TEST 3 Flashcards
dmitosis results
-Results in two diploid (two copies of each chromosome)
daughter cells
meiosis results
-results in four haploid gametes
Cristae of mitochondria
-folded internal membranes
-Contain enzymes needed for respiration and ATP production
Matrix of mitochondria
-innermost area of mitochondrion
-Contains citric acid enzymes
Thylakoids in chloroplast
-flattened membrane discs contain
chlorophyll and ATP synthetic components, form proton motive force
rubisco
-key enzyme for calvin cycle
-found in inner membrane of mitochondria
Endosymbiotic hypothesis
-Mitochondria and chloroplasts descended from respiratory and
phototrophic bacterial cells, that were enveloped and used with nonphototrophic eukaryal hosts
-mitochondria utilized before chloroplasts
eukaryote origins
-fusion of archaeal host and mitochondrial precursor
Microtubules
hollow tubes made up of a & b tubulin
25nm
-Maintain cell shape, moves cell chromosomes and organelles
microfilaments
polymer of actin
7nm
-Maintain and change cell shape
Intermediate filaments
fibrous keratin proteins
8-12nm
-Maintain cell shape and position organelles
golgi complex
-stacks of membrane-bound sacs
modifying ER products
lysosomes
-membrane-enclosed compartments
containing digestive enzymes and recycling cell
components
Endoplasmic reticulum
-a network of membranes continuous with nuclear membrane
-rough and smooth
-rough has ribosomes; processes glycoproteins
-smooth does not; processes lipids
flagella composition
-Bundle of nine pairs of microtubules surrounding a central pair of microtubules
-Dynein is attached and uses ATP to drive motility
-eukarya and prokarya flagella are different
first phototrophs
anaerobic
Stromatolites
fossilized bacterial communities
ozone shield
-02 gave rise to collection of 03 in atmosphere
-03 in atmosphere blocks suns harmful radiation (UV)
-allows for organisms to colonize land
Phylogeny
-Evolutionary history of related DNA
sequences
bacteria and archaea divergence in relation to eukarya
before the emergence of eukarya
bacteria and archaea divergence time
3.7bya
eukaryas divergence from archaea divergence time
1.5-2.7bya
-oxygen may have spurred evolution
last eukaryotic common
ancestor LECA characteristic
-4000 genes
2/3 from bacteria (metabolic)
1/3 archaea (info processing)
70% are genes only in eukaryotes
evidence for endosymbiont theory
-Chloroplasts and mitochondria about the same size as bacteria
and independently replicate
-Both contain their own genomes of bacterial genes and are
circular
-Both contain bacterial ribosomes
-16S rRNA are characteristic of Bacteria
-Antibiotics inhibit both bacterial and organelle ribosome function
Eukaryotic genes for DNA replication
derived from archaea
archaea is ancestor
Lokiarchaeota
-Genomes with eukaryotic features
-eukaryotic-like cytoskeleton
-ability to synthesize intracellular
membranes,
-which may have facilitated stable integration of an
endosymbion
Hydrogen hypothesis
-Eukaryotic cells arose from an H2-
producing bacterium and an H2- consuming Archaea
Symbiogenesis
-Eukaryotic cell arose from symbiotic
relationship between Bacteria and Archaea; bacterial
partner was engulfed to form mitochondria
Serial endosymbiosis
hypothesis
mitochondria and chloroplasts integrated into protoeukaryote after nucleus formed
Genetic drift
a random process that can cause
gene frequencies to change over time, resulting in
evolution in the absence of natural selection
mutation
changes in DNA sequence over time
evolution
change in allele frequency over time
Rhodobacter
anoxygenic phototrophic purple bacterium
rhodobacter loss of function example
-rhodobacter who have lost photoactivity do better in dark environments
-rhodobacter who keep photoactivity do better in light environments
duplication and deletions effects on genome
-regulates genome size
-regulates gene content, removing non essential genes and expanding functions
Homologous genes
-Genes that all descended from a single ancestral gene
Orthologs
-Homologus genes sharing the same function
Paralogs
-A single gene that diverges to many different functions in different organisms
deletion frequency compared to insertion/duplication
much more
horizontal gene transfer pathways
transformation, transduction, conjugation
Gene conversion
-homologous recombination results in replacement of recipient copy with donor copy
Mobilome
-Consists of all mobile genetic elements in a genome
-can shuffle genes between species (recombination between host genome and plasmid that is transfered to another species)
Insertion sequences
-Simple mobile elements made of transposase
-flanked by inverted repeats
Transposons
-mobile genetic elements
-have terminal inverted repeats and transposase
-gene
Integrons
-contain integrase gene which integrates extra chromosomal DNA into chromosome
Systematics
-Study of organisms and their relationships, links phylogeny with taxonomy
(characterizes, names, classifies organisms)
3 methods of approach to taxonomy
-phenotypic
-genotypic
-phylogenetic
sequence alignment
-positioning of codons is important
-establishes gaps in homologs
Homoplasy
-convergent evolution
-complicates phylogeneitc approach to taxonomy
horizontal gene transfer in relation to the phylogenetic approach to taxonomy
-complicates phylogenetic approach
phylogenetic taxonomy tests
-analyze SSU rRNA
-Multilocus sequence analysis
Average nucleotide identity
-estimates overall relatedness by aligning ~1000 bp fragments and
calculating average nucleotide identity
reduction potential
ability of a molecule to accept or donate an electron
fementation
-doesn’t need external electron acceptor
-excretes metabolic intermediates
respiration
-need external electron acceptor
-uses 02 as final electron acceptor
Assimilative
-integrates inorganic nutrients into cells which are the electron acceptors
-uses ATP
Dissimilative
-process conserves energy
-electron acceptor is reduced then excreted
-02 in respiration
Mixotrophs
-can utilize 2 different metabolism pathways for energy (photosynthesis and respiration)
-(autotroph and heterotroph)
autotrophs
-creates their own energy using inorganic materials usually sunlight or chemicals
calvin cycle
-most widespread pathway that fixes C02
-used by all oxygenic phototrophs
-uses rubisco
calvin cycle requirements
12NADPH & 18 ATP
calvin cycle products
fructose 6 phosphate
Carboxysomes
-Protein compartments filled with RubisCO
reductive calvin cycle
-reverse of calvin cycle
-24H & 10 ATP
photosynthesis
-Use of light energy to drive
biosynthesis
-those that use this pathway are photoautotrophs
-origininated in bacteria
-requires light sensative pigments such as cholorphyll to absorb light and convert energy
Tetrapyrroles
cytocrhome with magnesium at center instead of iron
chlorophylls absorb what colors
-red and blue
-transmits green as it doesnt absorb that color
Bacteriochlorophyll
-found in anoxygenic phototrophs
Antenna pigments
-absorb and capture and funnel the light, transferring it to reaction centers
Reaction centers
-where photosynthetic process take place
-where the light energy is transformed into chemical energy
thylakoid lumen
-space inside thylakoid
-creates pmf
thylakoid stroma
-surrounding matrix of thylakoid
Chlorosomes
-capture low light intensities
-in bacteria
-contains bacteriochlorophyll
Carotenoids
-most widespread accessory pigment
-yellow red brown or green
-absorbs blue light
-can transfer light to reaction center
-protects cell from photooxidation
Phycobiliprotein
-main light harvesting system in cyanobacteria and red algae
-red or blue/green tetrapyrroles
-allows cells to grow at low light intensities
oxidation of sulfur product
S04^-2
Sox system
-reduces sulfur to sulfate
-acidifies envrionment
Primary fermentation
-break down and ferment carbohydrate, protein, fat polymers and monomers to reduced products
Secondary Fermentation
-break down and ferment volitile fatty acids
Major substrate of fermentation in nature?
lactate
Syntrophy
-Two different microbes cooperate to perform
a reaction neither can do alone
-usually secondary fermentations
direct syntrophy
direct contact between cells to allow for syntrophy
Mediated syntrophy
diffusion of metabolic prodcuts allows for syntrophy
Metabolic diversity
L
Ecological diversity
-microbial interactions between organisms and
their environments
Phylogenetic diversity
-evolutionary relationships between organisms
Gene loss
-trait is present in a common ancestor is
lost during divergence over time
Convergent evolution
-trait has evolved independently in different lineages and is not encoded by homologous genes
Photosystem 1
-FeS in center of oxygenic phototroph
-can do photosynthesis w/o help from ps2 through anoxygenic photosynthesis
Photosystem 2
-Quinone in center of oxygenic phototroph
-transfers energy (electrons) to photosystem 1 in Z scheme
-oxidizes water into oxygen
-reduces hydrogen for pmf
phototrophic bacteria hydrogen produced per o2 in photosynthesis
12H+ per 02 molecule
cyanobacteria aquired ps1 & ps2 how?
through horizontal gene transfer
Purple sulfur bacteria
-Anoxygenic phototrophs that use
hydrogen sulfide as an electron donor for photosynthesis
-use bacteriochlorophyll and q types to harvest light
-uses 2 different ways to store excess sulfur
green sulfur bacteria
-nonmotile, anoxygenic phototrophs
-long/short rod shape
-Oxidize H2S to S and S04 for autotrophy
-uses bacteriochlorophyll in chlorosomes
-green and brown species
Methylotrophs
-grow using organic compounds lacking
C-C bonds as electron donors and carbon sources
-found in oceans/soils at interface of oxygenic and anoxygenic areas
Methanotrophs
-subset of methylotrophs that use
methane for growth
-only archaea
cyanobacteria
-oxygenic phototrophs that undergo photosynthesis as expected
-can be unicellular or filamentous
-5 morphological groups
-can fix nitrogen (dominant nitrogen fixer in oceans)
-can use gas vesicles/flagella/other cell motility structures
-uses thylakoids and pigments to harvest light
Consortium
two membered cell binding
epibiotic predators
attach to prey surface and
acquire nutrients from cytoplasm or periplasm
cytoplasmic predators
invade host
cells and replicate in cytoplasm, consuming prey from within
social predators
swarm and collectively feed upon lysed prey
Myxobacteria
-cell predator
-Most complex behavior
among known bacteria
-Life cycle results in
formation of multicellular
structures (fruiting bodies
Bdellovibrio
-cell predator
-Small, motile, curved
-preys on other bacteria and use host cytoplasmic contents as nutrients
-has 2 stages of penetration
-attacks exclusively gram negatives
-obligate aerobes
-NOT OBLIGATED TO PREDATE
Magnetotaxis
directed movement in a magnetic field
Magnetosomes
made of magnetic chains of particles
reaction center in photosystem 1
FeS
reaction center in photosystem 2
quinone
Fe3O4 magnetosome
aerobic magnetosome
Fe3S4 magnetosome
anaerobic magnetosome
common traits of archaea
-Ether-linked lipids
-Lack of peptidoglycan in cell walls
-RNA pol are complex like eukarya’s
Halophilic Cytoplasmic components
-Highly acidic
-Require K+ for activity
-Low level of hydrophobic amino acids and lysine (positively charged)
Bacteriorhodopsin
-membrane protein
-Absorbs light energy and pumps protons across the membrane
3 Methanogenic Pathways
-C02 reduction
-coenzyme M
-syntrophic w anaerobic bacteria
Methanogenesis products
2 pathways that create 2 different products
-either C02 and CH4
-Only CH4
Nanoarchaeum equitans
-smallest cellular organism
-coccoid
-cant grow in pure culture as its parasitic
-smallest genome
-thermophile
Primary Endosymbiosis
bacteria was aquired by ancestor of eukarya
-occured w obtaining of mitochondria and chlorophyll
Secondary endosymbiosis
-engulfing a green/red algal cell, retaining its chloroplast, and becoming phototrophic
Fungal Physiology
-multicellular creating network of hyphae
-heterotrophs
-lack flagella in most
mycelia
-several compact tufts hyphae w large surface area
conidia
-hyphae that extends above the surface of the ground
-pigmented
-resistant to death
Mycorrhizae
-help plants obtain phosphorus and nitrogen.
-associates w plant roots
3 forms of fungal asexual reproduction
-growth/spread of hyphael filaments
-asexual production of sprores
-simple cell division
fungal spores
-Sexual spores (diploid 2 diff fungi)
-Spores are resistant to drying, heating, freezing, and chemicals
fungal divergence time
1.5 bya
closest to animals than other eukaryotic organisms
rhizobia
nitrogen fixing bacteria
gram negative
alpha and beta proteobacteria genera
human gut affects on humans
immunity
vitamin synthesis
metabolism
gut-brain communication
deitary fiber
indigestible carbohydrate found in plants
can be fermented by gut bacteria
fructooligosaccarides
used as alternative sweeteners
30-50% as sweet as sugar
Gut-brain axis
-bi-directional communication between brain and gut
-gut-microbiota influence communication
-diet influences gut-microbiota
-changes in gut-microbiota can lead to mood disorders, changes in mood
bacterial species found in the gastric fluid
Firmicutes, Bacteroidetes, Actinobacteria
bacterial species found in the mucus of the stomach
Firmicutes, Proteobacteria
Helicobacter pylori
found in 50% of populations gut bacteria
found in gastric mucosa
large intestine function
undergoes fermentation
most microorganisms are restricted to the lumen here
majority of bacteria in gut
-Firmicutes, Bacteroidetes, and Proteobacteria are 98% of bacteria
-most people have mainly firmicutes or bacteroidetes bacteria in their gut
3 enterotypes of the human gut
(enterotype=main gut biome composition)
-bacteroidetes
-prevotella
-ruminococcus
how many microbes in gut biome
10^13
bacteria per square centimeter of skin
1 million
aging and gut microbiome
decreased microbiome diversity
Irritable bowel syndrome characteristics
-chronic inflammation
-lower microbiome diversity
-western diet
-antibiotics help develop it
virus
-genetic element that can only replicate with a host cell
-obligate intracellular parasite
virion
-single virus outside host cell
virulent infection
replicates destroying host
Lysogenic infection
-host cell genetically altered because viral genome becomes part of host genome
Capsid
-protein shell that surrounds the genome of a virus
Nucleocapsid
nucleic acid + capsid
Naked viruses
single layered capsid virus
enveloped viruses
multilayered capsid virus
Capsomere
proteins structured in repetative/presice shape to create capsid
helical capsid
rod shaped virus
length determined by length of nucleic acid
width determined by packaging
Icosahedral capsid
can be spherical/hexagonal
most efficient arrangment
requires fewest capsomeres
complex capsid
head & pilus virus
most complex
Lysozyme for viruses
-makes hole in cell wall to allow nucleic
acid entry, lyses bacterial cell to release new virions
Neuraminidases for viruses
-destroy glycoproteins and glycolipids, allow liberation of viruses from cell
Nucleic acid polymerases
-aid in virus genome replication
can be RNA/DNA/reverse transcriptases
Titer
number of infectious virions per volume of fluid
Plaque assay
-clear zones of cell lysis where successful
viral infections occur
5 steps of replication for a virus
1) attachment
2) penetration
3) synthesis
4) assembly
5) release
Early proteins
-proteins made early after infection
-usually enzymes
-usually made in small amounts
-includes nucleic acid polymerases that shut down host transcription/translation
late proteins
-proteins made late after infection
-made in large amounts
-includes structural and assembly proteins
prokaryotic viruses
only nucleic acid enters host cell
eukaryotic viruses
virion enters host cell
Viroplasms
-membrane bound viral factory
-forms in some eukaryotic
cells to increase virion assembly rate
and protect from host defense
viral infection of animal cells
-bind to host receptors
-some viruses only infect certain tissues due to the appearance of certain cell surface receptors
-cell membrane and virus membrane merge
-viral genome enters nucleus
-RNA viruses are converted into DNA in nucleocapsids
four outcomes of viral infection
1) transformation of host cell (tumor cell)
2) virulent infection (cell lysis)
3) persistant infection (host cell stays alice, slow release of virions)
4)latent infection (virus integrates into host genome, can trigger virulent infection)
plant infection of viruses
-plants have cell wall blocking viruses
-viruses infect through wounds usually from insects that transmit virus
DNA virus genome
smaller than cell genomes
RNA virus genome
smaller than DNA virus genomes
genome is mRNA
once virus infects host
-transcription of viral DNA occurs
-mRNA must be made by genome transcription
Baltimore Class 1
POX virus
-dsDNA
-replicates in cytoplasm
-largest animal virus
-pox viruses (small pox, cow pox)
-cell lyses and releases viruses
-used to make vaccines
Baltimore Class 1
herpes virus
-largest group of enveloped viruses
-latent, reappears under stressful conditions
Baltimore Class 2
-ssDNA
-infects plants animals bacteria
-circular genome
-a protein shuts down host DNA synthesis
-lysis occurs after shutting down of peptidoglycan synthesis of host
Baltimore Class 3
-dsRNA
-binds to receptor enters via lysosome
-replicates in cytoplasm
Baltimore Class 4
-ssRNA
-genome is the infectous agent
-replicates in cytoplasm
-lysis releases viruses
Baltimore Class 5
-ssRNA
-complex assembly
-released by budding
-RNA must be translated by host
Baltimore Class 6
-ssRNA
-uses reverse transcriptase (genome not used as mRNA)
-
Baltimore Class 7
Retroviruses
Baltimore Class VI, (+)ssRNA viruses
-need a DNA intermediate to complete replication
Hepadnaviruses
doublestranded DNA viruses
need RNA intermendiate to complete replicaiton
Vector
-agent that carries and transmits an infectious pathogen into another living organism
Zoonosis
animal disease transmissible to humans
Enzootic
present endemically in certain populations
Epizootic
incidences reach epidemic proportions in
certain populations
Baltimore class 5 rabies
ssDNA
infects CNS, proliferates in brain
enters through wound
Baltimore class 5 Hantavirus
hemmoragic fever with renal syndrome
sudden onset
mortaility rate is >40%
Rickettsia
-small bacteria that have intracellular
existence in vertebrates
-usually blood sucking arthopods
-cant be cultured in lab but in bugs
-three groups-
-typhus,
-spotted fever
-ehrlichiosis
Typhus group of Rickettsia
-transmitted by bite, contaminated by its feces
-mortalitiy rates ~30%
spotted fecer of rickettsia
-transmitted by dogs and wood ticks
-grows in nucleus/cytoplasm
-headach fever rash
Tickborne ehrlichiosis &
anaplasmosis
-flulike symptoms
-antibiotics treat it
-transmitted by tick bites
Lyme disease & Borrelia
-developed over months
-treated by antibiotics
-caused by spirochetes
Yellow Fever Baltimore Class 4
-transmitted by mosquitos
-endemic to tropical climates (africa/south america)
-no antiviral
-preventable by vaccination
-
Dengue Fever Baltimore Class 4
-transmitted by mosquitos
-endemic to tropical climates
-infected improve on their own
-no vaccine
-found in mexico latin america africa
Zika Virus Baltimore Class 4
-found in south america
-transmitted mother to fetus and mosquitos
-
West Nile Virus Baltimore Class 4
-transmitted to mosquitos
-seasonal
-no vaccine available
-meningitis
Black Death/ Plague
-Yersinia pestis, gram-negative,
facultative aerobic, rod-shaped bacteria
-fleas cause disease
Pneumonic plague
when the plague reaches the lungs
Septicemic plague
rapid spread of the plague throughout the body especially the blood stream
bubonic plague
-most common
-Local hemorrhage produce dark
splotches on skin and eventual
tissue necrosis (gives plague
historical name “Black Death”)
Sylvatic plague
plague endemic to rodents
Giardia intestinalis
-Flagellated anaerobic
parasite
-has mitosomes instead of mitochondria
-causes giarditis
Trichomonas vaginalis
-Flagellated anaerobic parasite
-Has hydrogenosomes in place of
mitochondria
-survives in moist areas (toilet seats, sauna
benches, and towels)
-asymptomatic in males
-vaginal
discharge, itching, and burning in females
Cryptosporidium parvum
-Parasitic coccidia
-Transmitted to humans through
fecally contaminated water
-protist that lives in warm blooded animals
-
Cyclosopra cayetanensis
-Parasitic coccidia
-Transmitted to humans through
fecally contaminated food
-protist that lives in warm blooded animals
-
Toxoplasma gondii
-Parasitic coccidia
-Transmitted to humans through
fecally contaminated food or water
-asymptomatic
-Damages eyes, brain, and other
organs in immunocompromised
individuals
-causes birth defects
-
Malaria
-Protist disease caused by Plasmodium spp.
-mosquitos cause disease
-found in tropical regions
-
Leishmania tropica & L. mexicana
-Flagellated protozoan
-transmitted by bite of sandfly
-infects and grows on macrophages
-
Leishmania donovani
Flagellated protozoan
-Related to trypanosomes
-transmitted by bite of sandfly
-travels to internal organs Damages liver, spleen, and bone marrow
-fatal if left untreated
Trypanosoma brucei
-African sleeping
sickness
–Transmitted by bite of tsetse fly
-Parasite multiplies in blood
and spinal fluid
-infects CNS
-
Trypanosoma cruzi
-Causes Chagas disease
-Transmitted by “kissing bug”
-Parasite affects heart,
gastrointestinal tract, and central
nervous system
-occurs in latin america
Schistosomiasis
-snail fever
-caused by trematode Schistosoma
-life cycle requires snails and humans
-occurs in tropical climates
Filariasis
-Transmitted by bite of
mosquito
-
symbiogenesis hypothesis
mitochondria was integrated into eukarya before nucleus first formed
infection
microorganism is established and
growing in a host
disease
tissue damage/injury that impairs hosts function
pathogen
Microbial parasites that cause disease or tissue damage in a host
Pathogenicity
ability of a parasite to inflict damage on the host
Septicemia
bloodborne systemic infection
Bacteremia
the presence of bacteria in the bloodstream
Virulence
ability of a pathogen to cause
disease
Attenuation
decrease or loss of virulence
Opportunistic infections
caused by
organisms that do not cause disease in healthy hosts
tissue destroying enzymes
Hyaluronidase
Coagulase
streptokinase
Hyaluronidase
breaks down host tissues
Coagulase
forms clots
streptokinase
breaks down clots
Exotoxins
Proteins released from the pathogen cell as it grows
-Cytolytic toxins
-AB toxins
-Superantigen toxins
AB toxins
blocks protein synthesis
A active domain
B binding domain
Enterotoxins
exotoxins whose activity affects the small intestine
cytolytic exotoxins
degrades cytoplasmic membrane integrity
causes cell lysis and death
superantigens
overstimulation of immune system
leads to shock and death
