Exam 3 Flashcards
Biofuels: Ethanol
Fermentation of sugars (corn, sugarcane) by yeast to produce alcohol.
Biofuels: Biodiesel
Transesterification of fats/oils with alcohol (e.g., methanol) to produce methyl esters
(biodiesel) and glycerol.
Biofuels: Bio gas
Anaerobic digestion of organic waste by bacteria, producing methane.
Biofuels: Algae-based
Harvesting lipids from algae and processing them into biofuel.
Biofuels: Cellulosic
Breaking down cellulose from plant materials into fermentable sugars via
enzymatic hydrolysis.
Biofuels
Biofuels are renewable fuels derived from biological materials such as plants, algae, or waste.
Transportation, heating, electricity
Bacteriophage Build
Head (contains DNA/RNA)
Collar
Tail (injects genetic material into host cell)
Tail Fibre (Specificity of phage is given by the proteins that are encoded in the tail fibre)
Bacteriophages Lytic Life Cycle
DNA injected as dsDNA, then converted to circular DNA; DNA fed to each head, tail attached to host cell is lysed; more cells infected / faster acting
Bacteriophage single cell
Lytic Cycle, Lysogeny/ carrier site, Chronic Infection
Bacteriophage population
what happens to the phages in our gastrointestinal tract. The health of our
microbiome is partly determined by the phages we have.
Steps in generation of scFv using phage display system
i. Isolate mRNA from B cells from immunized mice or infected/recovered Covid-19 individuals or use hybridomas secreting Mabs of know specificity
ii. Convert to cDNA and PCR amplify using degenerate primers to capture the VH and VL chains repertoire
iii. Clone PCR fragments into phagemid vector pComb 3
iv. Infect compatible strains of E. coli with the phagemid. Infect with helper phage to obtain
intact phage particles expressing VH and VL chains
v. Identify the phage particles of interest by panning using antigen or other substrates of
interest
vi. Convert phage DNA from particles of interest into plasmid DNA by restriction enzyme
digestion and relegation.
vii. Re-transform appropriate strains of E. coli for expression of soluble scFv specific to
antigen of choice
viii. Similar strategies can be used for expression of IgGs
How would you engineer a primer against SARS-COV2
i. Engineer restriction enzymes sites based on final destination expression plasmid
ii. Engineer linker sequence at appropriate ends of VL and VH amplicons
iii. Engineer FLAG tag or 6X- Histidine-specific sequence
iv. Engineer overlap sequence on appropriate ends of VL and VH amplicons for overlap PCR
and fragment assembly
v. Incorporate degeneracy as needed for obtaining the variable regions sequences
vi. If the primers are directed at VL and VH regions of antibodies from B cells from Covid-19 convalescent individuals – you are likely to express neutralizing antibodies against one or more proteins of SARS-CoV-2.
Live/Attenuated Virus
Cons
Requires immune system activation,
Reversion of virulence in bacteria,
Benefit
Longer lasting, greater immune response,
Reduce the need for boosters, do not require adjuvants,
produced at relatively low cost, and can be administered not just through IV, but orally.
Recombinant
Cons
require booster shots,
Benefit
Could be used for immunocompromised,
Strong immune response (not as much as attenuated),
greater stability for transportation.
Inactivated
Cons
less immune response,
requires boosters,
may increase allergic reaction,
Benefit
Cannot revert virulence in bacteria,
fewer side effects,
easy storage.
N2 Cycle
a. Cyanobacteria gets nitrogen fixation from atmosphere into NH3 and NH4+
b. Gets picked up by nitrosococcus and nitrosomonas and transformed into NO2 -
c. NO2- undergoes nitrification through nitrobacter nitrococcus into NO3-
d. Then, it goes back to NO2- through clostridium spp and e coli
e. Afterwards, it goes from either NO2- or N2 from the atmosphere to make ammonia, which makes
proteins from soil bacteria (Rhizobium) through ammonia assimilation
Quorum sensing
a. Second bacterial cell should have the ability to synthesize, to recognize the signals, and the ability to respond to signals.
b. Communication methods: Oligopeptides (gram +), AHL (gram -), and autoinducer-2 (interspecies “cross talk”)
c. Photopyrones (a-pyrones) example: the ones that have RFP are able to receive the signal and grow (kind of like gatekeeping info.)
Bioplastics
Bioplastics are usually derived from sugar derivatives, including starch, cellulose, and lactic acid
Examples include vegetable fats/oils, corn starch, straw, woodchips, recycled food wastes, agricultural by-products and used plastic bottles and containers treated with bacteria / microorganisms
Pseudomonas and disease
a. Ubiquitous soil bacterium
b. Infections in plants and animals
c. Produce fungicidal compounds
d. Helpful for bioremediation and burn wounds
e. Cystic fibrosis patients have reduced lung immune responses
f. Surgery, contact lenses, prosthetics at multiple sites
P. aeruginosa
i. Gram-negative, motile rod with an oxidative metabolism
ii. Non-fermenter
iii. High activity of electron transport chain of Pseudomonas - oxidase test
iv. NNN N’-tetramethyl-p-phenylenediamine tetrachloride- colorless to blue substrate
v. Blue green color -synthesis of pyocyanin, copious amounts
vi. Secondary metabolites
vii. Biofilm formation
viii. Linked by polysaccharide matrix
ix. Metabolically less active-less prone to antibiotics
x. Antibiotic Resistant to most antibiotics
P. aeruginosa Infections (predisposed)
Hot tubs: dermatitis
3rd degree burn: burn infection
long-wear contact lenses: eye infection
cystic fibrosis or inhalation of air during fire: lung infections
surgical wounds: nosocomial septicemia
urinary catheter: nosocomial UTI
Carbon cycle and how the biomass of earth does not change (that much)
i. Carbon dioxide fixation very important for generation of O2 (breathing)
ii. Regulates planet temp through carbon dioxide regulation
iii. Makes carbon available using photosynthesis
iv. Provides nutrients to animals, which is then given back to the organic carbon pool.
v. Biomass does not change much due to the high regulation of all parts of the carbon cycle
