exam 3 Flashcards
(151 cards)
1
Q
Origin of earth
A
origin of the universe:
-big band was 10-18 billion years ago
-carbon and higher elements formed first stars- main hydrogen and helium
-earth is about 4.5 billion years old
crust of eath became stable 3/9 billion years ago
2
Q
What constitutes life?
A
first evidence of life is about 3.8 bya
ability to ingest nutrients, secrete waste products, grow and reproduce
-obtain ebergy to drive chemical reactions
-generally capable of reproduction
-generally can evolve
3
Q
debates over the origin of life
A
1) temp: mesophilic or thermophilic
many uncatalyzed but biologically relevant reactions could have taken place much faster at higher temps
enzymes when they arose, provided optimal rate acceleration at lower temps
2) carbon metabolism: autotrophs vs heterotroph- availability of substrates to support heterotrophy is unlikely
3) complex cells early or late: trees and energetics suggest start with cells of low comoplexity
- early evolution was anoxic- oxygen is microbial invention
4
Q
monera
A
category for organisms poorly understood
kingdoms in the traditional 5 kingdoms: monera, animalia, protista, plantae, fungi
-very subjective, mostly based on morphological complexity
5
Q
prokaryotes
A
pro= before karyon= nucleus
possess basic life properties
- metabolic processes
- reproduction- using DNA, RNA, ribosomes
characterized by what they lack
- no nucleus
- no membrane bound organelles
6
Q
eukaryotes vs prokaryotes
A
Eukaryotes:
- organelles present- nucleus, mitochondria, chloroplasts
- diploid
- many are multicellular
- mitosis, centrioles present in many, mitotic spindle or microtubules
prokaryotes:
- no membrane-bound organelles
- haploid
- never truely multicellular
- cell division, no mitosis, binary fission or budding
7
Q
how to classify prokaryotes?
A
bacteria lack both morphological complexity and a fossil record
- SSU rRNA gene used for defining phylogeny
- rRNA is ubiquitous
- sufficiently conserved to relate all life
- multiple variable regions, good for discrimination
8
Q
archaea
A
comparisons of rRNA sequences allowed scientists to establish relationships among organisms
revealed a 3 domain tree
9
Q
reason for not using the word prokaryote
A
implies incorrect origin of eukaryotes
prokaryotes represent a paraphyletic group- where not all orgs come from last common ancestor
10
Q
endosymbiotic theory and evidence
A
postulates that mitochondria, chloroplasts and maybe some other subcellular organelles, originated when a bacterium established stable residence within the cytoplsm of a primitive bacterium established stables residence in the cytoplasm of a eukaryote and provided the cell with energy in exchange for a protective environment/nutrients
evidence: mitochondria and chloroplasts are about the same size of an average bacterium
-both organelles replicate by fission like bacteris. the duplication of both organelles takes place independently of nuclear division
both organelles have their own ribosomes and manufacture their own proteins. these ribosomes resemble bacterial ribosomes
cyanobacteria have a similar structure to chloroplasts and contain the same chlorophyls
mitochondria and chloroplasts have their own genome- these are circular molecules resembling bacterial chromosomes
-sequence the mitochondrion and chloroplasts genomes demonstrate that chloroplasts DNA is close to cyanobacteria and mitochondrial DNA close to typhus bacteria DNA- we see them on tree of life where we would expect if they had evolved from proteobacteria and cyanobacteria
11
Q
archaea- size and shape
A
0.1 um to 15 um in diameter
but usually very small
can form longer aggregates or filaments
they have a variety of cell walls but they don’t contian peptidoglycan, protein S-layers and preudomurein
various shapes- spherical, rod, spiral or lobed
12
Q
archaea DNA
A
single circular chromosome can have plasmids currently>1000 genomes finished or in production genome size range 0.5-5.5 reproduce asexually not known to produce spores most as yet uncultured
13
Q
archaea cell membrane
A
L-glycerol instead of D-glycerol
side chains bound by ether
side chains in the phospholipid bilayer is branched isoprene
archaea have cytoplsmic membrane, no outer membrane
14
Q
archaea similarities with bacteria
A
like bacteria:
- no nucleus
- no membrane bound organelles
- DNA in a signle loop
- genes grouped in operons
- genes in metabolism are similar
- size
15
Q
archaea similarities with Eurakyotes
A
- similar RNA polymerase
- methionine initiates protein synthesis (bacteria use formyl-methionine)
- histones (spools around which DNA winds)
16
Q
Archaea difference from Bacteria
A
bacteria have:
- simple RNA polymerase
- formylmethionine initiates protein synthesis
- control transcription initiation using sigma factors
17
Q
why study archaea?
A
- fuel production, food, antibiotics
- to understand their niche since it is so ddiverse
- archaea live in extreme environments so understanding their enzymes have many uses
they provide unique opportunities to gain insight into a number of fundamental problems in biology:
- such as extremophiles= biotech applications
- are imp components of biogeochemical cycles on earth and dominate special ecosystems of interes= methanogens
- offer insight into early evolution of life including origin of eukaryotes
18
Q
Methanogens
A
- methanogenesis only occurs in archaea
- polyphyletic- derived from more than one common evolutionary ancestor
- require complete anaerobiosis to frow
- major substrates and reactions include: H2 and CO2, acetic acid, methanol, methylamine
methanogens grow in: anaerobic soil of wetlands, rice paddies, landfills, rumen and GI tract of mammals, marine benthic sediments
hydrogen consuming methanogens: ecologically important in anaerobic environments: remove excess hydrogen produced by other pseices during fermentation (interspecies H2 transfer)
19
Q
Halophiles
A
extremophiles that can occur in environments with very high salt concentrations
- salt loving
-polyphyletic, they also occur outside of Archaea
some halophiles are capable of light-driven synthesis of ATP
-bacteriorhodopsin act as H+ pump- capture light energy and use it to move H+ acriss membrane= gradient made to make ATP- not photosynthesis since no synthesis
-survive by increasing osmolarity of the cell
>compatible solutes (organic compounds in cytoplasm)
>selective influence of K (salt-in strategy)
20
Q
Halophile salt strategy
A
“salt-in” strategy
- to use this strategy all enzymes and structural cell components must be adapted to high salt concentrations to ensure proper cell function
- based on optimal saline environments, halophilic organisms can be grouped into 3 categories: extreme halophiles, moderate halophiles, slightly halophilic or halotolerant organisms
- some extreme halophiles can live in solutions of 25% salt; seawater= 2% salt
21
Q
extremophiles
A
can occur in environments with high temps between 45-122 degrees C
enzymes function at high temps
membranes stable at high temps
include both obligate and facultative
22
Q
adaptations to life at high temps
A
stability of monomers
- protective effect of high concentrations of cytoplasmic solutes
- use more heat stable molecules ex: use of non-heme iron proteins ex: ferredoxins
- no significant changes in amino acid composition
protein folding and thermostability
- highly hydrophobic cores
- increased ionic interactions on protein surface
chaperonins -class of proteins that refold partially denatured proteins
DNA stability
- high intracellular levels of polyamines that stabilize DNA and RNA ex: putrescine, spermidine
- DNA binding proteins (archaeal histones) compact
23
Q
4 distinct phyla/groups of Archaes
A
based on small subunit ribosomal RNA sequences (less than 80% identity among them) that are well accepted among scientists Euryarchaeota Crenarchaeota Karoarchaeota Nanoarcheota
24
Q
Euryarchaeota
A
largest phylum of archaea
euryarchaeota means “broad-ranging archaea: dominated by methanogens
-have diverse habitats and physiologies, including methanogens and halophiles
-some extremely thermophilic aerobes and anaerobes
25
Crenarchaeota
-another phyum of archaea
means "scalloped archaea"
-often irregular in shape
all synthesize distinctive tetraether lipid called crenarchaeol
the number of cyclopentane rings increase with growth in temperature (more densely packed with more thermostable membranes)
occur in diverse habitats
abundant in marine systems
most lack histones (which are good for high temps)
include thermophiles- can grow up to 113 degrees C
stain gram negative
include sulfolobales: oxidize sulfur to sulfuric acid, found in hot springs
ex: sulfolobus solfataricus- thermophile that grows at 80 degrees C and pH of 3
26
Karoarchaeota
phylum of archaea
only known from sequence
and only known for extremely hot habitats
27
Nanoarchaeota
phylum of archaea
small
parasite
early-branching member of Archaea, lacks genes for all core molecular processes and thus depends on its host (Crenoarchaeote) for most of its cellular needs
28
```
cutoffs:
phylum/division
order
family
genus
species
```
these are cutoff established to group organisms togehter
Division/phylum: 80% small ribosomal subunit identity shared (still lots of diversity in phylum)
order: 90%
family: 92%
genus: 95%
species: 98%
29
Phylum cyanobacteria and photosynthesis/morphology/physiology
kyano= blue
commonly called blue-green algae
obtain energy throught photosynthesis, use oxygenic phototosynthesis- use water as electron donor for CO2 reduction
use Chlorophyll a
use phyycobillins: accessory photopigments,
are important in marine systems
-they are imp primary producers- 25% of global C fixation
-imp in N cycle- fix N2
morphologically diverse, but physiologically similar, and grow fast
have 6 orders
30
phycobillins
accessory photopigements in cyanobacteria
31
Phylum cyanobacteria, genus prochlorococcus
Phylum cyanobacteria, genus prochlorococcus
are extremely abundant and imp photosynthetic species in oceans
very small with an unusual pigmentation- chlorophyll B primariy absorbs blue lights
prochlorococcus occupies 2 distinct niches, leading to the nomeclature of the low light (LL) and high light (HL) gorups which vary in pigment
High light adapted strains inhabit depthes between 25-100m while low light adapted strains inhabit between 80-200m
these 2 strains differ in the amount of chorophyll a and B
LL strains have more chlorophyll b to a ratio which aids in the ability to abs blue light- blue light is next to UV light, so is higher in energy and penetrates deeper in the water column >200m
-their 16S are identical but photosynthesis pigments are different
32
cyanobacteria and earth's atmosphere
are likely responsible for Earth's atmosphere becoming rich in O2
-stromatolite- rock like deposition of carbonates and trapped sediments; formed by cyanobacteria and diatoms
-age is about 3/5 bya
growth-mineral depositions-growth-mineral deposition layers
33
cyanobacteria and N
filamentous often
some have heterocysts that permanently fix N, and have special mechanism to protect nitrogenase (Oxygen sensitive) from O2
some have resistant cells- akinetes: resistant to both cold and dessication
34
cyanobacteria: inhabituation, mutualisms, compounds produced
also occur on land- are very widely distributed
are in some lichens- mutualism between a fungus and photobiont
symbionts with some plants- "grene fertilizer" in rice fields in Asia
endosymbionts- chloroplasts in eukaryotes
many produce neurotoxins, hepatoxins
skin irritants, other toxins
surface water supplies- hepatotoxins (more widespread)/neurotoxins
35
biofuels and cyanobacteria- what makes organisms in this phylum appealing?
```
sun for energy/CO2 for C
no sugars needed
can grow in H2O- no competition for cropland
can make NH3 and AAs from N2 gas
grow fast
```
36
phylum firmicutes
```
formus= strong
cutis= skin
```
most have gram positive cell wall
but few also have porous-outer-membrane so stain gram-neg
commonly called low G+C gram positive bacteria
many form endospores= resistant to harsh conditions
>275 genera
-divided into 4 classes: Bacilli, Clostridia, Erysipelotrichia, mollicutes
-and has 11 further orders
-lateral gene transfer may be an issue, but there is support for these orders
37
4 firmicute classes
Bacilli
Clostridia
Erysipelotrichia
Mollicutes
38
Firmicute metabolism
metabolism:
heterotrophic lifestyle
usually anaerobic except Bacilli which are generally obligate aerobes
anaerobic metabolilsm is usually substrate level phosphorylation rather than anaerobic respiration
often lack complete electron transport chain
have a wide range of energy and carbon sources; wide range of fermentation products
39
firmicute morphology and habitat
morphology:
rods or cocci
can form chains (Bacillus and streptococcus)
endospores are a common unique feature of this group
Habitat:
soil, skin, mucous membranes, gut
40
Clostridia
```
class of firmicutes: clostridia
order: clostridiales
```
anaerobic
produce endospores
important genus:
- clostridium botulimus- causes Botulism
- Clostridium tetani- causes tetanus
- clostridium thermocellum- used in bioenery: cellulytic and ethanologenic- can break down cellulose and make ethanol
41
Mollicutes
```
class of firmicutes= mollicutes
order: mycoplasmatales
```
important genus is mycoplasma
lack cell walls= stain Gram neg
typically live inside cell of host= parasitic
the phylogeny of mollicutes is interesting: because of the degenration of the genome= reduction in genome size and the overall rate of evolution is uncharacteristically high
the evolution of mollilcutes into strict parasites has made much of their metabolic machinery obsolete (no longer used)
ex: mycoplasma genitalium has only 470 open reading frames
42
Bacilli
```
class of firmicutes
order: bacillales
```
are rod shaped
important genera: Bacillus, listeria, staphylococcus
imp:
- Bacillus anthracis- causes anthrax
- bacillus subtilis- used in science as model species
- Bacillus thuringiensis- is an inset pathogen
43
Staphylococcus aureus
is in the order Bacillales under class (of firmicutes Bacilli)
causes 100s of deaths in US
MRSA- methicillin resistant
-resistant to beta lactam antibiotics
-penicillind and cephalosporins
-resistance cand evelop by horizontal gene transfer of resistance determinants encoded by mobile genetic elements or by mutations in chromosomal genes
-horizontally acquired resistance can occir by:
1. enzymatic drug modification or inactivation
2. enzymatic modification of drug binding site
3. drug efflux
4. bypass mechanisms involving acquisitions of a novel drug-resistant target
- aquisition of resistance by mutation can result from:
1. alteration of drug target that prevents inhibitor from binding
2. derepression of chromosomally encoded multidrug resistance efflux pumps
3. multiple stepwise mutations that alter the structure and composition of the cell wall and/or membrane to reduce drug access to its target
44
Antibiotic resistance by horizontal gene transfer
- horizontally acquired resistance can occir by:
1. enzymatic drug modification or inactivation
2. enzymatic modification of drug binding site
3. drug efflux
4. bypass mechanisms involving acquisitions of a novel drug-resistant target
45
antibiotic resistance by mutation
- aquisition of resistance by mutation can result from:
1. alteration of drug target that prevents inhibitor from binding
2. derepression of chromosomally encoded multidrug resistance efflux pumps
3. multiple stepwise mutations that alter the structure and composition of the cell wall and/or membrane to reduce drug access to its target
46
Lactobacillales
order lactobacillales from class Bacilli (of firmicutes)
lactic acid bactera: convert lactose and other sugars into lactic acid
```
important genera:
lactobacillus
enterococcus
streptococcus: spherical
S. pneumoniae: bacterial pneumonia and meningitis
Lactobacillus spp. : foods
```
47
S. pneumoniae
genera of lactobacillales (order) from Bacilli (class) from Firmicutes (phylum)
cause bacterial pneumonia and meningitis
48
phylum bacteroidetes
large phylum with >140 genera
sacrharolytic- degrade complex polysaccharidea
are rod shaped cells
occur in soild, sea water, symbionts of animals and sediments
have 3 classes: Bacteroidia, Flavobacteria and Sphingobacteria
49
Bacteroidales
Bacteroidales are an order of Bacteroidetes (phylum):
most abundant gram-neg organism in the human gut
important genera is Bacteroides, Prevotella, and Porphyromonas
-porphyromonas gingivitis- causes inflammation of the gingiva
bacteroides and prevotella- commonly found in GI tract of animals. Privotella sp contain bacterial genes for cellulose and xylan hydrolysis (higher fiber diet=privotella)
50
Flavobacteriales
order= flavobacteriales
from phylum= Bacteroidetes
are areobic rods
causes disease in fish
51
Sphingobacteriales
order= sphingobacteriales
phylum= Bacteroidetes
little known
they synthesize spingolipids and incorporate then into their membranes otherwise found mostly in eukaryotes membranes; nervous system and incorporate them into their membranes= important for our immune systems
52
Actinobacteria
phylum
also called actinomyces
gram positive bacteria
-have high G+C content
form filaments
pharmaceutically very important- antibiotics and anticancer drugs: among bioactive compounds gotten from microbes, 45% are produced by actinomycetes, 38% from fungi and 17% from other bacteria
actinobacteira are very rich in secondary metabolites (reactions performed by organisms to kill and compete with other orgs like anitbiotics, or others to obtain nutrients)
very diverse
abundant in soils- cause soil to smell "earthy"- compound that does this is called Geosmin
help in decomposition of organic matter
are symbionts of insects
ecologically very imp but for the most part poorly studied other than from pharmaceutical perspective
ex: class- streptomyces- important antibiotics
mycobacterium tuberculosis- causes tuberculosis
genus bifidobacterium- prevalent in the guts of young kids (and adults)
important for probiotics- used in food industry
genus frankia- plant mutualists- fix N2
53
frankia
genus frankia of phylum Actinobacteria- plant mutualists- fix N2
54
bifidobacterium
genus bifidobacterium of phylum actonobacteria phylum- prevalent in the guts of young kids (and adults)
important for probiotics- used in food industry
55
streptomyces
```
class= streptomyces
phylum= actinobacteria
```
imp for antibiotics
56
Mycobacterium tuberculosis
is an actinobacteria
| causes tuberculosis
57
Spirochaetes
phyum of bacteria
are gram-negative
widespread in aquatic environments and animals
some cause diseases
highly coiled cells- defining feature
5-200um long, 0.1-0.5um wide (so pretty big- typically microbes arre about 1um)
58
spirochetes flagells
have internal polar flagella
-it is between the cell membran e and outer membrane- called an endoflagella
-number of flagella varies among species
runs lengthwise
-used for motility
-allows for enhanced motility in viscious substances
59
important spirochete generas
Treponema
Borrelia
Leptospira
60
Treponema
genus of spirochetes phylum
causes syphilis
infects only humans; enters thorough skin or mucous membrane where primary manifestations are seen
-is sexually transmitted
-is found in the microaerophile- thrives in low O2 levels
-first antibiotic used for this
Treponema are also found in human oral cavity- between teeth and gums, some can ferment cysteine to produced H2S
also associate with termites (in hindgut) and ruminants
61
termite, Spirochetes and protist symbiosis
Spirochetes resemble eukaryotic flagella. How would you test whether they are related structures?
termites have a symbiotic relationship with protists and bacteria
some of the protists have a sybiotic relationship with spirochetes which are also present in termites, attached at one end
movement of this "collective" is driven by movement of the spirochetes, but directed by the protists
to test relatedness: can look for molecular evidence- are the genes related ? (and they are not)
62
Borrelia
genus of the phylum spirochaetes
Borrelia bugdorferi
-causes lymes diseases (zoonotic vector borne disease transmitted by ticks)
most common disease transmitted by ticks in US
one of the few pathogenic bacteria that can survive without iron, having replaced all its iron-sulfur cluster enzymes with enzymes that use manganese
-since we use iron for electron transport chain for redox reactions, so this organisms is resistant to host attempts to kill it
has linear and small chromosomes- 900 genes
63
Leptospira
- genus of Spirochaetes (phylum)
- some species can cause leptospirosis which can lead to kidney damage, meningitis, liver failure, respiratory distress and even death
- obligate aerobes- use fatty acids as a source of C and energy
- commonly found in aquatic environments
- spread through the urine of infected animals
- wild and domestic animals carry the bacterium
- the bacteria can enter the body through the skin or mucous membranes. drinking contaminated water can also cause infection
- person to person transmission is rare
64
Proteobacteria
Phylum
thousands of described speices, well studied
gram neg
great metabolic diversity: there is no phenotypic trait that unites all proteobacteria; most are heterotrophs but also includes purple bacteria which are photosynthetic
most are facultative or obligate anaerobes
65
proteobacteria classes
grouped into 5 classes:
```
alphaproteobacteria
Betaproteobacteria
gammaproteobacteria
deltaproteobacteria
epsilonproteobacteria
```
there is molecular phylogenetic support for the groups
but the phylum proteobacteria is not monophyletic
66
alphaproteobacteria
-class of proteobacteria (phylum)
-important orders:
Rhizobiales
Ricketsiales
Rhodobacterales
- include phototrophs (anoxygenic photosynthesis- different from cyanobacteria who do oxygenic photosynthesis)
- metabolically versatile
67
Ricketsiales
Phylum: proteobacteria
class: alphaproteobacteria
order: Richetsiales
a genus of ricketsiales is Wolbachia
-these are endosymbionts of insects
-one of the most common parasitic microbes- can modify sexual behavior of insects
-its interactions with its hosts are complex, and in some cases have evolved to be mutualistic rather than parasitic
-Wolbachia is almost exclusively transmitted from mother to offspring via infected eggs
-modify host reproduction
-some host species can't reproduce without Wolbachia infection
-linked to viral resistance in drosphila melanogaster and mosquito species (new approaches for getting rid of the insects involves killing the endosymbiont)
-different Wolbachia species are being used to prevent mosquito transmitted diseases
wolbachia and other genera studied to understand evolution of genomes and symbiosis.
68
Rhodobacterales
order of Alphaproteobacteria which are a class of the phylum proteobacteria
- purple bacteria
- ex: rhodobacter
69
Rhizobiales
order of Alphaproteobacteria which are a class of the phylum Proteobacteria
- sumbionts of plants
- rhizobium
- nithrogen fixing mutualists
70
Betaproteobacteria
- class of the phylum of Proteobacteira
- mostly aerobic or facultative anaerobic
- they can degrade a wide variety of organic compounds
- some genera chemolithotropic ex: ammonia-oxidizing genus Nitrosomonas
- convert ammonia (NH3) to nitrite (NO2-). very important in N cycle for plants
0some human pathogens- ex: gonorrhoea- Neisseria gonorrhoeae, Burkholderia cepacia- an important pathogen of pulmonary infections in people with cystic fibrosis
- includes some important N2 fixing species
- Burkholderiales is common**
71
Burkholderiales
- is a betaproteobacteria
- is common
- Burkholderia cepacia is an important pathogen of pulmonary infections in people with cystic fibrosis
72
deltaproteobacteria
include:
- Myxobacteria
- sulfate and sulfur-reducing bacteria
- geobacter
73
Myxobacteria
- are deltaproteobacteria
- common in soil
- multicellular, social behavior- they communicate with each other and coordinate their movements through a cell-contact-dependent signal
- in the presence of nutrients, swarms of myxobacteira feed by sharing/cooperatively and can prey on other bacteria
- when the food supply runs low, they initiate a complex developmental program that culminates in the production of a fruiting body- social behavior as these fruiting bodies are multicellular
- fruiting body: cells in the head that differentiate into mycospores which are resistant to dessication, UV radiation and heat
- myxobacteria move by gliding
74
sulfate and sulfur reducing bacteria
are a type of deltaproteobacteria
genera: desulfovibrios, desulfobacter
widespread in aquatic and terrestrial environments that are anoxic
use oxidized sulfur compounds as terminal acceptors
H2S is an end product of their metabolism
cause iron corrosion
are found in the human gut (linked with inflammatory disease)
75
Geobacter
- are a genus of Deltaproteobacteria which is a class of phylum Proteobacteria
- consume oil-based pollutants and radioactive material with carbon dioxide as end product
- have already been used in environmental clean-up for underground petroleum spills
- metabolize insoluable substrates by creating pilli ("nanowire") between itself and the material
76
Epsilonproteobacteria
- class of phylum Proteobacteria
- common symbionts, occuring in GI tract of animals
- sequences found in hydrothermal vents
- some are pathogens: campylobacter, helicobacter**
77
Helicobacter pylori
- is a type of epsilonproteobacteria
- causes stomach ulcers but can also be beneficial in some places
- infections occur worldwide
- prevalence varies greatly among countries and population groupd
- 20-50% prevalence in middle age adults in industrialized countries
- >80% prevalence in middle age adults in developing countries
- highly adapted organism that lives only in gastric mucosa
- gastric antrum is most common site
- present in the mucus that overlies the mucosa
- can also be beneficial and help train the immune system against inflammatory disease
- only a small subset of infections develop into gastric cancer due to the range of alternate factors contributing to severity of infection.
78
Gammaproteobacteria
-class of phylum proteobacteria
-very important group- scientifically and pathogens
-disproportionaltely a large number of them are pathogens
important orders: Enterobacteriales, Legionellales, Pseudomonadales, Vibrionales
79
Enterobacteriales
- order of the class gammaproteobacteria of phylum proteobacteria
- rod shaped
- facultative anaerobes
- most have flagella
- many members occur in the guts of animals
- some important pathogens of animals and plants
- includes Salmonella and Yersinia (plague)
80
Vibrionales
- order of the class gammaproteobacteria of phylum proteobacteria
- have flagella
- facultative anaerobes
- found in fresh water and salt water
- most bioluminescent bacteria are in this order
- there are fish and squid that have specialized organs that provide bioluminescnet bacteria with both a safe place to live and a source of food. in return the animals can use the light that is produced by the microbes either as a means of camouflage, as an aid in hunting, or even as a way of attracting mates
-vibrio cholera- causes cholera
81
Pseudomonadales
- order of the class gammaproteobacteria of phylum proteobacteria
- diverse- greater than 150 species
- gram-neg bacilli
- have polar flagella*
- genus pseudomonas
- plant pathogens and mutualists of plants
- lung infections in CF patients
82
Chlamydia
- Phylum of Bacteria
- infect Eukaryotic cells
- obligate intracellular pathogens
- poor metabolic capactiy
- difficult to study
- very small*
- genus chlamydia
- cause STD chlamydia- can cause pneumonia
- chlamydia is most common sexually transmitted disease of bacterial origin
- easily cured but if left untreated can make it difficult for women to get pregnant.
83
infection cycle of Chlamydia
EB: Elementary body- rigid cell wall, nongrowing, infectious
RB: Reticulate body- fragile cell wall, mutiplying form, noninfectious
the EB is found in secretions, attaches to and enters cells such as an endocervical or urethral cells
within 8 hours the EB transforms into a RB ehich begins mutliplying in isolated area called an inclusion
within 24 hours, some RBs reorganize into EBs and as the cell wall bursts the EBs are released to infect adjacent cells or to be transmitted to and infect another person
84
Acidobacteria
phylum of bacteria
- biology poorly understood
- few isolates
- some phototrophs
- acidophillic
- abundant in soil
- monphyletic
- have been identified as a contaminant of DNA extraction kit reagents, which may lead to their erroneous appearane in microbiota or metagenomic datasets
85
Protists
- Eukaryotes
- ,eams "very first"
- genome analysis shows that some protists are derived from complex ancestors that aren't primitive at all
- it is an artifical group, single-celled eukaryotic orgs have been grouped together into this kingdom for convenience
- the "single-kingdom" classification of the Protista is not representative of their evolutionary relationships.
86
Generalizations about protists
they are eykaryotes that aren't animals, plants or fungi
are called the junk drawer of the kingdoms. they all have very little in common with each other, and very little is known about them.
can be:
-single-celled or multicellular
-nucleated microbes
-microscopic or very larger
-reproduce sexually or asexually
-O2 and waste production via diffusion and osmosis
-complex life cycles
-not a monophyletic group*- don't share a common ancestor
generally divided into 3 groups based on how they get their food:
-animal like: consume other organisms- heterotrophs, single-celled, not animals because animals are multicellular and animal-like protists are single-celled
-plant like: make their own food through photosynthesis- autotrophs
are single celled, colonial (live togehter in colonies) or mutlicellular (kelp)
not plants because they have no roots, stems or leaves
-Fungus-like: decompose other organisms, heterotrophs, can move some point in their life cycle whereas fungi cannot.
87
animal like protists
-animal like: consume other organisms- heterotrophs, single-celled, not animals because animals are multicellular and animal-like protists are single-celled
88
plant like protists
-plant like: make their own food through photosynthesis- autotrophs
are single celled, colonial (live togehter in colonies) or mutlicellular (kelp)
not plants because they have no roots, stems or leaves
89
fungus-like protists
-Fungus-like: decompose other organisms, heterotrophs, can move some point in their life cycle whereas fungi cannot.
90
Protist classification system
will likely change
some protists not closely related at all
molecular evidence supports re-classification of these organisms
-current tree is likely incorrect
91
why is the phylogeny of many protists poorly resolved?
because secondary and tertiary endosymbioses occured, and there was a huge lateral gene transfer event, fusion of nuclei occured which resulted in a huge transition in small amount of time
-both the mitochondrial and the plastid events were primary endosymbioses in whuch a bacterium was engulfed by another organism
secondary endosymbioses occurs when an organism that is already the product of primary endosymbioses gets engulfed by another organism
-the result is that the plastid is surrounded by 3 or 4 membranes instead of 2
-also, the genes from the primary endosymbiont leaves its nucleus and migrate to the nucleus of the engulfing organism
92
How would you establish ohylogenetic relationships among protists?
rRNA doesn't work to try to find conserved proteins and try to make smaller trees
93
Rhodophyta
-superphyla of protist
-red algae
-4000 species
-mostly multicellular
ancient, >2 billion years
-occurs worldwide
-especially diverse in deep tropical waters
>red because of the presence of the pigmen phycoerythrin (absorbs blue wavelength- the only light that makes it deep underwater
-some are edible seaweeds
-many important for reef building
-accumulate CaCO3
-important in reef ecology/food web since photosynthetic
94
Chromista
-superphyla of protists
-chromista means colored
-most are photosynthetic
-chlorophyl c and other pigments not found in plants
-includes:
>diatoms (up to 2mm long)
>giant kelps- not microbes, can be 50 meters long
>some can cause disease in plants: downy mildew ex:phytophthera infestans, potato blight caused irish potato famine where 1 million people starved to death
- important in marine ecosystems and industry
- diatoms imp for global C cycles and are grazed on by lots of organisms
- temperate coasts lined with kelp forests important for fish, shellfish etc
- kelps are used for the production of alginate- chemicals extracted from kelp used in paper production, toothpaste and ice cream where the alginate helps to improve texture and ensure uniform freezing and melting
95
Diatoms
a type of Chromista
up to 2mm long
10,000 species, both marine and freshwater
cells surrounded by frustules: hard and porous cell wall
sexual, most of life is diploid
-unicellular and filamentous
-most important aquatic microorganisms: abundant in the plankton and in sediments in marine and freshwater ecosystems
-photosynthetic: about 25% of all CO2 fixation on earth is done by diatoms (40% in oceams)
-imp food source for marine organisms
-some rocks are formed entirely of fossil diatoms, known as diatomaceous earth and used for:
>abrasives
>insecticide
>filters
>reflective paint
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Green algae
superphyla of protists
unicellular and multicellular
close relatives of plants
paraphyletic group
model system for studying the evolution of mutlicellularity
photosynthetic: contains 2 froms of chlorophyl (a and b)
primary aquatic
97
Alveolates
superphyla of protists
includes phyla:
-dinoflagellates- "red tides" that kill fish
-ciliata- most diverse group of heterotrophic protists
apicomplexa- diseases
-formaminifera
based on rRNA sequences
have similar surface: a system of sacs underneath their cell membrances called alveolli for strenth, temp regulation
98
dinoflagellates
phyla of alveolates which are a superphyla of protists
are marine and freshwater
like diatoms, are important in marine food web systems since are photosynthetic
unicellular
may be planktonic or may live within another organism
algae can accumulate rapidly during summer causeing red tides
toxin accumulate in water killing fish and disrupting the ecosystem
molluscsc concentrate toxins= cause shellfish poisoning for humans (the shellfish are fine)
- zooxanthallae are symbionts of coral, spnges and other protists
- they provide the host with photosynthesis-dervied nutrients
- coral bleaching =loss of zooxanthellae
- causes are not clear
99
Zooxanthallae
type of dinoflagellate which are a phyla of the superphyla alveolates of protists
100
Ciliates
- are a phyla of Alveolates which are a superphyla of protists
- have >7000 species
- found almost anywhere there is liquid water
- most are free-living organisms
- feed on microorganisms like bacteria, algae and yeasts
- have 2 nuclei- one for reproduction, one for cell function
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Apicomplexa
-are a phyla of Alveolates which are a superphyla of Protists
-are obligate parasites of animals
-have complex life cycles
-possess apical complex for penetrating host cells
-members include:
plasmodium (malaria)
toxoplasma (toxoplasmosis)
cryptosporidium
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Toxoplasma
- an example of an apicomplexa which is a phyla of alveolates which are a superphyla of Protists
- infects warm blooded animals, mainly cats
- infection usually occurs by eating undercooked contaminated meat, exposure from infected cat feces, or mother-to-child transmission during pregnancy
- intracellular parasite- replicates in a vacuole
- generally not fatal
- up to a quarter of humans are infected
- thought to alter behavior of host
- infected mice seek out cat urine= promotes risk taking behavior
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Plasmodium
genus= plasmodium
of phyla apicomplexa of superphyl Alveolates
parasites of vertebrates
mosquito vector
P. falciparum accounts for the overwhelming majority of malaria deaths
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Diplomonads
- primitive protists
- no mitochondria or golgi even though eukaryoties
- have mitosomes which are remnants of mitochondria
- heterotrophic
- mostly occur in animal intestines
- anaerobic
- one of the earliest eukaryotes
105
Parabasalids
- primitive protists
- only found in association with animals
- some are pathogenic
- most are commensal or beneficial to the host
- no mitochondria
- are anaerobic
- have a flagella
- most occur in intestines of insects ex:termites where the symbiotic bacteria help degrade cellulose
- cause STD Trichomonas vaginalis
106
kinetoplastids
- primitive protists
- have mitochondria
- have flagella
- includes the genus Trypanosoma
- parasites of animals including humans
- cause: African sleeping sickness, chagas disase, leishmaniasis
- transmitted by biting insects
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trypanosomes
| Trypanosoma Brucei
genus of kinetoplastids which are primitive protists (phylum)
Trypanosoma brucei= sleeping sickness
-transmitted by the Tsetse fly in Africa
-in the first stage the trypanosomes multiply in subcutaneoys tissue, blood and lymp causing fever, headaches, joint pains and itching
-in the second stage the parasites cross the BBB to infect the central nervous system causing changes in behavior, confusion, sensory disturbances and poor coordination, disturbance of the sleep cycle
-100% fatal without treatment.
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Trypanosoma cruzi
- genus of kinetoplastids which are primitive protists (phylum)
- Trypanosoma cruzi- causes Chagas disease
- transmitted by Reduviidae insects
- forms intracellular amastigotes (intracelular non-motile form in the vertebrate host)
- can damage neural and cardiac tissue
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Slime molds
superphyla of protists
two types:
>plasmodial slime molds:
-previously classified as fungi and called Myxomycota
-enormous single-cells- they are formed when individual flagellated cells swarm together and fuse
-thousands of nuclei
-they feed on microorganisms that live in any type of dead plant material. they contribute to the decomposition of dead vegitation and feed on bacteria, yeasts and fungi
>Cellular slime molds:
- have amoeboid single cell stage
- form swarms
- interest in evolution of cooportation- how cells interact to generate multicellular organism?
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plasmodial slime molds:
-type of slime mold which is a superphylum of Protists
>plasmodial slime molds:
-previously classified as fungi and called Myxomycota
-enormous single-cells- they are formed when individual flagellated cells swarm together and fuse
-thousands of nuclei
-they feed on microorganisms that live in any type of dead plant material. they contribute to the decomposition of dead vegitation and feed on bacteria, yeasts and fungi
111
Cellular slime molds
-type of slime mold which is a superphylum of Protists
>Cellular slime molds:
-have amoeboid single cell stage
-form swarms
-interest in evolution of cooportation- how cells interact to generate multicellular organism?
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Characteristics of fungi
- Eukaryotic
- non-vascular
- heterotrophic, do not have stomachs, they digest then ingest (animals ingest then digest)
- have diffuse, branched, tubular body (filaments)
- are multicellular
- some are yeasts
- reproduce through spores- both sexual (meiotic) and asexual (mitotic) spores
- have cell walls made of chitin
- non-motile
- store carbohydrates as glycogen (like animals) not starch
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1) Somatic
2) Hyphae
3) Mycelium
4) septa
Somatic: vegitative
2) Hyphae: hypha =web
- body of fungus
- microscopic and threadlike
- elongat by apical growth
3) mycelium: collective structures that make up the body of fungus
4) Septa= cross-walls within a hypha
- separates compartments
114
growth conditions for fungi
- fungi are widespread and versatile
- consume organic substrates- dead organisms, products of living organisms, living organisms
- fungi readily form symbiotic associations
- require free water for diffusion of nutrients-but some grow in salt water and others in very dry conditions
- optimal growing temperatures are 25-30C but some are thermophilic.
115
Plasmogamy
the cytoplams of 2 parent mycelia fuse together without the fusion of nuclei
-leads to the formation of dikaryon
plasmo=cytoplasm
116
dikaryon/dikaryotic
nuclei from 2 parents do not fuse, giving a cell an n+n nuclear condition
also called heterokarytoic
117
Karyogamy
fusion of nuclei
| kary=nucleus
118
anamorph
the asexual stage of the life cycle of a fungus
| most biology of fungus occurs in this stage
119
teleomorph
the sexual life stage of a fungus
120
generalized life cycle of fungus
asexual reproduction/Anamorph:
spore-producing structures->spores->germination->spore-producing structures
sexual reproduction/Teleomorph:
Mycelium-> plasmogamy/fusion of cytpolasm->Dikayotic (n+n)->Karyogamy->Zygote (2n)-> meiosis-> spore-producing structures->spores->germination->mycelium->repreat
121
fungi and animals similarities
both:
heterotrophic
-use glycogen
-DNA sequence
122
disc Q: ways in which fungi are a group of microbes that are critically important?
- food production (beer, cheese)
- antibiotics
- decomposers
- plant mutualisms and agroforestry
- yeasts used as model organisms
- plant pathogenic fungi and human pathogenic fungi, toxic side effects from anti-fungals
- contaminate buildings
- fungi produce mycotoxins
123
Chytridiomycota
phylum chytridiomycota of fungus
- about 100 genera and 1000 species
- have motile cells in some life stage
- coenocytic: non-septate
- many are endobiotic- occur inside host cells or tissues
- zoospore dispersal requires water
- chytrid fungus has been linked to global amphibian decline
124
Zygomycota
Phylum Zygomycota of fungus
125 genera, about 1000 species
important ecologically
>are symbionts:
- glomales- are vascular-arbuscular mycorrhizae
- trichomycetes-symbionts with insects
- entomophthorales- important pathogens of insects
- zoopagales-parasites of other fungi
>are saprobes:
-mucorales-weedy fast growing species (r-selected)
- no motile cells
- no flagellate cells
- aseptic hyphae (coenocytic)
- asexual reproduction by sporangiospores
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Zygomycota spores
produce thick-walled resting spores caleed zygospores
-zygos=yoked or joined
+spora= seed
zygospores= develop within zygosporangium
zygospores form as a result of fusion of 2 gametangia
126
Pilobolus
```
genus of Zygomycota
"hat thrower"
common on herbivore dung
stalk elongates rapidly
-forms sporangium at tip
phototropic-bends toward light
sub-sporangial vesicles acts as lens
```
127
Ascomycota
```
phylum of fungi
called the "sac" fungi
-have dikaryotic stage in life cycle
-septate hyphae
-conidia
sexual reproduction via ascospores in ascus
30,000 named species
groups based on reproductive structures
in general, are molds and yeasts
important plant pathogens
```
128
Ascomycota and humans
yeasts-bread and alcoholic beverages
penicilium-antibiotics, cheese
dermatophytes-ring worm and athlete's foot fungus
-chestnut nlight and Dutch Elm disease
-ergot- drugs, effect circulation and neurotransmission
129
Ascicarps
fruiting bodies of ascomycetes
130
Basidiomycota
```
club fungi
sexual reproduction via basidiospores on basidium
25000+ species
common mushrooms, puff balls, bracket fungi
plant pathogens
*have meiotic spores on basidium
*also have clamp connections
-no asexual cycle (vast majority)
```
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viruses general properties
small, infectious obligate intracellular parasites
depend on host cell to replicate
-because they lack the resources for independent existence, they exist on the borderline of the definition of life
-viral genomes consist of either RNA or DNA
they may be single or double or partially double stranded
the genomes may be circular, linear or segmented
-the virion (virus particle) consists of a nucleic acid genome surrounded by coat proteins (capsid) that may be enveloped in a host-derived lipid bilayer
132
virus unifying principles
- all viruses package their genomes inside the capside that mediates transmission of the viral genome from one host to the next
- viral genome contains the information needed for initiating an infectious cycle within a susceptible, permissive cell
- an infectious cycle includes attachment and entry of the particle, decoding of genome information, translation of viral mRNA by host ribosomes (no known viruses contain ribosoems). genome replication and assembly and release of particles containing the genome
133
what viruses need to do to survive/replicate?
- find and get into host cell: they are obligate parasites so they need to find the right type of cell for replication and invade cell, get their genome to the site of replication
- make virus proteins: all viruses are parasites of translation, virus must make mRNA
- make viral genomes: many viral genomes are copied using the cell's synthetic machinery in cooperation with viral proteins
- form progeny virions: virus genome, capsid and envelop proteins must be transported through the cell to the assembly site and the correct information for assembly must be pre-programmed
- spread within and between hosts:to ensure survival, virus must propagate itself in new cells
- overcome host defenses: virsuses have ways to fight back against host defenses. viral genomes encode for proteins that can block nearly every step of immune response= hard to treat
viral diseases are a consequence of the way each virus deals with these issues
134
challenges with viruses
- can;t survive outside of cells in historical samples
- viral polymerases of RNA genomes lack proofreading ability= high rate of mutation and evolution
- extremely high rate of replication
- many viral genomes are segmented- shuffling may occur
- viruses may be subjected to intense selective pressures- host immune response, antiviral therapy
- viruses invade diverse species
- the diversity of viral genomes precludes us from making comprehensive phylogenetic treee of viruses
135
why is difficult to establish phylogenetic relationships among viruses
- the diversity of viral genomes precludes us from making comprehensive phylogenetic treee of viruses
- there is no genetic equivalent in viruses to the rRNA or universal proteins that are common to bacteria, eukaryotes and archaea
- virus specific proteins are only found in subsets of viral groups
- protein phylogenies have only been useful to tentatively establish a classification for selected virus groups
136
origin of viruses hypotheses
1) progressive hypothesis
2) regressive hypothesis
3) virus-first hypothesis
137
progressive hypothesis
viruses came from mobile genetic elements ex transposons: fragments of DNA that gained the ability to leave their original cells and genomes and enter others
-this hypothesis explains retroviruses as they use integrase and reverse transcriptase to enter host cells
138
regressive hypothesis
viruses are remnants of more complex cellular organisms
| this supports the giant mimivirus tha gas genes that may be remnants of previous complete translation systems
139
virus-first hypothesis
viruses may have existed before cellular life rather than being derived frome xisting cells
self replicating units in the anceint virosphere may have gained the ability to form membranes and cell walls leading to evolution of 3 domains of life
140
viruses as drivers of evolution
they affect all life on earth, determining what will survive
the huge population of viruses combined with their rapid rates of replication and mutation makes them the world's leading source of genetic innovation
unique genes of viral origin may travel, finding their way into other organisms and contributing to `evolutionary change
141
how are viruses named?
randomly, based on:
- the disease they cause
- the type of disease
- geographic locations
- their discoverers
- how they were originally thought to be contracted
- combination of all of above
142
Baltimore classification system
```
based on genetic contents and replication strategies of virus
according to this system, viruses can be divided into:
-dsDNA virus
-ssDNA virus
-dsRNA virus
- (+) sense ssRNA
- (-) sense ssRNA
-RNA reverse transcribing virus
-DNA reverse transcribing virus
```
143
dsDNA virus
can use hosts' DNA/RNA polymerase
transcripts encoding viral proteins are translated using host machinery
capsid forms around newly formed viral DNA molecules and are released from cell
limit: need DNA polymerase so dependent on host cell replication
-some can encode their own replication machinery or make proteins that induce host cell replication'
-presence of virus and ciral growth-promoting proteins can drive host cell into unceasing growth and cell division= pattern of typical cancer cells
144
ssDNA virus
these face a problem as host cells polymerases don't recognize ssDNA so the first step is conversion of ssDNA to dsDNA using host cell DNA polymerase
(+)ssRNA is made by host cell RNA polymerase which is translated to make viral porteins
the replicated viral DNA is coverted back into a ssDNA genome and the virion is packaged for export
145
dsRNA viruses
distinct dsRNA geonmes
their virions carry an RNA polymerase that transcribes the dsRNA into a (+) ssRNA
this then serves as mRNA that is translated into the necessary viral proteins or they can act as template for (-)RNA strand synthesis to be converted back to dsRNA genome for packaging
146
ss(+)RNA viruses
identical to mRNA viruses
the host cell does not have mechanism to replicate RNA
they have direct acces to host ribosomes-> translation of virion RNA as mRNA
synthesis of (-) sense RNA on (+) sense template
synthesis of (+) sence RNA and mRNA using (-)sense RNA
translation of (+)sense and mRNA, synthesis of structural protein
assembly of structural protein and (+)RNA and maturation of virions
147
ss(-)RNA viruses
-largest group
-contains viral RNA-dependent RNA polymerase along with the (-) ssRNA genome within the nucleocapsid
-once inside the cell, the viral polymerase begins to worl on the (-)ssRNA making 2 kinds of (+) stranded viral RNA
some of thie (_) stranded RNA is made as short viral mRNAs that are then translated into viral proteins
some of it is made as full length RNA that is then replicated to make the (-) ssRNA that is needed for the proheny virions
-nucleocapsid assembly and maturation, budding of nucleocapsid through host membrane containing viral envelope proteins
148
RNA reverse transcrining viruses
after entering the cll the + RNA is not assiciated with ribosomes
instead the RNA is used as a template to make a DNA copy of viral genome which is done by reverse transcriptase
once the viral dsDNA is made it is transported into the nucleus where it is inserted and linked to the host chromosomal DNA (integrase) which can then be transcribed by the host cell into + RNA that is transported to the cytoplasm and used as mRNA in viral protein synthesis or as the genome for new progeny viruses
149
DNA reverse transcribing viruses
replication takes place i nboth cytoplasm and nucleus of host cells
viral DNA forms supercoiled mini-chromosome structires ipon entering host nucleus
the viral DNA is transcribes and RNA enters the cytoplams where it has 2 roles:
1)it can be used as a template for viral protein synthesis
2)it can undergo reverse transcroption by viral encoded reverse transcriptase to make dsDNA
as replication required use of RNA replication, viruses from this group are not true dsDNA viruses- instead they are termed DNA reverse-transcribing viruses
unlike reteroviruses, they don't need to be integrated into the host to replicate and for this reason their genome doesn't encode the enzymatic protein integrade
ex: Hep B virus
150
virus mutualism
Many parasitoid wasps lay their eggs in a living insect larva. The innate immune system of the larva would normally wall off the egg, forming an encapsulation structure that prevents the egg from developing, but the wasp genes carried by the polydnavirus virions suppress this response. without this suppression, the wasp eggs would not survive
151
Viruses as natural weapons
Many bacteria carry a viral genome (green) integrated into their own genome (blue). These lysogenic viruses remain dormant and render the host bacteria immune to lytic forms of the virus. If the lysogenic virus excises from the genome, it can reproduce rapidly, producing thousands of progeny and leading to the death of the host cell. •This releases the viruses into the extracellular environment, where they can kill competing bacteria (red) that are not lysogenic for the virus.
