91 Cards in this Set
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Alkaliphiles
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microbes classified as extremophiles that thrive in alkaline environments with a pH of 9 to 11 such as playa lakes and carbonate-rich soils.
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Dark Field Microscopy
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Scattered light makes objects appear white against a dark background. Helpful for examining very thin cells.
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Barophiles
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Microbes that thrive in very high pressure areas
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Acidophiles
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microorganisms that like very low PH conditions
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Halophiles
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Halophiles are extremophile organisms that thrive in environments with very high concentrations of salt.
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Psychrophile
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Low temperature loving microorganisms
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Hypothermophile
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Organisms that prefer higher temperatures
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Phase contrast microscopy
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Refraction of the image!
Phase contrast microscopy is an optical microscopy illumination technique that converts phase shifts in light passing through a transparent specimen to brightness changes in the image. Bacteria must be less that 0.2microm in size and have a refractive index di…
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microbes
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A microorganism or microbe is a microscopic organism that comprises either a single cell (unicellular), cell clusters, or no cell at all (acellular).
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Activation Energy
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the energy needed to bring the molecules involved in a recation to the reactive state
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Glucose
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Glucose ( or ; C6H12O6, also known as D-glucose, dextrose, or grape sugar) is a simple sugar (monosaccharide) and an important carbohydrate in biology.
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Citric Acid Cycle
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The citric acid cycle - also known as the tricarboxylic acid cycle, the Krebs cycle, or the Szent-Gyrgyi-Krebs cycle - is a series of chemical reactions used by all aerobic organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats and proteins into c…
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Antoni van Leeuwenhoek
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First to describe bacteria
Built simple microscopes with 300X magnification
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Bacteria
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Bacteria are a large domain of prokaryotic microorganisms.
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Archaea
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The Archaea are a group of single-celled microorganisms.
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Robert Hooke
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Built the first compound microscope
First to describe eukaryote organisms
Named the "cell"
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Cohn
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laid the foundation for bacterial classification
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Aristole
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theory of spontaneous generation: Life arises from inanimate objects
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Pasteur
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father of microbiology. 1860's ended the thoery of spontaneous generation as the origin of life.
created first vaccines for chicken cholera and rabies
Determined that yeast is responsible for consumption of sugars and fermenation in alcohol.
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Germ theory of disease
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The germ theory of disease, also called the pathogenic theory of medicine, is a theory that proposes that microorganisms are the cause of many diseases.
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Koch
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Provided experimental proof of the germ theory of disease, identified causes of antrax, tuberculosis and cholera
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Berijerinck
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Developed enrichment culture technique to isolate metabolically diverse bacteria
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Winogradsky
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Discovered autotrophic bacteria, proposed the concept of chemolithotrpohy.
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Transmission
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Light goes through without being shattered
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Absorption
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Object absorbs part of the light. Energy level raised in object
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Reflection
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The light bounces off the surface
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Refraction
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The light bends when it enters a substance that changes its speed
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Scattering
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Some of the light is scattered in all directions
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Bright field Microscopy
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Bright field microscopy is the simplest of all the optical microscopy illumination techniques. Light transmits throught the sample and some cell constituents absorb the light. Because the cells are mostly transparent to light, the image is poorly contrasted.
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Benefit of Oil Immersion
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Light is refracted by immersion oil so an increased amount of light passes through the specimen
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2 ways examine bacteria TEM
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Negetively stain whole cells or large molecules; shows cell surface texture and very thin appendages
Embedded in a polymer, thin-section, stain with heavy metal salts; show external coats, cell envelope and internal structures
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Scanning electron microscopy
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Image formation : detects electrons that have been reflected off the object surface. Sample preparation: coat specimen surface with gold.
Advantages: High depth of field, wide range magnifications, ideal for viewing surfaces colonized by bacteria.
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Phase contrast
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Provides contrast between unstained bacteria and surrounding medium .
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Fluorescence Microscopy
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Concept of fluorescence adapted to microscopy. Fluorescent cells apprear colored agains a dark background
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Electron Microscopy
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Used to study cell ultrastructure
Use an electron beam rather than visable light
Electron bean penetrates through the specimen in TEM, reflects the specimen's surface in SEM
Disadvantages:
Must operate in a vacuum
allow viewing of dead samples only
often need an electron-dense stain…
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Dark Field Microscopy
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Uses a cardioid condenser, produces a hollow cone of light, some of the light reaching the specimen is scattered, objects appear bright white against dark background
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Acid fast stain
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Differentiates the bacteria (myobacteria) that cause tuberculosis and leprosy from other bacteria, based on the precense of cell waxes (mycolic acid) that specifically bind the stain (carbol fuchsion) and retain it when treated with acid-alcohol (decolorizes non-acid fast bacteria)
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Chemotrophs
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Use chemicals for energy
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Phototrophs
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Phototrophs are the organisms that carry out photosynthesis to acquire energy.
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Anoxygenic
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Do not produce oxygen
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Oygenic
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Produce oxygen
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CO(2)O(0.5)N(0.2)
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Basic nutrients of a cell
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Advantages of Chemolithotrophs over Chemoorganotrophs
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No competition for organic compounds, and inorganic compounds used as sources of energy are often waste products from chemoorganotrophs
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Autotrophs
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(Includes phototrophs and chemiolitotrophs) Use CO2 as sole C source, "self feeders"
Primary Producers!
Most phototrophs and most chemolithotrophs are autotrophs
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Heterotrophs
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Use several to many (different) performed organic carbon molecules, eg, glucose, as C source (majority of microorganisms)
Consumers
*Chemoorganotrophs are by definition, heterotrophs
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Strict aerobes
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Can only grow in the presence of O2
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Strict anareobes
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Only grow in the absence of O2
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Facultative Anaerobes/facultative aerobes
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Can grow in the presence or absence of O2
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Primitive environment conditions of cells
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No O2 in the atmosphere or oceans
not many organic compounds
Environment rich in CO2, H2 and H2S
Deep Sea Environment
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What do you think can be a limitation of dark-field microscopy?
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Dust particles can make it difficult to distinguish bacteria
from particulates
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Which organisms were first grown in laboratories?
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Chemoorganotrophs
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Which organisms appeared first during evolution?
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Autotrophs
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Which are the most likely metabolic properties of primitive microorganisms?
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Chemolithotrophic, autotrophic, and anaerobic
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In the phylogeny of gamma-proteobacteria shown in the last page, the length of the Buchnera branch is longer than other groups. What could this?
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One of the assumptions for molecular clocks no longer applies in that branch.
-It turns out that all bacteria in the Buchnera branch are endosymbionts (they live inside another species’ cells.) They feed on the nutrients provided by the host cell and no longer need certain biosynthetic p…
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Why is the DNA-DNA hybridization method more sensitive to species variations than SSU rRNA sequencing?
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The SSU rRNA gene is among the most conserved genes. Related (but different) species can have identical SSU rRNA sequences. Most other genes in the genome accumulate more mutations and diverge faster in related species than the SSU rRNA gene
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T or F, this reaction requires energy (endergonic): A + B → C + D (A=-100, B=-70, C=0, D=-300)
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False, The free energy of the reaction is (-300 + 0) – (-100 – 70) = -130 kJ/mol
The free energy is negative, so the reaction produces energy. The reaction is exergonic, not endergonic
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Glycolysis
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The redox reaction catalyzed by glyceraldehyde-3-phosphate dehydrogenase releases enough energy for G3P to get phosphorylated. Glycolysis produces 2 ATP and 2 NADH
*Glycolysis consists of a succession of two stages: (1) energy investment and (2) ATP production
*Glycolysis is found in m…
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PPP
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The pentose phosphate pathway (PPP) uses hexoses to make pentoses and the redox coenzyme NADPH
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In organisms performing anaerobic fermentations, the production of which fermentation product allows the organism to make one ATP by substrate-level phosphorylation?
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Acetate
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What features of the CAC are the most important to remember?
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it oxidizes pyruvate completely to 3 CO2
Two redox reactions release enough energy to allow the formation of thioester bonds in acetyl-CoA and succinyl-CoA
It results in the formation of 3 CO2, one GTP, four NADH, and one FADH
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In aerobic respiration, the final electron acceptor is
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Oxygen
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Why can green bacteria grow in deeper waters than cyanobacteria or purple bacteria?
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They have the most efficient light harvesting antenna complexes, the chlorosomes
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Saying that a type of photosynthesis is oxygenic means that
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Oxygen is Produced
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The absorption of ... by reaction centers begins the process of ……
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Light energy
photosynthesis
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Why did it take until the 19th century for scientists to connect microbes with infectious disease?
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Bacteria were only discovered in the 17th century
Until the 19th century, many people believed in spontaneous generation
All healthy people contain microbes. Until techniques were invented in the 19th to isolate bacterial species from each other, it was impossible to discern the effect …
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In which part of the Winogradsky column are anaerobes more likely to grow?
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Bottom
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what type of culture medium would you use to enrich a culture with bacteria that are able to use cellulose as source of carbon for growth?
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A medium containing mineral salts, NH4+ as a nitrogen source and a cotton ball or shredded paper
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Phase contrast microscopy uses the fact that light refraction changes the angle of the light through the sample to create the phase contrast image
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False
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What kinds of research questions could you investigate using TEM?
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*Vertical organization of the cell envelope
*Organization of thylakoid membranes inside cyanobacteria
*Organization of the flagella motor in the cell envelope
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Compared to other types of light microscopy, what is the major limitation of bright field microscopy?
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It has poor contrast
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P.4, Lecture 3 in the Classes and Examples of Extremophiles Table, which 2 columns is most important?
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*Extreme (column 1) and Descriptive term (column 2)
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Mitochondria and chloroplast in eukaryotes probably originate from...
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bacteria
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By which evolutionary mechanisms can organism can acquire new functions?
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* Gene duplication
* Horizontal gene transfer
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In the subsurface hypothesis for the origin of life, H is described as an abundant source of reducing power primitive cells could use as a source of energy for growth. Which statements support the hypothesis that many primitive organisms (if not all) used H as a main source of energy?
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* Almost all most ancient archaeal and bacterial species (i.e., species close to the root of the phylogenetic tree) use hydrogen as an electron donor in their energy metabolism
* Sulfur compounds were abundant on early Earth. Biological reduction of molecular sulfur by hydrogen would …
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All eukaryotes contain...
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A membrane enclosed nucleus
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A reaction with a negative Gibb’s free energy is exergonic (True/false)
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True
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Enzymes are made of ...
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Protein or RNA
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Reduction is the....of an electron. Oxidation is the .... of an electron.
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Gain
Loss
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NAD+ is the reduced form of NAD
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False
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The strongest electron acceptor in the electron tower is
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O2
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In the NO3-/NO2- (+0.44 V) redox couple, NO2- is the …… In the NO2-/NH4+ (+0.43 V) redox couple, NO2- is the ………..
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Electron DONOR
Electron ACCEPTOR
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Koch's postules (in order)
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1st- isolate the suspected agent from a disease victim.
2nd- grow the agent in pure culture.
3rd- infect a healthy host and show that the organism produces the CLASSICAL CLINICAL DISEASE.
4th-ISOLATE the "same" organism from the new victim.
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T or F: Hemes are covalently attached to cytochromes
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True
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Why is 16s rRNA not the best to distinguish between dif. varieties of the same bacteria species?
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It is too conserved in highly related organisms
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T or F: Redox couples w/ the most elecropositive redox potential are most likely to give up e-
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False
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Give evidence in favor of the theory of endosymbiotic origin of chloroplasts and mitochondria?
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Mitochondria and chloroplasts contain small genomes of circular DNA
The DNA of mitochondria and chloroplasts encodes bacterial-type ribosomes
16S rRNA analysis shows that mitochondria and chloroplasts are phylogenetically related to bacteria
Mitochondria and chloroplasts are sensit…
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All eukaryotes contain:
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A membrane bound nucleus
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Phototrophic microorganisms that have …membranes surrounding their chloroplasts have acquired their chloroplasts through primary endosymbiosis
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Two
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Phototrophic microorganisms that have ………. membranes surrounding their chloroplasts have acquired their chloroplasts through secondary or tertiary endosymbiosis
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More than two
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T or F: Proteins from hyperthermophiles look very different from proteins of other species
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False.....As a matter of fact, it is often impossible to tell them apart by just looking at them
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Which mechanism is used by extreme halophiles to resist osmotic stress?
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They have intracellular ionic concentrations similar to those of the
surrounding growth medium
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Study Guide: Final Exam