Chapter 28 & 29 Flashcards
Bacteria
peptidoglycan in cell walls
Archaea
phospholipids in their plasma membranes
Enrichment cultures
- Growing a culture to a large enough size that you can study them
- Uses specific temperatures, substrate, nutrients and lightings
- Focuses on growing a type of bacteria and archaea
- Historically used the most
- Can be used to test theories or isolate types
- Used to test theory that bacteria could live beneath the surface of the earth
- Null prediction was that magnetite would not grow
- Magnetite did grow so one of the bacteria produced it and can live below the earth’s surface (860-2800 m)
Direct sequencing
Used when the bacteria or archaea can’t be grown in cultures
Isolates genes and determines if they are different from know gene databases
Direct sequencing lead to archaea
Use polymerase chain reaction to purify the DNA
Insert genes into plasmids
Grow a culture
Purify genes again
Sequence the genes
This method destroyed our understanding of extermeophiles
Molecular Phylogenies
Placing bacteria or archaea on trees allows scientists to understand the relationships of these small organisms
The trees are still being worked on
RNA
Biological impact
Ancient abundant and diverse
Oldest known fossil 3.5 billion years old bacteria
1.7 billion years prokaryotes ruled the earth
400 species = small intestine
128 species = stomach lining
500 species= mouth (200 unnamed or described)
Abundance
10^12 microbes on your skin and 10^ 14 in you stomach and intestines
10^3 cells make up your body
1 ml of seawater = 10,000-100,000 microbes
10% of the worlds mass of living material=dead sea microbes
Medical importance
Pathogenic bacteria are a fraction of the bacteria that live on your body, but they attack your bodies normal functions
There are several different lineages in the bacteria tree
Koch’s postulates
- Koch determined the link between diseases and bacteria
- Four postulates
- Microbe present in sick people only
- Microbe isolated and grown in a culture
- If the culture is put into a healthy organism they should get sick
- The microbe should be isolated again
Germ Theory
Koch’s postulates-> Germ theory
States that diseases are infectious
sanitation
What makes bacteria pathogenic?
Heritable trait
One pathogenic strain
The microbes then latch onto host cells and secrete toxins
Can cause different symptoms
Diarrhea or other expulsions from the body then leads to the microbes being spread even more if sanitation is poor
Antibiotics
can be used to target pathogenic bacteria using target sites
Amoxicillian
1949’s Penicillin
Since then antibiotic resistant strains
Amoxicillian
with a broad spectrum of bactericidal activity against many Gram-positive and Gram-negative microorganisms
MRSA (Methicillin-resistant Staphylococcus aureus)
vancomycin
Bioremediation
Fertilization to encourage natural bacteria and archaea growth
Seeding to make an area healthier
To gather oil or other pollutants
Example gulf oil spill
Extremophiles
- Has helped make sense of the tree of life
- Unique in the habiatats they live in
- pH less that 1.0
- Depths past 2500 M
- Anoxic environment
- 121 degrees celcius (highest)
- Live in areas that we believe are where life started
- Use extremophiles to model what possible alien organisms look like
- Commercial applications
Morphological diversity (Bacteria only)
Size: .15 micrometers^3 to 200X 10^6 micrometers
Shapes :filaments, chains, spirals
Motility: flagella and gliding (mechanism unknown)
Cell wall composition (bacteria)
Gram positive and negative
Gram positive
plasma membrane, peptidoglycan and a cell wall
penicillin, because it disrupts peptidoglycan
Gram negative
plasma membrane cell wall, phospholipid bilayer and peptidoglycan
erythromycin, poising the bacterial ribosomes
Cell walls
Knowing this allows us to treat the cells differently
Metabolic diversity
Three ways of ATP synthesis
Phototrophs
Chemoorganotrophs
Chemolithotrophs
Phototrophs
photophosploration and light
Chemoorganotrophs
oxidize organic molecules, cellular respiration or fermentation
Chemolithotrophs
oxidize inorganic molecules, cellular respiration
Photophosphorlation
Bacteria and archaea don’t have to use water as an electron receptor
Typically H2S
They can also complete anoxygenic photosynthesis (without or limited in oxygen)
Fermentation
Less efficiant
Typically a second option (not for bacteria and archaea)
Can use molecules other than glucose and can make molecules other than ethanol and lactic acid
Exp: rotting flesh smell is a by product of fermentation called cadaverine and putrescine
Cellular respiration
Requires: organic compounds, oxygen and water
Bacteria and Archaea do not follow these rules
Carbon synthesis
Two ways of getting building blocks
Autotrophs
Heterotrophs
Oxygen
21% of the atmospheric molecules
When the planet was formed there was none
Cyanobacteria: 1st photosynthetic bacteria
Nitrogen Fixation
Typically in cyano bcteria and in bacteria near plants
Nitrogen was a limiting factor
The evolution of the enzymes to fix nitrogen make the nitrogen usable
Nitrogen warning
Using nitrogen as a fertilizer is great until it reaches the water and causes mass cellular death due to blooms
Bacterial Lineages
will focus on six
- Firmicutes
- Spirochetes
- Actinobacteria
- Chlamydiae
- Cyanobacteria
- Proteobacteria
Firmicutes
- Low Guanine and Cytosine
- Gram positives
- Rod or spherical
- Chains or tetrads
- 1100 species
- Variety of ATP formations
- In the human gut
- Anthrax, botulism, tetanus, gangrene
- Insecticide,
- Yogurt and cheese fermentation
- decomposition
Spirochetes
Corkscrew shape and flagella
Outer sheath
Fermentation is the most common
Syphilis, Lyme,
Many live in anaerobic conditions
Actinobacteria
- High guanine and cytosine
- Gram positive
- Rods or filament
- Mycelia: long chains of filaments in soil
- Most heterotrophs some parasitic
- 500 antibiotics from Streptomyces alone
- Tuberculosis and leprosy
- Swiss cheese
- Break down of herbicides, nicotine and caffeine
Chlamydia
- 13 species
- Smallest group
- Spherical
- parasitic
- Called endosymbionts
- Most common cause of blindness in humans
- Urogenital tract infections
- Bird pneumonia
Cyanobacteria
- Dominate surface waters
- 80 species
- Forms colonies
- Photosynthesis
- Produce oxygen
- Bad smelling water
- mycrocystins
- Fix nitrogen
- Responsible for much of the O2 and nitrogen that is used in marine environments
Proteobacteria
- 1200 species
- Five major subgroups
- Alpha, beta, gamma, delta, epsilon
- Large morphological diversity
- No oxygenic photosynthesis
- Biotechnology ( E. coli), and gene transfer
- Cholera, legionaries disease, food poisoning,
Archaea
Three major Phyla
Korarchaeota
We will focus on: Crenarcheota and Euryarchaetoa
Korarchaeota
has never been cultured and is only known from direct sequencing
Crenarchaeota
37 species named
Many shapes
Most similar to original archaea
Sometimes the only life form present in extreme areas
Fermentation and cellular respiration
Euryarchaetoa
- 170 species so far
- High salt and pH habitats
- Methanogens and use 11 different organic compounds as an electronic acceptor
- Produce methane
- Gum disease, produce acid
Eukarya
Nuclear envelope
Large cells with many organelles
Cytoskeleton
Multicellular is common
Asexual reproduction is by mitosis
Many undergo meiosis and reproduce sexually
Protists
- All eukaryotes that are not fungi, land plants, or animals
- Not a monophyletic group
- They are a paraphyletic group meaning they represent some but not all of the descendants of a common ancestor
- No synapomorphy
Human health and welfare
Potatoes famine: 1845, Phytophthora infestans
- 1 million people died, many emigrated
Malaria: Plasmodium
- 30 million people per year in India
- 1 million people annually die
- Mosquito
- The parasite evolves quickly
- Has evolved to be drug resistant and the mosquitoes have evolved to be insecticide resistant
- No current way of controlling it
Algal blooms
- Typically due to dinoflagelletes
- Can cause toxins and discoloration in water
Ecological importance
Plankton are protists
Are a key part of aquatic food chains
Main primary producers in the top part of marine environments
Could fix global warming
Protists are the main way that carbon is taken from the atmosphere and placed into the ocean and finally the ocean floor
Iron fertilizations
Microscopy
- Traditionally used
- Organized protists according to overall shape, and organelles
- Exp: flagellum differ according to protists
- Synapomorphies: typically the supporting structures or feeding and movement structures
- Using morphologies 7 major groups
Direct Sequencing
- Same as with bacteria and archaea
- Isolating, purifying, growing, purifying and studying a specific set of genes
- 2001 first direct sequencing of eukaryotes
- Using this we proved that protists can be smaller than .5 micrometers
Morphological Innovations
Nuclear envelope
Mitochondria
Support and protection
Multicellularity
Nuclear Envelope
Proof
- In folding is seen in some current bacteria
- Nuclear Envelope and ER are continuous
Separated RNA and DNA were transcription and translation
Different Nuclei
Ciliates: diploid micronucleus that only reproduces and macronucleus that transcribes
Diplomanads: have two Nuclei that are identical, interaction unknown
Foraminifera, red algae, plasmodial slime molds: can contain multiple nuclei in calls
Dinoflagellates: no histones, chromosomes attach to the nuclear envelope
Endosymbiosis theory
the mitochondria originated separately from the bacterial cell and then was taken up by the cells perhaps for food
Natural selection
Some protists and bacteria have it today
Three alpha proteobacteria can be found in only protists
Mitochondria
- are the same size as alpha proteobacteria
- replicate through fission
- Have their own ribosomes
- Manufacture their own proteins
- Double membranes
- Own genes
- The genes are more closely related to bacteria than eukaryotes
why would a mitochondria make the survival of bacteria increase?
Host gave mitochondria protection
Mitochondria produced ATP
Different mitochondria
Diplomonads and parasalids: vestigial trait or lost
Euglenida and related species: cristae in the mitochondria are disc shaped
Opisthokonta : cristae are flat
Opisthokonta
cristae are flat
Structures for support and Protection
can have cell walls, support in membrane or shells
Most support structures are synapomorphies
Support and Protection
Diatoms: SiO2 box and lid structure
Dinoflagelletes: cellulose plates
Forminifera: CaCO3 shell
Forminifera: tiny pebbles
Parasiblids: internal support rod
Euglinids: Protien strips and microtubles on the membrane
Alveolates: alveoli sacs under membrane
Multicellularity
Not all cells express the same genes
Some bacteria form fruiting bodies
Most multicellular species are eukaryotic
Arose independently in multiple linages
When the same thing evolves separately it is called…
Food
Ingestive
Absorption
Photosynthesis
Ingestive Feeding
No cell wall -> feeding by engulfing, requires hunting
Psuedopodia
Yes cell wall-> latches to a place and filter feeds with cilia
Absorptive feeding
Nutrients are absorbed through the plasma membrane
Typically decomposers or parasites
Photosynthesis
How did the chloroplast occur…?
Secondary endosymbiosis
Chloroplasts are similar to bacteria like mitochondria
Four membranes
Many cyanobacteria in protists today
Chloroplasts have similar genes, membranes and organelles as cyanobacteria
Secondary versus primary
More than two membranes within protists
Only two membranes in plants
Photosynthesis lead to new species
pigments
Movement
Amoeboid motion: uses pseudopodia
Movement
Of cilia and flagella
Reproduction
Sexual reproduction evolved in protists
Typically they reproduce asexually but sometimes sexual reproduction occurs
Sexual reproduction is typically at a specific time or when crowding/lack of food dictates it
Why would a stressful environment cause sexual reproduction?
Lifecycles
Haploid dominated: normal chromosome number
Diploid dominated: double the chromosome number
Alternation of generations: gametophytes and sporophytes switch
Diploid dominated
double the chromosome number
Haploid dominated
normal chromosome number
Alternation of generations
gametophytes and sporophytes switch
Amoeboza-Myxogastrida
- Ameoboza- no cell wall, engulfing, ameboid motion, psuepodia, freshwater,
- Myxogastrida- plasmodial slime molds
- Supercell: many nuclei one cell
- Feed on dead cells
- Can form spores
Ameoboza-
no cell wall, engulfing, ameboid motion, psuepodia, freshwater
Myxogastrida
plasmodial slime molds
Supercell
many nuclei one cell
Excavata
- Feeding groove
- Unicellular
- No mitochondria, but have the genetic material from mitochondria
- Possible vestigial mitochondria
Excavata Parabasalida
- No cell wall or mitochondria
- Flagella connected to microtubules
- Non free living
- Termites and parabasalida
- Engulfing
*
Excavata Diplomonadida
Typically oxygen limited environments
Two nuclei
Some parasitic: humans, beavers
Eight flagella
No cell wall
Excavata Euglenida
410 million years old fossils
No cell wall, inner proteins
1/3 have chloroplasts most eat via engulfing (endosymbiosis)
Planktonic food chains
Plantae
Includes glaucophyte algae, red algae, green algae,
Land plants are not protists
All have engulfed a photosynthetic cyanobacteria
Plantae Rhodophyta
6000 species
Red because of the pigment in the chloroplasts
Why should red make living in water easier?
Alteration of generations is common
No flagella
Food and reef building
Rhizaria
No cell walls
Single celled
Shell like coverings
11 subgroups
Formanifera
Rhizaria Foraminifera
Shells that specify species
Floaters and engulfers
Numerous in marine habitats
The shells form fossils layers of sediment that eventually become limestone, chalk, or marble.
Foram species help in rock dating studies
Why would these fossils be helpful?
Alveolata
Small sacs called: Alveoli
Unicellular
Focus on: Ciliata, dinoflagellates, apicomplexa
Alveolata Ciliata
12,000 species
Two nuclei
Move with cilia
Conjugation or asexual
Digestive tracts of farm animals and marine plankton
Alveolata Dinoflagellata
Ocean dwelling
Some have bioluminescence
No histones and chromosomes are attached to the envelope at all times
Most planktonic
Two flagella: one around the cell in a groove and one coming out of the cell
Fix carbon, algal blooms, primary producers
Alveolata Apicomplexa
5000 species all parasitic
Apical complex: allows penetration of the membrane of the host
No cilia or flagella
Absorb nutriants from host
Malaria, infected chickens, pest control
Stramenopila (Heterokonata)
All have flagella with hollow hairs
Most unicellular
Contains the tallest marine organisms the kelp
Focus on: Oomycota, Diatoms, Phaeophyta
Stramenopila Oomycota
Thought to be fungi
- DNA, chitin and primarily aquatic habitat
- Convergent evolution
Absorb nutrients from dead hosts
Matures individuals are sessile
Unicellular, but form hyphae
Diploid
Caused potatoes famine
Can cause infections in Oaks
Stramenopila Diatoms
Form chains
Silicon rich, glassy like walls
Floaters, photosynthetic
Most important producer of carbon in water
Found in all aquatic habitats
Stramenopila Phaeophyta
Brown algae
Mostly marine
Photosynthetic and sessile
Alteration of generations
Algin-> cosmetics and paint
Used as a habitat for many species
