Studied by 2 people
E: Chemotaxis in E. coli
Methyl accepting chemotaxis proteins (MCPs) are polarized to one side of the bacterium, bind to an attractant and signal for a change in flagellar rotation
CheA and CheW autophosphorylate which leads to phosphorylation of CheYby CheZ which allows for random introductions of CW rotation (tumbles) otherwise the flagella defaults to CCW rotation (runs)
when MCPs are bound outside the cell, they stop the autophosphoylation of CheA so CheY isn’t phosphoylated so the flagella stays in the run mode going CCW
E: Chemotaxis Capillary Assays
substance is in a suspension in a tt and placed into a container w/ bacteria that flow in more if attracted, evenly if neutral, less if repellent
other forms of taxis include: oxygen or ____taxis or lining up at certain wavelengths in ______
aerotaxis, phototaxis
Some water-borne bacteria have _______ which confer ______ to the cell
gas vesicles, buoyancy
w/ gas vesicles, The bacterium is able to float up or down in response to ______________________________________________________
environmental changes (avail. of O2, light, etc)
what types of organisms can have a gas vesicle
Many phototrophs, some non-phototrophs, not euks
gas vesicle membrane is impermeable to ___ but permeable to __
water, oxygen
what is the oriC
origin of replication on chromosome
what binds and opens up double helix
DNAa proteins
how does binary fission work
binding of DNAa to oriC initiates DNA replication
the cell elongates
the septum forms
the z-ring forms
the cells separate
the ____ Directs synthesis of the septum
divisome
Fts proteins: ----- – forms the dividing ring
Fts stands for ---------
Other Fts proteins help form --------, etc.
FtsZ, __F__ilamentous __T__emperature __S__ensitive, peptidoglycan
anchors FtsZ ring to CM
zip A
min proteins do what
help guide FtsZ ring to the midpoint of the cell
mutants form minicells
what is the process of how the peptidoglycan wall forms
NEGs and NAMs are assembled in the cytoplasm but the pentapeptide attaches them to Lipid A which then enters the flippase which moves them across the CM where autolysin activity opens a hole in the existing structure and trans glycosylase activity adds it to the existing structure
transpeptidation then joins the NEGs and NAMs with peptide bonds
antibiotics inhibit both ‘trans’ activities
in what environments could you find each of the discussed temperature loving categories
psychrophiles- fridge
mesophiles- human body
hyper/thermophiles- hot springs
what does the preferred temperature for each organism determine
their environmental niche
E: 3 cardinal temperatures & effect on bacterial growth/molecular integrity
range is us. 30 d C
at minimum temp, membrane gels and cellular transport happens too slowly for life to exist
at optimum, enzyme rxns are occurring at the max rate
at max, pplbl collapses in thermal lysis, protein denaturation
what causes food poisoning
enterotoxin
what are facultative psychrophiles aka psychrotolerants
they can survive cold temps like lysteria
how do psychrophiles adapt for cold environments
proteins have more alpha helices, more hydropob and less polar amino acids, fewer weak interactions, and cryoprotectants like glycerol
have a high [] of unsat FA to stay fluid
what is an example of a thermophile
methanopyrus
thermus aquaticus
what adaptions do thermophiles have
proteins: more charged amino acids, with lots of interactions with hydrophobic interiors, chaperone proteins, less Gly, and protective solutes like phosphate to increase the osmolarity to increase stability,
genome has more DNA binding proteins to keep it tightly coiled
membrane has more sat FA, more hydrophobic with longer chains, some archea have a lipid monolayer that has specific hydrocarbons instead of FA
what do extreme pH orgs have
acidophiles- need more H+ for membrane stability
alkyphiles- are used in detergents
what do extreme pH guys do to keep a normal cytoplasmic pH
import/ export ions, HSPs are made when pH drops, and differences in the cell wall/ membrane
what does water activity (Aw) indicate and what is the lower limit of life
how much pure water is available for use, 0 pure, 1 no water, shows osmolarity
aquaporins are channels that allow for the fast transport of water to reduce osmotic stress
.6
________: require high NaCl concentrations
Marine organisms – 3.5% NaCl
-------– 15-30% NaCl (salt crystals)
________ (high sugar concentrations)
Xerophiles (___ environments)
_________: tolerate wide ranges of osmotic pressure
Halophiles, Extreme halophiles , Osmophiles, dry, Halotolerant
what is an example of a halotolerant organism
Staphylococcus aureus
Strict/obligate aerobes
require O2 to grow
Microaerophiles
only grow at low O2 levels
Strict/obligate anaerobes
die in the presence of O2
Facultative anaerobes
grow w/ or w/o O2 but grow better w/ it
Aerotolerant anaerobes
grow w/ or w/o O2 but use fermentation and are unaffected by O2
what is an example of an enzyme that destroys toxic oxygen species
catalase
what are the macronutrients needed for growth
CHNOPS
light for E, non-org for H donor, CO2 for C
Photolithoautotrophs
light for E, organic for H donor, organic for C
Photoorganoheterotrophs
chem E, non-org for H donor, CO2 for C
Chemolithoautotrophs
chem E, non-org for H donor, organic for C
Chemolithoheterotrophs
chem E, org for H donor, organic for C
Chemoorganoheterotrophs
what are the major micronutrients needed and what are they used for
Iron, zinc, nickel
making enzymes
fastidious need these supplied (like from tap water)
which micronutrient is the limiting thing in the human body
Fe
what are examples of organic growth factors
micronutrients, amino acids, purines, pyrimidines, vitamins
what are the uses of metabolism
Bringing in nutrients
Repair and maintenance
Release of wastes
Motility
Generation of PMF
Anabolism: building parts
Biosynthesis
Polymerization
Assembly
what is an anerobic organism
one that does not use O as its final e- acceptor
what is respiration
Organic or inorganic compounds are oxidized with oxygen or some other compound to make ATP
what is the most common form of glycolysis and what are the alternatives
Embden-Meyerhoff-Parnas pathway
Pentose Phosphate shunt, Entner–Doudoroff pathway
what is pyruvate used for
Further processed in the CAC in respiration
Reduced in fermentation
Used for biosynthesis
E: Why respiration in prokaryotes is more efficient than in eukaryotes
DNA is more available and no energy is needed to move through membrane bound organelles
euks do ETC in inner mito membrane while prok do in cytoplasmic membrane
E: Uses of the PMF (Proton gradient) in prokaryotes
powering ATP synthesis through OP
powers uni/sym/anti port, drug efflux pump
flagellar rotation
E: Complete oxidation of glucose
glycolysis: need- 2 ATP, 1 glucose, 2 NAD+, get- 4 ATP 2 pyruvate, 2 NADH +2H+ 2e’s
intermediate step: 2 pyruvate, 2 NAD+ 2 GDP, get- 2 Acetyl CoA, 2 CO2, 2 NADH + 2H+, 2 GTP 4e-s
CAC: 2 acetyl CoA, 6 NAD+, 2 FAD, get- 6 NADH + 6H+, 2 FADH2, 3 CO2, 2 ATP 16e-s
ETC: 10 NADH + 10H+, 2 FADH2, 6 O2, get- 34 ATP (finish with 38)
C6H12O6 + 6 O2 + 38 ADP + 38 Pi → 6 CO2 + 6 H2O + 38 ATP
E: How the proton motive force is generated
e- carriers are arranged so that H+ from water is separated from e-
e- carriers are arranged so that the next has a higher e- affinity than the last so the last carrier is the most pos reduction pot
carriers switch btwn reduced or oxidized forms
O is common final e- acceptor but there are some rare alternatives
meaning that NADH has more ATP gen potential than FADH2
happens through oxidation phosphorylation/ chemiosmotic theory
so ADP becomes ATP when H go down gradient
ATP synthase:
A.k.a. _____
Complex _ of ETC
Site of ____________
-------- per ATP produced
_______ complex
Catalyzes -------- phosphorylation of ADP to ATP
Reversible (---------- need to generate a PMF for motility and transport)
has changed _____ evolutionarily
ATPase, V, oxidative phosphorylation, 3 to 4 protons, F1 /Fo, reversible, strict fermentors, little
what are alternative final e- acceptors
nitrate, sulfate, carbonate
Forms nitrite, hydrogen sulfide, methane
what do faculative areobes do when they run out of O2
glycolysis then fermentation
what occurs in fermentation
No exogenous electron acceptor needed
Organic molecules only partly oxidized
Pyruvate converted to organic compounds
is inefficient w/ only 2 ATP per glucose molecule
NAD+ is restored for glycolysis
leads to a buildup of acid end products
E: Differences between prokaryotic and eukaryotic genetics
euk: nucleus, linear, haploid/diploid/poly, more protein encoding genes, histones, has introns, replicate DNA hours before mitosis, multi origins of rep
prok: nucleoid, circular, us haploid, less protein encoding genes, arch has histones bac has histone like, no introns in bac but introns in rRNA and tRNA of arch, replicate DNA just before BF, bac has one origin of rep but arch has multi
how are plasmids retained
must be transferred in conjugation to others or will be lost over time as they code for exogenous information, has an oriV center of replication
what do plasmids often code for
pilus on F-plasmid, enzymes for synthesis of unusual compounds, and/or genes for antibiotic resistance, virulence factors
what are segments of DNA that move from one location to another within other DNA molecules
transposable elements
where are transposable elements found
all 3 domains, in another DNA molecule like chromosomes or plasmids
how are transposable elements moved
transposition using transposase enzyme which moves DNA between inverted repeats
what are the 2 main types of transposable elements in bacteria
transposons and insertion sequences
both have genes to encode transposases and inverted repeated sequences to make them more recognized from multiple angles
what are transposons (Tn)
Larger than insertion sequences & have IRs at ends; also encode for transposase
May include genes for antibiotic resistance
Examples are Tn5 and Tn10
what are insertion sequences
Simplest transposable element with IRs at ends
Ca. 1,000 nucleotides long
Only gene is for the transposase
Found in plasmids and chromosomes of Bacteria and Archaea
Found in some bacteriophages
found in the chromosome and is basically a place to add genes
what is the physical exchange of DNA between genetic elements
recombination
what is the process that results in genetic exchange between homologous DNA from two different sources
homologous recombination
Recombination: A.k.a. _______________
________ transfer
Transfer of _ kinds of DNA
found in _______
----- forms (plasmids)
Must be maintained in a ------
as -------
Or --------- into chromosome, often via ----
Horizontal Gene Transfer (HGT), One-way, 2, Fragments, Stable, recipient cell, plasmids, recombined, IS’s
Homologous Recombination in prokaryotes is facilitated by letting strand invasion occur via _____
recA proteins, promotes base pairing btwn the 2 strands
E: Processes of, and differences between, transformation, conjugation and transduction
Transformation= Uptake of “free” DNA
donor cell is lysed and new cell can take up DNA, but new cell must have competence proteins in order to take it up, was used to determine that DNA is the vehicle of heredity, is often used as a genetic tool, virulence factor is transferred via a capsule, transferred as a plasmid or as a fragment, can artificially induce this, transformasomes allows for competent proteins to let a pillus form
Conjugation= 2 cells exchanging DNA
occurs through cell to cell contact through a pillus, conjugated or transferable plasmids have the genes for conjugation; F plasmid in e. coli codes for fertility factor that allows conjugation that sometimes also brings in host’s genome, tra genes encode for gene transfer that encode for the pillus and has multi IS sites and 2 origins of replication (oriT (rep in DNA transfer, everything behind this arrow is what is trans first) and oriV (rep of non-conjugating plasmid), transfer begins at the oriC), pillus only brings together the 2 cells, a conjugation bridge forms, DNA goes through tube where it is replicated on both sides, the cell then separates and both are now F+
Transduction= Via bacteriophages
bacteriophages takes up DNA from one host and inserts it into a new host
auxotroph vs prototroph
Auxotroph: Mutant strain requiring a growth factor (vitamin, AA, etc.)
Prototroph: Wt – typically does not require any growth factors
how are plasmids transferred in conjugation
Conjugation -Replication and Transfer Process
what differentiates F+ and F- cells
F+ cells mate only with F- cells
F-: No F plasmid
F+ cell: unintegrated F plasmid
F- becomes F+ after mating
F+ cannot mate with F+
Surface receptors altered so that cell can no longer act as a recipient in conjugation
what is the most common way antibiotic resistance is transferred between species
conjugation
E: Experiment of how transformation was discovered
Fred Griffith in 1928 used Streptococcus pneumoniae called it the transforming principle
had non-encapsulated bacteria injected in mouse- lived w/ encapsulated bac recovered
had encapsulated bac injected- died w/ a few non-en found
had heat killed encapsulated bac injected- lived w/ no colonies
added non-encapsulated to the dead encapsulated- died w/ encapsulated
E: Experiments of how conjugation was discovered
Joshua Lederberg and Edward Tatum 1946 saw that mixing 2 auxotrophs can make a prototroph
had tt of 2 opposite mixes of proto and auxos and a combo of both and plated on minimal media and only the combo grew
Bernard Davis 1950 saw that physical contact was needed for conjugation
put in tube that physically separated and didn’t happen so couldn’t be transformation
Note 
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