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

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