Bio 301 - Ch 1 Book Notes

  • microbes can be both harmful and helpful

    • if the pathogen is highly contagious or relatively unstudied, it may require containment at biosafety level 3 or 4 (BSL-3 or BSL-4)

    • the use of polymerase chain reaction has been helpful to detect small amount of DNA traces of blood or of fossilized bones

  • microbes are diverse in form and lifestyle - typically microscopic with exceptions

    • all kinds of life host viruses, some of which have preferences for a particular environment

    • they can consist of just a singular cell unit and have a genome used to reproduce its species

      • they acquire food, gain energy to build themselves and respond to environmental change

      • they evolve rapidly

    • microbial cells can range in sizes from 5 mm to <0.2 um

  • examples of diverse microbes that contradict the traditional definition

    • super-size microbial cells

      • can be seen by the unaided human eye (page 4)

    • microbial populations and communities

      • formation of complex multicellular assemblages like biofilm and fruiting bodies

      • two examples of multicellular organisms that require observation under a microscope but are not considered a microbe are mites and tardigrades

    • viruses

      • a noncellular particle containing genetic material that takes over the metabolism of a cell to generate more virus particles

  • the three domains of life: bacteria, archaea, and eukaryota

  • microbial genomes are sequenced

    • the use of advanced microscopy and sequencing of genome allowed for further insight to microbes

    • the genome reveals how the microbe grows and associates with other species

      • we can trace ancestry and close relatives to a species & potential evolution paths

    • metagenome: the sum of genomes of all members of a community of organisms

  • microbes and human history summarized

  • microbial disease devastates human populations

    • bubonic plague point in case wiped out 1/3 of Europe’s population

    • in the nineteenth century, tuberculosis was out here claiming many lives (and resistant strands of it are still present today)

    • influenza had a head count of a number larger than those killed in WWI

    • AIDS also be out here, killing about 35 million

    • COVID, the star of the show, killed 6 million deaths (hold your applause)

  • medical statistics & health disparities

    • Florence Nightingale recognized the significance of disease in warfare

      • founded the science of medial statistics and devised the “polar are chart” to represent mortality rates by certain causes

      • prompted the improvement of living conditions and standards of army hospitals

    • medical statistics bring insight to disparities that racial and ethnic groups face

      • caused by racism, lack of access to quality health care, and lower socioeconomic status

  • microscopes reveal the microbial world

    • Robert Hooke observes the microscopic world by building a compound microscope and published his drawings of the microbes he observed in Micrographia

    • Antonie van Leeuwenhoek observes bacteria with a single lens

      • grinded lens strength until he produced a lens stronger than Hooke’s

      • founded the fundamental idea that heat kills microbes

  • spontaneous generation

    • a theory that was supported in the 18th century due to the fact that the process seemed similar to the way chemicals changed during a reaction

    • Redi’s experiment of maggots found in decaying meat supported the theory of being the offspring of flies

      • argued against spontaneous generation

    • Spallanzani further warranted the opposition by showing that a sealed flask of meat broth that was sterilized failed to grow microbes

      • noticed that microbes appeared in pairs (asexual reproduction - parents)

      • demonstrated cell fission, a process of new cells forming by the splitting of preexisting cells

    • Pasteur’s experiments proved the theory that microbes did not arise by spontaneous generation (wasn’t believe yet though)

      • studied mirror chemistry & chirality

      • discovered that some organisms do not need oxygen to appear - one of the key components of why Spallanzani’s findings were rejected

      • used a swan neck flask that allowed air passage but prevented particle contamination to experiment

    • Tyndall performed Pasteur’s experiment but had heat-resistant bacteria, endospores, within his solution of hay infusion

      • the spore can only be killed by multiple rounds of boiling and resting

      • the invention of the autoclave gave way to a more efficient way to reduce microbial contamination by using steam pressure

  • life origins

    • components of early life included the following:

      • anoxic conditions (no oxygen)

      • presence of heat in the form of lightening or electrical discharge and ultraviolet rays

      • organic molecules that have a strong tendency to donate electrons

    • when a stimulation is run to test the necessary components of early Earth, it was found that amino acids were produced

  • medical microbiology

    • Koch devised the first scientific basis for the germ theory of disease

      • he studied anthrax because it took a toll on agriculture and livestock longevity

      • the pathogen can survive for an extended period of time in dormant conditions and in a desiccated endospore form

      • demonstrated the principle of the chain of infection which illustrated the transmission of a disease

    • Koch & his colleagues used this newfound information to apply to a dormant disease that had been quite deadly: tuberculosis

      • by following a series of steps from a starting stock of inoculated serum, they found that M. tuberculosis causes tuberculosis

    • Julius Richard Petri invented the Petri dish

    • Angelina Hesse recommended her husband use solidified agar in the petri dish as a gelling agent to remain intact at high temperatures

  • Koch’s postulates

    • because some organisms like intracellular pathogens and viruses cannot be grown in pure culture, Koch developed a set of criteria for establishing a causative link between an infectious agent and a disease

      • these postulates can be used to determine whether a given strain of microbes cause a disease

      • there are exceptions though, like Lyme disease, where the organism does not necessarily meet each criteria requirement

    • one difficulty with many human diseases is the absence of an animal host that exhibits the same disease

      • the two species may not show the same range of symptoms when inoculated which presents a limitation to testing and application

  • immunization can prevent the potential to get disease

    • it was found that the deliberate inoculation of individuals with the disease that was killing everyone proved to decrease the spread of disease

      • during a period outside the host, the virus becomes attenuated - it loses some of its molecular structure required for infection

    • the act of variolation led to vaccination, the inoculation from cowpox lesions

    • molecular components of pathogens generate immunity

      • Pasteur’s bitch ass recognized the significance of attenuation and extended the principle to other pathogens

      • the method to attenuate a strain depended on the pathogen present though heat treatment or aging for periods of time were the most effective approaches

      • vaccines today are constructed by molecular cloning of certain parts of pathogens

  • antiseptics and antibiotics

    • mortality rates are affected whether proper precautions are taken to prevent the spread of disease like sanitizing one’s hands after dissecting a cadaver

    • Lister found that carbolic acid was the most successful antiseptic agent to treat wounds and surgical instruments

      • sterilization processes became implemented to prevent the spread of pathogens and developed aseptic environments for surgery

    • in search for an antibiotic, it was found that microbes themselves produce antibiotic compounds

      • Alexander Fleming had accidentally discovered penicillin when he was culturing Staphylococcus

      • indiscriminate and broad use of common antibiotics has led to resistance of certain strains of major pathogens to those antibiotics & less effective

  • discovery of viruses

    • Ivanovsky had a porcelain filter that blocked known microbes from passing through

      • the agent of transmission to the disease he was observing wasn’t a microbe but an infectious noncellular particle

    • viruses consist of a helical tube of protein subunits containing its genetic material coiled within

  • Environment and ecology

    • Winogradsky columns are a wetland ecosystem model that maintain layers of niches for certain organisms to thrive in

      • at the top of the column, the conditions are rich in oxygen and usually house cyanobacteria and other photosynthetic organisms that require water, sunlight, and oxygen to metabolize

      • at the bottom of the column, the conditions are anoxic and sulfate rich; this layer houses sulfate-reducing bacteria

    • microbes cycle the many minerals essential for life like atmospheric nitrogen and oxygen

    • Earth’s ecology is microbial ecology since microbes can be found 3 km deep into Earth’s crust and 15 km out into the stratosphere

  • environmental microbes support ecosystems

    • in sewage, ammonia is oxidized by donating electrons to oxygen and in turn form nitrate; nitrate formation can be eliminated by antibacterial treatment

      • subclassification of microbes to be lithotrophs (rock-consuming)

    • Winogradsky cultured nitrifiers on inorganic solution containing silica gel and ammonia

      • an example of enrichment culture which is the selective growth media that support certain classes microbial metabolism

    • some microorganisms play roles in geochemical cycling processes like the nitrogen-cycle, the oxygen-cycle and the phosphorus cycle

    • extremophiles are set as a priority to study since they have valuable applications in industry and bioremediation purposes

      • these would include microbes that have the ability to digest toxic wastes or withstand extreme temperatures as well as extreme salinity or acidic environments

  • microbial endosymbiosis with plants and animals

    • endosymbiosis is the partnership of a host organism with its associated endosymbionts

    • endosymbiotic microbes make essential nutritional contributions to host animals and plants

      • nitrogen-fixing bacteria rhizobia within the root nodules of legume plants

      • invertebrates like hydras and corals harbor endosymbiotic phototrophs that provide products of photosynthesis in return for protection and nutrients

      • cattle and livestock have digestive bacteria that help them break down cellulose and other plant polymers

    • some intestinal bacteria grow as biofilms; play major roles in all ecosystems and within human body parts

    • all multicellular organisms have microbiota

  • microbial life on other plants

    • proposed by Oro due to prior experimentation, he theorized that the first chemical of life could have come from outer space and potentially carried by comets

    • rovers sent to Mars are exploring the presence or absence of water, organic compounds and other pieces of evidence of microbial life

  • the microbial family tree

    • Linnaeus classified every organism into his works by Kingdom, Phylum, Class, Order, Family, Genus, Species; Woese organized three addtional categories termed domains

      • bacteria, archaea, eukarya

  • challenges that biologist faced when tasked with naming microbes

    • the resolution of the light microscope revealed little more than the outward shape of microbial cells

      • vastly different kinds of microbes looked more or less alike

      • this challenge was overcome as advances were made in biochemistry and microscopy

    • microbes did not readily fit the classic definition of a species

      • they reproduced asexually, it was not a group of organisms that copulated

      • when they do exchange genes, they may do so with related strains or with distantly related species

    • the most useful classification defines relatedness on the basis of similarity of DNA sequence since it was believed there was a shorter divergence time from a common ancestor with more gene likeliness

    • taxonomists categorized organisms by only two classes: plant or animal

      • this was contradicting to the lifestyle, cell, structure, and biochemistry of those that could not fit those refined definitions

      • Haeckel proposed that microscopic organisms constituted a third kind of life that he termed Monera

      • this class was then further categorized by Copeland; Monera consisted of prokaryotes and eukaryotes

  • archaea differ from bacteria and eukaryotes

    • usually live in extreme environments like deep sea heat vents or salt pools

    • archaea are intermediates to bacteria and eukarya

      • they are prokaryotic like bacteria

      • they have gene expression machinery similar to eukarya

  • eukaryotes evolved through endosymbiosis

    • the major cellular components of plants and animals are chloroplasts and mitochondria which have double-membranes and have their own chromosomes

      • it is theorized that eukaryotes evolved by merging with bacteria to form composite cells by intracellular endosymbiosis, in which one cell internalizes another that grows within it

      • in the case of those two organelles, they were capable of independent existence

    • this theory was controversial because it implied a polyphyletic ancestry of living species

      • this was contradictory to the long-held assumption that species evolve only by divergence from a common ancestor

robot