final Flashcards
archaea characteristics
prokaryote cell structure
no disease causing species
can have monolayer
ether linked lipids
has ring structures
transmission electron microscope
scans cellular structures in side the cell
scanning electron microscope
scans the surface of cellular structures
three forms of transport across a membrane
simple transport
group transport
ABC transport
simple transport
have an integral membrane protein allowing diffusion through membrane
group transport
substance is chemically modified
ATP drives transport (usually)
ABC transport
-ATP has a binding site
-ATP drives uptake of substance
binding proteins guides substance into transporter protein into cell
gram negative
membrane + cell wall + membrane
gram postive
membrane + thick cell wall
hami
grappling hook pili
assists in surface attachment
cell inclusions
-Carbon Polyphosphate, Sulfur, and Carbonate Minerals Storage Polymers
-Gas Vesicles
-overall reduces osmotic stress
-prokaryotic only
endospore formation steps
activation, germination, outgrowth
endospore characteristics
dormant cells resistant to heat, radiation, chemicals, drying and lack of nutrients
Found ONLY in gram positive bacteria
archella
-smaller than flagella
-related more to pili than flagella
-uses atp to move
-moves slower than flagella
flagella structure
-rigid and helical
-reversible rotating machine
-uses proton diffusion to rotate flagella
-filament (tail)
-hook (connects tail to motor)
-basal body (motor)
surface motility
slower than swimming
requires type 4 pili
movement occurs away from colony
steps for surface motility
-extend from one cell pole
-attachment of pili to surface
-retraction of pili pulling cell towards grasping spot
gliding motility
-has helical intracellular protein track with adhesion proteins that allows for smooth motion across surface
chemoorganotrophs
gets energy from organic material
chemolithotrophs
gets energy from inorganic material
heterotrophs
gets carbon from organic materials
autotrophs
gets carbon from CO2
Substrate-level phosphorylation
substrate bond used
directly to drive ATP formation
Oxidative phosphorylation
electrons creates pmf used to make ATP
Photophosphorylation
light used to form proton motive force
two main stages of glycolysis
1-prep phase-forms key intermediate
2-redox phase- energy conserved w pyruvate
Defined media
exact chemical composition known
Complex media
composed of digests of microbial,
animal, or plant products
Selective medium
contains compounds that selectively
inhibit the growth of some microbes but not others
Differential medium
contains an indicator, usually a dye,
that detects particular metabolic reactions during growth
growth curve
-lag phase
-exponential phase
-stationary phase
-death phase
Sessile growth
growth attached to surface
Planktonic growth
growth in suspension of medium
stages of biofilm
attachment
colonization
development
dispersal
spread plate method
pipette desired microbes on top of agar plate
pour plate method
pipette desired microbes
then pour agar on top of microbes
Psychrophile
low, found in cold environments
Mesophile
midrange temperatures
Thermophile
found in high temperatures
Hyperthermophile
found in extremely high temperatures
Decontamination
The treatment of an object to make it safe to handle
Disinfection
kills and Directly targets pathogens, not necessarily all
microorganisms
Sterilization
The killing or removal of all living organisms and viruses
static
stops growth, eventually resuming growth
lytic
kills and destroys microbes
cidal
kills microbes, doesnt destroy them
DNA pol Family A
-DNA repair and Okazaki fragment maturation
-exonuclease activity
DNA pol Family B
-Main polymerase in eukaryotes
-exonuclease activity
DNA pol Family C
-Main polymerase in bacteria
-exonuclease activity
DNA pol Family X
-monomeric
-fills gaps for DNA repair
DNA pol Family Y
-low fidelity, translesion synthesis
-no exonuclease activity
translocation systems
sec and tat system
two component regulatory system components
Sensor kinase
Response regulator
how does the 2 component regulatory system terminate the responce?
A phosphatase removes phosphate from the response regulator
sensor kinase
-detects environmental signals and autophosphorylates at
specific histidine residue
-integral to cell membrane
response regulator
-DNA-binding protein that regulates transcription
-receives phosphate from sensor kinase
-in cytoplasm
what is this picture depicting?
-This picture shows the 2 component regulatory system
-the sensor kinase gives its phosphate to the response regulator which then blocks transcription of certain genes
Methyl-accepting chemotaxis proteins (MCPs)
proteins that sense attractants and repellents and interact with cytoplasmic sensor kinases
2 component regulatory system and flagella
counterclockwise-run
clockwise-tumble
-When MCPs bind repellent or release
attractant, a kinase is phosphorylated
interacts with flagellar motor to induce clockwise rotation and tumbling
-When MCPs bind attractant or release repellent, a kinase is unphosphorylated and not bound to the flagellar motor, resulting in
counterclockwise rotation and running
Acyl homoserine lactone (AHL)
autoinducer
gram negative only
autoinducer
-molecule that indicates to a cell that other cells are nearby
-moves freely about membranes of cells
-reaches high concentrations in a cell when around other cells
-binds to sensor kinases which activates specific genes
Quorum sensing
regulatory mechanism by which
Bacteria and Archaea
assess their population density near themselves
heat shock responce
global control mechanism to
protect cells from protein denaturation resulting from heat, high solvent levels, osmotic stress, UV light
heat shock proteins
proteins that counteract damage of denatured
proteins and help cell recover from stress
Global control systems
regulate transcription of many
different genes in more than one regulon
Enzyme repression
preventing the synthesis of an
enzyme unless the product is absent from culture
medium; excess of product decreases enzyme synthesis
Chaperones
catalyze macromolecular folding events
Open reading frame
AUG followed by a number of
codons and a stop codon
lac operon regulatory controls
negative control: lactose must be present to remove the repressor
positive control: cAMP must be present in high quantities to allow the activator to bind
endospore sporulation
-When Spo0A highly phosphorylated, sporulation
proceeds
-5 sensor kinases monitor envionrment
-turns into spore
endospore germination
germination receptors monitor environment
attachment of biofilm
-Random collision accounts for the initial attachment
-Facilitated by flagella and pili or by cell surface proteins
-Attachment is a signal for expression of biofilm-specific genes
-Once committed to biofilm formation, the cell loses flagella and becomes nonmotile
biofilm formation steps
Attachment, colonization, development,
and dispersal
Activation of endospore steps
-release of DPA
-rehydration of core
-transcription and translation increase
Germination of endospore steps
-removal of the cortex is a
major event
-full rehydration of core
-metabolically active
Outgrowth of endospore steps
-elongates allowing escape of spore from mother cell
-fully metabolically active
heterocyst
-dedicated cells to nitrogen fixation
-anoxic
heterocyst formation
-inactivation of photosystem
-grows thickened cell wall to prevent 02 diffusion
-expresses nitrogenase
-triggered by limited amount of fixed nitrogen
Pseudomonas aeruginosa biofilm
biofilm forms in high concentration of the same species
Vibrio cholerae biofilm
biofilm forms in low concentration of the same species
efflux pump
-transport molecules, including antibiotics, out of the cell
-lowers intracellular concentration allowing cell to survive at higher external cellular concentrations
Auxotroph
has an additional nutritional
requirement for growth compared to prototroph
prototroph
wild type bacteria, no additional requirement for life
Replica plating
-screens for nutritionally defective mutants
-transfers colonies from main plate
-if colony is unable to grow on medium
lacking a nutrient indicates mutation
Transduction
Transfer of DNA from one cell to another by a
bacteriophage
Transformation
Genetic transfer process by which free DNA is
incorporated into a recipient cell and brings about genetic
change
Specialized transduction
DNA from a specific region of
the host chromosome is integrated directly into the virus
genome, typically replacing some viral genes
Gene Transfer Agents (GTAs)
Defective bacteriophages that transfer DNA between prokaryotic cells
Conjugation
Horizontal gene transfer that
requires cell-to-cell contact
archaeal chromosome
usualy only have 1 circular chromosome
Heterologous expression
Expressing a gene in a
different host
Thermocycler
automated PCR machine
Cristae
folded internal membranes
matrix
-innermost area of mitochondrion
-Contains citric acid enzyme
Thylakoids
-flattened membrane discs contain
-chlorophyll and ATP synthetic components,
-forms pmf
symbiogenesis endosymbiosis
mitochondria was integrated before nucleus formation in eukarya chloroplasts were integrated after
Hydrogen hypothesis
Eukaryotic cells arose from an H2-
producing bacterium and an H2- consuming Archaea
Orthologs
Homologus genes sharing the same
function
Paralogs
A single ancestral gene diverges to many
different functions in many different organisms
Gene conversion
-homologous recombination results in
replacement of recipient copy with donor copy
Systematics
Study of diversity of organisms
and relationships, links phylogeny with taxonomy
Phenotypic analysis
morphological, metabolic, physiological,
chemical characteristics analysis
genotypic analysis
genome analysis
phylogenetic analysis
evolutionary analysis
Fermentation
-ATP generated primarily by substrate-level
phosphorylation
-Does not require an external electron acceptor
-Electron balance obtained by reducing metabolic
intermediates excreted as fermentation products
Respiration
-Requires an external electron acceptor
-ATP generated by oxidative phosphorylation
-ATP synthase harnesses pmf to make ATP
-Chemolithotrophs use inorganic electron donors for
respiration
Assimilative
processes incorporate inorganic nutrients
into cells
dissimilative
processes conserve energy
Mixotrophs
heterotroph and autotroph
pathways of c02 fixation
4
Primary fermentation
ferment carbohydrate, protein, fat polymers and monomers
to reduced products, CO2, H2
secondary fermentation
ferment fatty acids to produce co2 h2
Syntrophy
Two different microbes cooperate to perform
a reaction neither can do alone
Gene loss
A trait is present in a common ancestor is
lost during divergence over time
Convergent evolution
A trait has evolved
independently in two or more lineages and is not
encoded by homologous genes
Horizontal gene transfer
-Genes that code for a trait
are homologous and have been exchanged between
distantly related lineages
PS1
fe in center
can do photosynthesis alone
PS2
quinone in center
cant do photosynthesis alone
reduced h from h20 to create pmf
Lysogenic infection
host cell genetically altered because viral genome
becomes part of host genome
Virulent (lytic) infection
replicates and destroys host
Capsid
protein shell that surrounds
the genome of a virus
Nucleocapsid
nucleic acid + capsid
Naked viruses
have no other layer
Enveloped viruses
-have an outer layer
consisting of a phospholipid bilayer
(from host cell membrane) and
viral proteins
Capsomere
-individual protein
molecules arranged in a
precise and highly repetitive
pattern around the nucleic
acid making up the capsid
complex virus
head and tail virus
helical virus
rod shaped virus
Icosahedral virus
spherical/hexagonal
Lysozyme
makes hole in cell wall to allow nucleic
acid entry, lyses bacterial cell to release new virions
Neuraminidases
destroy glycoproteins and
glycolipids, allow liberation of viruses from cell
5 steps of viral replication
-Attachment
-Penetration
-Synthesis of virus
-Assembly of virus
-Release
prokaryotic entry of a virus
nucleic acid entry
eukaryotic entry of a virus
entire virus enters
Vector
agent that carries and transmits an pathogen
Infection
Situation in which a microorganism is established and
growing in a host, whether or not the host is harmed
Disease
Actual tissue damage or injury that impairs host function
Pathogens
Microbial parasites that cause disease or tissue damage in a
host
Pathogenicity
The ability of a parasite to inflict damage on the host
Partner Choice hypothesis
plants use prenodulation signals from rhizobia
to determine whether to allow
nodulation
Sanctions hypothesis
legumes cannot
recognize more parasitic or less N-fixing
rhizobia, have to counter parasitism
through post-infection legume sanctions
Primary symbionts
required for the host to
reproduce
secondary symbionts
not required for host reproduction
