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Lecture 1

BIO 1130 Lecture Notes - Lecture 1: Antimicrobial Resistance, Anaerobic Respiration, Biogeochemical Cycle

Course Code
BIO 1130
Jon Houseman

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BIO 1130
Study Notes
Semester 1
Bacteria and Archaea
Only about 6000 species (approximately 1%) of bacteria and archaea have been discovered
Almost nothing is known about the prokaryotes that live within the ocean (which takes up
about 70% of the Earth’s surface)
The only way to identify prokaryotes used to be to culture them, which was impossible for
those that require extreme physiochemical conditions, and to examine their physical
Techniques have now been created that allow for the DNA of prokaryotes to be cloned and
examined, allowing for identification without culturing —> metagenomics
Even with new techniques, it is still impossible to identify prokaryotes that occur in remote
environments (i.e. deep oceans, etc.)
Prokaryotes make up two of the three domains of life —> Bacteria and Archaea
Bacteria are the most well known prokaryotes, they are responsible for diseases as well as
production of several common foods
Archaea were just discovered and are not as well known
Archaea have characteristics of both eukaryotes and bacteria, as well as characteristics unique
to only archaea
Prokaryotes are the smallest organisms in the world (between 1um and 2um long on average)
It is estimated that the diversity of prokaryotes is in the billions and that their biomass
exceeds that of eukaryotes and potentially plants, despite prokaryotes’ small size
Prokaryotes inhabit every part of the world, including other organisms
The bacteria in and on the body outnumber all other cells
Prokaryotes were the only life form on Earth for approximately 3 million years, hanse why
they are so diverse
Coccoid (spherical), bacilli (cylindrical/rod shaped), and spiral (spirilla) cell shapes are
common among both bacteria and archaea
Some archaea have also been known to have square shaped cells
Prokaryotic cells seem more simple than eukaryotic cells at first glance (cell wall, plasma
The chromosome is packed into a nucleotide region within the cell
There are no organelles equivalent to the ER or the Golgi complex
Generally, functions carried out by organelles in eukaryotic cells are complete by the plasma
membrane and the cytoplasmic solution in prokaryotic cells
Macromolecules (i.e. proteins) are packed into the cytoplasm, making it viscous
It has recently been shown that prokaryotes have cytoskeletons that perform the same general
functions as eukaryotic cytoskeletons, but are not the exact same in structure
Some prokaryotic cells (i.e. those that oxidize ammonia for energy) appear to have organelles
that carry out specialized functions
Most prokaryotic cells have a single circular strand of DNA (some, i.e. in the bacteria that
causes Lyme disease) have a single linear chromosome)
Most contain smaller circular pieces of DNA called plasmids
Plasmids replicate independently and are able to easily transfer genes (i.e. those for antibiotic
resistance) to other prokaryotic cells and even those of other species via horizontal gene
Peptidoglycan (polymer of sugars and amino acids) cross-linkages give the cell wall its
structure and rigidity —> penicillin blocks the formation of these cross-linkages

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BIO 1130
Study Notes
Semester 1
Gram positive bacteria have a thick peptidoglycan layer and therefore retain a purple colour
after being stained
Gran negative bacteria have a thin peptidoglycan layer as well as an outer membrane
(containing lipopolysaccharides), gram negative does not retain a purple colour after being
The outer membrane protects gram negative cells from potentially harmful substances (i.e.
penicillin) making it less sensitive
Archaea are made from a molecule that is related to peptidoglycan, proteins, or
Different archaea respond differently, meaning that the gram-negative/positive staining
method ors not work for them
Prokaryotic cell walls are surrounded by a capsule (layer of polysaccharides)
The capsule is “sticky” and works to protect the prokaryotic cell from things such as harsh
environments and molecules (such as antibiotics) that may try to harm them
Capsules can be the difference between a nonvirulent and virulent from of bacteria (i.e. a
bacteria with a capsule is virulent and one without is nonvirulent)
Prokaryotic flagella are whip-like extensions that allow for the organism to perform a
swimming motion through liquid
Prokaryotic flagella are composed of rigid helical proteins, some which work as propellors/
motors which rotate the flagella
Archaeal flagella are essentially the same as bacterial flagella, however the two develop
differently, are coded for by different genes, and contain different components
Pili are rigid protein shafts that extend from the cell wall and allow the cell to stick to different
surfaces (i.e. sex pili which adhere two cells together and allow for the movement of plasmids)
Bacteria and Archaea Metabolism
Classification of organisms is based on intake of carbon as it is the backbone of all organic
Autotrophs = synthesize organic carbon using inorganic carbon (i.e. plants)
Heterotrophs = get carbon from organic molecules (i.e. animals)
Photoheterotrophs = use light as an energy source and obtain carbon from organic molecules !
= i.e. some prokaryotic organisms
Chemoautotrophs = obtain every by oxidizing inorganic substances, use CO2 for carbon !
= i.e. prokaryotes that live in deep sea hydrothermal vents
Photoautotroph = use CO2 for carbon!
= i.e. some bacteria, some protists, and most plants
Photoheterotroph = use organic molecules to gain carbon !
= some bacteria
Some prokaryotes use oxygen as a final electron acceptor, as do humans, and are therefore
aerobes (aerobic organisms)
Aerobic organisms cannot survive without oxygen
Some prokaryotic organisms ‘breathe’ oxygen, meaning that they use metals as the final
electron acceptor, using anaerobic respiration

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BIO 1130
Study Notes
Semester 1
Aerobic respiration can also involve other inorganic molecules like nitrate or sulfate as final
electron acceptors —> only prokaryotic organisms are capable of this process
Obligate Anaerobes = poisoned by oxygen, use only anaerobic respiration
Facultative Anaerobes = use oxygen when it is available, but under anaerobic condition
Bacteria and Archaea in Biogeochemical Processes
Prokaryotes’ ability to recycle elements (i.e. carbon and nitrogen) makes them essential as
elements move through an ecosystem (biogeochemical cycle)
As elements go through the biogeochemical cycle, they go from one form to another; this is the
job of prokaryotic organisms (i.e. in the nitrogen-fixation cycle
In nitrogen fixation; N2 —> NH3 —> NH4+
Nitrogen fixation is the only method of replenishing the nitrogen used by organisms and is
carried out by prokaryotic organisms (i.e. cyanobacteria)
Nitrification; NH4+ —> NO3-
Metabolic versatility allows prokaryotes to be abundant and persistent
Asexual Reproduction
Asexual reproduction is normal in prokaryotes and allows for rapid population growth
Parent cell divides (via binary fission), producing two daughter cells that are exact genetic
copies of the parent cell
Binary fission allows populations to grow rapidly; some prokaryotes can complete the process as
in little as 20 minutes and can start another round of division before the first is complete,
meaning that, if given good conditions, a single cell can produce a population of millions
within only a few hours
Quick reproduction and short genomes mean that mutation is more common among
prokaryotes (approximately 100 times as many mutations per gene as eukaryotes per unit of
The increased amount of mutation contributes greatly to the amount of prokaryotic diversity
The ability of prokaryotes to adapt to nearly any environment also contributes to their great
Pathogenic Bacteria
Exotoxins = toxic proteins secreted/leaked from bacterium, present in gram-positive bacteria
(i.e. the exotoxin that causes botulism)
The botulism exotoxin is used commercially under the name ‘Botox’
Endotoxins = lipid A portion of the LPS molecule, works to overstimulate the host’s immune
system, triggering inflammation and often lethal responses, present in gram-negative bacteria
Each endotoxin is different based on the bacterial species and site of entry
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