Microbiology 1220 Mid Term 1 – Flashcards
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Define Spontaneous Generation |
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The theory that organisms arise spontaneously from non-living material |
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What is the scientific contribution of Hooke? |
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Hooke saw microobes in 1665 |
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What is the scientific contribution of Leeuwenhoek? |
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Leeuwekhoek saw bread mould in 1674 |
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What is the scientific contribution of Pasteur? |
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Pasteur disproved spontaneous generation in 1861 |
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What is the scientific contribution of Tyndall? |
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Tyndall discovered endospores in the 1860's. |
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What is the scientific contribution of Jenner? |
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Developed smallpox vaccine in 1796 |
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What is the scientific contribution of Koch? |
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Developed protocols for handling bacteria in lab, established rules to be used to determine causative agent of disease (Koch’s Postulates) in the 1800s |
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What is the scientific contribution of Ehrlich? |
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Started chemotherapy to treat diseases in the 1900s |
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What is the scientific contribution of Fleming? |
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Discovered Penicillin in the 1900s |
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How do the three Domains differ in size? |
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Bacteria (0.3-2µm) Archaea (0.3-2µm) Eucarya (5-50µm) |
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Which domains have nuclear membranes? |
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Eucarya |
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Which domains have peptides in the cell wall? |
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Bacteria |
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Which domains have membranous organelles? |
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Eucarya |
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Which domains are prokaryotes? |
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Archaea |
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Define Prokaryote |
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Single celled organism with no membrane bound nucleus or lipid bound organelles with DNA in a nucleoid |
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List the organization of biological hierarchy, from greatest to least specificity |
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DKPCOFGS (Don’t Kick Police Cars, Otherwise Fools Get Shot) - Domain Kingdom Phylum Chordata Order Family Genus Species |
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Define Algae |
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Diverse single and multi celled organisms that have chloroplasts, undergo photosynthesis, have flagella and are found primarily in water |
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Define Fungi |
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Single and multi celled organisms that gain energy from degrading organic material and are found primarily on land |
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Define Protozoa |
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Single celled organisms with un-rigif cell walls that are found on both land and water and require organic compounds as food which they ingest as particles. |
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Define virus |
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Nucelic acid with a protein coat, that can only multiply inside a host and is therefore an obligate intracellular parasite |
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Define viroid |
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An organism that consist of short RNA segment without a protein coat that can only multiply inside a host |
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Define prion |
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An organism consisting of protein without nucelic acid |
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Define Helminth |
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A parasite such as round and tape worms |
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How do viruses, prokaryotes and eukaryotes differ in size? |
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Viruses (10nm-100nm) Prokaryotes (100nm-1000nm) Eukaryotes (10m-10mm) |
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What 6 elements make up 99.5% of living material by weight? |
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CHONPS |
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Define Molecule |
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2 or more atoms with a chemical bond |
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Define Compound |
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2 or more different elements bonded together |
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How are ionic bonds created? |
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Two or more elements trade electrons, join as ions |
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How do ionic bonds fare in water? |
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Break at room temperature, 100x weaker than covalent |
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What defines an organic compound? |
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Covalent bonds with C and H |
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How do Polar and Non-polar covalent bonds differ? |
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Polar have slight pos. and neg. charges (OH/NH/OC/NC) versus no charges (CC/CH/HH) |
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How are Hydrogen bonds formed? How strong are they? |
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H+ attracted to negatively charged atom. Weak, constaltly breaking and forming at room temperature |
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Why is water considered a universal solvent? |
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Dissolves polar compounds - splits them into ions (polar sides attract - ion, etc) |
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What is the concentration of OH and H ions in solutions that are Basic, Acidic, and Neutral? |
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Basic (10[OH-], 10^14[H+]), Acidic (10^7[OH-], 10^7[H+]) , Neutral (10^14[OH-], 10^0[H+]) |
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What is the function of proteins? |
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Catalyze enzyme reactions, determine structure/shape of ribosomes, take nutrients in/out of cell |
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What is the general structure of an amino acid, and how many are there? |
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Amino + side chain + carboxyl. 20 different ones that differ by side chain |
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How do hydrophobic and philic proteins differ? |
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Phobic - nonpolar, many CH3 groups. Philic - polar, few CH3 groups |
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What is the function of carbohydrates? |
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Food, building block of DNA |
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What is the ratio of CHO in carbohydrates? |
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1:2:1 |
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What are the two types of monosaccharides and how do they differ? |
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5-carbon (Deoxy/ribose), 6-carbon (gluocose, galactose, fructose) |
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What are 2 examples of disaccarides? |
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Lactose, sucrose |
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What are 2 examples of polysaccarides? |
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Cellulose, glycogen |
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Define Oligosaccarides |
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Polymer containing 3-6 monosaccarides |
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What is the structure of DNA |
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N-ring base (purine) with deoxy base and a phosphate backbone, wound around histones |
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What is the structure of RNA |
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Single stranded DNA with ribose base and U instead of T |
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Are lipids hydrophilic or hydrophobic? |
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Hydrophobic, non-polar |
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How do simple lipids differ from carbohydrates? |
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Different ratio of CHO |
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What are Fats composed of? |
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Fatty acids and glycerol |
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How can you determmine if a fat is a mono/di/triglyceride? |
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Count the number of fatty acid chains |
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In what case is a simple lipid unsaturated? |
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Double bond s are present in a fatty acid chain (liquid at room temperature) |
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What is the structure of compound lipids? |
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Fatty acids + glycerol + other |
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What is the structure of Phospolipids? |
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Phosphate + fatty acid + glycerol |
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What is the maximum magnification of a light microscope? |
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1000x |
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How does light go from the lamp to eyes in a light microscope? |
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Specimen, magnifying lens |
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What Domains are viewable under a light microscope? |
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Eucarya and Bacteria - good for up to 10µm |
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What is the maximum magnification of an electron microscope? |
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100,000x(+) |
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What acellular organisms are viewable under an electron microscope? |
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Viruses |
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What are the TEM and SEM used for viewing in a cell? |
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TEM (internal cellular structures), SEM (surface structures) |
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What is the purpose of an atomic force microscope? |
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View objects at the atomic level |
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How are magnification and resolution different? Which would provide better resolution - an electron or light microscope? |
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Magnification is image enlargement, Resolution is the degree to which fine detail can be distinguished. Light microscope will provide better resolution. |
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How does a simple stain work? |
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Basic dye for color, negatively charged nucleic acids and proteins are stained with a positively charged dye |
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What is a differential stain used for? |
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Distinguishing between bacterial groups |
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What function does a gram stain serve? |
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Determine if a cell is gram + or -, which reflect differences in cell wall structure. 1st stain - Purple 2nd stain - Pink |
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What genus would you be trying to detect by using an acid-fast stain? |
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Mycobacterium |
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Why is a capsule stain used? |
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Capsules don’t take up certain stains, this used to make capsules stand out against background |
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Why is an endospore stain used? |
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Stains endospores, which do not stain easily |
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Why is a flagella stain used? |
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Coats thin flagella, visible under light microscope |
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What are the steps in a Gram stain? |
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Flood smear with primary stain, rince, flood with dilute iodine, rince, add 95% alcohol to decolor gram negative, counterstain added to stain gram negative |
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What are the 4 bacterial shapes? |
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Cocci (spherical), Bactillus (columnar), Spiral, Pleomorphic (varying in shape) |
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What is the function of the cytoplasmic membrane? |
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Selectively permeable barrier made of phospholipids with embedded sterols and hopanoids. |
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What is the fluid mosaic model? |
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Proteins are not static, dynamic nature means the cytoplasmic membrane is constantly changing and fluid |
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What is the structure of peptidoglycan? |
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AA/sugar mesh with covalent bonds, alternating NAG/NAM sugar units cross linked to AA's |
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Peptidoglycan, found only in the cell walls, is the target of... |
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Antibiotics and Lysosome (a product of the body) |
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What is the structure and function of the membrane outsode of the peptidoglycan layer in Gram Negative bacteria? |
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Consists of LPS (endotoxin), phospholipids and proteins, plays a role in fever/inflammation |
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How do capsule and slime layers differ? What is their function? |
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Gel like layers that function as protection/attachment. Capsule layer (distinct/gelatinous) Slime Layer (diffuse/irregular) Function in adhereing to surfaces are thwarting innate defense system |
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What is the function of flagella? |
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Protein structure responsible for mobility, spin in propellar like fashion |
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What is Chemotaxis? |
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Phenomenon where bacteria sense and move according to chemical attractants (cells move towards) or repellants (cells move away) |
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What is the function of pili and how do they differ from flagella? |
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Attachment to surfaces/bacterial mating. Shorter/thinner than flagella and can't been seen under light microscope |
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What is a plasmid? |
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Circular, supercoiled double stranded DNA that the cell does not actually need, but may provide an advantage (can encode enzymes that destroy antibiotics) |
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How are bacterial ribosomes different from eukaryotic ones? Why is this useful? |
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Size/composition. Exploited for drug design |
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What are storage granules? |
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Polymers of nutrients stored until required |
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How are glucose, carbon and phosphate stored as granules? |
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Glycose (glycogen), Carbon (Poly-B-hydroxlbutrate), Phosphate (Volutin granules) |
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What is an endospore and why is it advantageous? |
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A resistant form of life some bacteria (particularily Bactiuus/Clostridium) can differentiate to, advantageous as it allows cells to lie dormant until conditions improve |
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Describe a spore |
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DNA surrounded by many levels of cytoplasmic membtrane/peptidoglycan. Can't reproduce or grow, will revert when conditions improve |
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Define microtubles |
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Long hollow cylinder form mitotic spindle, make up cilia and flagella framework along which organelles move |
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Define actin filaments |
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Enable cytoplasm to move |
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Describe intermediate filaments |
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Function like ropes, strengthening cell mechanically, enable cell to resist physical stresses |
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How are flagella different/simmilar? |
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Protein appendages that appear to project out but are covered by cytoplasmic membrane extension, flagella give mobility, cilia help move material away/towards cell |
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Describe the structure of the nuclear envelope |
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Two lipid bilayer membranes, protein strucures (nuclear pores) |
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Where is mRNA synthesized? |
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Nucleolous |
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Describe the structure of the mitochondria membrane |
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Two lipid bilayer membranes (inner/outer), inner highly folded (cristae) to increase surface area, enclosed by inner is the matrix |
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What is the stroma in chloroplasts analgous to in mitochondria? |
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The matrix (inner space) |
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Define generation/doubling time |
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The time for a population to double in number (generally bacteria) |
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What do the variables in the function: Nt = N0 x 2n represent |
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N0 - original number of cells, Nt - number of cells at given time t, n - number of divisins during time t |
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Define sterile |
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free of microbes |
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Define Aseptic techniques |
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procedures that minimize chance of organisms being introduced |
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What is agar used for? |
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Solidifying a liquid culture medium |
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Describe the streak-plate method |
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Sterilized loop dipped in bacteria, and drawn across a plate three times at different angles to dilute the concentration of cells |
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What is a stock culture? |
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A culture stored for later use |
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Define a closed/batch culture |
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A culture in which nutrientsare not renewed and wastes are not removed |
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Define an open/continuous culture |
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A culture in which nutrients are added and wastes removed regularily |
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What are the phases in bacterial growth in a culture? |
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Lag, exponential (log), stationary, death, prolonged death (LESDP) |
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Describe the lag phase |
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Bacterial culture diluted/transferred, cells not rapidly increasing for the moment (synthesizing macromolecules) |
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Describe the exponential (log) phase |
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Cells divide at a constant rate, generation time measured, primary and secondary metabolites synthesized in early/late log phase. Endospores form in late log phase if possible |
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Describe the stationary phase |
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No more energy or nutrients, number of cells constant because some die and release contents and are cannabalized |
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Describe the death phase |
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Decrease in number of viable cells, exponential but slower than growth |
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Described the prolonged death phase |
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99% dead, days to years, cannibalizing continues, survival of the fittest |
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Define optimum growth temperature |
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Temperature at which growth is fastest |
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Define psychrophiles |
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OGT 15-30 |
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Define psychtrophs |
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OGT 20-30, cause food spoilage |
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Define mesophiles |
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OGT 35-40, found in human body - most common pathogens |
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Define thermophiles |
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OGT 45-70, hot springs/compost/water heaters |
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Define hyperthermopiles |
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OGT 70+, archeae |
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Define obligate aerobes |
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Absolute oxygen requirements |
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Define obligate anaerobes |
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Capable of growth in the absence of oxygen |
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Define facultative anaerobes |
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Growth better with oxygen |
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Define microaerophiles |
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Small oxygen requirements, more inhibitory |
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Define aerotolerant anaerobes |
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Oxygen indifferent |
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Why do all cells attempt tp maintain a cytoplasmic pH near 7? |
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Preserve enzyme function |
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Define neutrophiles |
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Prefer pH near 7 |
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Define acidophiles |
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Prefer pH 5.5 or lower |
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Define alkalophiles |
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Prefer pH 8.5 or higher (exchange internal Na ions for internal protons) |
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Define plasmolysis |
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Solute concentration higher out of cell - cell dehydrates |
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Define halotolerant |
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Tolerate high salt concentrations |
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Define halophiles |
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Require high salt concentrations |
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What is the function of the cell wall in maintaining water homeostasis? |
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Enables bacteria to survive hypotonic enviornment while preventing osomtic lysis |
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How do cells prevent plasmolysis |
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Increase internal solute concentration |
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Define heterotroph |
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Use organic C |
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Define autotroph |
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Use inorganic C (CO2) |
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Define phototroph |
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Use energy from sun |
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Define chemotroph |
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Use energy from oxidizing chemical compounds |
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Define complex media |
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Contains variety of ingredients |
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Define defined media |
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Contains precise amounts of pure chemicals |
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Define differential media |
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Contains substances that bacteria change in a recognizable way |
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Define direct cell count |
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Includes total number of cells (living and dead) |
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Define viable cell count |
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Includes viable cells, 24 hour incubation required |
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Describe the process of doing a plate count |
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Sample diluted in 10 fold increments, 0.1-1mL transferred to sterile petri dish, mixed with agar, when agar hardens - plate incubated and colonies farm (multiple layers) |
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Describe the process of doing a spread plate |
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Plate count where 0.1-0.2 mL dilution spread on hard agar plate with sterile glass rod, after incubation colonies form on surface (1 layer) |
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Define Sterilization |
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Process of destroying all micro-organisms/viruses through physical/chemical means |
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Define Disinfection |
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Process that eliminates most/all pathogens in the material |
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Define Antiseptics |
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Disinfectant non-toxic enough to be used on skin |
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Define Sanitization |
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Process that substantially reduces microbe population to meet health standards |
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Does Pasteurization sterilize? |
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No, pasteurization reduces the number of organisms |
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What is the HTST form of Pasteurization? |
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High temperature, low time - 72 degrees for 15 seconds |
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What is the UHT form of Pasteurization? |
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Ultra high temperature (sterilizes) 140 degreece for 12 seconds |
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What does an autoclave do? |
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Sanitizes and kills endospores - pressurized steam at 121 degrees at 15 psi for 15 minutes |
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How does canning work, and what is the process for home and commercial canning? |
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Moist heat/Anaerobic Chamber. Home (115 @15 min) Commercial (121 @ 2.5 min) |
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What do drying ovens do? Give an example of something sterilized by drying ovens |
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Oxidize cell components, denatures proteins, high temp/time required versus moist heat. Lab glassware (160@2-3 hours) |
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Give some examples of physical methods of destroying organisms |
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Steriliants, high/intermediate/low level disinfectants |
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Define steriliants and provide an example item that would require their use |
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Destroy all microbes (including endospores and viruses), 6-10 hours, used on scalpels |
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Define High Level Disinfectants and provide an example item that would require their use |
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All viruses and vegetative organisms (not endospores), sterilants used for 30 minutes. Used on gastrointestinal endoscopes. |
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Define Intermediate Level Disinfectants and provide an example item that would require their use |
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Destroy vegetative bacteria, most viruses (not endospores). Used on stethoscopes |
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Define Low Level Disinfectants and provide an example item that would require their use |
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Destroys fungi, vegetative bacteria, enveloped viruses |
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What are some considerations to take into account when selecting a disinfectant? |
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toxicity, activity in presence of organic matter, compatibility, residue, enviornmental risk, cost/availbility, storage/stability |
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How do Alcohols work? What are they effective against, and provide an example |
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Damage membrane lipids. Effective Against: VB/F (~E/V). Example: Ethanol/Isopropanol Alcohol |
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How do Aldehydes work? What are they effective against, and provide an example |
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Sterilants, inactivate proteins/nuc acids. Effective Against: M/V. Example: 2% Glutaradehyde |
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How do Biguanides work? What are they effective against, and provide an example |
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Disruput cell membranes. Effective Against: VB/F, some V. Example: Chlorohexadine |
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How do Volatile Chemicals work? What are they effective against, and provide an example |
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Gas sterilants for large items, damage proteins. Effective Against: M/V. Example: Ethylene Oxide |
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How do Halogens work? What are they effective against, and provide an example |
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Disinfectant, oxidize proteins/cellular components. Effective Against: M/V. Example: Cl, Bleach, Iodine |
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How do Metal Compounds work? What are they effective against, and provide an example |
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Affect protein function, toxic to humans in effective concentrations. Effective Against: M/V. Example: Silver Nitrate, Mercury, Zinc |
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How do Oxidizing Agents work? What are they effective against, and provide an example |
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Oxidize cell components. Effective Against: Anaerobic Organisms. Example: Ozone, Hydrogen Peroxide |
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How do Phenals work? What are they effective against, and provide an example |
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Destroy Cytoplasmic Membrane, denature proteins, disinfectant. Effective Against: Most VB. Example: Lysol, mouthwash, cleaning up blood on hospital floor |
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How do QUATS work? What are they effective against, and provide an example |
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Detergent, destroy Cytoplasmic Membrane and denature proteins. Effective Against: VB, some V. Example: Detergents |
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Name some methods of preserving perishable products |
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Low temperature (enzyme reactions slowed), addition of salt/sugar (dehydrate cells), dessication (remove water), lycophilization (freeze dry) |
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How does anabolic metabolism work? What does it require? |
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Builds larger molecules from smaller ones (biosynthesis). Requires: energy source, B12, biotin, folic acid, Vitamin E |
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What is anabolic metabolism required for? |
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Replicating working molecules in cell, growth/division, secretion of cell products |
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Explain how anabolic/catabolic pathways and ATP/ADP fit together to form a cycle |
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ADP is filled up with energy by enzymes in catabolic pathways to form ATP which is then broken down in anabolic pathways to form ADP |
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What are the products and reactants of glycolysis? What is required for glycolysis? |
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Reactants: glucose Product: Pyruvic Acid. Enzyme niacin required |
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Bacterial break down pyruvic acid to _____ and _____ |
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Carbon dioxide and water |
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During fermentation, how many molecules (approx.) of ATP are gained for every glucose? Why is fermentation not efficient? |
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36-38 Not efficient because it produces ATP only by glycolysis. |
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Summarize what happens in the Kelvin/Citric Acid Cycle (KCAC) |
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P.A. --> CO2, some ADP --> ATP. H atoms are provided for next step. Coenzyme NADH created via oxidization. Thiamine/riboflavin/niacin/pathothenic acid all essential |
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What happens in the electron transport chain? |
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ATP generated using oxygen (Aeroic respiration) |
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Summarize the electron transport chain process |
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NADH transfer H to EXC ( e-/p+ to carrier proteins), E- transferred NADH->O2, E- carried along EXC by carrier proteins, p+ shuffled out of cell (proton gradient created), aerobic respiration (carrier protein transferes 2 protons to oxygen to form water), ATP synthase allows outside protons in (proton motive force creates some ATP) |
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What do hydrolic enzymes do? |
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Break bonds by adding water |
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What do cellulases, amalayses and B-galactosidase digest? |
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Cellulose, starches, lactose (glucose+ galactose) |
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What are fatty acids digested by? |
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B-oxidization reactions |
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What breaks peptide bonds between amino acids? How are amino groups removed? |
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Proteases, Deamination |
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Define genome |
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Complete set of genetic information for a cell |
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Define gene |
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functional unit of genome |
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Define gene product |
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gene encoded protein |
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Define genetics |
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study of function and transfer of genes |
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Define genomics |
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study and analysis of nucleotide sequencing of DNA |
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Define DNA replication |
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DNA duplication before cell division |
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Define expressed |
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decoded DNA information |
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Define translation |
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interprets information carried by RNA to synthesize encoded protein |
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Define transcription |
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copies info in DNA to RNA |
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What is the central theory of molecular biology |
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flow of information from DNA->RNA->Proteins |
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Define retrovirus |
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RNA genome that copies information in form of DNA |
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DNA has a _' and _' end, the strands are ______. Seperating the strands is ____. |
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3, 5, antiparallel, denaturing |
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With regards to RNA, what is a "transcript"? |
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A fragment of RNA synthesized from DNA |
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What is the function of mRNA |
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Encodes proteins |
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DNA replication is _____, as each of the 2 newly created DNA strands is half original and half new DNA |
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Semi conservative |
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What is the function of DNA Gyrase? |
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temperature breaks DNA down |
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What is the function of DNA Ligase? |
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joins DNA, forms covalent bond between sugar and P of adjacent nucleotide |
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What is the function of DNA Polymerase? |
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synthesizes DNA helix ahead of replication fork |
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What are Okazaki Fragments? |
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nucleic acid fragments that are generated during the discontinuous replication of amino acids |
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What is the origin of Replication? |
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region of DNA where replication begins |
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What is the function of Primase? |
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synthesizes small RNA fragments to serve as primers for DNA synthesie |
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What is a Primer? |
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nucleic acid fragment to which DNA polymerase can add nucleotides |
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What is the Negative (-) strand |
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DNA template strand, for RNA synthesis, RNA is complementary |
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What is the Positive (+) strand |
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strand complementary to negative, RNA analogous |
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Define Promoter |
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nucleotide sequence to which RNA polymerase binds to begin transcription |
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Define Sigma factor |
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component of RNA polymerase that recognizes promoter region |
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Ribosome Binding Site |
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sequence of nucleotides to which ribosome bonds |
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Define monosistronic |
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Transcript carrying only one gene (poly=multiple) |
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What is a core enzyme? |
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RNA polymerase without a sigma factor |
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What happens in termination? |
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Terminator encountered, ribosome falls off |
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What happens during transcription initiation? |
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At start codon, initiation complex forms |
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What happens during transcrption elongation? |
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Ribosome has 2 sites (P/A). Initiating tRNA binds to P, tRNA recognizing next codon binds to A, enzyme binds with peptide bond, translocates one codon, tRNA released through E (exit) site |
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What happens during transcrption termination? |
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Stop codon encountered, enzymes called release factors free tRNA |
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What are the function of chaperones? |
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Help fold protein into final shape |
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How are proteins meant to travel outside the cell differentiated? |
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Signal sequences added at the ends (tagged for export) |
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What are spontaneous mutations |
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Mutations that occur in a cells natural enviornment in an exteremely (1 in 10k to 1 in 1T) |
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Define reversion |
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The random reverseal of mutation (to a non mutated form) |
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Define base substitution |
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Incorrect base incorporation into DNA |
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Define silent mutation |
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A base changes but due to degenerate gene code, new codon specifies same amino acid |
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Define missense mutation |
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New codon specifies new amino acid. Leaky - cell grows slowly, as encoded protein still partially works |
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Define nonsense mutation |
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New codon is stop, protein truncated |
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Define null/knockout mutation |
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Inactivates gene |
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What is used to increase the frequency of base mutations? |
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Reactive forms of oxygen |
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Why is adding 1 or 2 bases worse than 3? |
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Frame shift mutation if 1 or 2 added/removed -- causes ALL following codons to be wrong |
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Chemicals that affect _________ _______ in DNA will result in higher mutations |
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Hydrogen Bonds |
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Define intercalcating agents |
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Mutagens that fit between N bases in DNA and distort the structure |
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How do UV rays affect DNA? |
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Cause covalent bonds to form between adjacent thiamine bases (thiamine dimers) |
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How do X rays affect DNA? |
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Cause single and double strands to break (lethal deletions) |
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What keeps the mutation rate in DNA low, aside from a low frequency of occurance? |
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DNA repair (pre or post replication), if heavy damage SOS repair |
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Define DNA-Mediated Transformation |
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Genetic exchange allowing DNA to move bacterium |
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How does DNA enter bacteria cells? |
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Binds to receptor cells on "competent" (state requiring high bacteria concentration, etc.) cells, one strand enters, other is degraded by nucleases |
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How does donor DNA integrate into the host genome? |
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Homologous recombination - If donor DNA has a homologous region in cell genome, it will take its place |
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What does transduction allow? |
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Bacterial DNA to transfer to another bacteria, mediated by bacteriophage |
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Define phage |
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DNA/RNA with protein coat, infect by injecting nucleic acid |
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Describe the process of transduction |
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Injection, nucleic acid removes host DNA, phage coat proteins synthesize, phage DNA replicates, some phage heads envelope bacterial DNA and infects another cell, bacterial DNA integrates into chromosomes by homologous recombination |
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What does conjugation allow? |
answer
Bacterial DNA transfer, requires physical contact (bacterial sex) |
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What does conjugation involve? |
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Mobilization of DNA transfer, plasmid transfer, synthesis of functional plasmid inside recipient/donor cells |
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Light of a _______ wavelength will provide better resolution because these waves can more easily fit between individual objects in the specimen. |
answer
Shorter |
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True of False: Differential media suppresses the growth of unwanted bacteria but promotes the growth of wanted bacteria |
answer
False |