Exam 3 Flashcards
Phylogeny
shared common ancestry
Why do we need a species system?
Organization Communication Different contexts and languages
What are the requirements for life?
Carbon source, energy source, water, nitrogen, phosphorus, cell membrane
What are the environmental characteristics for life?
Temperature, O2 level, pressure, salt concentration, pH
Steps to life
- Abiotic synthesis of organic molecules 2. Building polymers from monomers 3. Packaging polymers, separating self from non-self (cell membrane) 4. Self-replication and inheritance
Miller-Urey experiment
using electricity and atmospheric gasses to produce amino acids
shock synthesis
comet impact creating organic molecules
montmorillonite
clay that may have catalyzed the formation of RNA polymers
RNA World Hypothesis
early forms of life used RNA as their genetic material
What did protocells use to protect their RNA?
Phospholipids
Vesicle vs. Micelle
What is a cell membrane important for?
Establishing protein gradients
RNA replicase
makes RNA from a template
Why does the use of DNA for long term storage make sense?
More chemically stable than RNA (chemically selected), mutates less
Where could life have started?
Surface, deep sea vent, geyser
Who could have been the first replicates?
Viruses
What are the oldest fossils we have?
Cyanobacteria Not the oldest form of life
Are prokaryotes simple?
Nope just specialists
What is the difference between metabolic processes in prokaryotes and eukaryotes?
Eukaryotes do things pretty much the same (chemoheterotroph and/or photoautotroph) Prokaryotes’ processes are diverse and complicated
What is the size difference between prokaryotes and eukaryotes?
Prokaryotes are 1/10 the size of eukaryotes
How do prokaryotes and eukaryotes move molecules inside the cell?
eukaryotes: endomembrane system prokaryotes: diffusion
Organelles
membrane-bound sub-cellular structure eukaryotes have a common set, prokaryotes don’t
Why can’t the biological species concept be applied to prokaryotes?
Asexual reproduction
How do we ID bacteria in clinical labs?
metabolic tests, not very useful for novel species
Carl Woese
proposed using 16S rRNA gene for molecular phylogenies Led to discovery of archaea domain
What are genetic changes caused by?
(A)sexual reproduction mutations horizontal gene transfer
Why are rRNA genes useful?
Every cell has them There are regions that are highly conserved and regions that are highly variable
MLST
Multi-locus sequence typing analyze several housekeeping genes
At the molecular level, archaeal proteins are more similar to:
eukaryotes, not bacteria
Difference in membrane lipids in archaea?
Archaea have ether linkages, can have bi- or monolayer Eukaryotes and bacteria have bilayer ester linkages
Difference between G+ and G- bacteria?
G+ has thick peptidoglycan layer and thin lipid layer G- has thin peptidoglycan layer and thick lipid layer
Do archaea have a cell wall?
Some do, they are highly variable with diverse components and no outer membrane
Why don’t we know more about archaea?
Little research money since they aren’t infectious
How did the G+ state come about?
Convergent evolution, evolved independently
Why don’t we change the names of microorganisms?
Healthcare Consistency Keeping track of where microbes go
Archaea shapes
round, rod, spiral
Swarmers and stalkers
Caulobacter crescentes In swarmer form, uses motile flagella to move Once it finds a surface, attaches via stalk and loses flagella Stalk cell divides to produce new swarmers
Akinete
cyanobacteria dormant cell type thick cell wall storing lots of food vegetative cells actively conduct photosynthesis and reproduce, akinetes don’t
endospores
dormant cell type extremely resistant to environmental damage formed when conditions go bad when dividing, makes 1 new endospore instead of 2 new cells usually G+
heterocysts
cyanobacteria, not dormant Nitrogen-fixers anaerobic cell in an aerobic environment since oxygen inhibits n-fixing enzymes 3 layered cell wall and degradation of photosystem 2
Mycococcus Xanthus
hunts in predatory wolfpack forms fruiting bodies when they run out of food
Magnetoglobus Multicellularis
Found in groups of 10-40 cells Removing one cell kills the rest Each cell contains about 80 bullet-shaped magnetosomes Displays negative phototaxis
Anammoxosome
membrane-bound organelle that uses ammonia for energy special lipids in membrane (“ladderanes”) protect rest of cell from harmful chemicals
Do eukaryotes outweigh prokaryotes?
No, prokaryotes also outnumber eukaryotes
Termite digestive system
termites can’t digest cellulose protists break down wood into smaller pieces bacteria (endosymbiotes) secrete digestive enzymes to break down cellulose Archaean methanogens produce methane as a food source for bacteria
Humane Microbiome Project
National Institute of Health project aimed at developing a reference set of microorganisms, disease state vs. healthy state
How do we sample diversity?
Metagenomics, meta-metabolomics
How do we acquire our microbiomes?
Caregivers Environment (breathing in, eating) Medications can disturb it
Steps to biofilm formation
adherence to surface monolayer formation and production of slime microcolony formation, other species join formation of polysaccharide “mushroom”, some cells split off and revert to planktonic cells
Methanogens
obligate anaerobes, only need CO2, N2, and H2O
What is the electron donor in oxygenic photosynthesis?
H2O
What is the electron donor in anoxygenic photosynthesis
H2S
Difference between chlorophyll a and b?
Chlorophyll a is found in all photosynthetic eukaryotes and cyanobacteria Chlorophyll b is the synapomorphy for viridiplantae
Phycobilins
pigments that help absorb wavelengths not absorbed by chlorophyll a and b, useful in low light situations like deep underwater
Chlorosomes
organelle found in green sulfur bacteria Obligate anaerobes, live in extremely low light Photoheterotrophs that use light for energy and carbon to build cells
Types of gene transfer
vertical - parent to offspring horizontal - transfer between cells of the same generation
Types of horizontal gene transfer
transformation, conjugation, transduction
Transformation
cell picks up DNA from environment that was released when a cell died Can be forced in the lab by damaging a cell, will cause it to pick up DNA near it need way of killing those that didn’t pick up new DNA, antibiotic resistance usually included
Conjugation
One cell directly transfers DNA to another using Fertility pilus Copy plasmid and send to recipient
Transduction
virus infects cell A, DNA from cell becomes part of viral particle and spreads with it virus infects cell B which incorporates DNA from cell A into genome
Why is horizontal gene transfer important?
foundation of genetic engineering medicine, research viral transfer of DNA results in 15-20% of cancers
Who and what disproved spontaneous generation?
Louis Pasteur and Germ Theory of Disease
Robert Koch
developed organized method for demonstrating link between microbe and illness (Koch’s postulates)
Koch’s postulates
- Organism must present in all states of disease 2. Isolate pure culture of microbe 3. Observe disease characteristics in test subject 4. Isolate same pure culture from test subject
How did Koch’s postulates hold back virology?
They were followed too strictly
How was tobacco mosaic virus isolated?
First thought to be toxin, crushed and filtered leaves resulted in filtered water harming plants but not leaves, thought that filter stopped bacteria Then realized that it replicated in plants when any dose produced same results, didn’t follow dose response curve
Are viruses living organisms?
No cell membrane No growth or metabolism Do replicate and evolve Require a host organism to replicate
Components of virus
DNA or RNA genome Capsid - protein coat Envelope - typically protein, not always present, glycoprotein spikes for attachment
Types of viral envelopes
Helical Polyhedron Enveloped Complex
How do viruses limit host cell diversity?
Kill 1/2 of all bacterial cells each day Keep diseases at bay
Emerging viruses with a threat to humans
SARS from Asia MERS from middle east
Steps to viral replication
Attachment Entry (Integration) of viral genome into host genome Synthesis of viral proteins and genome Assembly Release
Helper-T cells
Cause body to produce antibodies, activates cytotoxin cells to destroy infected cells, attacked by HIV
Acute infection
short-lived, get sick and get better, common cold
chronic infection
get sick and never get cured, Hepatitis C
latent infection
get sick, symptoms get better, symptoms show up again later, can last for a lifetime, Herpes, HIV
Phage therapy
using bacteriophages to fight infection
What causes chronic and latent infections to show up?
Injury or harm to host cell can trigger replication
How can viruses cause cancer?
If they integrate their DNA close to genes controlling growth, cells can replicate uncontrollably
oncogenes
genes that normally are tightly controlled and related to growth, viruses can cause them to lose control and cause cancer
Similarities and differences between bacteria, archaea, and eukaryotes in:
Chromosome structure
Nucleosome structure
Chromosome segregation
Introns in genes
Ribosome number
Initiator tRNA
Operons
Capping of mRNA
RNA Polymerases
Promotion of Structural Genes
Cell compartmentalization
Membrane Lipids
What is the defining characteristic of eukaryotes?
nucleus
nucleus
membrane bound organelle containing DNA, site of RNA synthesis
must have ribosomes to be true nucleus
exists only in eukaryotes
What is the difference in RNA synthesis between prokaryotes and eukaryotes?
Prokaryotes have simulataneous transcription and translation all in cytoplasm, no introns/exons
Eukaryotes transcribe RNA in nucleus, then introns stay and exons recombine and go to cytoplasm to create proteins
Cons of using nucleus for protein synthesis
DNA takes up a lot of space, can be problematic with many or large chromosomes
Endosymbiosis
theory that mitochondria and chloroplasts originated from bacteria that took up residence in a primordial eukaryotic cell
Anagenesis
Straight line from A to B
New species from many small accumulations over time
Cladogenesis
Divergence between species over time, Darwin’s finches with geographical division
Reticulate evolution
Sharing of genetic material results in new species
Types of reticulate evolution
Horizontal gene transfer - a few genes move
Hybridization - entire genome moves
endosymbiosis - entire cell moves
Sites of DNA in a cell
nucleus, mitochondria, chloroplasts
Sites of RNA synthesis in a cell
cytoplasm, mitochondria
Mitochondria function
oxidize food residues to produce usable energy
Chloroplast function
reduce CO2 molecules to produce sugar
Pros and Cons of Mitochondria
Pros:
More energetic organisms, gave rise to predators
19x more energy, metabolic efficiency
Cons:
Habitat restrictions, need oxygen
Pros and cons of chloroplasts
Pros:
Energy independence
Less energetic demands
More resources for reproduction, more offspring produced
Cons:
Makes you into food
Habitat restrictions, need sunlight
T/F: eukaryotic plastids are more closely related to their cell’s nucleus than bacteria
False
Cyanobacteria and plastids form a:
monophyletic grouping (clade)
What group are we a member of? What else is in that group?
Opisthokonta, fungi and metazoa
Where did the first endosymbiotic capture occur?
Archaeplastida
Parasymbiosis
Two organisms undergo symbiotic relationship side by side
Who controls each membrane in archaeplastida plastids?
Nucleus controls outer
Plastid controls inner
Glaucophyte
Plastid contains peptidoglycan (cell wall of bacteria) in membrane
Only chlorophyll a
Requirements for endosymbiosis
- Obligate relationship, mixing of DNA caused by horizontal gene transfer
- Cell, not organism, living inside another cell
- Passed through vertical transmission
Cryptomonads
Provide evidence for secondary endosymbiosis
cyanobacteria inside eukaryote inside eukaryote
3 sets of genetic material in one cell
Dinoflagellates
Show secondary and tertiary levels of endosymbiosis
Plastid can’t survive without cell, cell can’t survive without plastid (obligate relationship)
Hatena
When they divide, 50% of cells are photosynthetic and 50% are heterotrophs
In the wild, they eat nephroselmis and use their chloroplasts and eyespot for energy
If digested, swells up feeding hole so it can only be photosynthetic
synapomorphy
evidence for a monophyletic group
presence of a plastid in archaeplastida
feature that only that group has from a common ancestor
3 clades of archaeplastida
viridiplantae
rhodophyta
glaucophyta
What is the synapomorphy for chlorophytes?
Chlorophyll b
Chlamydomonas
Vegetative, normal states are haploid
Enters a sexual reproductive state when environment toughens, 2 haploids combine to form diploid zygote
Undergoes meiosis to produce 4 new cells
Isogamy
two identical, undifferentiated gametes
Oogamy
two different gametes come together to form zygote
iteroparity
ability to reproduce more than once
semelparity
organisms that only reproduce once in lifetime
genetic load
recessive, harmful alleles building up in a population’s gene pool
two primary synapomorphies of streptophytes and what they allow
phragmoplasts
rosette proteins
allowed for the development of life on land
Phragmoplasts
microtubular assemblages that move chromosomes, guide movement in cell, arrange material
Difference between phragmoplasts and phycoplasts
Phragmoplasts let cells fully divide, true multicellularity
Phycoplasts keep cells connected but still individuals so only allows unicells and colonies
