What is mineralizing
conversion of organic matter to inorganic substiuents
What performs minerlization
microbes
T/F: The body consists of as many microbes as human cells
FALSE a lot more microbes
T/F: Microbes help perform bodily fucntions
True
“the invisible presence”
microbes
the life force of the planet
microbes
The origins of life are based on
First principles
Name the hypothesis of water
degassing-condensationcomets and asteroids bringing ice
The first microfossils appeared when
3.5-3.8 bya
6 essential characteristics of life
-membrane-aqueous-catalysts-energy flow/storage-anabolic pathways (polymerizing molecules)-RNA/DNA
describe the membrane characteristic
layer separating outer environment and inner
describe aqueous
water-based organism
describe catalysts
speed up reactions
describe energy flow/storage
metabolism (ATP -> ADP Pi)
describe anabolic pathways
monomers -> macromolecules
describe RNA/DNA
info carriers/storage + translation apparatus
Name the 3 Theories of life
Gaia HypothesisVital Force ViewMechanistic View
What is the Gaia Hypothesis
earth is a living entity - its biosphere maintains its homeostasis
What is the Vital Force View
science cannot explain life forces (not testable) and does not include physics and chemistry
What is the Mechanistic View
Life is chemically based with same chemicals from environment, just in a particular and unique arrangement
Can some forms of life form from inanimate matter?
Nopes
Which two guys disproved spontaneous generation
Redi and Pasteur
Redi’s exp
flies and rotten meat in a jar
Pasteurs exp
Broth and swan-neck flask
Origins Hypothesis I is
panspermia
What is panspermia
extra terrestrial life was brought here in the form of germs/spores
Origins Hypothesis II is
Chemical Evolution (life is unique to Earth)
Stages of Chemical Evolution
1) Nucleotide/Amino Acid formation2) Polymerization3) Polymers in membranes4) Living
Explain the 3 ways of nucelotide/amino acid formation
E.T. input -> water and organic material delivered by comets and asteroidsReducing atmosphere air contained CH4 NH3 CO2 H2S, H2, NOO2Hydrothermal Vents: Chemicals interact with energy from heat (CH4 NH3)
Explain the stage of polymerization
[difficult with no enzymes present]Energy for polymerization could be possible from:1) pyrite2) hydrothermal vents3) hot pools
What is pyrite
sillicate in clay that condense to catalyze
what is a hydrothermal vent
vent that consists of metas, iron and nickel, that could catalyze
What are hot pools
places where water evaporates and leaves more concentration of materials to interact with each other
Explain the stage of polymers in membranes
Membranes form around the polymers and the result is a protobiont
What is a protobiont?
aggregate of organic molecules that perform metabolism
Catabolism
breaking down materials
Anabolism
synthesizing materials
What are coacervates
specific protobionts that have lots of sugars and proteins
What is the coacervates relationship to the environment?
its internal chemistry is sginificantly different than the surrounding environment
The catalyst that allowed protobionts to become living
RNA ribosyme (ribosome)
Information carriers in the living microbe
RNA and (Hydrogen bonds)
T/F: Ribozyme is an enzyme
FALSE it is only made of nucleotides (amino acids) not proteins
Catabolism
breaking down materials
Anabolism
synthesizing materials
What are coacervates
specific protobionts that have lots of sugars and proteins
What is the coacervates relationship to the environment?
its internal chemistry is sginificantly different than the surrounding environment
The catalyst that allowed protobionts to become living
RNA ribosyme (ribosome)
Information carriers in the living microbe
RNA and DNA
T/F: Ribozyme is an enzyme
FALSE it is only made of nucleotides (amino acids) not proteins
Other things that allowed microbes to be classified as living
RNA/DNA (hydrogen bonds) (translation/transcription apparatus)
Two forms of dating
relative and absolute
Relative dating
straiographic layers (sediment layers and fossils)
Absolute dating
Half-life (radioactive isotopes)
Linnaen Classification
Kingdom - Phylum - Class - Order - Family - Genus - Species (most specific)KPCOFGS
Characteristics conserved over all 3 domains
RNA/DNATranslation/Transcription apparatusGlycolysisRibosomesSemi-conserved DNA ReplicationPlasma Membranes
Which of the 3 domains is most different from the others
bacteria (archaea and eukarya most similar)
Evolutionary Distance
different base pairs/ total base pairs (presented in %)
What are all prokaryotes?
Microbes
What is the size range of prokaryotes?
100 nm to 100 micrometers
What portion of Eukaryotes are microbes? Examples?
1/3Protists and fungi
What is the advantage prokaryotes have over multi-cellular eukaryotes?
Individual cells can survive by themselves (while other cells need to communicate)
Advantages to being small
less competition for spacesmaller surface area/volume to move nutrients, excrete wasteless nutrients needed to maintain
Phytoplankton is what percent of the earths biomass? What % of the Earths oxygen do they produce?
0.2% biomass45-5-% oxygen
What type of organism is phytoplankton?
photoautorophs
What type of organism is bacterial plankton?
heterotroph
2 other names for autotrophs, derived from what?
chemo-autotrophschemo lithotrophsderived from converting inorganic materials and CO2 –> organic and oxygen
What are ribozymes?
selt-catalyzing strands of RNA that also carry information
Proteins become specific to
control reactions
RNA folding leads to
stabilization of H-bonds in 3D form
What is a reducing atmosphere?
Atmosphere created by desne gasses (volcanic out-gassing) H2O, ClH2, CH4, H2S, NH3, CO2
Miller-Urey experiment? Did it work?
Emulated conditions of early Earth (reducing atmosphere) to try and create organic compounds. Produced nucleotides and AAS
Nucleotides and AAs are precursors for
DNA and proteins/enzymes
Hydrothermal vents created first organic compounds through (specific terminology)
Thermal gradients and “plume chemistry”
Some factors for extinction and evolution
continental drift, climate change, volcanic activiy, unidirectional change in O2, external events.
Taxonomy
Theory and practice of classifying organisms
Phylogeny
classifying organism based on evolutionary history
Systematics
the science of studying diversity of organisms and reconstructing phylogeny
2 ways changes in living organisms happen
Genetic exchangeEnvironmental change
Properties of rRNA that help construct phylogenies
its a structural genehighly conservedsufficient variability
T/F: Not all prokaryotes are microbes
FALSE
How many entire domains are microbes?
2 (bacteria and archaea)
Domains are set based on which rRNA gene sequences?
16s and 18s
Characteristics of Microbes
sing cell or clusterstand alone organismscapable of living independent of tissue (growth, energy generation, reproduction)
Traits that set microoganisms
metabolism, reproduction, differentiation, communication, movement, evolution
Common features all microbes share
live in waterfood for higher trophic levelssmall
T/F: Microbes are not the most abundant organisms in the biosphere
FALSE they are bro
T/F: Microbes have a vast physiological diversity (functions)
True
2 physiologies of Macrobes
photosynthesis (chloroplasts)heterotroph (mitochondria)
2 basic metabolic strategies
photosynthesisrespiration
Another name for photosynthesis and formula. Example?
photoautotrophyCO2 + nutrients –> organic matter + O2Phytoplankton
Another name for respiration and formula. Example
Heterotrophyorganic matter + O2 -> CO2 + nutrientsBacterioplankton
What is the base of the food web at Hydrothermal vents?
Sulfur oxidizing bacteriaH2S + 2O2 –> SO4 + 2H
The element most associated with mircobes
nitrogen
Macro nutrients
C,H,O,N,P,S
T/F: Cells are at equilibrium
FALSE, they are non-equilibrium systems
5 Huge impacts of microbes
Majority of earths biomassVarious functionalityBiogeochemical agentsControl human historyIndustry
Advances in microbiology come from
technological develoments
Most early microbe work focused on aspects related to
humans
How old of a science is microbiology?
young science
Who created the first microscope
Leeuwenhoek
What did he call the first observed bacteria
animicules
What is a major technological development in the microbiology world?
optics
2 terms of microscopy?
magnificationresolution
Magnification does what?
increase the viewing size ONLY
Resolution does what
distance between two points, used to gain information
Disproved spontaneous generation
Pasteur and Redi
Got microbes into culture
Pasteur
Worked on vaccination
Pasteur
proved microbes were responsible for degradation.
Pasteur
showed different microbes made different products
Pasteur
Guy who started medical microbiology
Koch
Who developed pure culture technique
Koch
Who was an environmental micobiologist
Winogradsky, Beijernick
What is chemolithotrophy
obtaining energy from the oxidation of inorganic compounds (CO2 as carbon source)
Organisms who use chemolithotrophy are
autotrophs
Who developed the idea of chemolithotrophy
Winograsky
Who developed enrichment cultures
beijernick
whats enrichment culturing
eh?
Who used rRNA genes to construct phylogenies
Woese
Who created PCR (polymerase chain reaction)
Mullis
What polymerase is used in PCR
Taq polymerase
Attributes of Taq Polymerase
thermally stable
Who discovered Taq Polymerase? From where?
Brock and FreezeIsolated from hot springs
Cultivation independent techniques formed by who?
Pace
How to ID an organism via rRNA genes
1) isolate plasmids2) Sequence3) Assess variability4) construct phylogeny
What is genome?
entire genetic make-up (sequence) of an organism
Metagenome is?
study of genomic material from a mixed population
Steps of Random Shotgun Sequencing Approach
1) library construction2 DNA sequencing3) Assemble fragments
Main attributes of prokaryotes (3 things)
cell wallsno organelles (no microtubules)nucleoid and free ribosomes (ciruclar DNA)
Main attributes of eukaryotes (3 things)
organellescytoskeleton-microtubulescan digest material internallypretty much opposite of prokaryotes
What is lateral gene DNA transfer?
the gene of one species incorporated into another
3 mechanisms for prokaryotic gene recombination
TransformationConjugationTransduction
DNA transfer for eukaryotes and prokaryotes
eukaryotes - sexualprokaryotes - asexual
3 main shapes of prokaryotes
Cocci - sphereBacilli - rod Spirochetes - spiral
Describe Bacteria cell membrane. What type of linkage?
phospholipid bilayer (glycerol, fatty acid, membrane protein)Ester Linkage
Describe archaea cell membrane. What type of linkage?
phospholipid mono- or bilayer, NO fatty acidsether linkage
2 types of bacteria
Gram +Gram -
What process is used to separate bacteria into 2 groups? What group retains what color?
Gram stainingGram+ = violetGram- = pink/red
Properties of Gram +
simple thick cell wallless phsiologically diverseexotoxins
Properties of Gream -
more complexlipopolysaccharides (LPS) attachedendotoxins
Bacteria cell wall is made of
peptidoglycan
what is peptidoglycan cell wall made of?
muramic acid
T/F: Archaea also have organisms with peptidoglycan walls
FALSE
How to differentiate bacteria from archaea?
Use a strong base and see reaction (reacts with acid wall in bacteria and bubbles)
Nutritional requirements for anabolism
Energy and carbon
If an organism uses CO2 it is an _____ if it uses organic C it is a ____
autotrophheterotroph
T/F: All organisms generate ATP
True
What is fermentation
substrate level phsophorylationno electron acceptor
What is Oxidative/Electron Transport Level Phosphorylation (ETLP) ( 2 types)
Anerobic - use non O2 elements as e- receptorAerobic - uses O2 as e- acceptor
The ETLP uses what two forces to create ATP
electron transport systemproton motive force
What is photophosphorilation?
light energy generates a proton gradient and proton motive force
What force drives photophosphorilation
proton motive force
What is the proton motive force?
electron carriers are oriented in the membrane that separate protons from e-
Bacteriorhodopsin?
a protein used (by archae) in synthesis of ATP withouth chlorophyll pigment
Primitive photophosphorlyation?
pretty much photosynthesis
What bacteria are phototrophs?
purple and green bacteria
Phototropic properties of purple and green bacteria
anaerobic, photosystem I anoxygenic
What are purple sulfur bacteria? (in terms of trophic level)
photoAUTOtophsbacteria that use CO2 to split H2S and H2 instead of water
What are purple non sulfur bacteria? (in terms of trophic level)
photoHETEROtrophsuse light and organic carbon
What are cyanobacteria?
bacterial that go through photosynthesis(obligate photoautotrophs)(a huge source of O2 on earth, one of the first to largely produce O2)
What attacks bonds of organic matter?
oxygen
Obligate aerobe
Organic C + O2 –> CO2 + water
Microaerophiles
aerobic respiration
Facultative Anaerobe
Respiration with O2Fermentation with out it
Obligate anerobe
Anerobic respirationsulfate oxidation/fermentation
Examples of Chemoautotrophs
Sulfur oxidizers (microbial miners)
conversion formula for sulfur oxidizers and where are they found
H2S + 2O2 -> SO4 + 2Hhydrothermal communities
A majority of prokaryotes are what?
chemoheterotrophs
Examples of chemoheterotrophs
SaprobesParasites
What to saprobes feed on?
dead organic matter
Type of microbes in relation to increasing temperature
psychophiles <0-20mseophiles 20-48thermophiles 42-68hyperthermophile 65-110
3 Main domains
Bacteria, Archaea, Eukarya
How many branches of bacteria are there and what are they?
5ProteobacteriaCyanobacteriaFirmicutesSpirochetesChlamydiasCCFPS
How many branches of Archaea and what are they?
2 branchesCrenarchaeotaEuryarchaeota
Sub-categories of proteobacteria
purple bacteriarhizobiumenteric bacteria
Firmicutes are what type of bacteria and what do they consist of?
Low gram positive (GC) endospores
Spirochetes and Chlamydias are what type of bacteria?
Gram negative
Crenarchaeota properties
hyperthermophilesacidophiles
Euryarchaeota properties
methanogens (produce methane)halophiles
History wise, what are protists?
ancient eukaryotes
Difference between prokaryotes and eukaryotes
organizedd nucleusribosome studded internal membranecytoskeletondigestive vesiclesorganelle formation
What environment are most protists?
aquatic environments
T/F: Protists only have one source of nutrition
FALSE they got nutritional diversity
Protozoas are similar to ____ and algae to ____
animal likeplant like
Locomotion for protists
pseudopodciliaflagella
Method of ingestion of protozoa and its subcategories
Endocytosis-pinocytosis (dissolving)-phagocytosis (englufing whole)
The contractile vacuole of the protists does what?
assist in osmoregulation
T/F: Most protists have similar cell surfaces
FALSE, they are diverse
What are endosymbionts? and do protists fall under the category?
organisms that live within other organismsyes protists are included
Sarcodines are a class of
amoeba (pseudopods)
Examples of Endosymbionts
forminiferaradiolariansacantharia
What is the reproduction process of protists? Is it sexual?
AsexualIt is sexual but NOT a “sexual” process
Genetic recombination of protists is called
conjugation
T/F: protist life cycles don’t have an alternation of generations
False!
2 types of alternation of generations and what do they do?
heteromorphic - haploid and diplod are differentisomorphic - haploid and diploid are the same
Describe Diplomonads and parabasalids
lack mitochondriaobligate parasites
Describe Euglenids
no cell wallheterotrophic and photoautotrophic
What is bacteriorhodopsin
synthesis of ATP without chlorophyll pigment using light
Bacteriorrhodopsin use ____ phosphorliation, What is that?
Primitiveabsorb light and pump protons out for a gradient to make ATP
What groups are closely related to dinoflagellates?
Ciliates and apicomplexans (Plasmodium)
Describe dinoflagellates
2 flagella of different sizesbioluminescentred tidesendosymbiontsauto, mixo, and heterotrophs
What type of eukaryote causes malaria?
Apicomplexans
In the Theory of Endosymbiosis aquisition of what leads to protozoa/animals and algae/plants
proteobacteria and cyanobacteria
What type of protist has two types of nuclei?
Ciliates
Conugation is what type of protists way of genetic recombination?
paramecia
Alveolates include which protists?
Dinoflagellates and apicomplexas
Phytoplankton is what type of protist?
dinoflagellates
Paicomplexans are ___ of animals which use ___ for reproduction
parasitesspores
the defining structures of the apicomplexas is the ____ use to ___
apical complex that is used to burrow into host tissue or cells
T/F: Apicomplexas have a simple life cycle
FALSE, its intricate
Two types of stramenopila
diatoms, brown algae
Properties of diatoms
cartenoids, yellow/brown, silica shells, important marine phytoplankton, asexual/sexual reproduction, harmful algal blooms
Properties of brown algae
photoautotrophsfucoxanthin pigmentmulticellular (seaweed)
Describe Coccolithophorids (haptophytes)
foudn in calcium carbonate plates ) coccolithsauotorophicocean acidification will have major effect
Eukaryote group plantae is the ____ to all plants
precursor
Ancestral trait of plantae
endosymbiosis of cyanobacteria to make chloroplasts
Another name for green algae
chlorophytes
The red algae, and the key pigment that makes it red
rhodophytaphycoerythrin
Do rhodophyta have flagellated stages? Are the multi or unicellular or both? What chemical do they secrete
NOall multicellularcalcium carbonate
Properties of excavates and what groups of protists do they include?
-mostly heterotrophsinclude:-kinetoplastids-diplomonads-euglenids
Properties of Rhizaria
marinemost heterotrophic-ameoboids with complex shell-skeletonsinclude: forminifera and radiolarins
What are the radiolaria and forminifera shell-skeletons made out of?
raidolaria - silicaforminifera - Calcium carbonate
Two groups of unikonts
ameobozoachoanoflagellida
Describe ameobozoa
move by pseudopodsheterotrophic - phagocytosis Ex: plasmodial slime molds
Describe choanoflagellida
closest relative to animals similar to sponges (colonial)
Fugi are ____trophic. And in which domain?
heterotrophic/chemoorganotrophicEkaryotes (unikonts)can be unicelluar or multi
Relationships of fungi to other organisms
saprobicparasiticmutualistic
Fungi have ____ in cell walls
Chitin
What do fungi produce for reproduction?
spores
T/F: Fungi have tolerance to hypertonic environments as well as low and high temperatures
True!
Fungi are good ____ and produce _____ chemical byproducts
degraders and produce secondary chemical byproducts
T/F: Fungi can alternate between uni- and multicellular form and unicellular members are present in all fungal groups
True
How do fungi alternate between uni- and multicellular forms?
alternation of generations
What is the mycelium?
the body of a multicellular fungus
What is mycorrhizae?
associations between vascular plant roots and fungal mycelia
Different characteristics of hyphae
spetate- incomplete cross walls (pores)Coenocytic - no septaHaustroia- push into cells - parasite
Fungi multiply by ____ and ____
reporduction and sporulation
Dikaryote stage is seen in ____ fungi
higher “crown”
Fruiting bodies are called
sporangia
Hyphae are what part of the fungi
the “roots”
Fungi are good ____ and produce _____ chemical byproducts
degraders and produce secondary chemical byproducts
T/F: Fungi can alternate between uni- and multicellular form and unicellular members are present in all fungal groups
True
How do fungi alternate between uni- and multicellular forms?
alternation of generations
What is the mycelium?
the body of a multicellular fungus
What is mycorrhizae?
associations between vascular plant roots and fungal mycelia
Different characteristics of hyphae
spetate- incomplete cross walls (pores)Coenocytic - no septaHaustroia- push into cells - parasite
Fungi are tolerant to ____-tonic environments and high/low ____
hypertonichigh and low temperatures
the prime terrestrial remineralizers
Fungi
T/F: Not all fungi are heterotrophs
False - they all are
Fungi reproduce asexually in _____ conditions while sexual in ____ conditions
asexual - favorablesexual - unfavorable
T/F: Mating for fungi are based one male and female
False- mating TYPES
Instead of a diploid phase (2n) fungi have a _____ phase (n + n)
Dikaryon
The symbiotic relationship between fungi and algae/cyanobactiera
Lichen
The “pioneer” organism
Lichen
Name the main groups of fungi (5)
ChytridsZygomycotaGlomeromycotaAscomycotaBasidiomycota
The type of fungi under glmoeromycota
mycorrihzae
The fungi with flagella, and no dikaryotic stage
Chytrids
Which group of fungi is the most important step to colonization of land?
Glomeromycota : mycorrhizae
The fungi that have rapid spreading growth (mold)
zygomycota
Sac fungi (fruiting bodies), include plant pathogens and have septate hyphaeMake penicillin
Ascomycota
The typical mushroom falls under what class fungi
Basidiomycota
Animals originated from the acquisition of
proteobacteria
Describe Koch’s Postulates (medicinal microbio)
1) suspected pathogen should be present in the infected and absent from the healthy2) the pathogen should be isolated and grown in pure culture3) this culture should cause the disease in the healthy organims4) when reisolated, the pathogen should be identical to the orignal