Question Answer What are the super domains Prokara and Eukarya two domains in prokarya bacteria and archaea What is the difference between the old kingdoms and the new domains The old kingdoms are based on phenetic observations: membrane size, cell size and cell organization
the domains are based on phylogenetic sequences:
rRNA, DNA and protein rRNA sizes eukaryotes have 18S and prokaryotes have 16S finction is identical in all organisms rRNA function three distinctions about prokaryotes 1. only unicellular organisms
2. lacks membrane bound organelles
3. DNA is not bound by a membrane thus known as a nucleoid three distinictions about eukaryotes 1. orgainisms are uniclellular and muti-cellular
2. have membrane bound organelles
3. DNA is bound by a membrane thus called a nucleus Bacteria contain what peptidoglycan bateria reproduce how binary fission Bacter is motile how flagella or flagellum Domain archaea lacks what peptidoglycan archaea reproduce how binary fission archaea is motile how flagellum or flagella what is the domain that is saprophytic domain eukarya domain eukarya include mushrooms, molds and yeast Algae explain aquatic, contains pigments for photosynthesis (autotrophic) explain protists some are autotrophic and some are heterotrophic, terrestrial and aquatic,
some have CaCO3 and some have silica cytoskeletons,
motile by flagella, cillia or psuedopodia RNA world hypothesis chemicals interact with one another creating enzymes, proteins and DNA what are ribozymes RNA with catalytic activity like enzymes what is LUCA last universal common ancestor
bacteria is the root of all three domains
lacks fossil evidence endosymbiotic hypothesis mitocondria, chloroplast, hydrogenosomes likely evolved from prokaryotic symbiotes of eukaryotic partners Survival of the fittest Eukaryotes vs Prokaryotes eukaryotes: vertical sexual reproduction
prokaryotes: horizontal asexual reproduction binomial nominclature is invented by linnaeus species vs genus there can be many species within a genus Lucretius and francastoro diseases were because of invisible living creatures van leeuwenhoek men's haberdasher that discovered animalcules by means of the first microscope 300x magnification Redi disproves spontaneous generation by three experiments
1. meat open to the air–maggots and flies
2. meat covered with paper–no maggots or flies
3. meat covered with gauze–maggots on the gauze but not the meat spallazani sealed glass flask and boiled sat_flash_1s
said air either carries the organisms OR air is required for germs to grow schwann flasks with boiled broths are left open and air passes through red-hot glass tubes
concludes air carries germs schroder flask with boiled broth is stopped with serilized cotton/wool
germs are stopped by serilized wool/cotton Pasteur created swan-neck flask to catch the germs
results:spontanteous generation is solidly disproved–he was a wine maker and his wine was turning into vinegar before he did this tyndall Hypothesizes that some forms of germs may be more resistant to heat Cohn demonstrates the existance of heat-resistant germs (endospores) bassi showed that disease affecting silk worm production was caused by fungal infection–only worms without infection could produce silk Lister found an antiseptic for infection–carbolic acid and heat serilized his instruments Koch Germ theory of disease
1. microbe must be present in every disease and absent in healthy
2. microbe must be isolated and grown in pure culture
3. same disease must result when inoculated into a healthy host
4. same micro must be reisolated and grown Germ Theory 1. microbe must be present in every disease and absent in healthy
2. microbe must be isolated and grown in pure culture
3. same disease must result when inoculated into a healthy host
4. same micro must be reisolated and grown Koch and pure cultures used agar because it could withstand high temps and most bacteria didnt use it vaccine against anthrax and rabies using what and developed by who using attentuation which is weakening of germs (successive passage through hosts and heat) pastuer what do microbes do make me sick, make and preserve foods, fertilize soils, bioremediation bioremediation GEM– genetically engineered microbes
like for the oil spill types of microscopes light and electron how electron microscopes work use electron radiation to capture and reproduce images light microscope magnification 1000x four types of light microscopes 1. brightfield
2. dark field
3. phase contrast
4. flouresence Brightfield Light microscope:
specimen appear dark and background is white
specimen need either natural color or to be stained–not good for live specimen Dark field Light microscope:
Specimen are light and background is dark
no need for stain or pigment–good for live specimen
light is scattered by a disc (patch stop) Phase Contrast Light microscope:
Image is bright background is dark
good for live material
Produces images in which the dense structures appear darker than the background and a glow around their edges Fluorescence Light microscope:
use dyes or natural pigments that produce light
some work for live specimen
pigments and dyes create a different wavelength and see them glow two types of electron microscopes scanning and transmission
1000x better magnification than light microscopes
can be expenseive because materials are often coated with gold or platinum transmission electron microscope:
electron beam penetrates specimen and scatters
intracellular details are studied this way scanning electron microscope:
beams hit surface of coated specimen
surface structure studied this way
100x better than light microscopes oil for microscopes almost no refraction and increases resolution
like mineral oil at work fixation kills and adheres microbes to slides
toughen cell walls and perserves the cell structure methods of fixation heat and chemical explain the methods of fixation heat:
air-dried and passed through flame
preserves the morphology of cell but not the internal structures
if not dired completely then cell can lyse
keeps internal structures in tacked
some chemicals are toxic

types of dyes and explain basic and acidic
basic: Carry a positively charged chromophore group is attracted to negatively charged components of cells, Most common dyes in lab
acidic: carry negative charge chromophore group is attracted to positively charged parts of the cell four staining techniques positive
differential positive stain cell is stained and background remains the same negative stain cell stays the same and background is stained simple stain positive or negative
only one dye is used differential stain two or more dyes are used
positve or negative examples of differential stains gram stain and acid fast stain differences of acid-fast stain and gram stain acid fast:
based on presence of waxy mycolic acids
end result is fushia or blue
gram stain:
most widely used method
based on peptidoglycan sat_flash_1 is purple or red
end result is how does a gram stain work primary stain: crystal violet
all cells are purple
Mordant: Gram's iodide
decolorizer: ethanol
Dissolves lipopolysaccharide layers in cell walls
counterstain: safranin
turns vacant cells pink gram stains–what each color is Pink–lipopolysaccarides
purple–peptidoglycan gram stain important factors Lipopolysaccharides are easily dissolved by ethanol, Peptidoglycan is not easily deteriorated by ethanol,After decolorization, Gram – cells take up counterstain

how does acid-fast stain work Primary stain: Carbol fuchsin
heat is used to soften the mycolic acid
Mordant: Cooling
Decolorization: Acid alcohol
Dissolve the walls of non-acid fast bacteria
Counterstain: Methylene blue
Blue cells–non acid fast
Pink cells–acid fast

capsules Capsules are layers of polysaccharides which are slimy and starchy
Nigrosin or India ink is used
The visibility of cells can be increased by counterstaining endospores it's the dormant stage of bacteria and is nonreproductive and difficult to stain
resistant to heat and chemicals, when conditions are favorable, the spore germinates to produce a vegitative cell how does an endospore stain work Primary stain: Malachite green
Mordant (physical): Cooling
Decolorizer: Water
Counterstain: Safranin
Turns vegetative cells pink/red

Flagella use electron microscopes to see monotrichous one flagellum at one pole bitrichous two flagellum at one pole lophotrichous a tuft of flagellum at one pole amphitrichous one flagellum at each pole peritrichous flagellum around the perimeter amphilotrichous a tuft of flagellum at each pole bacterial morphologies coccus, bacillus, vibrio, spirilla, pleomorphic and appendages (have tubes or stalks) bacterial arrangements strepto–chain
tetrads–squares of four
sarcina–packets of eight bacterial cell sizes nanobacteria
giant bacteria bacterial cytoplasm 70 to 80% water
mix of amino acids, sugars and salts bacterial cytoskeleton microtubules (tublin in E), microfilaments (actin in E), and intermediate filaments (laminin in E) **look at notes** bacterial intracytoplasmic membrane observed in photosynthetic and nitrifying bacteria
similar to endoplasmic reticulum and golgi apparatus, derived from invagination of plasma membrane and is part of complex structures in Eukaryotes (mitochondria and chloroplast) bacterial nucleoid usually a single cellular chromosome
contains genes that are essential for survival bacterial plasmids genes that are nice to have but not neccesary for survival
are double stranded DNA
replicate seperately from chromosomes
genetic recombination (episome) plasmid types conjugative–horizontal gene transfer (carry antibiotic resistant genes)
virulence–carry virulence genes
metabolic–carry genes for alternate metabolic substratescol–carry genes for colicin production

bacterial inclusions granuoles or gas "vacuoles"
primarily formed for storage purposes
membranes may be phospholipid bilayers or proteins oligotrophic inclusions store low or scarce nutrients examples of inclusions PHB
sulfur granuoles/globuoles
cyanophycin granules
gas vacuoles
ribosomes PHB lipid-like, carbon and energy source
found in purple photosynthetic bacterial
surrounded by single layer of protein and phospholipids glycogen starch like, carbon and energy source
in many bacteria volutin stores phosphate
used to be called metachromatic granules sulfur granules energy and electron source
found in purple photosynthetic bacteria cyanophycin graules used to be called blue/green algae
polymer of arginine and aspartic acid
stored nitrogen source carboxysome contain Rubisco and CO2 for carbon fixation reactions
surrounded by protein coat magnetosomes orientation for navigation toward nutrients
found in magnetic bacteria gas vacuoles aggregates of many gas vesicles
impermeable to water but permeable to gas
provides buoyancy for aquatic bacteria
each is composed of a single protein repeating ribosomes site of translation
made of two separate components Bacteria and Archaea ribosomes subunits 30+50S = 70S total Eukarya ribosomes subunits 40+60S = 80S total endospores (Sporulation) develope in unfavorable conditions
most are gram +
clostridium–tetnus, botulism and gangrene
bacillus–anthrax and food poisoning endospore (water sat_flash_1) water sat_flash_1 is VERY low how to eliminate endospores sterilization what contains dipicolinic acid endospores endospores: seven stages 1.axial filament of DNA formed
2.cell membrane forms septum
3.double layered membrane=protection
4.cortex forms around forespore
5.spore coat synthesis starts
6.spore coat complete–true endospore
7.released endospore dormant endospores transform to vegetative cells in three stages activation–usually heat
germination–spore swells and coat ruptures
outgrowth–cell returns to vegetative state bacteria cytoplasmic membrane boundary between cell and environment
flexible phospholipid bilayer
contain hoponoids to stabilize structure (are steroid like) peripheral and intergral proteins peripheral–loosly connected to cytoplasmic membrane, hydrophilic
intergral–amphipathic, extend from the inside of the cell to the outside cytoplasmic membrane analogous to eukarya site for enzyme interactions
regulates transport for sugars and salts
houses components for etc cell wall–bacteria prevents cell from lysis and holds shape
gram + and gram – Peptidoglycan for gram + and gram – gram + has lots of peptidoglycan
gram – has little peptidoglycan peptidoglycan backbone alternating amino sugars NAM and NAG
(chain of a metal fence) chain between NAM and NAG tetrapeptide chains composed of peptide bonds
(chain link fence) gram – peptidoglycan backbone DAP linked to D-alanine
DAP is unique to bacteria gram + peptidoglycan backbone interpeptide bridge formed (5 glycines) from D-alanine to L-lysine gram + cell walls teichoic acid aids in stability
lipoteichoic acid connect peptidoglycan to cytoplasmic membrane lipids gram – cell walls outermost edge is lipopolysaccharides
contains porins–channels for small molecules
large periplasmic space gram – antibiotics cells recognize antibiotics and pump them out by porins lysozyme weakens existing peptidoglycan found in tears and saliva
forms protoplasts (gram +) and spheroplast (gram -)
more effective on gram + glycocalyx expolysaccharide (EPS)
is used for energy storage and protection
not all bacteria
examples are capsules and slime layers S-layers primarily on archaea (usually the only form of protection)
like bubble wrap
pattern like floor tiles
protection bacterial flagella swimming
may aid in attachment
threadlike propellars
protein made of flagellin prokarya flagella hollow axial filaments in spirochetes flagella in periplasmic space bacterial flagella structure filament, hook, basal body tumble pattern of flagella counterclockwise–run
clockwise– tumble and direction change
proton motive force produces energy flagella motors Rotor:
turns in a cylindrical ring of electromagnets
Stator: electromagnetic ring made of MotA and MotB that anchor to peptidoglycan and form channel in plasma membrane fimbriae and pili hair like appendages thinner and horter than flagella fimbriae Velcro
attach bacteria to solid surfaces (dental plaque) Pili allows transfer of plasmids from one cell to another Nutritional requirements microelements (trace elements), macroelements, and growth factors (organic compounds that cannot be synthesized like amino acids, vitamins and purines and pyrymidines) autotrophs carbon source
make own organic compound heterotrophs carbon source
must get organic compound from somewhere else (us) phototroph energy source
light chemotroph energy source
break down chemicals lithotroph elcetron source
inorganic organotroph electron source
organic flexability of purple nonsulfur bacteria O2 at normal levels: follow chemoorganoheterotrophy
O2 absent: follow photoorganoheterotrophy
O2 at low levels: follow a mix of both pathways diffusion high to low concentration to reach homeostasis (equilibrium) four nutrient transport mechanisms passive diffusion
facilitated diffusion
active transport
group translocation passive diffusion concentration high to low
for O2 and CO2 facilitated diffusion carrier proteins
concentration high to low
(50000 fans through 12 gates) facilitated diffusion carrier proteins permeases
intergral proteins
change conformational shape when it binds
gradient must be maintained facilitated diffusion waste waste is exported through reverse mechanism faciliated diffision prokaryotes not the primary mechanism of nutrients active transport energy is required
primary is ATP
secondary is energy from gradients (proton and sodium pumps)
low to high
most common uptake of microbes
energy comes from breaking the phosphate bond active transporter paths three types uniport
antiport (two molecules different direction)
symport (two molecules same direction) ABC transporters requires a solute binding protein
permease has two domains
spans the phospholipid bilayer (transport
one in cytoplasm (nucleotide binding)
binds to ATP cleaves to ADP so solute can pass through Proton and Na pumps coupled anti and symport
antiport: Proton-motive force drives expulsion of Na+ from the cell as H+ enters
Conformational change in carrier occurs to release Na+ and solute inside the cytoplasm group translocation molecule is being transported into the cell while being chemically altered
break a phosphate bond, make a phosphate bond group translocation example PEP or PTS transport
PEP becomes pyruvate (substrate for kreb cycle)
May also play a role in chemotaxis
Mechanism widely distributed in prokaryotes agars complex polysaccharide but bacteria dont eat it
extracted from seaweed
remains stable at human pathogen incubation 37 degrees C chemical types of media complex
chemically defined chemical types of media explain complex: contains material that we do not know the exact ingredients to and varies from batch to batch such as meat extract
chemically defined: we know the exact formula for it special purpose media: selective allows growth of some organisms but inhibits others
example: Thayer-Martin agar used for STD screening with antibiotics in it special purpose media: differential everyone can grow
growth is differentiated special purpose media: sel/dif Example: MacConkey Agar
does not grow gram +
differentiation is based on fermentation of lactose
fermenters (break down lactose)–pink
non fermenters–off white bacterial colonies all cells arise from single parent cell
all protegy are identical
binary fission three ways to isolate pure cultures streak plate doesnt enumerate
spread plate enumerates
pour plate enumerates what is microbial growth increase in number
achieved by binary fission (bacteria) and budding budding two unique cells mother and daughter bacterial cell cycle c phase: replication
d phase: delayed phase getting pulled to either side of the cell
cytokinesis: septation complete chromosome replication begins at origin
bidirectional replication makes two copies chromosome partitioning MreBmodel in rod shape bacteria (actin in E)
form spiral complex inside the cell
chromosome separate to either pole as they move down the MreB helix steps in cytokenisis in E. coli 1. select site where septum will form
2. assemble of Z ring
3. link Z ring to plasma membrane
4. assemble cell wall machinary
5.constict cell and form septum batch culture growth phases lag
death lag phase cells are metabolically active but no increase in number
adaption: chromosome replication and synthesis
increase in cell size
length of phase varies with environment and species log phase (exponential) population doubles with each generation
average is 20 minutes
asynchronous–not all at once
growth rate is saturated stationary phase curve becomes horizontal
population stays the same–new cells gorm as old cells die
very common reasons for stationary phase nutrition or O2 limitations
accumulation of toxic waste
cell density death phase viable cells decrease exponentially
inability to grow
may experience a new lag and log phase because it relieves cell o2/space/nutritional limitations what causes cell death build up of toxin
survival of the fittest
current theories:
Viable but not Culturable (VNBC)
programmed cell death VNBC viable but not culturable
"bacterial coma"
dormant without change in morphology
inability to grow unless environment changes
public health threat Programmed cell death suicide of cells to provide more space and nutrients to surviving cells
it triggers an enzyme to break down it's own cell wall and die cell number calculation Nt = N0 x 2^n

Nt–the number in the population at time t
No–the originial population number
n–the number of generations in time t two ways to measure microbial growth by cell number and by cell mass microbial growth–cell number viable vs total
direct microscope counts microbial growth–cell mass calculations and conversions
total cell weight and turbidity direct microscope counts Petroff-Hauser Counting Chamber
counts number of cells per 0.1ml but cant distinguish between viable and dead cells cell counters automated counting device ex. coulter counter
cant distinguish live and dead and cant distiguish between a cell and small debris flow cytometry automated counting device
cant distinguish live and dead and cant distiguish between a cell and small debris viable counts measures colony forming units turbidity (cell mass) measures the amount of light scattered by cells
more mass=more scatter
uses spectrophotometer to measure optical density of the cell six chemical and physical factors determining growth solutes and water activity
o2 availability
radiation osmotic pressure four types moderate halophile:marine bacteria
extreme halophiles:found in hypersaline places
osmotolerant: growth over wide range (skin bacteria)
saccharophile: yeast and mold effects of osmotic pressure osmotic pressure and water activity are inverse
low water activity causes metabolic limitaions
high water activity may lyse cells because too much water in them–cell wall helps with protection pH requirements acidophiles– 1-5.5pH
neutrophiles (most)– 5.5-8pH
alkalophiles– 8.5 – 11.5pH keeping the cytoplasmic pH neutral neutrophiles exchange of K for h
alkalophiles exchange of na for h
synithesize special proteins in acidic conditions
acid shock proteins use ATP to export H out of cell
export waste out of cell
fermentation pruduces acids

temp requirements (4) psychrophile 0-20 degrees
mesophile 15-45
thermophile 45-70
70-120 degrees c psychrophile causes soilage of food in the fridge mesophile include most human pathogens 37 degrees thermophile found in compost heaps hyperthermophile hot springs major groups based on o2 availability obligate areobe
facilitative anaerobe
obligate anaerobe
areotolerant anaerobe
microareophiles abligate aerobes o2 required so live at top of test tube facilitative anaerobe in a test tube dense at top but growth everywhere
in presence of o2 more atp=more growth
lack of o2 less atp=less growth obligate anaerobe test tube they are mostly at the bottom with some alittle above the bottom
oxygen is toxic to them obligate anaerobes catalase breaks down hydrogen peroxide to h2o and o2 obligate anaerobe peroxidase converts peroxides to water and NAD+ aerotolerant anaerobes no toxic affect of O2 to to SOD
in test tube they can live everywhere microaerophiles too high of o2 is damaging
require 2-10% o2 and atmosphere has 20%
many are respiratory pathogens
Grow with other organisms to float through the atmosphere
test tube–all near the top but not at the top hydrostatic pressure land or surface water: 1 atm
deep sea bacteria: 600 to 1100 atm barotolerant adaptable to pressure barophiles grow better with higher pressure than the atmosphere
ones that grow in high temps are archaea and one that grow in cold temps are bacteria radiation damages DNA
mutations indrectly lead to cell death
Thymine dimers are easy to break individually but together it’s much harder to break all of the covalent bonds radiation ultraviolet rays uv light DNA damage can be repaired
dark reactivation
read slide 46 chapter 7 ionizing radiation atoms lose electrons
x-rays and gamma rays
low levels cause mutation
high levels are lethal
often used as a sterilizing treatment