lec 4 - microbial biotech Flashcards
1
Q
define
microbes
A
microorganisms (bacteria, viruses, fungi, algae, protozoa)
2
Q
define & characteristics (3)
bacteria
A
- first life forms on earth
- resilient: can live in harsh environments
- less than 1% of all species identified, cultured, studied
3
Q
define
eukaryotic microbes
A
yeast, algae, protozoans
4
Q
list (2)
prokaryotic microbes
A
bacteria and archaea (share both eukaryotic and prokaryotic properties)
5
Q
list (5)
structure of microbes
A
- small (1-5um)
- no nucleus –> DNA in circular chromosome (plasmid)
- cell wall: peptidoglycan (protection)
- lack membrane-bound organelles
- capsule: outer layer of carbs
6
Q
list (4)
advantages of microbes
A
- grow and divide rapidly (every 20 mins)
- millions grown on small agar dishes
- liquid cultures or fermenters
- easy to engineer or mutate
7
Q
list (2)
microbial enzymes in industrial biotech
A
- food production
- molecular bio research
8
Q
define
Taq DNA polymerase
A
heat stable, isolated from thermophile
9
Q
define
cellulase
A
degrades cellulose –> more digestible food
10
Q
list (3)
advantages of microbial enzymes
A
- improve yield
- reduce costs
- environmentally cleaner products
11
Q
define
bioprospecting
A
looking for new species with new genes and functions we can harness
12
Q
define
microbial proteins as reporters
lux genes
A
marine organisms generate light thru lux genes (visual indicator) coding for different subunits of luciferase –> study gene expression
13
Q
define
microbial proteins as reporters
in-vivo fluorescent bioassays
A
take saliva with tuberculosis –> bacteriophage with GFP reporter infects bacteria –> glows
14
Q
define
microbial proteins as reporters
edible sensor pills
A
monitor disease –> fluoresce in response to heme
15
Q
process
fusion proteins
A
gene for protein of interest cloned into expression vector and tagged with GFP –> protein purified by affinity chromatography
16
Q
define and advantages (3)
yeast
A
- single-celled eukaryotic fungi
- antibiotics and drugs that lower cholesterol
- mechanisms of gene expression resemble human cells
- grows in presence or absence of oxygen
17
Q
define
chymosin
A
- first recombinant DNA food ingredient –> curds to make cheese
- less expensive and easier to produce
- traditionally made with rennin from stomach of calves
18
Q
list (7)
how to choose a system to use
A
- promoters (inducible vs constitutive expression)
- maximize yield (toxic at high levels?)
- cost
- stability of protein in host cell
- cellular location of final product
- post-translational modifications of protein
- efficient translation of foreign protein (codon bias)
19
Q
therapeutic protein production
insulin
A
- genetech cloned human insulin gene in bacteria –> express each subunit in different bacterial cultures
- produce beta-gal insulin fusion proteins –> affinity column with antibodies to purify
- cut protein from beta-gal –> active insulin
20
Q
tackling malaria
A
- bacteria secreting harmane, halts development of malaria in mosquito guts
- avoids safety concerns about releasing edited organisms into wild
- doesn’t affect mosquito survival or offspring –> no resistance
21
Q
spider silk
A
- recombinant miniature spidroins form self-supporting, transparent hydrogels at 37 degrees –> immobilization of active proteins, delivery of functional proteins, controlled release of drugs, regenerative medicine
- stronger than steel but still super flexible
22
Q
microbial weaving
A
- bacteria produces nanocellulose
- engineered to self-dye by producing melanin
- 2D yarn scaffold –> submerge in bacteria –> weaves a sneaker
23
Q
define
antibiotics
A
- e.g. penicillin –> colonies of mold inhibited growth of another bacteria –> treats infections
- inhibits cell wall synthesis, protein synthesis, and enzymatic activity
24
Q
define
antibiotic resistance
A
- improper antibiotic use
- resistance to one antibiotic leads to resistance of many others
- must develop new antimicrobials that act in novel ways
25
technology convergence
- using machine learning to accelerate innovation
- screen 100 million chemical compounds in days --> determine potential antibiotics that kill bacteria using different mechanisms than existing drugs
- trained model on 2500 molecules (1700 FDA approved drugs)
26
# tech convergence
halicin
kills resistant bacteria by disrupting its ability to maintain electrochemical gradient across cell membrane
27
# tech convergence
conjugated oligoelectrolytes (COEs)
small, synthetic molecules that spontaneously interact with lipi bilayer to disrupt functions
28
phage therapy
- naturally or genetically modified to have particular features (synthetic)
- phage attack doesn't overlap with common mechanisms of antibiotics
- can be engineered to target specific pathogens
29
phage therapy challenge + solution
- bacterial cell walls contain endotoxins that must be removed during phage purification
- solution: generate viral particles in test tude instead of actual phage --> library of phages
- isolate bacteria from patient --> match phage --> cell free system produces it
30
living medicine
modified, non-pathogenic version of pneumonia that attacks antibiotic-resistant bacteria
31
microbial safety concerns
- microbes enter environment through accidental or intential release
- horizontal gene transger (spread of genes to related microbes) --> could be irreversible
32
microbial genome project (MGP)
sequence entire genomes of microorganisms that have potential applications in environmental biology, research, industry, health
33
# list (5)
goals of MGP
indentify genes involved in microbial cell metabolism, cell division, and genes that cause human illnesses
- new and rapid diagnostic methods & treatments
- identify disease causing organisms in food & water
- bacterial genes for bioremediation, synthesis or degradation of plastics, biosensors
- detect biological weapons
34
first complete sequence of microbial genome
haemophilus influenza
35
synthetic genome
- synthesized bacterial genome in test tubes --> introduced into another bacterial cell
- easier to upgrade many organisms for industry, agriculture, medicine
36
# synthetic genome
george church's lab
- re-engineer genetic code of bacterial strain (Syn 61) to repurpose 3 of 6 codons (serine and STOP) --> added genes coding for novel tRNAs that insert unnatural aas whenever they encountered new serine
- add novel aa to protein: new ways to synthesize antibiotics and antitumor drugs
37
syn 61 advtange
- cannot read all codon in WT code
- code-decoder system creates bidirectional genetic firewall that protects synthetic organisms from contamination with mobile genetic elements and prevents genetic transfer to natural organisms
38
biofuels/biorefineries
convert cellulose from stalks and other biomass into sugars used to make ethanol sustainably
39
gut microbes & cancer immunotherapy
- gut microbes shape responses to cancer immunotherapy (some repond well, others don't)
- solve using fecal microbial transplant from responder to non-responder
40
chemotherapy drug (irinotecan)
- severe diarrhea in some patients bc bacterial enzyme turns drug into toxic compound
- animal models don't always predict drug toxicity in humans --> different gut microbes
41
microbial diagnostics
- techniques used to detect and track microbes
- PCR and DNA sequencing
42
bioterrorism
use of biological materials as weapons to harm humans or food sources
43
how many organisms can feasibly be used for bioterrorism?
12
44
bioterrorism prevention
- countries must have antibiotic and vaccine supply
- vaccines must be administered before exposure
45
bioterrorism concern
synthetic biology --> organisms engineered against conventional treatments or unknown organisms --> no way to prevent
