Exam 3

Question 1

Biofuels: Ethanol

Answer 1

Fermentation of sugars (corn, sugarcane) by yeast to produce alcohol.

Question 2

Biofuels: Biodiesel

Answer 2

Transesterification of fats/oils with alcohol (e.g., methanol) to produce methyl esters
(biodiesel) and glycerol.

Question 3

Biofuels: Bio gas

Answer 3

Anaerobic digestion of organic waste by bacteria, producing methane.

Question 4

Biofuels: Algae-based

Answer 4

Harvesting lipids from algae and processing them into biofuel.

Question 5

Biofuels: Cellulosic

Answer 5

Breaking down cellulose from plant materials into fermentable sugars via
enzymatic hydrolysis.

Question 6

Biofuels

Answer 6

Biofuels are renewable fuels derived from biological materials such as plants, algae, or waste.

Transportation, heating, electricity

Question 7

Bacteriophage Build

Answer 7

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)

Question 8

Bacteriophages Lytic Life Cycle

Answer 8

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

Question 9

Bacteriophage single cell

Answer 9

Lytic Cycle, Lysogeny/ carrier site, Chronic Infection

Question 10

Bacteriophage population

Answer 10

what happens to the phages in our gastrointestinal tract. The health of our
microbiome is partly determined by the phages we have.

Question 11

Steps in generation of scFv using phage display system

Answer 11

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

Question 12

How would you engineer a primer against SARS-COV2

Answer 12

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.

Question 13

Live/Attenuated Virus

Answer 13

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.

Question 14

Recombinant

Answer 14

Cons

require booster shots,

Benefit

Could be used for immunocompromised,

Strong immune response (not as much as attenuated),

greater stability for transportation.

Question 15

Inactivated

Answer 15

Cons
less immune response,

requires boosters,

may increase allergic reaction,

Benefit

Cannot revert virulence in bacteria,
fewer side effects,
easy storage.

Question 16

N2 Cycle

Answer 16

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

Question 17

Quorum sensing

Answer 17

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.)

Question 18

Bioplastics

Answer 18

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

Question 19

Pseudomonas and disease

Answer 19

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

Question 20

P. aeruginosa

Answer 20

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

Question 21

P. aeruginosa Infections (predisposed)

Answer 21

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

Question 22

Carbon cycle and how the biomass of earth does not change (that much)

Answer 22

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