Tree of life
3 Domains – Bacteria, Archea, Eukaryote, Microbes in all 3 and we are just a small blip on the homo sapien, eukaryote branch.
bacterial cells and those that are pathogenic
Only 5-7% of microbes are known to cause disease out of millions of bacteria.
Early microscopists and their contributions
Van Leeuwenhoek – Built first microscope
Koch’s disease postulates
These postulates stated that to establish that an organism is the cause of a disease, it must be found in all cases of the disease examined. Additionally, it must be absent in healthy organisms prepared and maintained in a pure culture capable of producing the original infection, even after several generations in culture retrievable from an inoculated animal and cultured again.
Roles of microbes, use in research
Antibiotics, Biotech and Disease research, Bioremediation (oil spills) – microbes help clean up - Cheap and easy to use
Enzyme structure and function and how this related to pH and temperatur
Lower activation energy – primary, secondary, tertiary and quaternary structure create a specific active site that allows a specific substrate to bind to create the product. Because the activation energy is lower, the reaction can occur much faster. But this is dependent on the optimum environment including pH and temperature.
Polyhydroxyalkanoates, or PHAs, are linear polyesters produced in nature by bacterial fermentation of sugar or lipids. They are produced by the bacteria to store carbon and energy. More than 150 different monomers can be combined within this family to give materials extremely diverse properties. These plastics are biodegradeable and are used in the production of bioplastics. They can be either thermoplastic or elastomeric materials, with melting points ranging from 40 to 180 °C. The mechanical qualities and biocompatibility of PHA can also be changed by blending, modifying the surface or combining PHA with other polymers, enzymes and inorganic materials, making it possible for a wider range of applications.
Break down of larger molecules to smaller ones and does not require energy
The buildup of smaller molecules into larger ones and requires energy.
a classification of bacteria based on how they obtain energy, Autotrophs make their own food by using the energy of sunlight or chemical reactions
a classification of bacteria based on how they obtain energy, Heterotrophs obtain their energy by consuming other organisms.
Phototrophs are organisms that carry out photon capture to acquire energy
a class of organisms that obtain their energy through the oxidation of inorganic molecules, such as iron and magnesium.
Shapes of bacteria
Bacillus - Rod ; Coccus = Sphere ; Vibrio = Comma Curve ; Spirillum = Spiral ; Spirochete = Ribbon curl
8 cells, 4 on top and 4 on the bottom
When a cell endocytoses another cell, i.e. a bacterium. The bacteria is engulfed into the cell and provides some beneficial features to the cell so instead of killing the bacteria or getting rid of it some way, they cohabitate. There is evidence to this in that Mitochondria have their own membrane and own DNA, which can be traced back to at one point mitochondria must have an independent organism that was engulfed by a larger one. They also believe cyanobacteria was engulfed by early plant cells and it is the reason they have chloroplasts.
Sizes of bacteria
Millimeter = 10-3 , Micrometer = 10-6, Nanometer = 10-9
Wavelength vs Resolution
The shorter the wavelength the better the resolution, visible light has a longer wavelength than electrons
Bouncing of light
Bending of light (through a substance)
Taken into an object
Readmitted at a different wavelength
Leaves a small hole and bends
positive ions and basic that bind to negatively charged microbes
negative ions an acidic that bind to positive charged microbes
Used to divide bacteria into two main groups (gram neg and gram pos). The reaction is based on the amount of peptidoglycan found in the cell walls of bacteria. Gram-positive bacteria (purple) have many layers of peptidoglycan which has many molecules of teichoic acid. The teichoic acid reacts with the crystal violet and iodine used in the staining process. This reactions creates a molecule that is larger and difficult to remove with the decolorizer (alcohol) so gram positive bacteria retain this color of the crystal violet.
Characteristics of DNA
double stranded 5’ and 3’, Nitrogenous bases (Adenine, Thymine, Guanine, Cytosine) with hydrogen bonds, sugar phosphate backbone.
rRNA (ribosomal) a structural molecule that makes up over half of the mass of a ribosome and aids in protein synthesis. tRNA (transfer) recognizes a codon on mRNA and brings the appropriate amino acid to that site. mRNA (messenger) Translation is the process where a ribosome decodes mRNA into a protein.
A specific version of a gene, differing in sequence from other alleles of the same gene (blue eyes, green eyes)
A piece of DNA, circular = bact/arch, linear = euk
The passing of genetic info to one’s progeny
Helicase separates the DNA to form a replication fork at the origin of replication where DNA replication begins. Replication forks extend bi-directionally as replication continues. Okazaki fragments are formed on the lagging strand, while the leading strand is replicated continuously. DNA ligase seals the gaps between the Okazaki fragments. Primase synthesizes an RNA primer with a free 3'-OH, which DNA polymerase III uses to synthesize the daughter strands.
Silent – No change to the first 2 bases of 3 part sequence (AAG) Missense – Change to the first 2 bases of 3 part sequence (AGG) Nonsense – Change AA to a stop codon
Frame Shift Mutations: (Bigger issue)
Insertion: Add a base ; Deletion: Delete a base ; Translocation: Move one part to another chromosome.
3 genes are part of operon that oversees metabolizing lactose when present (lacZ, lacY, lacA). LacI protein is a repressor that blocks transcription by binding to the operator, thus inhibiting RNA polymerase from starting transcription. However, when lactose is present, the LacI protein binds to that instead, releasing the operator and allowing the transcription to proceed.
Anything that is undefined (beef broth, who knows what’s in it).
know exactly what it is
has chemicals included that inhibit the growth of some microbes
Takes advantage of biochemical reactions of the specific microbe, however all microbes can grow, it used to differentiate between their growth
freeze them in glycerol
Bacterial Growth Chart
Cells break up after creates a spore, spore protects all the important stuff so when conditions are better spore coat will disintegrate and bacteria will continue to grow normally
direct and individual counting
(microscopic), Direct counting methods are easy to perform and do not require highly specialized equipment, but are often slower than other methods.
direct and bulk Counting
indirect and individual counting
colony counting), The spread plate relies on bacteria growing a colony on a nutrient medium so that the colony becomes visible to the naked eye and the number of colonies on a plate can be counted. Selective media can be used to restrict the growth of non-target bacteria. The pour plate method can be used when the analysis is looking for bacterial species that grow poorly in air, for example water samples. Counting the number of colonies that arise on a spread plate or a filter can calculate the concentration by multiplying the count by the volume spread/filtered.
indirect and bulk counting
most probable number, turbidity, nutrient uptake
Low temp (0-20˚C)
High Temps (PCR)
pH 2 or less
Bacteria grows at top because it needs O2
Bacteria grows at bottom because it does not need O2
grows in the middle because it uses O2 every once in awhile
Grow all over can go with or without O2
Individual bacteria use quorum sensing to communicate across species to determine friend or foe, population density, breeding grounds etc. based on the secretion of certain signaling molecules.
Grow a bunch of cultures, put it in a liquid medium and dilute it until enough cultures you can count.