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179 Cards in this Set
- Front
- Back
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What is the causative agent of a) trachoma, b) genital chlamydia
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Chlamydia trachomatis
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How does PID occur?
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STDs progressing up the fallopian tube into peritoneum
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List 2 structural characteristics of elementary bodies
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0.2 um in diameter
no peptidoglycan no ATP synhtesis |
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Why is penicillin not an effective antibiotic against chlamydia?
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Penecillin cannot diffuse into host cell
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Which is the odd one out: chlaydia, syphillis, gonorrhea, herpes
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Herpes because it is viral
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What microbes are hypothermophiles and what can they do?
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Archaea. They grow with optimal temperatures above 80
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Name three molecular adaptations that allow bugs to grow at high temps
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lipid monolayers
high percentage GC heat tollerant enzymes |
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Give the name of the bug that can grow at 113
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Pyrodictium sp
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What is the mode of nutrition of this bug?
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it's a hydrogen bacterium. Oxidizes H2 t H then reduces S to H2S as terminal electron acceptor
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Explain what Taq is and where it comes from
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It's the DNA polymerase from Thermus Aquaticus used in the PCR
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Made three products made in mixed acid fermentation
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Lactic acid/succinic acid/CO2/H2/formic acid/acetic acid
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Name 5 genera that can grow anaerobically
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Escherichia, Bacteriodes(obligate), Desulfovibrio (obligate), Clostridium, Propionibacterium, Saccharomyces
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What produces bubbles in swiss cheese/
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Propionibacterium/CO2
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Give the full binomial name for the common yeast
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Saccharomyces cerevisiae
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What is an endospore and name a genus which produces them?
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Highly resistant, survival stage formed inside the cell. Clostridium
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Name the genus responsible for 25% of primary productivity in many oceans?
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Synechococcus
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How does this organism photosynhtesize? Name the electron donor, the products, the absorption maxima and the key enzyme used for carbon fixation
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Oxygenically, non-cyclically
H2O, O2/NADPH2, 680-700, RuBisCo |
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Where do you find Chloroflexus spp. and how does it photosynthesize
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In hot springs. Cyclically/ photoheterotrophically
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What is the typical depth profile of photosynthesizing prokaryotes found in freshwater lakes?
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Cyanobacteria - Purple S (Chromatium)- Green S (Pelodictyon)
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Name two genera that perform cyclic photophosphorilation
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Chromatium, pelodictyon, Chloroflexus
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What is the difference between VISA and MRSA?
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Vancomycin intermediate S.aureus (resistant to Van but still susceptible to other antibiotics)
Methicillin resistant S. aureus. (resistant to all other antibiotics except van) |
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Explain two mechanisms bacteria use to become antibiotic resistant
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Natural selection - a resistant bug appears by chance mutation
Transfer of R-plasmids |
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Name three diseases that S.aureus can cause and the organs effected
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Pneumonia - lungs
Food poisoning - GI Pyelonephritis - kidneys Endocartis - heart |
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What is the role of enterococci in the vancomycin story/
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The enterococci (streptococcus fecalis) carry van resistant plasmids
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Distinguish between methanogens and methylotrophs. Give on application of each group
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Methanogens - obligate anaerobes/produce Ch4
Application - anaerobic sludge digester Methylotrophs - aerobs/consume CH4 Application - bioremediation |
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Why is CH4 important as a greenhouse gas
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25 better at heat retentio that CO2 and 85% produced biogenically
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Name the four starting compounds that can be used in methanogenesis
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CO2, H2, CH3OH, CH3COOH
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Where do you find methanogens in aquatic sediments
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Deep down in highly reduced layers, usually greater than 100cm
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What is MMO
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Methane monooxygenase
It is the first step in methylotrophy and used in bioremediation |
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Which of the pathogenic protists have cysts? Where do they excyst?
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Giardia lablia and Entamoeba histolytica
Both excyst in the small intestine |
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Which of the protists is a parabasalian, lacks mitochondria through secondary loss, is a kenetoplasmid?
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Trichomonas vaginalis
Entamoeba histolytica Trypanosoma brucei |
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Why is sleeping sickness so difficult to treat
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Cassette shuffling of the outer antigen of the trypanosome
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What is the approximate number of annual deaths due to malaria?
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2 million
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What causes the cyclic fever of malaria
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The merozoites rupturing en masse from the red blood cells
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What is the causative agent of lyme disease?
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Borrelia burgforferi
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What is the tick vector of this disease?
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Ixodes dammini - deer tick
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In N.S., dog tick nymphs metamorphose from waht, when and the nymph feeds on what host
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From larvae, metamorphosing typically in the spring of Year 2. Feeding primarily on white footed mice.
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Is the "bulls eye rash" a good diagnostic aid?
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Not definitive, only about 40% of patients show this rash
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Why are deer ticks more threatening to human health than dog ticks
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All life stages of the deer tick have mouthparts capable of penetrating human skin. Only the adult dog tick can do this, and in NS this species appear to carry no disease
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Name two genus that do not have cell walls
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Mycoplasma, chlamydia
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Life cycle of chlamydia?
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elementary bodies invade the host cell and infect -> once inside change to reticulate bodies which divides inside host cell until host cell is full and bursts
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3 fermenters and their end product
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E.coli - CO2, mixed acid fermentation
Clostridium - butanol, isoproponal Propionibacterium - CO2, propionic acid, acetic acid |
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Why is clostridium used as a fermentor in industry?
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produces butanol and isoproponal and endospores
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Difference between cyst and endospore
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Endospores are formed inside the cell
Cyst cannot tollerate as much as edospores |
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Cinicococcus photosynthesis
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oxygenic, absorption spectrum, uses chlorophyl a
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VRSA
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vancomycin S. aureus
Resistant to van but also resistant to everything else |
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What produces methane biogenically
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methanogens
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Example of parabosalian
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trigamonas
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Two ways that mitochondria can be lost in protists
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Primary - never had it - never needed it
Secondary - radiated after mitochondria, then went into anaerobic environment so didn't need it |
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Biology of Malaria?
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Vector is the mosquito
When mosquito bites the plasmodium gets inside host and infects liver cells, 24 hours later infects the red blood cells |
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How do scientists make the modern tree of life
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Look at 16s and 18s rRNA, and look at the number of nucleotide changes
The more nucleotide changes means a longer branch |
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Difference between phenetic and phylogenetic
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Phenetic is based on visual characteristics
Phylogenetics based on genotype sequences and shows evolutionary classificaiton |
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Examples of aerobic chemolithotrophs
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Nitrosomonas, nitrobacter, thiobacillus
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Examples of aquatic bacteria
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Purple S, Green S (Peliodictium, chlorobium), Rhodopseudomonas
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Genus that is found in chen. archeota
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Pyrodictium
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Dictostillium
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slime mold
several ameoba come together to form a fruiting body |
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Okazaki fragements
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DNA polymerase can only add nucleotides in the 5-3 direction. So lagging strand must be synthesized in fragments. Then are joined together by ligase
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Sigma factor
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component of RNA polymerase that recognizes the promoter and initiates transcription
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RNA Polymerase
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enzyme that catalyzes the synthesis of RNA using a DNA template
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R plasmids
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plasmids that encode resistance to one or more antibiotics
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Advantage of direct screening of mutation
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All that grow is the mutant strain because the entire parent population is killed off
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Transduction
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Mechanism of gene transfer between bacteria in which bacterial DNA is transferred inside a phage
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Importance of Rhixobium in nature
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fixes nitrogen into a usable form
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Endospore formation
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Plasma membrane forms around piece of DNA, membrane forms around forespore so have two membranes, have layer of peptidoglycan around forespore, endospore coat forms around forespore and endospore is released
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Bidirectional replication
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open chromosome at OriC, replication proceeds all the way around to an identical point on the other side
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Primer
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Fragment of nucleic acid layed down at each 5' end so that DNA polymerase can add nucleotides
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DNA gyrase
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temporarily breaks the strands of DNA and relieves tension
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DNA ligase
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joins two fragments of DNA by forming a covalent bond
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Helicases
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unwinds the DNA helix ahead of the replication fork
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Primase
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synthesizes small fragments of RNA to serve as primers for DNA synthesis
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Transcription
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initiation by sigma factors and promoters, termination by Rho dependent or independent
uses dsDNA as a template to create ssmRNA which can leave the nucleus |
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Translation
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converting triplet code into amino acid sequence
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tRNA
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brings amino acids to the ribsosome during translation,
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Process of translation
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Initiation by initiation factor (mRNA, tRNA, IF, small subunit)
elongation - amino acid brought into A site, carried by tRNA into P site Termination - release factors recognize stop codons |
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Eukaryotic gene expression
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introns and exons
poly-a-tail 5' cap |
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Transcription repressors
(negative control) |
Repressor binds to the operon so it is switched OFF
Switched on when an inducer interracts with the repressor before it can bind so it can no longer bind to the operon, RNA polymerase can interract with promoter and start making mRNA |
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Transcription activators
(transcription off) |
activator cannot bind to the activator binding site - RNA polymerase cannot bind to the promotorand initiate transcription
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Transcription activators
(transcription on) |
an inducer binds to the activator and changes its shape, enabling the activator to bind to the site
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Endospore formation
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Plasma membrane forms around piece of DNA, membrane forms around forespore so have two membranes, have layer of peptidoglycan around forespore, endospore coat forms around forespore and endospore is released
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Bidirectional replication
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open chromosome at OriC, replication proceeds all the way around to an identical point on the other side
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Primer
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Fragment of nucleic acid layed down at each 5' end so that DNA polymerase can add nucleotides
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DNA gyrase
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temporarily breaks the strands of DNA and relieves tension
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DNA ligase
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joins two fragments of DNA by forming a covalent bond
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Helicases
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unwinds the DNA helix ahead of the replication fork
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Primase
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synthesizes small fragments of RNA to serve as primers for DNA synthesis
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Transcription
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initiation by sigma factors and promoters, termination by Rho dependent or independent
uses dsDNA as a template to create ssmRNA which can leave the nucleus |
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Translation
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converting triplet code into amino acid sequence
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tRNA
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brings amino acids to the ribsosome during translation,
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Process of translation
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Initiation by initiation factor (mRNA, tRNA, IF, small subunit)
elongation - amino acid brought into A site, carried by tRNA into P site Termination - release factors recognize stop codons |
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Eukaryotic gene expression
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introns and exons
poly-a-tail 5' cap |
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Transcription repressors
(negative control) |
Repressor binds to the operon so it is switched OFF
Switched on when an inducer interracts with the repressor before it can bind so it can no longer bind to the operon, RNA polymerase can interract with promoter and start making mRNA |
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Transcription activators
(transcription off) |
activator cannot bind to the activator binding site - RNA polymerase cannot bind to the promotorand initiate transcription
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Transcription activators
(transcription on) |
an inducer binds to the activator and changes its shape, enabling the activator to bind to the site
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Lac operon
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lac operon contains three genes. transcription is controlled by regulatory proteins
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glucose present - no lactose
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transcription not activated and blocked
CAP cannot bind, repressor bound to operon |
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glucose present - lactose present
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Transcription not activated
CAP cannot bind, but inducer prevents repressor from binding to the operon |
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no glucose - no lactose
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transcription activated but blocked
CAP binds to activator, repressor is bound to operon blocking polymerase |
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no glucose - lactose present
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transcription activated
CAP binds to activator binding site, inducer prevents repressor from binding |
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Archaeal enzymes
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have chaperone proteins that coat enzymes and protect them
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Thermus
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used in the PCR because it does not denature at high temperatures
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Aquifex
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several flagella at one end, lives by eating hydrogen
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Thermotoga
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ferments sugars at high temperatures, has empty pockets on either side
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E.coli
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coliform bacteria - gram negative, ferments lactose
10^6 g/feces need e.coli in gut in order to digest tourista - change in the e.coli population |
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Mixed acid fermentation
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get lactic acid, succinic acid, formic acid, acetic acid, CO2, H2
only produces 2 ATP |
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Bacteriodes
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most dominant in the large intestine (find 10^10 g/feces)
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Propionibacterium
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produces CO2, acetic acid, propionic acid
also found in arm pit - gives the odor |
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Desulfovibrio
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sulfate reducing, not a fermenter (Anaerobic respirer)
pulls electrons off lactate to CO2 uses S as terminal electron acceptor |
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Lac operon curve
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initially will grow on glucose, will plateau when glucose is used up andthen will grow on lactose
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Base substitutions
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DNA polymerase can make a mistake and if not found will go into next round, will produce a different amino acid
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Frameshift mutation
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Another bp has been inserted into the codon so messes up everything below that codon
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Chemical mutation
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modify the chemistry to make a different amino acid
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Indirect mutant selection
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have master plate with bacteria - pressed onto velvet - velvet pressed onto complex medium and synthetic medium - auxotrophs do not grow on synthetic medium so can see position
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Direct mutant selection
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Have streptomycin resistant and streptomycin senstive, plate on a medium containing strep and one without, only mutants will grow
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Transformation
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Transforming DNA attaches to host cell - ss donor DNA enters - pairs with homologous region of host chromsome - transformed cells multiply
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Transduction
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Phage DNA enters host cell - degredation of host DNA into small fragments - phage DNA replicated - phage heads may take in fragments of bacterial DNA - phage carrying bacterial DNA infects another cell and can then be integrated and reproduced
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Conjugation
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F+ donor cell has F plasmid with origin of transfer - cell grows a sex pilus which joins to the F- recipient cell - Fplasmid is transfered as a ssDNA molecule - both are F+ and have a sex pilus
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Methanogens in humans
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Methanobrevibacter smithii
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Methane
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accounts for 18% of greenhouse gasses
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Applications of methanogens
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digester - for sewage, sludge (digest sludge anaerobically)
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Methanotrophs
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Methylobacter spp.
Methylococcus spp. Methylosomonas spp. |
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Natural vs. Artifical classification
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natural looks at the evolution of species
artificial is clumping all species together |
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Genomic typing: RFLP
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use restriction enzymes to detect different sequences and then chops DNA into different size fragments, some will be different and some will be the same
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Phage typing
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detect by plaquing - grow on agar plate and if phage recognizes bacteriait will infect it, so will have a zone of no growth
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Internal vs. external nodes
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internal represent ancestor species
external represent what is alive today |
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branch lengths
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represent the evolutionary distance or the degree of relatedness
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Genotype characteristics
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%GC must be similar, at least 70% DNA reassociation
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Distance matrices
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look at the differences between strains,
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Branches close to bottom of tree...
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if branches are down by the root it represents primitiveness (aquifex)
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Anoxygenic phototrophs
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purple bacteria (use organics as electrons acceptors)
green bacteria (use sulfur as electron acceptors) |
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Aerobic chemolithotrophs
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thiobaccillus
beggiatoa |
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Obligate aerobes
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pseudomonas
micrococcus |
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Faculatative anaerobes
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enterobacteriaceae
e.coli |
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Fruiting bodies
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Myxobacteria - function is to capture food, but when food becomes limiting produce stalk which releases spores
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Agrobacterium
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produces a tumor - when plant becomes wounded inserts the Ti plasmid
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Rhizobacterium
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produces pockets at roots where rhizobium grows and fixes nitrogen, so plants benefit
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Mucous membrane
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Bacteriodes
Mycoplasma |
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No mitochondria
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Microsporans
Diplomonads Parabasalians |
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Economic importance of fungi
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synthesize antibiotics
production of beer, wine, and bread |
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Life cycle of slime molds
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spores germinate myxamoeba - plasmodium - fruiting body - fruiting bodies release spores - spores germinate ameoba
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Archaeal cell walls
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can stain positive or negative
SL - globular proteins on th surface no muramic acid no D-amino acids |
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Archael lipids and membranes
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has hydrocarbon attached to glycerol by an eshter linkage
in bacteria/eukaryotes have fatty acids attached to glycerol Hydrocarbon has hydroxyl groups at either end so glycerol can bind to both ends making it a mono layer |
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Archeal genetics
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chromosomes are smaller than bacterial cells
have one chromosome per cell have eukaryotic initiator methionine |
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Archaeal ribosomes
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70s
shape different from bacterial and eukaryote |
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Chren archeota
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extremely thermophillic
acidophiles sulfur dependent grow in heated water or soils pyrodictium |
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Euryarcheota
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divided into five groups:
methanogens - methanococcales halobacteria thermoplasms extremely thermophilic sulfur metabolizers - thermococci sulfate reducers - archaeoglobi |
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Importance of methanogens
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importance of wastewater treatment, produce methane, oxidize iron
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Halobacteria
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require 1.5M NaCl
aerobic chemoheterotrophs |
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Extremely thermophillic
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motile by flagella, strictly anaerobic
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Nutrient acquisition
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light energy - producers - dead organic matter - decomposers - consumers - CO2
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Streptococcus mutans
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when matabolizing sugar producesa thick glycocalyx, once have this other things get embedded in layer - once get a thick layer that contains obligate anaerobs so have fermenters that produce acidic biproducts
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Antagonism
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two bugs get together in close proximity so one strain produces something that inhibits the growth of the other
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Bacteriocin vs. antibiotic
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anti has a wide target - bacterioci has more of a narrow target
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PCR
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find a certain sequence by finding primers that border the target sequence
extract DNA - add primer - goes through PCR - take out product and run it on gel |
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Get information in sequences:
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1) denaturing gel
2) sequence |
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Thermal stratification
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epilimnium
thermocline hypolimnium |
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Rhizosphere
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nutrients are coming out of the root so it changes the nature of the soil
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Carbon cycle (aerobic)
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start with CO2 (gas or bicarbonate) - fixed into organic compound - organics respired off (microbes mostly do decomp)
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Carbon cylce
anaerobic |
CO2 fixed by anaerobic microbes - purple and green S fixed CO2 to organic - when released resired by fermentation or anaerobic respiration
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Nitrogen cycle
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start with N2 gas - nothing can use it until it is fixed by prokaryotes into organic form - organic nitrogen in plants is eaten by animals then is excreted and decomposed
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Sulfur cycle
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start with SO4 - assimilated by plants to organic form - either goes to organics in animals or right to decomp to release H2S - oxidation to S and again to SO4
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Mycorrhizae and plants
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fungi growing on plants roots
ecto increases the surface area of the plant to capture more nutrients |
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Ixodes dommini
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carries lyme disease - deer tick, much smaller than dogs ticks
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How does it get here
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Feeds on birds - all brids which migrate south carry the disease and stop in NS and drop ticks off
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Life cycle
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eggs (femals feeding on mammals) - in early summer eggs hatch - larvae slowly digests the blood through the winter - goes through metamophisis in spring - nymph bites more animals - in fall metamorphoses into adult - lays eggs in spring
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How do they infect host
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look for moist places for 24 hrs - scratch through skin and pump out anesthetic - cement themselves in - during feeding can pass on lyme disease through salica
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Lyme disease
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spirochete up to 100um long, early symptoms are fatigue, headache, late lyme disease is arthritis
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Treatment
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early - tetracycline
late - Ceftriaxone |
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Beaver fever
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giardia lamblia
diplomonad amitochondrial goes into resting form called cyst that is hard to treat (only way is to boil or filter) cramps naseau diarreah |
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Amoebic dysentry
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entamoeba histolytica
secondary loss of mitochondria bloody diarreah |
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Trachomoniasis
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trichomonas vaginalis
parabasalian no mitochondria passed by sexual intercourse |
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Sleeping sickness
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Trypanosoma brucei
grows inside tse tse fly and grows in gut - when bites the human injects the disease |
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Malaria
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Plasmodium falciparum
tubular mitochondria goes through the female Anopheles mosquito |
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Applications of genetic engineering
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Clone segments of DNA into bacteria for further study
Bacteria produce pharmaceutical proteins, vaccines, etc. Study gene function and regulation |
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Applications of nucleic acid hybridization
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DNA probe
Colony blots Southern blots Fluorescence in situ hybridization (FISH) |
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Applications of DNA sequencing
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Determine the sequence of a gene
Use gene sequence to determine the amino acid sequence of a protein Identify genetic alterations Study evolutionary relatedness |
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Applications of PCR
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Amplify selected sequences
Thermophilic enzyme Used to identify pathogens (Neisseria gonorrhoeae) |
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Photosynthetic sulfur bacteria
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obligate anaerobes
cyclic, H2S is electron donor |
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Purple non-sulfur
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cyclic, anaerobes, organic is electron donor - rhodopseudomonas
chloroflexus |
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Thermoproteus
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thermoacidophiles
anaerobic metabolism |
