Microbiology Flashcards
Basics of organizing the microworld
- How Cyanobacteria changes the world:
There’s an organism that changed the world. It caused both the first mass extinction in Earth’s history and also paved the way for complex life. By sending the first free oxygen molecules into our atmosphere,and they did all this as single-celled life forms. They’re cyanobacteria, that don’t even have nuclei or any other organelles.
Earth’s atmosphere wasn’t always the oxygen-rich mixture we breathe today. A really long time ago, the atmosphere was mostly N2, CO2 and NH4. Almost all oxygen was locked up in molecules like water, not floating around in the air. The oceans were populated by anaerobic microbes. Those are simple, unicellular life forms that thrive without oxygen and get energy by scavenging what molecules they find.
Then, cyanobacteria, a photosynthetic microbe, evolved. They can obtain sunlight to create their own energy. They started polluting the atmosphere with a new waste product: oxygen. At first, O2 was eliminated by Fe2+/Fe3+ buffer system in the ocean. O2 then became abundant, replaced NH4. However, O2 was toxic to the anaerobic species –> Great Oxidation Event.
Eventually, life adjusted. Aerobic organisms, which can use oxygen for energy, started sopping up some of the excess gas in the atmosphere.
The oxygen concentration rose and fell until eventually it reached the approximate 21% we have today.
They still pump oxygen into the atmosphere, and they also pull nitrogen out to fertilize the plants they helped create.
General characterization of microorganisms
Introduction of animal and plant viruses, bacteriophages
Virus carries their own genetic materials, can be DNA or RNA, ds or ss. The genetic materials can be circular or linear. The protein cell that enclosed the genetic materials is capsid
General and comparative introduction of microorganisms belonging to the Archaea domain
Introduction of Bacteria domain I.: Chloroflexi, Chlorobi, Cyanobacteria, Chlamydiae strains
Introduction of Bacteria domain II.: Spirochaetes, Proteobacteria, Firmicutes, Actinobacteria strains
- Spirochaetes:
- Gram - strains
- Contain anaerobic and aerobic species, free-living and parasite species
- Long, helically coiled (Corkscrew-shaped)
- Distinctive diderm (Double-membrane)
- Chemoheterotrophic (Obtain energy by breaking down macromolecules like carb, proteins; Carbon souce is from organic molecules or from other organisms)
- Reproducing: Asexual transverse binary fission => Duplication of genetic materials of a parent cell starts the process (Asexual). The cytoplasm separates transversely between 2 pairs of nuclei (Transverse), forming 2 identical daughter cells with the same number of chromosomes (Binary fission).
- Example: Leptosfia –> cause Leptospirosis (Blood infection in human and animals) - Proteobacteria: Biggest single phylum, very high number of species
- Gram - strains, although in practice maybe Gram + or Gram-variable
- Diverse morphology, motility, metabolism
- Morphology: Cocci, Bacilli …
- Motility: Non-motile, Gliding, …
- Metabolism: Chemoautotroph, Heterotroph, Phototroph (Purple bacteria)
- Divided into 6 groups based on rRNA sequences, from alpha to zeta. Including some well-known genera- Pathogenic: Salmonella, Escherichia (E.coli)….
- Free-living (Non-parasitic): Bacteria responsible for N fixation (Oxidizing NH3 to Nitrite –> plant function)
- Causes disease: Diarrhea …
- Firmicutes, now called Bacillota
- Gram +, some are Gram - becuase they have a porous pseudo-outer membrane (Megasphera). Some don’t posses cell walls (Mycoplasma) –> No Gram stain
- They are found in various environments, and the group includes some notable pathogens
- A low GC content group (Less stable than high GC)
- Cocci or Baccilli
- Many produces endospores (a tough structure which is triggered from lacking of nutrients) –> Resistant to desiccation and can survive extreme conditions
- Heliobacteria produce energy through anoxygenic photosynthesis (No O2 product)
- Divided into 2 classes: Clostridia (anaerobic) and Baciili (obligate or facultative anaerobic)
- Related to diabetes, obesity …
- Found in human gut
- Lactic acid bacteria belongs to Bacilli class. They usually found in decomposing plants and milk products, produce lactic acid as the major metabolic end product of carbohydrate fermentation - Actinobacteria
- Gram +, high GC content (G linked with C by triple bond –> DNA structure is more stable)
- Found in terrestial or aquatic habitants
- Important because agriculture and forest depends on their contribution to soil system. They help to decompose the organic matter of dead organisms –> New molecules can be taken up by plants
- Some soil bacteria live symbiotically with plants whose roots pervade the soil, fixing N for the plants. Plants exchange for access to plant’s saccharides
Example: Frankia
- Important pathogens: Mycobacterium –> Cause disease in human (Tuberculosis -> Affects lung and other body parts)
Introduction of the structural types of fungi
Ergosterol in plants have the same function with cholesterol in animals. Ergosterol is a sterol that resides on the cell membranes of fungi and acts to maintain cell membrane integrity
- Hyphae are the tubular projections of multicellular fungi that form a filamentous network (mycelium)
Fungal hyphae release digestive enzymes in order to absorb nutrients from food sources
Morphology of fungi:
- Hypha form (Filamentous structure): hypha (Septate - each cell is separated, has septum / Aseptate: No septum) or mycelium (Branched hyphae)
- Yeast form: Yeast or Pseudomycelium (Yeast cells cling together or form branches)
Sexual, asexual and parasexual reproduction of fungi
A fungus’s thallus is commonly referred to as a mycelium
Symbiosis of fungi and plants, fungal pathogenesis of insect and human hosts
Introduction of the role of microorganisms in the formation and maintenance of terrestrial life
Mention also N and C cycle
How Cyanobacteria changes the world
The carbon cycle in nature. Carbon dioxide and methane utilization
Energy production mechanisms in the microworld
Substrate transport mechanisms of prokaryotic and eukaryotic cells: uptake, release
- Vesicle transport.
Vesicle: A small sac formed by a membrane and filled with liquid. - Passive transport:
b. Facilitate diffusion
- Channel proteins: span the membrane and make hydrophilic tunnels across it, allowing their target molecules to pass through by diffusion. Channels are very selective and will accept only one type of molecule (or a few closely related molecules) for transport. Passage through a channel protein allows polar and charged compounds to avoid the hydrophobic core of the plasma membrane, which would otherwise slow or block their entry into the cell.
- Osmosis: The movement of water from high concentration area to low concentration area. There are more H20 outside the cell, less H20 inside the cell –> H20 moves from outside the cell to inside the cell. It is just dependent upon the concentration of water but also on the concentration of solute. Inside the cell, there are a lot of NaCl and tiny NaCl outside –> Higher NaCl conc inside and lower on the outside
Water also loves to move from low solute conc to high solute conc.
–> The transport protein allows H20 to move in and out of the cell membrane is “Aquaporins”.
- Carrier protein: they will change shape in response to binding of their target molecule, with the shape change moving the molecule to the opposite side of the membrane. They simply provide hydrophilic molecules (which are charged and polar) with a way to move down an existing concentration gradient (rather than acting as pumps).
-> In general, channel proteins transport molecules much more quickly than do carrier proteins. This is because channel proteins are simple tunnels; unlike carrier proteins, they don’t need to change shape and “reset” each time they move a molecule.
- Active transport
a. Primary active transport:
- Active, directly uses ATP
- From lower conc gradient to higher conc gradient –> Go against its concentration gradient –> That is why energy is needed to pump against.
- Na+/K+ pump: Inside the cell: Low Na+, high K+, Oustide the cell: High Na+, low K+. Inside the cell, the pump takes up 3 Na+ –> Triggers the pump to breakdown (hydrolysis) ATP –> Release Pi, it attaches to the pump –> Causes the pump to change its shape, facing outward, releasing 3 Na+ outside
Outside the cell, the binding of 2 K+ triggers the removal of Pi to the pump –> Change its shape again, facing inward, release 2 K+ inside the cell
b. Secondary active transport:
- Active, indirectly uses ATP, the free energy needed to perform active transport is provided by the concentration/electrochemical gradient of the driving ion => Truly dependent on primary active transport pump (Na+/K+ pump)
- A transporter couples the movement: One molecule moves from high to low concentration –> down its concentration gradient, usually Na+. This molecule provides energy for the another molecule to be pumped against its concentration gradient. Another molecule moves from low to high concentration –> Against its concentration gradient, can be Glucose, H+,…
- Example: Na+/H+ antiporter, in kidney. Because of the pumping of Na+/K+ pump, outside the cell, the Na+ conc is really high now. Na+ moves down its concentration gradient, from high to low, H+ moves against its gradient, from low to high
- Symport: 2 molecules moving the same direction
- Antiport: 2 molecules moving the opposite direction
Nitrogen assimilation, nitrogen metabolism, denitrification
The physiological significance of sterols and lipids
While glycogen provides a ready source of energy, lipids primarily function as an energy reserve
Sterols
- they pass on messages received from outside the cell to effect changes inside the cell
- Cholesterol is found in many biological membranes and is the main sterol of animals
- Ergosterol in plants have the same function with cholesterol in animals. Ergosterol is a sterol that resides on the cell membranes of fungi and acts to maintain cell membrane integrity, similar to mammalian cholesterol.
