Microbiology

Characteristics

• Prokaryotes
    * flagella:: bacteria use to propel themselves
    * pili:: allow prokaryotes to stick to substrates or exchange DNA
• Bacteria
    * no membrane bound organelles, no nuclear envelope, circular chromosome
    * ^^peptidoglycan in cell wall^^, one kind of RNA polymerase, inhibited by antibiotics, can’t survive in extreme temperatures
      * antibiotics:: many target peptidoglycan and damage bacterial cell walls
      * gram stain:: used to classify bacteria into gram-positive and gram-negative groups based on cell wall composition
• Archaea
    * no membrane bound organelles, no nuclear envelope, circular chromosome
    * ^^polysaccharides and proteins in cell wall^^, many kinds of RNA polymerase, not inhibited by antibiotics, can survive in extreme temperatures
• bacterial photosynthesis:: bacteria have modified cell membranes that allow them to perform photosynthesis or respiration, unlike plants who use membrane bound organelles such as the chloroplast
    * endosymbiotic theory - this evolved when cells engulfed photosynthetic/aerobic bacteria

Bacterial Genetics

• bacterial genetic material:: chromosomes are a singular circular piece of DNA, extra DNA is stored in plasmids, small ribosomes
• horizontal transfer:: the exchange of genetic information between bacterial cells
• binary fission:: rapid asexual production; bacterial chromosome replicates, cell divides, daughter cell is a clone
• conjugation:: sex pili form a tunnel between bacteria, copies of chromosomes move from one bacteria to another
• transduction:: bacteria acquire new DNA from a phage infection (virus)
• transposons:: mobile sections of DNA that replicate themselves, splice themselves out, and insert themselves in another locations; turns genes on and off → genetic diversity
• transformation:: bacteria take in plasmids from the environment, sometimes incorporated into the bacterial chromosome, recombinant DNA is formed
    * ex. if one bacteria cell has resistance to an antibiotic, the resistance can spread to all bacteria in a hospital by releasing its DNA for other bacteria to pick up

Manipulating Bacterial Genes

• plasmid vectors:: plasmids used as tools to clone, transfer, and manipulate genes
• reporter genes:: used to visualize that the foreign DNA is incorporated and being expressed in the transformed organism (ex. glowing green protein)
• selection genes:: inserted genes that allow for the isolation of the transformed organisms (ex. antibiotic resistant genes)

Bacterial Ecology

• bacteria are everywhere and in every ecosystem; most species can’t be grown in a lab
• thrive anywhere; there are autotroph species and heterotroph species
• microbiome:: in humans, affects genes, immunity, health, etc.; improved with probiotics and prebiotic foods
• relation to multicellular organisms
    * parasitism:: some bacteria live in host organisms and obtain food from/at the expense of the host
    * commensalism:: one organism benefits while the other does not benefit nor is harmed (ex. gut bacteria don’t benefit but humans do)
    * mutualism:: both organisms, bacteria and host, benefit from the relationship
• signal transduction:: how cells respond to substances in their environment with signaling molecules on the surface and inside the cell

Viruses

• viruses aren’t considered to be living because they can’t live or reproduce without a host
• have DNA or RNA as genetic material
• capsid:: protein shell, encapsulates viral genome
• some have membranous envelopes
    * viral enveloped:: surroup capsid, derived from host membrane, combo of viral and hos molecules
• glycoproteins:: on surface of virus, host specific, help virus enter host cell
• DNA viruses:: replicate with host cell’s machinery, less mutation because more accurate replication
• RNA viruses:: replicate with RNA polymerase, less proofraeding, more mutations, rapid evolution so they are difficult to control with vaccines
• phages:: prokaryotic viruses, eat bacteria lawns, specific to bacteria
• Lytic Cycle
    * virulent phages, most common cycle
    * infection, synthesis, assembly, lytic release
    * degrades the host DNA, host cell lyses
• Lysogenic Cycle
    * temperate phages
    * phage DNA splices into chromosome
    * when cell replicates, phage DNA replicates with it
    * switches to lytic cycle when conditions change
• Retroviruses
    * RNA genome, use reverse transcriptase to convert DNA and integrate into host cell
    * attaches, infects, reverse transcriptase, integrate into host DNA, synthesis, assembly
    * reverse transcriptase is error prone & lacks proofreading, so there is much mutation
• viral fossils:: virus infections integrate DNA into our genomes; some end up doing nothing, the integrated viral DNA becomes a part of our own

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