Notes in Molecular Capstone

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Published	10/11/2023	What does ELISA stand for? {{c1::Enzyme-linked}} {{c2::Immunosorbent Assay}}
Published	10/11/2023	Where do antibodies come from? {{c1::B-cells}}/{{c2::From the immune system}}
Published	10/11/2023	Two major branches of the immune system: {{c1::innate}} and {{c1::adaptive}}
Published	10/11/2023	The {{c1::innate}} immune response is always ready to react, {{c2::no prior exposure to a pathogen is needed}}, can detect alot of different path…
Published	10/11/2023	The {{c1::adaptive}} immune system reacts to antigens, {{c2::'remembers'}} an invader, {{c2::highly specific}} to an antigen, {{c3::takes time to acqu…
Published	10/11/2023	{{c1::Beta}} cellssecrete {{c2::antibodies}}come from the {{c2::bone marrow}}mount the {{c1::humoral}} immune response
Published	10/11/2023	{{c1::T}} cellsattack cells infected with {{c2::bacteria or viruses}}{{c2::cell-mediated}} immune response
Published	10/11/2023	{{c2::Antibodies}} very large {{c1::proteins}}bind to foreign invading particles called {{c1::antigens}}
Published	10/11/2023	{{c1::Epitopes}} are the part of {{c2::antigens}} that antibodies actually bind to.
Published	10/11/2023	An antibody molecule is {{c1::Y}}-shapedHas {{c1::two}} antigen-binding sitesAlso called {{c2::immunoglobins}Has a {{c2::constant regio…
Published	10/11/2023	Antibody Applications: {{c1::protein purification}}: used in column chromatography to catch a certain protein from a serum{{c2::protein visualiza…
Published	10/11/2023	Antibodies are made by using living systems:{{c1::take your protein of interest and inject it into an animal}}{{c1::animal has adaptive immune respons…
Published	10/11/2023	When an antigen is injected into an animal, a {{c2::mixture}} of antibodies is produced. Each antibody recognizes a {{c2::different, specific epitope}…
Published	10/11/2023	{{c1::Monoclonal}} antibodies are identical antibodies to a specific epitope of a protein.
Published	10/11/2023	{{c1::ELISA}} is a diagnostic tool that tracks pathogens in animals, plants, etc.
Published	10/11/2023	{{c2::Primary}} antibodies bind {{c1::directly to the antigen}}
Published	10/11/2023	To make {{c2::monoclonal}} antibodies: take out an animals {{c1::B-cells}}fuse B-cell with cancer cells and plate one cell per well ({{c1::cell c…
Published	10/11/2023	Monoclonal antibodies serve as {{c1::drugs}}!
Published	10/11/2023	Monoclonal antibody drugs have a name ending in -{{c1::mab}} and are {{c1::super expensive, $500,000 for one dose}}.
Published	10/11/2023	{{c1::Secondary}} antibodies bind to the {{c1::primary}} antibody and can fluoresce/cause a color change because they have an {{c1::enzyme}} atta…
Published	10/11/2023	Primary and secondary antibodies HAVE to be made {{c1::in two different animals}}.
Published	10/11/2023	The secondary antibody recognizes {{c1::the constant region}} on primary antibodies.
Published	10/11/2023	{{c1::Elisa}} Applications: diagnose diseases, COVID, HIV, Lyme diseasedetect viruses in veterinary medicinedetect plant virusestest indoor air q…
Published	10/11/2023	ELISA is {{c1::not sensitive}}, so don't always trust the results
Published	10/11/2023	{{c1::Blocking reagent}} is used in ELISA methodology to prevent nonspecific binding of antibodies. Antibodies are {{c2::VERY sticky}}), increasing th…
Published	10/11/2023	In ELISA the secondary antibody is coupled to an enzyme called {{c1::Horseradish peroxidase (HRP)}}.
Published	10/11/2023	In ELISA, {{c1::False positive}} is a result that looks positive (demonstrates a color change) but really isn't. This can be due to:{{c2::contaminatio…
Published	10/11/2023	In ELISA, a {{c1::false negative}} is a result that does not demonstrate a color change but the subject is positive for the infection. This can b…
Published	10/11/2023	{{c2::Ethics}}: {{c1::conforming to accepted and professional standards of conduct}}.
Published	10/11/2023	Ethics are developed by {{c1::professional communities}}.
Published	10/11/2023	{{c1::Standard Operating Procedures}} (SOPs) detail procedures for dealing with spills, emergencies, and exposure incidents.
Published	10/11/2023	Principles of Biosafety: RRCBDR: {{c1::Risk assessment}}R: {{c1::Risk groups}}C: {{c2::Containment}}B: {{c2::Biosafety levels}}D: …
Published	10/11/2023	We assess risk so that we can {{c1::categorize it qualitatively}}. Takes pathogenicity, route of transmission, concentration, agent stability, etc. in…
Published	10/11/2023	Agents are split into {{c1::four}} risk groups based upon their {{c21::relative pathogenicity}} to healthy adult humans.
Published	10/11/2023	Risk group 1: agents are {{c1::not associated with disease}} in healthy human adultsRisk group 2: agents are associated with disease {{c2::which is ra…
Published	10/11/2023	{{c1::Containment}} is {{c2::safe methods for managing infectious materials}} to {{c2::reduce or eliminate exposure}} to lab workers, other persons, a…
Published	10/11/2023	{{c1::Primary}} containment is the {{c2::protection of personnel and the immediate laboratory environment}}. Example: PPE
Published	10/11/2023	{{c1::Secondary}} containment is the {{c2::protection of the environment external to the laboratory}} from exposure. Example: Facility design
Published	10/11/2023	Capstone labs are a biosafety level {{c1::2}}. For each risk group we have a biosafety level.
Published	10/11/2023	Each biosafety level {{c1::builds on and includes all safety measures from the previous levels}}.
Published	10/11/2023	Biosafety Level 1: {{c1::Standard}} practices ({{c1::things we must do in lab}})Wash handsWear {{c2::PPE}} Prohibit eating, drinking, and smoking…
Published	10/11/2023	Biosafety Level 2 is the same as BSL-1, with emphasis on: {{c1::Face/eye}} protection{{c1::Gloves}}Mechanical {{c2::pipetting}}Attention to&…
Published	10/11/2023	Biosafety level 2 introduces biosafety {{c1::cabinets}} a.k.a. {{c1::hoods}} for work with infectious agents.
Published	10/11/2023	Biosafety level 2: Special PracticesPolicies and procedures for {{c1::entry}}{{c1::Biohazard warning signs}}{{c2::Biosafety manual}} specific to …
Published	10/11/2023	Biosafelty Level 3 Facility Design: {{c1::Secondary}} containment barriers{{c1::Ante-room}} (room inside of a room){{c2::Negative}} air flow{{c2::Auto…
Published	10/11/2023	Biosafety level {{c1::4}}: {{c2::Positive pressure}} personnel suit with segregated air supply{{c2::UV}} room, multiple showersAll air and water …
Published	10/11/2023	Disposal of Hazardous Waste:Orange bags: {{c1::Biohazard}}Red bags: {{c1::Infectious Waste}} We use these in our lab
Published	10/11/2023	{{c2::Orange}} BagsSterilization cycle in the autoclave at {{c1::250F}} for at least {{c1::90}} minutesNo carcasses, large organs, etc.NO {{c2::s…
Published	10/11/2023	{{c1::Red}} Bags:Incinerated by special facilitiesSerious stuff!
Published	10/11/2023	Our material safety data sheets (MSDS) is kept {{c1::?}}
Published	10/11/2023	An immune response is the ability of an organism to both {{c1::defend}} itself and {{c1::recognize}} itself.
Published	10/11/2023	Humoral Immune Response (That of the B-cell):Lymphocytes (type of white blood cell that is part of the immune system) originate from stem cells in the…
Published	10/11/2023	Immunoglobulins or {{c1::antibodies}} are secreted by {{c1::B-cells}}.
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Published	10/11/2023	How ELISA works: {{c1::Antigen}} {{c1::Primary}} Antibody{{c1::Secondary}} Antibody and {{c2::Enzyme}}Chromogenic {{c2::enzyme substrate}}
Published	10/11/2023	Microplate strips made of polystyrene bind proteins via {{c1::hydrophobic interactions}}.
Published	10/11/2023	ELISA Color changing process: {{c1::HRP}} will cleave {{c1::TMB}} in the presence of {{c1::hydrogen peroxide}} creating a bluebyproduct – allows …
Published	10/11/2023	DNA Characteristics: contains the information for the development and function of all living organismstwo polynucleotide strands bonded together …
Published	10/11/2023	DNA in plant cells is located in the nucleus{{c1::mitochondria}}{{c1::chloroplasts}}
Published	10/11/2023	PCR ({{c1::Polymerase Chain Reaction}} is a very powerful molecular technique for {{c1::amplifying DNA}}.
Published	10/11/2023	PCR mimics in vivo replication:DNA {{c1::unwinds}} and ssDNA is exposed to be copied{{c1::Primer}} used to initiate replication{{c2::DNA polymera…
Published	10/11/2023	PCR is similar to in vivo DNA replication in that it uses the same ingredients and methods, but is different in that it uses {{c1::temperature ch…
Published	10/11/2023	Three steps of PCR:{{c1::Denaturation}}- usually at a high temperature (94C), {{c2::breaks apart}} the DNA strands{{c1::Annealing}}- much lower temper…
Published	10/11/2023	DNA is always synthesized from {{c1::5' to 3'}}.
Published	10/11/2023	PCR temperatures are too high for DNA polymerase, so we use {{c1::Taq}} polymerase, a polymerase isolated from a {{c1::bacterium living in hot springs…
Published	10/11/2023	Other necessary PCR components: {{c1::Magnesium chloride}} - Taq polymerase co-factor{{c1::Reaction buffer}} containing salt to maintain pH
Published	10/11/2023	GMOs are made by {{c1::identifying}}, {{c1::isolating}}, {{c2::engineering}} a specific gene, and {{c2::inserting}} the gene into crops.
Published	10/11/2023	GMO genes may be from a species of another {{c1::kingdom}}.
Published	10/11/2023	GMOs are used for: {{c1::Herbicide}} and {{c1::Pest}} ResistanceIncrease {{c1::nutrient value}} in crops (golden rice)Increase {{c2::yield}}…
Published	10/11/2023	PCR creates {{c1::exponential}} amplification ({{c1::2n}}).
Published	10/11/2023	Instagene matrix contains {{c2::-}} charged beads that bind {{c2::divalent cations}} (Mg2+) so that these cations cant be used as {{c1::nuclease cofac…
Published	10/11/2023	The goal of scientific writing is to {{c1::get funded}}.
Published	10/11/2023	{{c2::Electrophoresis}} allows {{c1::DNA}} molecules of {{c1::different sizes}} to be separated from one another.
Published	10/11/2023	DNA is {{c1::negatively}} charged. Attracted to the {{c1::anode}} pole in an electric field.
Published	10/11/2023	{{c2::Agarose}} is a {{c1::polysaccharide}} polymer made from {{c1::seaweed}} extract.
Published	10/11/2023	{{c2::Smaller}} DNA fragments move {{c1::faster}} through the gel. {{c2::Larger}} DNA fragments move {{c1::slower}} through the gel.
Published	10/11/2023	{{c1::Ogston Sieving}} regards the DNA like {{c2::a tangle of thread}} where smaller molecules fit into more pores and thus travel faster.
Published	10/11/2023	{{c1::Repation}} regards the long DNA molecule as {{c2::a snake}} and thus the longer the DNA strand the longer it takes because {{c2::its route is mo…
Published	10/11/2023	Loading Buffer characteristics:{{c1::Colored Dye}}: tracks the progression of the samples down the gel{{c1::Thickening Agent}}: samples need to be den…
Published	10/11/2023	{{c1::Nucleases}} {{c2::destroy DNA}}, by using EDTA we take out {{c2::magnesium (Mg2+)}} which is a cofactor for {{c1::nucleases}}
Published	10/11/2023	3 Tips to load a gel: {{c1::Support your hand with the other to keep it steadyGo slow when you are emptying the pipetteWatch where the tip of you…
Published	10/11/2023	When running a gel, it is important to select the correct voltage. Higher voltage = {{c1::faster}}, but too high and {{c1::gel will mel…
Published	10/11/2023	{{c1::Ethidium bromide}} {{c2::binds to DNA}} and a UV light illuminates the dye, this is also why its {{c1::CARCINOGENIC}}!
Published	10/11/2023	Size of the bands used in our gel electrophoresis:Photosystem II primer (PSII): {{c1::455}} base pairsCaMV 35S primer: {{c1::203}} base pairsNOS termi…
Published	10/11/2023	{{c1::Morphological}} species defines two individuals as the same species because {{c2::they look alike}}.
Published	10/11/2023	{{c1::DNA barcoding}} looks at the genome, often to determine species.
Published	10/11/2023	Drawbacks of using {{c1::morphological}} species:Individuals can exhibit {{c2::sexual dimorphism}}, where the male and female individuals look very di…
Published	10/11/2023	{{c1::Biological}} species categorize two individuals to be the same species if {{c2::they can mate and have a fertile offspring}}.
Published	10/11/2023	Drawbacks of using the {{c2::Biological}} species definition: If you are dealing with {{c1::fossils}}, {{c1::extinct creatures}}, or {{c1::very l…
Published	10/11/2023	{{c1::Phylogenetic trees}} show the evolution of species over time.
Published	10/11/2023	{{c2::Phylogenetic}} species definition uses {{c1::genetic code}} to determine species.*
Published	10/11/2023	A benefit of using the {{c1::phylogenetic}} species definition is that {{c2::we dont need the whole animal, we just need a part and not even one in go…
Published	10/11/2023	{{c1::DNA Polymorphisms}} are small changes to the DNA between individuals.
Published	10/11/2023	A single nucleotide polymorphism {{c1::takes a single nucleotide and replaces it with a different base type}}. (What does it do to DNA?)
Published	10/11/2023	{{c1::Insertion-deletion}} mutations change the length of the DNA code by {{c2::adding or removing nucleotides}}.
Published	10/11/2023	Changes in DNA between species usually occur {{c1::during the DNA replication process}}.
Published	10/11/2023	The most common type of damage to DNA is {{c1::base}} damage. This results in a base {{c1::change}} or {{c1::loss}}.
Published	10/11/2023	We are {{c1::99.9}}% the same at the genetic level. However, these small changes can be significant for {{c2::human disease}} and {{c2::how we pr…
Published	10/11/2023	When mutations in individuals {{c1::increase in frequency}}, they can become {{c1::fixed}}, so that all individuals in a population or lineage has the…
Published	10/11/2023	{{c3::DNA Barcoding}} steps:{{c1::Extraction}}{{c1::Purification}}{{c2::Gel Electrophoresis}}Pull samples for SequencingSequencingAnalyze using {{c2::…
Published	10/11/2023	The DNA Barcoding community chose certain genes to generate libraries for because these genes {{c1::are absolutely vital to the physiological function…
Published	10/11/2023	The genes used for DNA barcoding have {{c1::high interspecies variation}} (different between different species) and {{c1::low intraspecies variation}}…
Published	10/11/2023	We are using the {{c2::CO1, Cytochrome C Oxidase subunit I}}, gene for our DNA Barcoding. This gene is {{c1::vital to mitochondrial function}}.
Published	10/11/2023	We need to purify DNA to {{c1::remove contaminants like PCR reagents}}.
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