Exam 1 Mindmap Flashcards
endosymbiosis
bacteria and archaea was engulfed and evolved to be mitochondria and chloroplasts in eukaryotes
koch’s postulates
rules for determining the link between microbe and disease
1. microbe is present in ill cells and not in healthy cells
2. when isolated and cultured inside hosts, no other microbes are present
3. healthy people injected with isolated microbe become sick
4. microbe can be isolated and cultured from those newly sick individuals
pasteur’s experiment
a broth was boiled and microbes were killed, and after 100 years, no microbes were present in broth but they accumulated in an attached tube
once the gathered microbes were tipped into the nutritious broth, they multiplied quickly (disproves spontaneous generation)
common ground between archaea and bacteria
no nucleus or membrane bound organelles
common ground between bacteria and eukaryotes
membrane composition
common ground between eukaryotes and archaea
genetic makeup and machinery
microscope purpose
useful to see how microbes interact with eachother
resolution
smallest distinguishing distance between 2 things
detection
ability to determine prescence of object
magnification
(what we resolve through) increase in apparent size to distinguish objects
spherical bacteria
coccus
rod shaped
bacillus
box shaped
arcula
appendaged
additive portion of bacteria
what gives us information on the type of bacteria?
shape of bacteria and colonies
what can we see with light microscopes?
eukaryotes, prokaryotes sometimes (without sub cellular structures), NOT phages and viruses (too small)
conditions to resolve an object
contrast, wavelength, magnification
wavelength rule
can be maximum 2x the object (the size of the object must be at least half of the wavelength)
focal point
where refracted light meets (and where we can see)
immersion oil
use with microscope’s 100x lens, it has the same refractive index as glass (so it cancels), more waves absorb and less escape
wet mount bacteria
in its natural state
smear bacteria
stained and dead
simple stain
colors cells
ex: methylene blue
differential stain
stains some cells and not others (to differentiate)
ex: gram stain
fluorescence microscopy
specimen absorbs light and emits longer wavelengths
used to identify specific bacteria if they are too small to resolve
chemical imaging
detects activity of cells and uses its mass to identify microb
dark field
used when size is too small to resolve with light or when the cytoplasm is transparent (uses phase contrast and scattered light)
electron microscopy
2 types: transmission and scanning
electrons are equal to lightwaves and the object (which is fixated and coated with metal - besides cyro EM) absorbs electrons. used to observe shapes
transmission EM
observes internal structures
scanning EM
observes externally
fundamental traits of bacteria
think and complex outer envelope, compact genome, tightly coordinated functioning (for efficiency and quick replication in compact state)
cytoplasm
gel with DNA, RNA, proteins and solutes (unique structural filaments: MinC and MinD)
cell membrane
encloses cytoplasm
nucleoid
non membrane bound area of cytoplasm containing chromosomes (looped coils)
cell wall
rigid external structure to prevent bursting
specialized structures
flagellum and chemosensors for motility
gram negative bacteria
lots packed into the plasma membrane- the cell envelope is key to interaction with host and environment
cell components
water, proteins, nucleic acids, peptidoglycan, essential ions (dictactes what is transported across the envelope)
membrane composition of bacteria
phospholipids: made up of glycerol (carb), with ester links to hydrophobic tails and phospholipid head group
phospholipids in archaea
more rigid, more ether links
fluidity of bacterial membranes
adaptable by modifying fluidity
unsaturated (cis) bonds increase fluidity
cyclic structures reduce fluidity (more rigid)
teichoic acids
found in gram positive bacteria, holds together the layers of peptidoglycan and consists of glycerol and phosphodiester chains
Gr+ cell envelope
cell membrane, peptidoglycan, S layer, glycosyl chains
Gr- cell envelope
inner membrane, peptidoglycan (periplasm), outer membrane, liposacchrides
liposacchrides
found in Gr- bacteria: endotoxins that are healthy for bacteria but if the cell is lysed, dangerous for host (difficult to target because antibiotics repel due to hydrophobicity)
inner membrane proteins
YjpP and YjgQ (transport liposacchrides to the surface of the cell)
mutations in the cytoskeleton
can cause shape change, function, complications, and death!
bacillus mutation
mutated mreB (rods to bubbles)
creS mutation
makes curved cells straight
FtsZ
forms complex around middle of cell (Z-ring) to help develop round shape
MreB
guides peptidoglycan elongation
crescentin
polymerizes along inner curve to create curved shape
ribosomes
made of RNA and proteins in cytoplasm
svedburg units
measures size and density
bacterial ribosomes: 70S
eukaryote ribosomes: 80S
pilin
protein monomers that attach to envelope and cytoplasm (cause gonorrhea)
chromosome
double stranded circular DNA aggregated in the nucleoid (viruses can be single stranded)
plasmid
non essential pieces of DNA (important in genetic engineering which produced insulin production), passed onto offspring, exchange antibiotic resistance
O2 and CO2 (small and uncharged molecules)
passively permeate through the membrane
H2O transport
uses aquaporins (proteins) to cross membrane via osmosis
weak acid and base transport
pass uncharged through the membrane and then become charged
active transport
low concentration to high concentration (requires energy)
passive transport
high concentration to low concentration
coupled transport
uses concentration gradient of one substance to power another against its gradient (can be symport or antiport)
ABC transport
ATP binding proteins dephosphorylate (making ADP) and uses that released energy to transport across
sidrophores
used to transport rare nutrients
group translocation
fools gradient (uses phosphate)
what is resolution dependent on?
density of photoreceptors in observer’s eye
peptidoglycan
a target for antibiotics, because it is in the cell wall of bacteria. a polymer of NAM and NAG sugars that are interconnected
S-layers
crystalline layers of proteins for extra protection
capsule
polysaccharides and glycoproteins- protect cell from drying out and being eaten (phagocytosis)
carboxysomes
bodies packed with Rubisco for CO2 fixation
gas vesicles
protein bound gas filled structures to make things float
flagella
spiral filament of protein monomers rotated by a proton motive force
chemotaxis
flagella moving!
clockwise = tumbles (flips/switches directions)
counterclockwise = moves forward
essential nutrients
must be supplied from the environment
macronutrients
major elements in cell macromolecules
cofactors
magnesium, iron, and potassium
micronutrients
trace elements necessary for enzyme function
autotrophs
fix CO2 and assemble into organic molecules (producers)
heterotrophs
use preformed organic molecules (consumers)
(chemo)organotrophs
use organic molecules for e- (most heterotrophs)
(chemo)lithotrophs
use inorganic molecules for e-
phototrophs
obtain energy from chemical reactions triggered by light
chemotrophs
obtain energy from redox reactions (two types: lithotrophs and organotrophs)
mixotrophs
can use multiple methods to exist
heterotrophy metabolism
external C sources cause energy transfer and C breakdown for other machinery (carbon cycle generates energy)
autotrophy metabolism
energy generated is used to fix CO2, molecules are reassembled into glucose
bacteria grown in liquid or broth
useful for studying the growth characteristics of a pure culture
solid
useful for trying to separate mixed cultures from clinical specimens or natural environments
dilution streaking
a loop is dragged across the surface of an agar plate
spread plate
serial dilutions are performed on a liquid culture, a small amount of each dilution is then plated
complex media
nutrient rich but poorly defined
minimal media
contains only nutrients that are essential for growth of a specific microbe
enriched media
complex media to which specific components are added
selective media
favors growth of one organism over another
differential media
exploits differences between species that grow equally well
growth factors
specific nutrients required by not all, but some species (needed to grow in lab media)
unculturable microbes
species that adapted so well to their environment that we cannot grow them in lab (may depend on growth factors that other species produce), or we may give too much!
optical density
measures growth in real time; bacteria in a tube of liquid medium can be detected by how cloudy medium appears as the cells scatter light
-quick and easy approximation of cell density
-decreased intensity of light due to scatter by a suspension is measured as optical density
light microscopy
direct counting of living and dead cells
-counted directly by placing dilutions on a special microscope (hemocytometer)
fluorescence microscopy
direct counting of living and dead cells
-living cells may be distinguished from dead cells using chemical dyes
(dead = red from propidium, live = green from syto-9 which can enter all cells)
flow cytometry and cell sorting
direct counting of living and dead cells
-light scatter correlates to cell size and granularity
-fluorescence measures live and dead cell content
how do most bacteria divide?
binary fission: one parent cell splits into two equal daughter cells
some divide asymmetrically (caulobacteria has a stalk and swimmer cell, and hyphomicrobium divides by budding)
growth rate
rate of increase in cell numbers or biomass is proportional to the population size at a given time (exponential growth never lasts indefinitley)
generation time
time it takes for a population to double
final cell number for binary fission equation
Nt = N0 x 2^n
Nt = final cell number
N0 = original cell number
n = number of generations
cyanobacterial heterocysts
every 10th anabaena cell- makes nitrogenase, forms a specialized barrier from O2, degrades photosynthetic machinery, allowing it to fix nitrogen anaerobically at night and maintain oxygenic photosynthesis during the day
gliding motility
myxococcus uses gliding motility - starvation triggers the aggregation of 100,000 cells which form a fruiting body (cells inside differentiate into dormant microspores)
what determines ability for rate and growth?
nutrients available, physical parameters, chemical and biological control agents (may stress response or adapt)
normal conditions
pressure: sea level
temperature: 20-40 degrees C
pH: near neutral
salt concentration: 0.9%
ample nutrients
what can microbes control?
pH, osmolarity, sometimes O2
what can microbes not control?
internal temperature and pressure
microbe temperature
matches its environment —> affects nutrient transporters, DNA/RNA stability, enzyme structure and function
osmolarity
number of solute molecules (opposite of water activity)
water activity
how much water is available (becomes water as solutes increase, fungi can grow with lower activity)
hypertonic medium
osmolarity greater inside than outside the cell, water flows inside
hypertonic medium
osmolarity greater outside than inside, water flows outside
how do halophiles avoid high internal salt concentration?
using Na+/K+ antiporters (special ion pumps excrete sodium and replace it with a compatible solute)
mechanosensitive channels
leak ions out of cell to avoid an influx of water
how do alkaliphiles maintain a neutral internal pH?
rely on Na+/H+ antiporters to bring protons into the cell, peptidoglycan and lipid modifications reduce OH permeability, has sodium motive force (to power flagella motility)
how do acidophiles maintain a neutral internal pH?
proton motive force is present, membrane permeability changes to reduce H+ entrance, K+(in)/H+(out) antiporters
strict anaerobes
die in the presence of oxygen have different acceptor in the electron transport chain
aerotolerant
can grow in O2 while functioning in fermentation
microaerophiles
only grow at low O2 concentration
faculatative
can grow with or without O2 (both types of respiration)
probiotics
restore balance in intestinal microbiome
phage therapy
aims to treat infectious diseases with a virus targeted to a pathogen
halophile
high salt
barophile
high pressure
hyperthermophile
above 80 degrees C
thermophile
between 50-80 degrees C
disinfection
killing/removing antigens from inanimate objects
sterilization
kills all living cells, spores, and viruses
antisepsis
kills/removes pathogens from surface of living tissues
antimicrobials
bacteriostatic = inhibits growth
bactericidal = kills bacteria
lag phase
bacteria are preparing cell machinery for growth
log phase
growth approximates an exponential curve
stationary phase
cells stop growing and shut down their growth machinery while turning on stress responses to retain viability
death phase
cells die with a “half life” similar to that of radioactive decay, a negative exponential curve
rod shape
envelope elongates + peptidoglycan chains track around the cell (DNA synthesis, then separation)
sphere
septation by Z ring generates cell envelope (splits then expands)
archaea
more closely related to Eukarya
- unique DNA compaction
-unique and chemically distinct cell walls
-certain genetic sequences only found in rRNA
psychrophiles
cold
what shows distance in ancestry?
nitrogen bases in rRNA
macronutrients
C, H, N, O, P, S
micronutrients
Co, Cu, Mn, Zn, Mb, Ni
cations necessary for enzyme function
cofactors: K+, Fe2+, Mg2+
cell signaling: Ca2+
autotrophs
fix carbons for themselves through CO2 (glucose through fixation)
heterotrophs
obtain carbon for organic molecules (to glycolysis)
phototrophs
energy from light
chemotrophs
energy from redox reactions
chemolithotrophs
use inorganic molecules for electrons
chemoorganotrophs
use organic molecules for electrons
how are bacteria defined?
by similarities within traits
serotype
stimulate distinct response of antibiotics
subspecies/strain/type
same species with different characteristics
growth cycle
bacteria divides by binary fission; one cell divides into 2 equal daughter cells (some divide asymmetrically)
growth factors
specific nutrients required by some but not all species
mixotrophs
can use multiple methods to obtain energy and carbon
liquid culture
best to see growth
solid culture
best to see seperation of species
isolation techniques
streaking and spread plate (dilution)
batch culture
liquid culture within a closed system (best for seeing change in environments)
continuous culture
all cells in a population achieve a steady state, which allows detailed study of bacterial physiology
adds and removes equal amounts of culture medium (ex: stomach)
biofilms
protect the cells from drying out; specialized, surface attached communities (defense against stress). can be cued by environmental signals in different species (pH, iron, temperature, oxygen, amino acids)
steps to forming biofilms
- a signal induces a genetic program in planktonic cells, cells attach to surfaces
- adhered cells. coat surface and more cells attach, communicate via quorum sensing
- cells form extracellular matrix (polysacchrides, DNA, proteins)
- columns, streaks, and channels form
- individuals detach when nutrients become scarce
