms which uses only one dye - Differential Staining: the use of two or more stains to categorize cells into groups

What are the three major classes of transport systems in prokaryotes and how do they differ from each other?

- Simple transport --Driven by the energy in the proton motive force - Group translocation -- Chemical modification of the transported substance driven by phosphoenolpyruvate - ABC system -- Periplasmic binding proteins are involved and energy comes from ATP - All require energy in some form, usually proton motive force or ATP

X Cell Size and the Significance of Smallness: What is the size range for eukaryotic and prokaryotic cells? size of most cultured rod-shaped bacteria? Name two large prokaryotes.

- Size range for eukaryotic cells: 10 to > 200 μm in diameter - Size range for prokaryotes: 0.2 μm to > 700 μm in diameter - Most cultured rod-shaped bacteria between 0.5 and 4.0 μm wide and < 15 μm long - Few very large prokaryotes; Epulopiscium fishelsoni Thiomargarita namibiensis

Communicate: How can some cells communicate?

- Some cells can communicate with each other via chemicals that are either released or taken up

Scanning Electron Microscopy (SEM): Specimen are coated with thin film of what? What scans the object? What are collected by a detector and what happens as a result? T/F only very small specimens can be observed? What is the magnification range?

- Specimen coated with thin film of heavy metal (e.g. gold) - Electron beam scans the object - Scattered electrons collected by a detector and the image is produced - False: even very large specimens can be observed - Magnification range of 15X - 100,000X -- Supplemental info: only the surface of an object is typically visualized

Bright-field microscopy: how are specimen visualized? How many sets of lenses form the image and what are they called? How is total magnification calculated? Approximately what is the maximum magnification?

- Specimens are visualized because of differences in contrast (density) between specimen and surroundings - Two sets of lenses form the image (objective lens and ocular lens) -- Total magnification = objective magnification x ocular magnification -- Maximum magnification is ~2,000x -- supplemental info: Since the microscope has an objective lens and an ocular lens, the microscope is called a compound microscope

Phase-Contrast microscopy: How are the specimen seen? T/F It improves the contrast of a sample with the use of a stain. phase-contrast microscopy allows for the visualization of what? What is the resulting image?

- Specimens stand out against background -- False: It improves the contrast of a sample without the use of a stain -- Allows for the visualization of live samples -- Resulting image is dark cells on a light background - Supplemental info: It is widely used in teaching and research for the observation of wet-mount (living) preparations

Resolution: What is resolution?

- The ability to distinguish two adjacent objects as separate and distinct - Supplemental info: -- Determined by the wavelength of light used and the numerical aperture of lens -- Limit of resolution for light microscope is about 0.2 micrometers -- resolution is the limiting factor in our ability to see objects. Although magnification can be increased virtually without limit, resolution cannot because resolution is a function of the physical properties of light.

Louis Pasteur's experiment: Pasteur used what type of flask for the experiment? What did he use to eliminate contaminants (bacteria and other microorganism) and what is that process called today? How did proponents of spontaneous generation criticize his experiment? What was the result of using this type of flask? What was observed that finally disproved the notion of spontaneous generation?

- The defeat of spontaneous generation: Pasteur's swannecked flask experiment. The flask is now called a Pasteur flask. - Pasteur used heat to eliminate contaminants. Killing all the bacteria and other microorganisms in a process we now call sterilization. - Proponents of spontaneous generation criticized such experiments by declaring that "fresh air" was necessary for the phenomenon to occur. - In the flask, nutrient solutions could be cooled, air was allowed to renter, but the bend in the neck prevented particulate matter (including microorganisms) from entering the nutrient solution and causing putrefaction. - The teeming microorganisms observed after particulate matter was allowed to enter at the end of the experiment disproved spontaneous generation

Cytoplasmic Membrane Composition: What is the general structure of the membrane?

- The general structure is a phospholipid bilayer -- Contain both hydrophobic and hydrophilic components Supplemental info: - Can exist in many different chemical forms as a result of variation in the groups attached to the glycerol backbone - Fatty acids face inward, form hydrophobic environment - Hydrophilic portions remain exposed to external environment or the cytoplasm

X Physiological Diversity of Microorganisms: The phylogenetic diversity we see in microbial cells is the product of how many years of evolution? Microorganisms also have a tremendous amount of metabolic diversity, what does that mean? How evolved are microorganisms? (e.g. temp, pH, hydrostatic pressure, salinity, heavy metals)

- The phylogenetic diversity we see in microbial cells is the product of almost 4 billion years of evolution - Microorganisms also have a tremendous amount of metabolic diversity so microorganisms have exploited every conceivable means of "making a living" consistent with the laws of chemistry and physics - Just as evolved as we are

DNA processing includes what two main events?

- The production of RNAs (transcription) and the production of proteins (translation)

X Groups branching early within Bacteria: Origin of life?

- These groups are not closely related, but all are thermophiles, growing near the boiling point of water. -- Aquafex -- Thermotoga - Thought to be modern descendents of very ancient bacterial groups.

Sterols and Hopanoids: What is the purpose of sterols and hopanoids? In which cells are sterols and hopanoids found?

- They are membrane strengthening and stabilizing agents: -- Sterols => Rigid, planar lipids found in eukaryotic membranes. -- Hopanoids => Structurally similar to sterols => Present in membranes of many Bacteria

The Cytoplasmic Membrane: I general terms, what is it? How thick is it? It's a vital barrier that separates what? What does it enable concentrations of and excretion of? As a result, it can be describes as what kind of barrier?

- Thin structure that surrounds cell - 6-8 nm thick - vital barrier that separates cytoplasm from environment - Enables concentration of specific metabolites and excretion of waste products - A highly selective, permeable barrier

Atomic Force Microscopy (AFM) 3D: What is placed close to the specimen and what does it measure?How does the computer generate an image of the specimen?

- Tiny stylus placed close to a specimen - Stylus measures weak repulsive forces between it and specimen - Computer generates image based on data received from the stylus - Supplemental info from textbook: Images obtained from the microscope appear similar to those from the scanning electron microscope, but the AFM has the advantage that the specimen does not have to be treated with fixatives or coatings. The AFM thus allows living specimens to be viewed, something that is generally not possible with electron microscopes

X Protein Export: Translocases: Sec translocase system and the type III secretion system:

- Translocases: responsible for exporting proteins through and inserting them into prokaryotic membranes -- Sec translocase system: Both exports proteins and inserts integral membrane proteins into the membrane -- Type III secretion system: common in pathogenic bacteria; secreted protein is translocated from the bacterial cell directly into the host. e.g. a human cell

Growth/Reproduction: turning chemicals and energy into what? All cells come from where?

- Turning chemical and energy into new cells - All cells come from preexisting cells - Where and how was life created?!?

Uniport, Symport, and Antiport Transport:

- Uniporters transport in one direction across membrane - Symporters function as co-transporters - Antiporters transport a molecule across membrane while simultaneously transporting another molecule in opposite direction

Metabolize: Uptake of what from the environment? T/F there is transformation within the cell? Involves the removal of what? Cells are considered what, which allows them to exchange with the environment?

- Uptake of chemical and energy from the environment - True: Transformation within cell - Removal of waste - Cells are open systems exchanging with the environment

Electron Microscopy: What does electron microscope use to image cells and structures? What are the two types of electron microscopes?

- Use electrons instead of photons to image cells and structures - Two types of electron microscopes -- Transmission Electron Microscopes (TEM) -- Scanning Electron Microscopes (SEM)

Phototrophs: What do they use as an energy source? T/F The mitochondria allows them to use light as an energy source? What does oxygenic photosynthesis produce? What type of photosynthesis does not produce oxygen? T/F They are found in only a few select habitats?

- Use light as energy source - False: they contain pigments that allow them to use light as an energy source - Oxygenic photosynthesis produces oxygen - Anoxygenic photosynthesis does not produce oxygen - False: phototrophs do not have to compete for energy sources and so are found in a wide variety of habitats.

Microbiology as a basic biological science:

- Uses and develops tools for probing the fundamental processes of life.

Confocal Scanning Laser Microscopy (CSLM) 3D: Uses computerized microscope coupled with what to generate a 3D image? What can the computer focus the laser on? What are compiled to show a 3D image? What is the resolution?

- Uses computerized microscope coupled with laser to a fluorescent microscope to generate a 3D image - Computer can focus laser on single layers of specimen - Layers are compiled for a 3D image - Resolution is 0.1 micrometers

Transmission Electron Microscopy (TEM): What does it use instead of light rays? What function as lenses? What does it have to operate in to function? What is the magnification and resolution? It's able to visualize structures at what level which allows what to be seen? In what two ways must the specimen be prepared to use this type of microscopy? How are heavy metals involved in this process?

- Uses electrons instead of light rays - Electromagnets function as lenses - Operates in a vacuum - High magnification and resolution (0.2 nm) - Visualization of structures at the molecular level -- Proteins and nucleic acids may be seen - Specimen must be very thin (20 - 60 nm) and be stained -- Specimens are stained, usually with heavy metals (eg. osmium, lead)

X The 2 phyla of Archaea: Crenarchaeota: Vast majority of cultured Crenarchaeota are what? Where do they live?

- Vast majority of cultured Crenarchaeota are hyperthermophiles - Live in marine, freshwater, and soil systems

Fluorescence microscopy: Used to visualize specimen that fluoresce, what does that mean? Do cells fluoresce naturally? What do you call cells that can fluoresce after they have been stained?Fluorescence microscopy used in microbial ecology for what reason?

- Visualize specimens that fluoresce -- Emit light of one color when illuminated with another color of light - Cells fluoresce naturally (autofluorescence) - Cells can also fluoresce after they have been stained (DAPI) - Used in microbial ecology for enumerating (listing) bacteria in natural samples

Microorganisms are All Cells (Except for Viruses): What is a cell? What is present in all cells and determines influx and efflux of molecules? What is the name of the structure that stores genetic information in the form of DNA (hint: is has a different name depending on cell type)?

- a fundamental unit of life - Has a cell membrane: -- Present in all cells -- Defines the cell's boundary -- Determines influx and efflux of molecules - Has a nucleus (eukaryote) or nucleoid (prokaryote): -- Stores genetic information in the form of DNA

Microbiologists: What have scientists learned from microorganisms and what can that generalize to?

- a sophisticated understanding of the chemical and physical basis for life. - These features make them excellent experimental systems for illuminating life processes common to multicellular organisms. - They can grow microbial cells to extremely high densities in small-scale laboratory cultures, making them readily amenable to rapid biochemical and genetic study.

Endosymbiosis: Explain What it is:

- a type of symbiosis in which one organism lives inside the other, the two typically behaving as a single organism. It is believed to be the means by which such organelles as mitochondria and chloroplasts arose within eukaryotic cells

What are the five different types of microbes?

- bacteria, viruses, archaea, fungi, protists

(Not In Slides) Differential Interference Contrast (DIC) 3D: It employs what in the condenser to produce polarized light? What is polarized light? What appears to be more 3D because of this effect? DIC is typically used for observing what?

- employs a polarizer in the condenser to produce polarized light. -- The beams pass through different substances with slightly different refractive indices, the combined beams are not totally in phase, but instead create an interference effect. - polarized light: light in a single plane - Thus cellular structures appear to be more 3D - It is typically used for observing unstained cells -- because it can reveal internal cell structures that are nearly invisible by the bright field technique

Alkaliphile: Extreme; Genus/Species; Domain; Habitat

- extreme: high pH - genus/species: natranobacterium gregoryi - domain: archaea - habitat: soda lakes

Hyperthermophiles: Extreme; Genus/Species; Domain; Habitat

- extreme: high temperature - genus/species: pyrolobus fumarii - domain: archaea - habitat: hot, undersea hydrothermal vents

Psychrophiles: Extreme; Genus/Species; Domain; Habitat

- extreme: low temperature - genus/species: polaromonas vacuolata - domain: bacteria - habitat: sea ice

Barophile: Extreme; Genus/Species; Domain; Habitat

- extreme: pressure - genus/species: moritella yayanosii - domain: bacteria - habitat: deep ocean sediment

Halophile: Extreme; Genus/Species; Domain; Habitat

- extreme: salt - genus/species: halobacterium salinarum - domain: archaea - habitat: salterns

Acidophiles: Extreme; Genus/Species; Domain; Habitat

- extreme: they live in a very low pH environment - genus/species: picrophilus oshimae - domain: archaea - habitat: acidic hot lakes

Robert Hooke (1635-1703): He was the first to describe what? What made this a contribution to microbiology?

- first to describe mold - this was the first known description of microorganisms

There are 3 advantages to being a small cell:

- small cells contain more surface area relative to cell volume than large cells (i.e., higher S/V) -> as size increases SA decreases - support greater nutrient exchange per unit cell volume - tend to grow faster than larger cells

What is meant by the description of cells as machines and as coding devices?

- the description of cells as machines: Cells can be viewed as biochemical catalysts, carrying out the chemical reactions that constitute metabolism - cells as coding devices: Replicating DNA and then processing it to form the RNAs and proteins needed for maintenance and growth under the prevailing conditions.

What is microbiology? The science of microbiology revolves around what two interconnected themes (these would be considered two reasons for studying microbiology)?

- the study of small life - 1. Understanding the living world of microscopic organisms / understanding basic life processes -- Simple -- Reproduce quickly -- Grow densely - 2. Applying our understanding of microbial life processes for the benefit of humankind and planet earth.

Magnification: What is magnification?

- to enlarge

Describe Koch's 4 Postulates:

1. The disease- causing organism must always be present in animals suffering from the disease, but not in healthy animals 2. The organism must be cultivated in a pure culture away from the animal body. 3. The isolated organism must cause the disease when inoculated into healthy susceptible animals. 4. The organism must be isolated from newly infected animals and cultured again in the laboratory, after which it should be seen to be the same as the original organism.

Move: T/F All cells are capable of self propulsion? T/F cells can propel themselves only toward a stimulus?

• False: some cells are capable of self propulsion • False: Either toward or away from stimulus

Differentiate: Some cells can form special structures called what? This special structure is generally highly resistant to what?

• Some cells can form special structures such as spores • Generally highly resistant to heat, dehydration, etc.