Microbes Flashcards
(150 cards)
1
Q
What is life?
A
Life is a self-sustaining chemical system capable of Darwinian evolution.
Here, self-sustaining implies that a living system should not need continuous intervention but a higher entity (e.g. a graduate student or a god does something physical) to continue as life.
2
Q
Eating something else is considered to be part of…
A
The self-sustaining system even if it’s a parasite.
3
Q
There are two concepts for life, one is…
A
Self-sustaining. Which by this definition, means for something to be alive, it’s a chemical system so there’s some kind of boundary to it and it has to be able to sustain itself. It has to be able to do some sort of metabolism that allows it to replicate and divide and make more copies of itself. Fire replicates and grows but doesn’t have Darwinian evolution which makes it nonliving.
4
Q
Darwinian evolution requires these three things…
A
Multiplication, Heredity and Variation
5
Q
Multiplication means…
A
When they do that, they make something that is like themselves
6
Q
Heredity means…
A
In general, when these entities replicate, they will make something that is like themselves
7
Q
Variation means…
A
There also must be some variation, there must be some kind of change or difference (mutation), things that are occasionally different from everything else. Which can lead to a population to having this mutation more in the future or less in the future. This is evolution.
8
Q
Where did abiotic synthesis of organic molecules happen?
A
It’s the changing of basic carbon molecules into more organic molecules - something more complex. Still being studied. How close can we get to replicating the conditions on Earth that generated peptides for making proteins, amino acids to make those peptides, nucleotides to make DNA and RNA…
9
Q
How did we get these basic building blocks?
A
Maybe there was some sort of infusion of energy? Maybe it was important to have some sort of interface that made chemistry more likely to happen between these different types of chemicals that were floating around.
10
Q
So these basic building could have happened through…
A
1) Hydrothermal vents. Very deep water, heat and mechanic energy coming out of the ground but at the floor of the deep ocean
2) Rocky pools or hot springs. Lots of energy, lots of concentration of different chemicals
3) Water-land interface. Little micro-water-drops taking place near the ocean’s surface, there is this certain type of very tiny electricity that passes between them and maybe that very first surface chemistry with electricity may have lead to it.
4) Sandy porous clays. Look in textbook. 5) Outer space with comets or meteorites. Maybe it happened elsewhere, maybe the building blocks of life formed on other planets and somehow transported here via meteorites.
11
Q
(blank) are some of the potential energy sources that may be driving these types of interactions to create organic molecules.
A
Lightning and UV radiation
12
Q
An experiment tested the hypothesis that chemical conditions thought to be on early Earth allowed abiotic synthesis of organic molecules. They found…
A
they made amino acids and other organic monomers. But now, we need polymers to make the foundation for life.
Organic monomers (amino acids) > Polymers (DNA, RNA, Proteins)
How could the first polymers have formed without the help of enzymes? Polymerization occurs when dilute solutions of organic monomers are dripped onto hot sand, clay or rock. An experiment was done doing this, the water vaporised and allowed more concentration of the monomers. In some cases, this allowed bonding of the monomers into polymers. Polymerization to form polypeptides called proteinoids.
13
Q
Central dogma is…
A
DNA is an information-bearing molecule that then acts as a template for RNA and through the process of transcription, DNA is used to make RNA molecules. RNA is then used as a template to make protein through the process of translation.
14
Q
What came first in life, RNA or DNA?
A
The biggest reason we focus on RNA being the first information-bearing molecule is that RNA has the capacity to be both information-bearing (a sequence that can be read out as proteins) and it can also (depending on the proteins or enzymes) be turned into DNA. It is something that can go in both of those directions. The last reason is that RNA itself can be catalytically active so RNA is a molecule that unlike DNA can do enzymatic-like catalysis.
15
Q
RNA forms…
A
RNA is a reproducible molecule. RNA exists in different forms; mRNA, rRNA, tRNA, snRNA and ribozymes.
RNA exists in different forms, including ribozymes. Ribozymes also have the ability to be catalytic. RNA has self-splicing. RNA molecules are catalysts: Synthesis of new RNA, intron splicing, formation of peptide bonds between amino acids during translation. The ribosome does the majority of protein creation, inside it is mostly RNA, these do the chemical heavy lifting.
16
Q
Catalytic means…
A
In chemistry, a catalytic substance or a substance with catalytic properties is a substance that increases the speed of a chemical reaction.
17
Q
The RNA world…
A
No enzymes or DNA. RNA as rudimentary genes and catalysts. Heredity, exists in such a system and with this natural selection can work. May have the capacity to conduct its own replication. At some point, because RNA is vulnerable to things such as mutation and variation, the DNA molecule evolved.
18
Q
DNA became the primary information-bearing molecule because…
A
DNA is much more stable than RNA, from maybe it’s stability, DNA outcompeted RNA as the primary information-bearing molecule. At some point, DNA takes over as the primary information-bearing molecule and we get the central dogma. DNA as the central information-bearing molecule, RNA as the signal amplifier and protein as the primary enzymatic worker. This is all possible because these molecules as a population went through heredity, variation and multiplication.
19
Q
Stages in the origin of life…
A
Abiotic synthesis of organic monomers
Abiotic synthesis of organic polymers
The origin of self-replicating molecules
20
Q
Protocells are…
A
they are the basic building blocks we have before cells (the building blocks of the membranes that can contain chemistry). In a protocell, the building blocks, catalytic machinery and self-replicating molecules are contained in a membrane. Protocells can form spontaneously when lipids or other organic molecules are added to water.
21
Q
Simple cell properties…
A
Selective permeability, Membrane potential (energy storage), reproduction (budding)
22
Q
How would a protocell divide?
A
Protocell growth can be accomplished through the addition of free-floating membrane elements. The filling of it by molecules, eventually, when big enough, the cell will split in two. Protocells keep growing and start to enclose these systems, competing with each other and having different forms, which may be the start to things like bacteria or archaea.
23
Q
So, oxidizing without oxygen?
A
Sulfur came from volcanic activity, light sulfur isotopes, hydrogen sulfide (H2S) and sulfur dioxide (SO2), metabolised, releasing oxygen to begin oxygenating Earth’s atmosphere.
24
Q
How early was life? Two primary early signs of life…
A
1) Oldest evidence of life is parokaryotic: stromatolites- fossilised microbial mats of ancient prokaryotes 3.5 BYA. Still found forming in some warm, shallow, salty bays.
2) Isotopically light carbon, possibly formed via biological activity, as far back as 3.85 BYA.
25
The influential Miller-Urey experiment showed that...
with just water, ammonia, hydrogen and methane – and electric sparks to mimic lightning – you could form several of the protein precursors necessary for life on Earth. Stanley Miller and Harold Urey’s aim was to recreate the chemical conditions of early Earth.
26
Scientists hypothesise that chemical and physical processes could have produced simple cells through a sequence of 4 main stages:
1) The abiotic (nonliving) synthesis of small organic molecules such as amino acids and nitrogenous bases
2) The joining of these small molecules into macromolecules, such as proteins and nucleic acids.
3) The packaging of if these molecules into protocells, droplets with membranes that maintained internal chemistry different of that from their surroundings.
4) The origin of self-replicating molecules that eventually made inheritance possible.
27
Single-stranded RNA molecules can make a variety of specific...
3D shapes mandated by their nucleotide sequences. In a given environment, RNA molecules with certain nucleotide sequences may have shapes that enable them to replicate faster and with fewer errors than other sequences. The RNA molecule with the greatest ability to replicate itself will leave the most descendant molecules. Occasionally, a copying error will result in a molecule with a shape that is even more adept at self-replication. Similar selection events may have occurred on early Earth. Thus, life as we know it may have been preceded by an ‘RMNA world, in which small RNA molecules were able to replicate and to store genetic information about the vesicles that carried them.
28
Eukaryotic cells have...
a nuclear envelope, mitochondria, endoplasmic reticulum, and other internal structures that prokaryotes lack. Also, unlike prokaryotic cells, eukaryotic cells have a well-developed cytoskeleton, a feature that allows them to change their shape and thereby surround and engulf other cells.
29
How did eukaryotes evolve from prokaryotes?
Current evidence indicates that the eukaryotes originated by endosymbiosis, when a prokaryotic cell engulfed a smaller one that would evolve into an organelle found in eukaryotes (the mitochondrion). It’s an example of an endosymbiont, a cell that lives within another cell, called the host cell. It may have happened as undigested prey or a parasite.
30
Bacteria are...
One thing we can use to define bacteria is the fact that they do not have a nucleus. They are mostly small and divide through binary fission, they reproduce asexually.
31
Bacteria can be...
spherical (cocci), rod-shaped (bacilli) or spiral (helix) shaped
32
Microorganisms can…
Cause disease, proterct you from bad bacteria, help you digest food, cheat (against one another), make us happier (releases happy chemicals), glow in the dark, make yogurt, follow geomagnectic fields, live in nuyclear power plants (can have its genome entirely ripped apart by the radiation and slowly piece it back together), fix nitrogen from the air, eat oil and do photosynthesis.
33
Microbiome =
the collection of microorganisms living in and on a host organism’s body and their genetic material. These are primarily mutualists with whom we evolved.
34
There are many bacteria that are beneficial such as:
Lactic acid bacteria like lactobacillus that makes yogurt, Lactococcus that makes cheese and environmental bacteria like cyanobacteria that makes oxygen.
35
Most bacteria will have just one cell membrane. Most bacteria have a peptidoglycan...
cell wall (pretty firm barrier against things pressing against the bacteria. Bacteria is more stiff due to this wall). A plasma membrane that surrounds a cytoplasm. This cytoplasm in bacteria contains DNA and RNA (RNA template > Amino Acids = Proteins), no separation between these two.
36
In gram-positive bacteria, they’ll have a...
plasma membrane, and then they’ll have a really, really thick peptidoglycan cell wall.
37
In gram-negative bacteria, they will have...
two of these plasma membranes, an outer membrane and an inner membrane with a thin peptidoglycan cell wall.
38
In gram stains...
The purple dye gets caught in the thick peptidoglucan walls of Gram-positive bacteria, which causes them to appear purple.
39
The DNA in bacteria isn’t like that in eukaryotes. Generally, eukaryotic chromosomes is...
linear and they have many, but in bacteria, almost always the chromosome is circular. When replicating, instead of replicating from many places at once in the chromosome like eukaryotes, bacterial chromosomes will start replication at a single point (likely the origin) and that replication continues bilaterally towards the terminus. Replication takes 50 minutes to 1.5 hours.
40
Bacteria will replicate much faster with better...
nutrients, but in low nutrients, it’ll be much slower. Some bacteria can divide in 20 minutes. But bacterial DNA can be circular, linear or both, but most have a single circular chromosome.
41
How accurate is DNA replication in bacteria?
Spontaneous replication. The chances of a mutation in a particular gene is 1 in 10 million per cell division (1 x 10-7 ). Sounds small but there are 2 x 1010 new cells in your intestine each day (2 billion).
Therefore, (2x1010) x (1 x 10-7) = 2,000 bacteria with mutated genes.
42
Bacteria has a way of evolving that most eukaryotes do not. They do...
1) multiplication, 2) heredity, 3) variation but they also do 4) horizontal gene transfer.
43
Horizontal gene transfer can take place in 3 different ways:
transformation, conjugation and transduction.
44
Horizontal gene transfer reproduction of transformation is...
Property of many bacteria. Sucking up DNA from the environment, chopping it up into little pieces of DNA then harvasting the nucleotides. It inherits a bunch of new genes.
1) Naked DNA in the environment is ‘delicious’ 2) Some bacteria are ‘competent’ to take it up 3) This novel DNA is sometimes recombined into the bacterial chromosome 4) If expressed, this can give the recipient new genes/traits from another species.
45
Horizontal gene transfer reproduction of conjugation is...
Mediated by plasmids. Plasmids are small, double-stranded, circular pieces of dsDNA, natural parasites. They are independent origins of replication and can replicate themselves inside cells. Conjugative plasmids can mediate their own transfer between strains or species. Plasmids have been modified to aid in the genetic modification of bacteria. Basically selfish genetic elements. They transfer their own replicated selves into other cells. They can also help genes move around very quickly.
46
Horizontal gene transfer reproduction of transduction is...
1) Bacteriophage mistakenly packages bacterial DNA 2) Next, infection round DNA is injected 3) This is sometimes recombined into bacterial chromosome. Relies on the viruses of bacteria. What a bacteriophage should be doing is infect a cell, cause that cell to make 100 copies of that phage, and then go on to infect a bunch of new cells (replicating it’s own DNA). Sometimes, it does a bad job by packing the host cell’s DNA instead of their own. So they burst the cell but spread and package the host DNA as well.
47
Consequences of Horizontal Gene Transfer:
DNA that has been transferred can be Disadvantageous (decrease the fitness of the individual cell, Neutral (not affect the fitness of the individual cell), or Advantageous (increase the fitness of the individual cell). This will affect how the cell fares competitively.
48
Selection for Horizontal Gene Transfer:
1) New genes! Toxicity, metabolic and so on. 2) New combinations mean new novel niches
3) Fast forward evolution
Horizontal Gene Transfer is accidental, it’s believed to happen because viruses exists, plasmids exists and eating DNA exists.
49
A key feature of nearly all prokaryotes is the...
cell wall, which maintains cell shape, protects the cell and prevents it from bursting in a hypotonic environment. In a hypertonic environment, most prokaryotes will lose water and shrink away from their wall, losing water inhibits cell reproduction. This makes salt a great way to preserve food.
50
The cell walls in prokaryotes are different than those in eukaryotes:
they instead have cell walls that contain peptidoglycan (a polymer composed of modified sugars cross-linked by short polypeptides. This molecular fabric encloses the entire bacterium and anchors other molecules that extend from its surface. Archaeal cell walls contain a variety of polysaccharides and proteins but lack peptidoglycan.
51
The cell wall in many prokaryotes is surrounded by sticky layer called...
a capsule. It can be dense and well defined or a slime layer if not well organised. Both kinds enables prokaryotes to adhere to their substrate or to others in the colony. These layers also protect against dehydration and pathogenic prokaryotes use this to shield themselves from the host’s immune system.
52
Another way of withstanding harsh conditions, prokaryotes can produce...
endospores. The original bacterium cell produces a copy of its chromosome and surrounds it with a multilayered resistant structure, forming an endospore. Water is then removed from it so metabolism halts. The original bacterium then lyses, releasing the endospore. These endospores then rehydrate and start metabolising when conditions are right.
53
In transformation, the genome in prokaryotes is...
altered by the uptake of foreign DNA from its surroundings.
54
In transduction, bacteriophages...
carry prokaryotic genes from one host prokaryotic cell to another. In most cases, transduction results from accidents that occur during the phage replicative cycle. A virus that carries prokaryotic DNA may not be able to replicate because it lacks some or all of it;s own genectic material.
In conjugation, DNA is transferred between two prokaryotic cells (usually the same species) that are temporarily joined. In bacteria, the DNA transfer is always one-way: One cell donates DNA, the other receives it. A temporary structure is formed between the two cells, called the ‘mating bridge’.
55
A handful of elements are considered macronutrients:
carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur (CHONPS).
56
Phototroph =
obtain energy from the light
57
Chemotroph =
obtain energy from chemicals
58
Autotrophs =
requires CO2 as a carbon source
59
Heterotrophs =
requires organic nutrients as a carbon source
60
Nitrogen is important because...
it is key, it is one of the predominant molecules. Nitrogen is a colourless, odorless and tasteless gas that makes up 78.09% (by volume) of the air. N2 can’t be used for nitrogen for most organisms. N2 is “fixed” into more readily available forms, such as ammonia (NH3), through the process of nitrogen fixation by bacteria.
61
The two kinds of nitrogen-fixing bacteria are...
1) those associated with plants, 2) ones that are free-living in the soil. These two groups are important for N2 being recycled back into a form that other organic lifeforms can use.
62
Endotoxins are lipopolysaccharide...
components of the outer membrane of gram-negative bacteria. In contrast to exotoxins, endotoxins are released only when the bacteria die and their cell walls break down.
63
Diazatroph =
Organisms that can fix N2
We have both free-living diazotrophs and symbiotic diazotrophs. This chemical process takes a lot of energy. Takes 16 ATP proteins just to turn one N2 into NH3.
64
Cooperation between Rhizobia and plants...
1) microbes loose in the soil 2) start to colonise around the root hair, putting out these nod factors. 3) The bacteria forms an infection thread, a single bacteria wide thread down the root hair into the deep tissues of the plant 4) Once the thread is established, the bacteria begin to replicate inside the plant tissues. 5) Plant captures and imprisons the bacterium inside a root nodule. The bacteria goes through a procss called terminal differentiation (become a new form of the same cell, taking on a different shape. Becomes a bacteriod. They will never replicate again) 6) The bacteria converts the N2 into NH3 which the plant needs. Plant gets nitrogen, bacteria gets photosynthesis products.
This is a symbiotic relationship between the two.
65
What is the big deal with oxygen?
Oxidative atmosphere. Reducing or natural atmosphere. Oxygen is at the heart of photosynthesis. “Oxygen strips organic molecules of electrons, often shredding molecules.” Earth didn’t use to have much oxygen.
66
Where was all the oxygen?
In rocks, the process of releasing it from the rocks involved volcanic activity and organisms taking advantage of the oxygen. Oxygen is described as molecule that likes to grab onto things. There are some organisms, like those in our guts that will die even with just a little bit of oxygen around. Oxygen is still only 20% of the atmosphere we have today.
67
Reduction refers to the...
addition of electrons from an atom or molecule. Oxidation refers to the removal of electrons from an atom or molecule.
68
Combustion =
hydrogen oxidation, this reaction produces energy, the oxygen is stripping electrons from hydrogen. Produces a huge amount of energy, hence a combustion. Nitrogen reduction, when hydrogens are added, they coat the molecules. “Reduction has the blanketing effect of a fresh coat of paint.” Also takes a massive amount of energy. Hydrogen carrier- Hydrogen would escape from cells. This big molecule allows the cell to trap hydrogen.
69
NADH...
We see this a lot in the chemical reactions we’ll look at. NAD becoming DH. Hydrogen becomes increasingly important. There is an needed ability of keeping hydrogen in one place in a membrane until it can be used to start molecular reactions. NADH is a big molecule that cannot just pass through a membrane so the addition of the H on the molecule means it cannot pass through the membrane by itself anymore. A good way to build up a concentration of hydrogens on one side of the membrane that can’t cross back again.
70
Before oxygen was enriched, energy generation mechanisms that microbes like bacteria came up with were…
1) Fermentation of an organic compound (not O2) is the terminal electron (or hydrogen) acceptor. Allowed just 2 ADPs to be generated, so not a whole lot of energy generation, just a little bit. If the glucose went through an additional step, alcohol could be fermented. We think these were the first kind of metabolism bacteria developed.
2) Anaerobic respiration where a compound other than O2 serves as a terminal electron acceptor. A second stage, developed from the first. Through a process called glycolysis. But still only a small amount of energy if produced.
3) Some photosynthesisers. H2O is an electron acceptor and NADPH is the terminal electron acceptor. There are two different centers for photosynthesis. Some just had one set of the centers, but were still able to generate energy, it was just half but enough. Some prokaryotes only have half the system for photosynthesis. Some bacteria just have the set 1, some just have set 2 and some have both.
71
What is photosynthesis?
6 waters and 6 carbon dioxides + solar energy allows these to become glucose and oxygen. The opposite of that reaction is cellular respiration, which we all do right now, taking oxygen and glucose in our cells, transforming them into energy and having carbon dioxide and water left over.
Photons (light energy) are used to split the water into O2, H+ and electrons. The electrons are used to power enzymes that increase the concentration of H+ (hydrogen) within the membrane until H+ is finally accepted by NADP. The H+ gradient is used to turn the ATP Synthase, generating ATP (energy currency).
We are taking light energy and using that to elevate the energy of electrons, and we’re doing work with that energy; that work is moving protons across the membrane. An active process of building concentrations of protons down here, so that eventually that proton gradient (which wants to flow in the opposite direction) can be used to crank a machine like the ATP synthase. This is a machine that as those hydrogens are allowed to pass back in the direction they would like to go (which is against this gradient), then energy is being generated for that cell. Happens in the plasmids or chloroplasts in the membranes, like the thylakoid membrane (these membranes can be within the cell, even in photosynthetic prokaryotes).
The important thing to remember is the proton gradient is being developed through the use of energy and electron energy through membranes. This is being used to drive protons in one direction and they are released in the opposite direction which generates ATP, using that ATP synthase.
Photosynthesis predates plants. Happened long before we had the separation of prokaryotes and eukaryotes. Likely took place in the prokaryotes.
72
Cyanobacteria are the only...
oxygenic phototrophic prokaryotes, they built the world. They contain certain chlorophyll and accessory pigments required for photosynthesis. Conducts photosynthesis in thylakoid membranes (similar to what we see in plasmids or chloroplasts). They do other interesting chemistry, like being able to fix CO2 in carboxysomes and many fix N2, in specialised cells called heterocysts. Maintain buoyancy independently using gas vesicles so they have enough access to light. Huge diversity of these bacteria (sometimes called blue-green algae but they are bacteria). An example of a bacterial cell that is multicellular, differentiating into different cells and cooperating as a single organism. Have what looks like a lot of intracellular structures, they have lipid bodies with thylakoid membranes and carboxysome bodies. People once thought they were eukaryotic because they have a lot of structure inside the cell.
73
Cyanobacteria play key roles in many ecosystems...
Environmental change may cause colonial cyanobacteria Trichodesmium to form giant blooms. These are an indicator species, a bloom may take place when a lot of nutrients end up in the ocean. A sign of some kind of nutrients end up in the ocean and what happens with these blooms is that the cyanobacteria starves everything else of oxygen. This is because their populations grow such great numbers that they take all the oxygen for their own metabolism. It can take place when the sewage overflows into the water system and then the cyanobacteria take over, killing all the fish. Benficial but can become harmful when there is no balance.
74
Bacterial metabolism is way more than just O2.
Bacterial metabolism is way more than just O2.
Aerobic respiration:
Electron receptor: O2 Products: CO2, H2O
Anaerobic respiration:
Electron receptor: FeIII Products: FeII
Electron receptor: SO42- Products: HS
Electron receptor: NO3- Products: N2
Electron receptor: MnIV Products: MnIl
Electron receptor: CO2 Products: Acetate (C2,H3O2-)
These have developed and are still successful in some places. There are lots of non-oxygen-related respiration that have byproducts like aerobic respiration. Hot springs can have bacterial metabolism that has never been seen before.
75
Once oxygen is enriched, we get...
cellular respiration and anaerobic cellulular respiration (citric acid cycle). Oxygen is consumed, CO2 is produced, yields huge amounts of ATP! After this was created, many organisms adopted this kind of metabolic machinery and taking off. Much better energy yields than the slow fermentation that was done before it. So metabolism evolution occurred in this order: 1) Fermentation 2) Anaerobic respiration 3) Some photosynthesisers 4) Aerobic respiration.
There are many areas in the world where all these metabolisms are being done, they haven’t gone extinct. There may be more metabolism types we haven’t discovered or has gone extinct.
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Obligate aerobes must use...
O2 for cellular respiration and cannot grow without it.
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Obligate anaerobes are...
poisoned by O2 and some live exclusively on fermentation, others extract chemical energy by anaerobic respiration (in which some substances other than O2 such as nitrate ions (NO3-) or sulfate ions (SO42-) accept electrons at the ‘downhill’ end of electron transport chain).
78
Facultative anaerobes use...
O2 if it is present but can also carry out fermentation ot anaerobic respiration in an anaerobic environment.
79
Nitrogen is essential in the production of...
amino acids and nucleic acids in all organisms. Whereas eukaryotes can obtain nitrogen only from a limited group of nitrogen compounds, prokaryotes can metabolise nitrogen in many forms.
80
In terms of nutrition, nitrogen-fixing cyanobacteria are some of the ...
most self-sufficient orgasnisims since they need only light, CO2, N2, water, and some minerals to grow.
Nitrogen fixation has a large impact on other organisms. For example, nitrogen-fixing prokaryotes can increase the nitrogen available to plants, which cannot use atmospheric nitrogen but can use the nitrogen compounds that the prokaryotes produce from ammonia.
81
Cooperation between prokaryotic cells allows them to use
environmental resources they could not use as individual cells. In some cases, this cooperation takes place between specialised cells in a filament. For instance, the cyanobacterium Anabaena has genes that encode proteins for photosynthesis and for nitrogen fixation. However, a single cell cannot carry out both processes at the same time because photosynthesis produces O2, which inactivates the enzymes involved in nitrogen fixation. Instead of living as isolated cells, Anabaena forms filamentous chains. Most cells only carry out photosynthesis, while a few specialised cells called heterocysts carry out only nitrogen fixation. Intercellular connections allow heterocysts to transport fixed nitrogen to neighbouring cells and to receive glucose.
82
Metabolic cooperation among the cells of one or more prokaryotic species often occurs in surface-coating colonies known as...
biofilms. Cells in a biofilm secrete molecules that recruit nearby cells, causing the colonies to grow. The cells also produce polysaccharides and proteins that stick the cell to the substrate and to one another; these polysaccharides and proteins form the capsule, or slime layer. Channels in the biofilm allow nutrients to reach cells inside and wastes to be expelled.
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Substrate =
The surface or material on or from which an organism lives, grows, or obtains its nourishment.
84
The microbiome of the Tundra is a...
significant variable that affects the future trajectory of climate change. Appears to be a positive feedback loop for climate change. Tundra contains 50% of the world’s Soil Organic Carbon (SOC) storage and temperature is rapidly increasing. Short-term warning stimulates rapid, microbe-mediated decomposition of tundra soil carbon. The microbiome of the Tundra is a significant variable that affects the future trajectory of climate change.
85
All microbes communicate with members of their own species and between species. This type of communication, called...
quorum sensing, allows bacteria to form rich social networks with their neighbors. Bacteria use quorum sensing to keep tabs on the density of members of their species in relation to the density of other species in order to perform fantastically synchronous events that they could never accomplish working in isolation--like the successful invasion of a host.
86
V. fischeri is a bioluminescent bacteria that glows under...
high density conditions. For example, if this bacteria is cultured in a dilute medium, it won’t produce light at all. How exactly does V. fischeri know when and when not to shine in all its glory? It knows this because each bacterial cell releases highly specialized molecules (gram positive bacteria use small peptides) called autoinducers that diffuse in and out of each cell. Since each bacteria is constantly secreting these molecules, the more bacteria present in solution, the higher the concentration of the autoinducer. Once a minimum autoinducer threshold is detected (via cytosolic receptors) by V. fischeri, every single species member changes their gene expression in unison producing luminescence.
87
On the ventral side of the squid is a light organ...
On the ventral side of the squid is a light organ. This organ houses ~10^10 to 10^11 V. fischeri cells--that's a huge culture of bacteria--and this microbiologist of a squid maintains its bacteria culture daily. Since the bobtail squid is nocturnal and lives in a few feet of water, moonlight and starlight easily penetrate to its depth. However, this squid has evolved a pretty neat trick in order to get around at night undetected. The squid can detect the amount of starlight and moonlight coming in, and using its ink sac as a shutter over the light organ, the squid can match the exact amount of moonlight and starlight coming into the water with the luminescence from its light organ, thus producing no shadow as it swims.
The squid also needs to do something about its dying culture in the light organ. When the sun rises and the squid burrows itself into the sand, (s)he dumps out more than 90% of its culture into the ocean. The few remaining V. fischeri cells left are not enough to meet the minimum autoinducer threshold and therefore do not produce luminescence from the light organ.
88
Single 16S rRNA molecule. Very long, single strand, folds and complements itself. Ribosomes:
1) Necessary for life (all life has it, makes it a good benchmark or tape measure to compare sequence evolution. Complementary, whole thing is under intense selection for function) 2) Slowly evolving (Interdependencey keeps the molecule evolving slowly, because if bulges in the wrong places, ribosomes stop working which is bad for life) 3) Interdependent (Complementary means interdependence, so if there is a mutation one one side of the branch, there needs to be one on the other side or else there’d be a bulge) 4) Recognisable (Every cell in the world has 100,000s of copies of this exact ribosomal RNA, because it’s a machine that’s used for every single protein production). Abundance in all cells, all cells must have it, cells need it to live.
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The achaea:
Can have lipid monolayers. Cell walls can be made out of pseudopeptidoglycan, polysaccharides, glycoproteins or protein-based cell walls (which is very unusual for prokaryotes). They are extrophobes and live in very unexpected places such as hydrothermal vents, terrestrial hot springs
90
We don’t know how to grow 99% of prokaryotes in a lab, so only...
1 inn 100 will grow on the media we try them out on. The reasons may be: 1) Temperature, too hot or too cold 2) Wrong nutrients/environments, like some can only grow without oxygen or some need certain nutrients 3) Cross-feeding, can also cause lack of nutrients.
91
Cross-feeding:
Some cells that have existed in a certain environment for a long time will sometimes develop an interdependency on one another. For example one cell through active or passive transport, put out some sort of metabolite or waste product and another bacterium has adapted to that product as a nitrogen or carbon source. So this cell may not grow because it’s not getting the product it gets from another cell, which it has adapted to rely on to grow. Lots of ways for exchange in a cell.
Some archaea are extremophiles, some are not.
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What are Eukaryotes like?
1) Cells with nuclei surrounded by a nuclear envelope with nuclear pores. This is the only trait all eukaryotes have. A nuclear pore is a highly specialised gate that keeps molecular riff-raff out of the nucleus. Part of the reason or consequence of the nucleus is that you have this membrane barrier between the cytoplasm (where the RNA needs to get to, where translation happens, where proteins are produced). So the DNA is protected behind the membrane that makes the nucleus. Has big consequences in how these sort of organisms have evolved. So horizontal gene transfer which is common in prokaryotes, is much less common in eukaryotic cells, partially because of the nucleus and the very important nuclear pore (permeable barrier to the right types of molecules).
2) Most have Mitochondria. They are ubiquitous (found everywhere), but not all eukaryotes have one. Mitochondria are usually shown as bean shapes, but this is incorrect. Due to how cells are cut, to view them, it distorts their shape. Mitochondria are more spaghetti-like structures, a dispersed network.
3) Cytoskeleton of microtubules and microfilaments. The “railway of the cell”. More consistent among eukaryotic cells, but there are some missing this feature. They are these networks allow proteins to kind of march and deliver things from one side of the massive cell to the other. But they also allow cells to do the sort of active things like grabbing things that’s all coordinated by the pushing of the microfilaments.
4) Flagella and cilia. Many eukaryotic cells, especially in this protist world, will have some way of moving themselves. In the amoeba, its stretching and moves the pushing of its actin filaments. Some protists have what we see in bacteria: Flagella or cilia. Cilia are short little things that sort of beat to make movement happen and the flagella has larger movement to move around.
5) Chromosomes organised by histones. The biggest difference between eukaryotes and prokaryotes is that eukaryotes have organised their DNA with histones. That is something at least the bacteria will never have. It’s one of the things that makes a big difference between the prokaryotic and eukaryotic worlds.
6) Mitosis.
The idea that you have complementary DNA, you replicate that, you separate it, and then you complete cell division to have two daughter cells that are equivalent to the mother cell. Common in many eukaryotes but not in all of them.
7) Sexaul reproduction
Not many protists do this, more so an animal thing but some insects don’t even reproduce sexually.
8) Cell walls. We find these in plants but also some fungi. Some eukaryotes will have cell walls. They are found but not necessarily found in eukaryotes.
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Protists have over...
100,000 species described. They are polyphylectic (have many ancestors). The protists are embedded in the tree of life. They are not a single group. They are at the root of many different groups.
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The Nucleariids are an example of...
single-celled motile protists that is an extant example of something that is probably what the fungi were before they became fungi.
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Acathamoebae castellanii:
1) Model organism. Classic amoeba, well-studied, completely sequenced. Lots of copies of its genome so we can sequence it to study it easily. Very simple, it has a dormant state where it’s in a cyst-like form. It comes out of the dormant form when it senses it is in a good environment, then it eats bacteria. If stressed, starving or in bad place it goes dormant. Used in many lab studies as it’s similar to human immune cells.
2) Common in terrestrial and aquatic environments.
3) An opportunistic pathogen that can cause a severe encephalitis (inflammation of the brain, often caused by viral or bacterial infections) in immunocompromised patients.
4) Genetically tractable. It can be used for DNA by adding or editing its genes.
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Dictyostelium discoideum:
1) Model organism. Cellular slime mould. Well studied, completely sequenced. Used to understand a lot of things in microbiology and larger. They have a spore state first. They go from a single-celled amoeba and aggregate (because of starvation) to form a slug (all these single-celled organisms go to one spot thanks to a signal). The slug can be seen with the naked eye, it crawls in the opposite direction of gravity towards light and then forms this thing called the fruiting body which is a huge conglomeration of single-celled organisms coming together to make this stalk. The cells in the stalk are sacrificial to the first cells that made the fruiting body (these cells are the only ones that can go on to survive and reproduce). Studied for cellular aging, cellular cooperation, cytoskeleton, chemotactic motility, fungal or bacterial pathogenicity.
2) Common in terrestrial environments.
3) Pathogenicity is not observed.
4) Genetically tractable. Can be made fluorescent.
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Paramecium caudatum:
1) Model organisim. Classic paramecium. Well studied. Cilia motility (propels them through water) and feeding. Tough organism that has a hard cell wall. Has a hole in their side or groove that allows bacteria to be tossed in to digest.
2) Common in marine, brackish and freshwater environments.
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Phytophthora agathidicida...
Believed to have been single-celled fungi, due to zoospores (small motile spores that allow colonisation of roots). They then form a sporangium that releases more zoospores. This is a protist and in New Zealand is affecting Kauri trees, causing them to die off.
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Extremophiles are...
organisms that live in environments so extreme that very few other organisms can survive in. The name means lover of extreme conditions. Extreme halophiles live in highly saline environments such as the Great Salt Lake in Utah. Extreme thermophiles thrive in very hot environments like deep-sea hot springs (hydrothermal vents).
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Methanogens are archaea that release...
methane as a by-product of how they obtain energy. Many methanogens use CO2 to oxidise H2, a process that produces both energy and methane waste.
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Bacteria vs Archaea vs Eukarya:
Characteristic: Nuclear envelope.
Bacteria: Absent, Archaea: Absent, Eukarya: Present
Characteristic: Membrane-enclosed organelles.
Bacteria: Absent, Archaea: Absent, Eukarya: Present
Characteristic: Peptidoglycan in the cell wall.
Bacteria: Present, Archaea: Absent, Eukarya: Absent
Characteristic: Membrane lipids.
Bacteria: Unbranched hydrocarbons, Archaea: Some branched hydrocarbons,
Eukarya: Unbranched hydrocarbons
Characteristic: RNA polymerase.
Bacteria: One kind, Archaea: Several kinds, Eukarya: Several kinds
Characteristic: Initiator amino acid for protein synthesis.
Bacteria: Formylmethionine, Archaea: Methionine, Eukarya: Methionine
Characteristic: Introns in genes.
Bacteria: Very rare, Archaea: Present in some genes, Eukarya: Present in many genes
Characteristic: Histones associated with DNA.
Bacteria: Absent, Archaea: Present in some species, Eukarya: Present
Characteristic: Circular chromosome
Bacteria: Present, Archaea: Present, Eukarya: Absent
Characteristic: Growth at temperatures > 100oC
Bacteria: No, Archaea: Some species, Eukarya: No
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Endosymbiosis:
(inside) (living together). It can be parasitism, not always balanced or positive. Just means living together inside.
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Genomes:
Mitochondria and bacterial clades - alpha-Proteobacteria and Pastid- Cyanobacteria.
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Nature of Mitochondria:
1) Cannot live independently today (outside the cytoplasm).
2) Have their own genomes. Extremely reduced.
3) Genomes are circular (like bacteria).
4) Ribosomes and transfer RNAs are similar to bacteria.
5) Genes are similar to alpha-Proteobacteria.
6) Some genes have moved to the nucleus.
7) Two membranes like bacteria.
8) They do aerobic respiration (to generate ATP).
9) Binary fission (like bacteria).
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Nature of Plastids:
1) Cannot live independently today (outside the cytoplasm).
2) Have their own genomes. Extremely reduced.
3) Genomes are circular (like bacteria).
4) Ribosomes like cyanobacteria.
5) Genes are similar to cyanobacteria.
6) Some genes have moved to the nucleus.
7) Two membranes, some have peptidoglycan.
8) Have thylakoids and chlorophyll (photosynthesis).
9) Binary fission (like bacteria).
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Timeline on Earth:
We do not have a complete picture of life now. We do not have a complete picture of life then. We don’t know how Eukaryogenesis came about. People have very strongly held beliefs about this despite our lack of information.
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Phagocytosis...
(as a stepping stone to evolving eukaryotes in prokaryotes) is thought to be impossible as it takes a lot of microtubules and microfilaments to get the prey. But in 2019, the first prokaryotic cell was discovered doing phagocytosis. So we now know that it is possible for prokaryotes to do this. Now we think phagocytosis was present in these prokaryotes, which led to eukaryogenesis.
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Chytridiomycota:
Simplest fungi, hangs out with protists, very similar to protists. 500 million years old. Evolved even before land plants evolved.
Zygomycota:
Includes bread mould. They have a sporangium full of sporangiospores.
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Fungi are a single branch of...
eukaryotes. 5 major phyla. They are heterotrophic (they use complex organic compounds such as energy and carbon like us mammals). Their cell walls are made of chitin (like arthropods). They store energy as glycogen (like in animals and bacteria). They absorb nutrients across a surface (like bacteria). Single cell, through wall. Multi-cell, through hyphae walls. Hyphae are present in the stalk, but also are in the roots, the hyphae does the bulk of the work of the fungi (the nutrient exchange of the environment). The hyphae don’t do anything active; they just grow. A mass of hyphae is the mycelium. Fungi acts as decomposers (like bacteria).
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Glomeromycota:
Soil-borne. Mycorrhizal associations with plants. 80% of plants have some kind of relationship with this fungus. Glomeromycota form Arbuscular mycorrhizas. Fungal network below the ground with different fungi. They have a reciprocal exchange: organic carbon is fixed by the plant through photosynthesis which comes down to the fungal networks. In exchange, the fungi siphon soil-derived water and inorganic compounds containing phosphorus, nitrogen, sulphur and other essential nutrients. In the arbuscule is where the two organisms meet. Fungi forms a tube to access inside the plant, the knot is where the exchange of nutrients takes place.
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Ascomycota:
Includes Morel and Neurospora crassa. Spores in sacs (at a microscopic level) are called asci.
It also includes Saccharomyces cerevisiae, a single-celled and buds. Also called “Brewer’s yeast”. Powerful model organisation. Also makes bread, beer, etc. 23% of genes are homologous (similar) to humans. ~500 can be exchanged for human genes. So can add human genes into it and still grow beer from it.
It also includes Penicillium roqueforti, which is found in blue cheese and Roquefort. Also includes Penicillium chrysogenum, the source of the first antibiotic (penicillin).
Lastly, it includes Ophiocordyceps unilateralis or Cordyceps. This is often referred to as the “Zombie-ant fungus”. These are able to take over and control the behaviour of insects.
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Basidiomycota:
“Club fungus” includes the infamous death cap mushroom (Amanita phalloides). Club; produces club-shaped structures (basidia) that contain spores. Inside the gills of these spores are the basidium, a way to recognise the deadly deathcap mushrooms.
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Fungi as a mutualist:
Lichens
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Fungi as a parasite:
Cordyceps
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Symbiosis:
A close, prolonged association between two or more different biological species.
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Linchens are in a type of...
Symbiosis (living together) called a Mutualism in which organisms benefit from their association.
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Some kind of complex structure that mounts amd combines the bulk for some kind of microorganism Mutualism. This mutualism is composed of...
fungal hyphae and inside this is an algal zone (this does the photosynthesis. The zone can contain either algae or cyanobacteria. Algae (or cyanobacteria) do photosynthesis, this creates nutrients for the fungus. The fungus (Ascomycete) provides minerals, water and shelter. The organisms can be grown separately, but lichens cannot be grown in the lab (you cannot get the two to cooperate in the lab like they do in nature). We are still not entirely aware of how these organisms benefit or provide for each other (what they do exactly and what nutrients they provide each other) as they cannot be grown together in a lab. In July of 2016, we learned what we were missing. two structures within the fungi, a cyanobacteria or algae and now a yeast dotted around.
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Cicadas (and many other insects) often rely on...
bacterial endosymbionts/have important relationships with endosymbionts. 50% of insects have this crucial relationship where they are completely reliant on bacteria. There are long term associations. Common in insects (ants, aphids, flies). Insects have special organs called “Bacteriomes” inside these organs is where the bacteria is. Insects eat sugars, it and provides sugar to bacteria. Bacteria provide insect with (this varies) vitamins, amino acids. Some insects have completely lost the ability to produce needed amino acids or vitamins because it's always been provided by their inner bacteria. Has membrane where bacteria is hosted. Some insects have have a lot of their internal area occupied by these organs.
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Endosymbiont does not mean...
“beneficial”, it just means living within
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Wolbacteria is an example of an...
endosymbiont that isn't beneficial. It is a reproductive manipulator, so it stops the insect from doing different types of reproduction. Sometimes they cause parthenogenesis, cytoplasmic incompatibility, feminisation and male-killing of offspring.
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FISH:
Fluorescent in situ hybridisation. Used to take a closer look at DNA, helps to understand where different types of microorganisms are found. Thin slice of sample is prepared on slide, then the microscope slide is subjected to different heat and chemical treatment. What the heat does it allows the DNA to become single stranded, the heat allows the DNA to open up (denaturing the DNA). A single probe is then added with a single modified base. That modified base is going to have some sort of chemical nature to it that allows it to then react to something that you then apply to the slide which is a fluorescent property. So if this particular DNA is present anywhere, it will light up.
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A sign of yeast is a single-celled organism that...
does budding. Fungi will often form these long structures of hyphae, but if you see one large eukaryotic cell that looks like it has budding, then it's a sign of a yeast. These fungi are closely related to Ophiocordyceps… the yeast like fungi that takes over the brains of some cicadas.
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Much of the protistan diversity can be traced to...
endosymbiosis. Over time, early heterotrophic and photosynthetic eukaryotes have given rise to four highly diverse supergroups of eukaryotes: the Excavator, the SAR, the Archaeplastida and the Unikonta.
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The cytoskeleton provides the...
structural support that enables eukaryotic cells to have asymmetric (irregular) forms as well as to change in shape as they feed, move or grow. In contrast, prokaryotic cells lack a well developed cytoskeleton, this limiting the extent to which they can maintain asymmetric forms or change shape over time.
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Viruses genomes made up of...
4 genes (maxium), which is why they cannot be put onto the Tree of Life (Phylogenectic Tree). We don’t know if viruses have done the life processes, if they came about many times or risen once. Every form of life has viruses, even bacteria.
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Viral structure:
Requires a host cell for replication - they are parasites. This is a key defining feature for viruses.
Most are small, <20nM, smaller than a ribosome!
Can have lots of different types of nucleic acid in the protein (sometimes lipid), DNA, RNA, SSRNA, SSDNA. Can be single stranded DNA/RNA or double stranded RNA/DNA.
Generally small genomes; 2,000-100,000 bp (1,181,404 basepairs exception).
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Viruses have classification based on their target:
Viruses of bacteria = bacteriophage or phage
Viruses of animals = viruses
Viruses of plants = viroids
Viruses of fungi = mycoviruses
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Structure of viruses:
Capsid = Protein coat of virus. All viruses have capsids.
Capsomere = Subunits of the protein that make up the capsid.
Viruses vary in size and shape. Generally just one or two types of proteins used to make capsid. The capsid wraps up or encloses the genome.
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Viral reproduction:
Viruses are obligate parasites - they lack the ability to do active things intentionally, the enzyme inside them only does things when injected into a host, they are inert particles until then.
They lack metabolic enzymes, they lack proton movative force (the ability of cells to generate energy, hydrogen proton on one side of the membrane to the other. This generates energy).
Their host range is usually narrow (we think, we don’t know unless it’s tested who the virus can infect). Host attachment is specific to the ‘receptor’, this determines how well a virus can jump between hosts and exchange genomes to jump between hosts.
Their lifycyle begins with nucleic acid injection or endocytosis or membrane fusion.
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These occur in eukaryotic/animal viruses...
Virus is absorbed into host cell, then a few different possible outcomes can occur. Cytocidal infection resuls in cell death through lysis. Persistent infection may last many years. Cytopathic effects, degenerative changes, abnormalities. Transformation to malignant (cancer) cell.
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Where do emergent viral diseases come from?
Mutations. Increased dissemination of existing strains. Spread from animals to humans (recombination). 10-20% of cancers are associated with viral infection.
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10 times more bacteriophages than there are...
bacteria.
Bacteriophage can lie dormant in bacteria with the lysogenic cycle. When it gets a signal (chemical damage, DNA damage, cell starvation) they will then switch to the lytic infection cycle.
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Advantages of Phage Based Therapies:
Specific (can just destroy infection and not normal microbiome), Numerous (so many around), Recyclable (causes no harm in the enviroment).
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Disadvantages of Phage Based Therapies:
Specific (finding the right phage for the infection), Numerous (we "know" about 3000 of these), Recyclable: (Delicate, won’t work if damaged), Old School (we are still learning about them).
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The Human Microbiome:
The microbiome - the commensal microbes that inhabit our skin and gastrointestinal tract; bacteria, archaea, yeast and even viruses contribute to the microbiome.
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Commensal =
an organism that uses food supplied in the internal or external environment by the host, without establishing a close association with the host. An example of this is a monarch butterfly on a milkweed, both rely on each other but aren’t intracelluluar or attached.
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The Microbiota =
microorganisms. Used interchangably with Microbiome.
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The Microbiome =
DNA of those organisms. Used interchangably with Microbiota.
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The Holobiont:
Host (human) + microbiota.
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We believe all microbiomes are...
unique (no core), so there is no set of bacteria that is present in everyone's gut. There are "core" functions filled by various organisms these genes for these function are present in many different bacteria.
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The prokaryotes in you microbiome:
Liberate nutrients from otherwise inaccessible dietary substrates, promote differentiation of host tissues, stimulate the immune system, and protect the host from invasion by pathogens.
Liberate nutrients from otherwise inaccessible dietary substrates.
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Probiotics:
live micro-organisms that are supposed to confer a health benefit. The long term residence of probiotics in the gut has not been clearly demonstrated.
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Prebiotics:
subtrates that are intended to selectively feed micro-organisms in the gut. The long term effects of prebiotics on health are highly speculative.
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The vagus nerve...
goes all the way from the brain to the bowels. There are all sorts of signals that are generatedf by bacteria in the gut, which is received by the vagus nerve endings and transferred to the brain. Because of this, the gut can have an affect on the brain.
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Two way communication
communication, direct and indirect.
These are all chemicals, peptides and hormones that are produced by microbes in the gut and transferred to the brain. Oxytocin a neuropeptide hormone, social bonding, childbirth. GABA (Gamma aminobutyic acid) an inhibitory neurotransmitter. Reduces neuron excitability. BDNF Brain derived neurotrohpic factor Maintains neurons.
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Bacteriodes is very common to find in the...
human gut. Things that cah change the microbiome in the gut are diet changes, antibiotics, illnesses and the environment.
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Antibiotics can effect the...
microbiome ... a bit. Outcomes vary but microbiomes generally recover
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Microbiome and Antibiotics:
Clostridium difficile. Common pathogen, harmless at low levels. Can be resistant to certain antibiotics. Reduction of microbiota can allow it to take over. This is usually caused by the use of antibiotics.
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Clostridium difficile Infection (CDI):
Asymptomatic or diarrhea or toxic megacolon (where a healthy guy has a bunch of toxins injected into it by a bacteria and becomes inflamed). 29,300 deaths from C. difficile (CDI) each year. Some patients infected in the hospital (spores). Can be from the person’s own gut but it’s allowed to flourish because of antibiotic use.
Antibiotics are not effective in 15-26% of patients. Recurrent infections are often not treatable.
Vancomycin (last resort) prescribed but this Disrupts the microbiota, Selects for AB resistance, Does not affect the spores. This can be a very dangerous and worrisome infection for some patients.
Fecal Transplants:
93.8% of repeat CDI patients cured without relapse.
What changed? Microbial diversity was restored in treated patients
