Micro Exam 1
Cytoskeleton
internal protein framework of the cell
MALDI-TOF
measures the masses of various components using mass spectrophotometer
Simple Diffsuion
movement from high to low concentration
Biotechnology
use of microbiological and biochemical techniques to solve practical problems
Bioremediation
using microorganisms to hasten decay of pollutants
Describe the characteristics of cyanobacteria, including how nitrogen-fixing species protect their nitrogenase enzyme from O2.
- 1. providing an important source of USABLE NITROGEN and CARBON in NUTRIENT POOR ENVIRONMENTS 2. limiting atmospheric CO2 BUILDUP
Compare and contrast Agrobacterium species and rhizobia.
- Agrobacteriumgram - rods, attack plants and cause tumors - Rhizobiagram - rods, fix nitrogen, live in nodules on roots, nitrogen is food for plants
Compare and contrast the algae, fungi, and protozoa.
- Algae: Primarily live-in water, single celled or multicellular, rigid cell wall, many have flagella, photosynthetic, - Fungi: Energy from degradation of organic material, primarily live on land, single or multicellular - Protozoa: Most exist in organic compound, no rigid cell wall, single celled, complex, larger than prokaryotes, most motile
Describe the general structure of an atom and its isotopes.
- An atom is made up of 3 major components: Neutrons (uncharged) Protons (positively charged) and Electrons (negatively charged)
Describe how the cytoplasmic membrane is involved with proton motive force.
- Analogous to the energy stored in a battery. The energy of a proton motive force can be harvested when protons are allowed to move back into the cell. This is used to drive certain cellular processes, including ATP synthesis.
Describe the structure and function of the eukaryotic cytoplasmic membrane, comparing and contrasting it with the prokaryotic counterpart.
- Ancestors of mitochondria as well as chloroplasts were bacteria residing within other cells in a mutually beneficial partnership.
Describe the cell walls of archaea.
- Archaea have a variety of cell wall types since they inhibit a wide range of environments - Do not contain peptidoglycan in their cell wall - Many have S-layer which are sheets of flat protein, self-assemble
Compare and contrast characteristics of members of the Bacteria, Archaea, and Eukarya.
- Bacteria: Prokaryotic, with no membrane-bound organelles, ribosomal RNA, Unicellular, cell wall containing peptidoglycan - Archaea: Prokaryotic, with no membrane bound organelles, Ribosomal RNA, Unicellular, no peptidoglycan - Eukarya: Eukaryotic, include nucleus and other membrane bound organelles, Ribosomal RNA, Uni or Multicellular, no peptidoglycan (Contain fungi, algae, protozoa)
Describe five distinct methods to distinguish different strains.
- Biochemical typing: identify various species of bacteria - Serological typing: proteins and carbohydrates that vary among strains can differ - Molecular typing: gel electrophoresis can be used to detect restriction fragment length polymorphisms, whole genome sequencing - Phage typing differ in susceptibility based on various types of bacteriophages - Antibiograms: antibiotic susceptibility patterns can be used to characterize strains
Describe two multicellular associations of bacteria.
- Biofilms and fruiting bodies
Describe the role of buffers.
- Buffers help stabilize pH of solutions
Compare and contrast the structure and function of capsules and slime layers.
- Capsules: a distinct and gelatinous layer - Slime Layer: diffuse and irregular
Describe the special stains used to observe capsules, endospores, and flagella.
- Capsules: the common procedure darkens the background, the capsule stands out as a clear area surrounding the cell - Endospore: a type of dormant cell that does not readily take up stains - Flagella: adheres to and coats the otherwise thin flagella, making them visible with the light microscope
Describe how SSU rDNA sequences, DNA hybridization, and DNA base ratios are used to classify microorganisms.
- SSU rDNA: regions of 16S in bacteria and archaea can determine distant relatedness of diverse organisms - DNA hybridization: the extent of nucleotide sequence similarity between two isolates can be determined by measuring how completely single strands of their DNA hybridize to one another - G + C content: offers a crude comparison of genomes.
Anaerobic Chemotrophs
-don't need oxygen; live in anoxic environments- - likely used anaerobic respiration or fermentation
Discuss the principles and importance of magnification, resolution, and contrast in microscopy.
- Magnification: apparent increase in size - Resolution: resolving power, or ability to distinguish two objects that are close together - Contrast: determines how easily cells can be seen
Describe the properties of water and explain why it is so important in biological systems.
- Makes up 50% of all living organisms by weight - Polar molecule - Hydrogen bonding explains ice and liquids Hydrophilic= water loving Hydrophobic = water fearing
Compare and contrast the characteristics and habitats of methanogens, sulfur- and sulfate-reducing bacteria, Clostridium species, lactic acid bacteria, and Propionibacterium species.
- Methanogens- Anaerobic Chemolithotrophs, Members of the Archaea bacteria that oxidize hydrogen gas, using CO2 as a terminal electron acceptor to generate methane. - Sulfur and Sulfate-reducing bacteria- Anaerobic Chemoorganotrophs, Anaerobic Respiration. Use sulfate as a terminal electron acceptor, generating hydrogen sulfide. Found in anaerobic muds rich in organic material. Gram negative. - Clostridium species- Endospore-forming obligate anaerobes. Inhabitants of soil. Gram positive. - lactic acid bacteria- Produce lactic acid as the major end product of their fermentative metabolism. Aerotolerant anaerobes. Several genera are used by the food industry. Gram positive. - Propionibacterium- Obligate anaerobes that produce propionic acid as their primary fermentation end product. Used in Swiss cheese production. Gram +.
Describe how phenotypic characteristics—including microscopic morphology, culture characteristics, metabolic capabilities, serology, and protein profile—can be used to identify microorganisms.
- Microscopic morphology: shape, size, staining characteristics can give suggestive information on identity - Culture characteristics: colony morphology can give initial clues - Metabolic capabilities: a set of biochemical test can be used to identify a microorganism - Serology: proteins and polysaccharides that make up a microorganism are sometimes characteristic enough to be considered identifying markers - Protein: sorts an organism protein by mass, generating a profile that provides a fast method of identification
Describe the characteristics of the different groups of carbohydrates.
- Monosaccharides: single unit can exist in alpha or beta depending on location of hydroxyl group - Disaccharides: two monosaccharides, joined by covalent bond. o Common: Sucrose, fructose, glucose - Polysaccharides: chains of monosaccharides, made of glucose
Describe the representative obligate aerobes and facultative anaerobes.
- Obligate: cannot ferment, must have oxygen presentFacultative: prefer to use O2 but can ferment
Explain how the cell wall affects susceptibility to penicillin and lysozyme.
- Penicillin prevents cross-linking of adjacent glycan chains - Lysozyme breaks the bonds that link the alternating subunits of the glycan chain.
Describe the chemistry and structure of peptidoglycan.
- Peptidoglycan is found only in bacteria - The basic structure is an alternating series of two major subunits released to glucose: NAM and NAG
Compare and contrast the structure and function of fimbriae and sex pili.
- Pili: a string of protein subunits arranged helically to form a long molecule with a hollow core. Many types of pili, fimbriae, allow cells to attach to specific surfaces.
Compare and contrast the factors that affect protein structure and function.
- Polymer chains composed of a limited number of different amino acids - One or more long polypeptides - Covalent bonds - Enzyme catalysis - Signal reception - Motility
Describe how nucleic acid probes, NAATs, and sequencing 16S rRNA genes can be used to identify microorganisms.
- Probes: locate nucleotide sequence characteristic of species or group - NAAT: used to increase number of copies of specific DNA sequence. Allows detection of small number of organisms form body fluid, soil, food and water. - Sequencing ribosomal RNA: relatively stable
List three commercial benefits of microorganisms.
- Production of antibiotics, dairy, bread, aid in digestion, development of immune system response, prevent diseases by competing with pathogens
Compare and contrast the characteristics of the purple bacteria and the green bacteria.
- Purple: gram-neg; photosynthetic apparatus in cytoplasmic membrane; purple sulfur bacteria are large, sometimes motile cells; may have gas vesicles, store sulfur in granules, use Hydrogen Sulfide (some just H2) to generate reducing power - Green bacteria: gram-neg, some use sulfur, some don't; found mostly in aquatic habitats; often grow in big mats
Osmosis
Diffusion of water through a selectively permeable membrane
Antony Leeuwenhoek and Robert Hooke
Discovered microbes. Hooke was first to describe love processes under a microscope
Phylogeny
Evolutionary history of a species
Describe the family Enterobacteriaceae and explain what distinguishes coliforms from other members of this family.
Gram-negative rods-most reside in the intestinal tract-facultative anaerobes that ferment glucose-coliforms ferment lactose
Molarity
Molarity of solution is number of moles dissolved in 1 liter of H20
Compare and contrast the examples of bacteria that use animals as habitats.
Obligate intracellular parasites cannot reproduce outside of host cell; rickettsia (rocky mountain fever), chlamydia (sexually transmitted disease) ex.. Staphylococcus sp.
Describe the structure and function of the chromosome, plasmids, ribosomes, storage granules, gas vesicles, and endospores.
- Chromosome: a single, circular, double-stranded DNA molecule that contains all the genetic info required by a cell - Plasmid: have a structure similar to chromosome but are typically smaller. - Ribosomes: involved in protein synthesis, where they facilitate the joining of amino acids. - Storage granules: accumulations of high molecular weight polymers synthesized from a nutrient that a cell has in relative excess - Gas vesicles: for aquatic organisms, small, rigid, protein bound compartments that provide buoyancy to the cell - Endospores: a unique type of dormant cell produced by certain bacterial species. Resistant to temperature, chemical, UV, and pH changes.
Describe the common bacterial shapes and groupings, and their significance.
- Coccus (cocci)-- sphere shaped - Bacillus (bacilli) -- rod shaped - Spirillum (spirilla) -- spiral shapes Groupings: - Diplococci— cocci that usually occurs in pairs - Streptococci— long chains of cocci - Staphylococci—cluster of cocci
Compare and contrast the chemical compositions, structures, and major functions of DNA, RNA, and ATP.
- DNA: information storage of genes o Double stranded o Nucleotides are 3 parts: Deoxyribose, Phosphate group, nucleobase - RNA: decoding info in DNA to assemble a sequence of amino acids to build proteins o Mostly single stranded o Sugar is ribose o Uracil in place of thymine o mRNA, tRNA, rRNA - ATP: energy currency of cell o Adenosine triphosphate o Built from using nucleobase o 3 phosphate groups in a row, negatively charged o Inherently unstable, when broke they release energy that can drive cellular process
Describe the role of microbes in disease, including examples of past triumphs and remaining challenges.
- Damage can occur as a direct result of the of pathogens growth and products, or because of the body's defense mechanism. - Past triumphs include the viral disease smallpox, killing over 10 million people. The plague was also a major disease that killed over 25 million people within 4 years. Antibiotics made the treatment of this disease possible. - Remaining challenges include emerging infectious disease which is an infectious disease (EID) that has become more common in the last 35 years. EID include MERS, Hepatitis C, SARS, and Ebola.
Explain how the successful challenge to the idea of spontaneous generation led to the Golden Age of Microbiology.
- Ferdinand Cohn discovered endospores and when Spontaneous generation was disproved, the golden age was born. The principle that microorganisms cause diseases known as Germ theory of Disease
Describe the structure and arrangements of flagella and explain how they are involved in chemotaxis.
- Flagella have basal body which anchors the structure to the cell wall and cytoplasmic membrane. The hook is flexible curved segment that extends out from the basal body connecting to the filament.
Describe the benefits of using fluorescent dyes and tags.
- Fluorescent dyes: bind to compounds found in all cells; others bind to compounds specific to only certain types of cells - Fluorescent tags: antibodies to which a fluorescent molecule has been attached are used to tag specific molecules
Describe the key experiments of scientists who disproved spontaneous generation
- Francesco Redi: Demonstrated worms on rotting meat came from eggs of flies landing on meat. - Louis Pasteur: "Father of Microbiology" Demonstrated air is filled with microorganisms and filtered air through cotton plugs. Also developed swan-necked flask. Disproved spontaneous generation. - John Tyndall: Sterilizing broths required different times and realized broths made from hay contained heat-resistant microbes
Compare and contrast the structure and chemistry of the Gram-positive and Gram-negative cell walls.
- Gram + cell walls contain a thick layer of peptidoglycan, teichoic acids, they lack an outer membrane - Gram - cell wall contain; a thin layer of peptidoglycan, no teichoic acids, and contain an outer membrane
Explain how the cell wall affects Gram staining characteristics.
- Gram + cells retain the dye because their cell wall prevents crystal violet iodine complex from being washed out by the decolorizing agents. Gram - cells lose their color easily.
Describe the scientific method, using Pasteur's swan-necked flask experiment as an example.
- He demonstrated that broth boiled in a swan-neck flask was protected from airborne microbes by the curve in the flask's neck, which trapped invading microbes. But if he broke off the swan neck and waited a couple of days, microbe growth occurred. Nothing wrong with the boiled broth or its air!
Describe how microorganisms are identified, classified, and assigned names.
- Identified: process of characterizing in order to group - Classified: arranging organisms into similar/related groups - Nomenclature: system of assigning names
Describe the importance of valence electrons.
- In the outer shell of an atom and are important in bond formation. The govern the atoms electronegativity, which leads to things like covalent and ionic bonds
Compare and contrast ionic bonds, covalent bonds, and hydrogen bonds.
- Ionic bonds: formed by atoms gaining or loosing electrons. o Deals with salts (electrolytes), o weak bonds o Cations (positively charged, loses an electron) o Anions (negatively charged, gain an electron) - Covalent bonds: from when atoms share electrons o One pair of shared electrons = one covalent bond o Organic compound: molecules that contain at least 1 carbon and hydrogen o Polar bond= unequal sharing electrons o Nonpolar bond = equal sharing of electrons o Strong bonds - Hydrogen bonds: weak bons when a hydrogen atom in a polar molecule is attract to an electronegative atom in the same or another polar molecule o May be short lived o Numerous bonds add strength
Compare and contrast light microscopes, electron microscopes, and atomic force microscopes.
- Light microscope: can magnify 1000X. Uses a visible light and a series of lenses to magnify an object - Electron microscope: can magnify more than 100,000X. Uses electromagnetic lenses, electrons, and a fluorescent screen to produce magnified image - Atomic force: can produce images of individual atoms on surface
Explain the significance of lipid A and the O antigen of LPS.
- Lipid A: anchors the LPS molecule in the lipid bilayer. The body recognizes as the sign of invading Gram - bacteria - O antigen: the portion of the LPS directed away from the membrane, at the end opposite lipid A.
Describe the examples of the four mechanisms aquatic bacteria use to maximize nutrient acquisition and retention.
- Sheath: chains of cells encased within a tube. The sheath plays a protective role, and helping the bacteria attach to solid objects - Prosthecate: Gram negative bacteria, have projections called prosthecae (extensions of the cytoplasm and cell wall) Increased surface area to facilitate absorption of nutrients - Bacteria that derive nutrients from other organisms - Bioluminescent bacteria: Emit light which helps themselves and their host
Compare and contrast the structure and function of simple lipids, compound lipids, and steroids.
- Simple lipids: contain carbon, Hydrogen, oxygen. Triglycerides: fats or oils composed of 3 fatty acids linked to a 3-carbon glycerol molecule - Compound lipids: contain fatty acids and glycerol as well as other besides carbon, hydro, oxygen - Steroids: simple lipids. 4 ring structures. Cortisol, estrogen, testosterone.
Describe the principles of a wet mount, a simple stain, the Gram stain, and the acid-fast stain.
- Simple stain: a basic dye is used to stain cells. Easy to increase the contrast between otherwise colorless cells and background - Gram stain: used to separate bacteria into gram+ and -. - Acid fast stain: used to detect organisms that are not easily take up stains
Explain why prokaryotic cells must secrete certain proteins.
- Some proteins are enzymes that function outside of the cell break down macromolecules in the external environment into their respective subunits.
Describe the significance and processes of sporulation and germination.
- Sporulation: complex sequence of changes that begin when spore forming bacteria experience limiting amounts of carbon or nitrogen - Germination: can be triggered by a brief exposure to heat or certain chemicals
Explain how the scientific name of an organism is written.
- The binomial name consists of a genus name and specific epithet. The scientific names of species are italicized. The genus name is always capitalized and is written first; the specific epithet follows the genus name and is not capitalized. EX) Canis lupus
Describe the structure and chemistry of the cytoplasmic membrane, focusing on how it relates to membrane permeability.
- The cytoplasmic membrane is selectively permeable, meaning only certain substance can cross it.
Explain why life could not exist without microorganisms.
- There are many benefits (nitrogen fixation, oxygen production, degradation of material)
Describe why microorganisms are useful research tools.
- They are cheap and easy to grow in the lab, they use the same metabolic rate pathways as eukaryotic cells, and they can be grown in large numbers very easily
Compare and contrast viruses, viroids, and prions.
- Viruses: Consists of either DNA or RNA, surrounded by a protein coat. Obligate intracellular agents that use the machinery and nutrients of host cells to replicate - Viroids: Consists only of RNA, no protein coat. Obligate intracellular agents that use the machinery and nutrients of host cells to replicate. - Prions: Consist only of protein, no DNA or RNA. Misfolded versions of normal cellular proteins that cause the normal versions to misfold.
Compare and contrast the characteristics of sulfur-oxidizing bacteria, nitrifiers, and hydrogen-oxidizing bacteria.
- aerobic chemolithotrophs, located around hot springs
Compare and contrast the characteristics and habitats of the extreme halophiles and extreme thermophiles.
- alt lakes, soda lakes, brims; red/pink patches; halo bacteria
Explain the role of an enzyme in chemical reactions.
- are biological catalysts that speed the rate of reactions - bind to one or more reactant molecules - Position them in such a way that certain bonds are more likely to be broken or to form - Reactants in enzyme-catalyzed reactions are referred to as substrates
Explain the concept of pH, and how the pH of a solution relates to its acidity.
- pH is the measure of [H+] in mol/L - more acid (lower pH) - more basic (high pH)
Hans Gram
-Attempted to find cause of pnemonia - Developed gram stain
Species
A basic unit, group of morphollogy similar organisms capable of producing fertile offspring
Macromolecules
A very large organic molecule composed of many smaller molecules
Spontaneous Generation
Life comes from on-living material
Scientific theory
an explanation supported by a large amount of evidence
Pili
are shorter than flagella
Polymers
formed via dehydration synthesis (remove water)
Chromosome
forms gel like region... nucleoid
Ribosomes
protein synthesis
Hydrolysis
reverse reaction (requires addition of water)
Taxonomy
the science that studies organisms to arrange them into groups