Biotechnology of Extremophiles and Astrobiology/Exobiology Flashcards
Extremozymes: a Definition
Extremozymes are enzymes that work normally at extremes of temperature, pH, salinity, metal concentrations and other conditions that would otherwise denature typical enzymes. Therefore they are or can potentially be used in many biotechnical applications in the pharmaceutical, chemical, energy, agricultural, environmental, food, health and textile industry.
For each application, an enzyme has often to fulfil numerous requirements related to features such as activity, stability and substrate specificity.
Optimisation of Extremozymes
Extremozymes can display polyextremophilicity i.e. stability and activity in more than one extreme condition.
Error prone PCR- mutations are introduced into gene, screen colonies- random process and has limitations - time consuming. Process of choice
Structure based protein engineering- need atomic structure- if you didn’t have structure, not much to optimise
Alpha fold - game changer but there’s limitations- can spot frauds- make funny translations
What are the four categories ectoines can be used for
- Macromolecule protection (enzymes, antibodies, DNA)- protect them by using them as an additive in the buffer- use for retroviral vectorism - adding increased half life time to 185 days
- Therapeutic uses (Alzheimer’s disease, CJD)- ectoine when you add it to fibres- ectoine by interacting with the surface- prevents initiation from fibre formation and also slows down process in vitro- in vitro prevents initiation and polymerisation of the fibres- ectoine is non disruptive and non toxic- doesn’t interfere much with other proteins or other cellular processes- helps water retention
- Cell protection (desiccation, thermotolerance)
- Skin protection (anti-ageing, photoprotection)
How are ectoines produced and isolated
Ectoine is produced using Halomonas sp. and hydroxyectoine is produced using Marinococcus.
Its isolated via bacterial milking- grow bacteria at high salinity until they reach a high cell density and contains massive amounts of intracellular ectoine. You then re-suspend the cells in low salinity medium and they will excrete the ectoine into the medium where it can be collected by filtration. Cells are then returned to high salt medium, grown to a high cell density and the whole process is repeated.
Other strategies include “leaky mutants” and over expressing the ectoine genes in E. coli
What is astrobiology
Astrobiology or exobiology is an interdisciplinary field of research that explores the origin, early evolution, distribution and future of life in the universe. As such it studies the condition and events that support the formation of life and is interested in developing methods to detect molecular signatures that would allow to detect these life forms
Whats the Hadean period and what was the temperature
The condition on Earth during the Start of Life
Temperature: No definitive answer exists, not least because, apart from a few ancient zircons, almost all the evidence has been obliterated by later geological processes. Critical factors would have been the rate of crustal recycling, the rate and distribution of heat from radioactive decay, the extent and intensity of the greenhouse effect, the onset of plate tectonics, rates of magmatic differentiation, and the role of water in the early crust.
Some temperature estimates include:
- Early mantle, ca. 1650-1850 oC
- Late Hadean zircons from Jack Hills, West Australia, 700 oC
- Crustal rocks with plate tectonic under-thrusting, 600 oC
Probably not far short of 2000oC
What did Zircons reveal
Early geochemistry of Earth
Analysis of ancient zircons reveal that liquid water was present by 4.3 Ga and that at 4.4 Ga Earth’s mantle was near its current redox state (balance of oxidants and reductants). Likewise, Earth’s atmosphere was likely redox neutral
What happens during Zircon exposure to hydrothermal fluids
Natural zircons from igneous rocks are present in mantle melts. These zircons can transport upward into the crust where they can be exposed to- and altered by- hydrothermal fluids. Fluid sources include rainfall or seawater that circulate fluids into and out of the crust
What happens during Zircon crystallization
A zircon crystal present in the crust can dissolve into its elemental constituents in a hydrothermal fluid. Consequently, its age, as determined by uranium (U) decay into lead (Pb) is lost. However, zircons can recrystallize, trapping certain constituents of the environment. This process “records” the geochemistry of the fluid and resets its age.
What was the atmosphere during the Hadean period and what experiment did they use
The early atmosphere likely began as a region of escaping hydrogen and helium. It is generally thought that ammonia, methane, and neon were present sometime after the crust cooled, and volcanic outgassing added water vapour, nitrogen, and additional hydrogen.
Miller-Urey Experiment:
The experiment used
- water (H2O),
- methane (CH4),
- ammonia (NH3),
- hydrogen (H2).
What are the signature molecules of life
- Amino acids: Simple molecules. Found in meteorites and therefore should be be able to be generated under abiotic conditions.
Major problems: how were the proteinogenic amino acids selected and what explains the preference for L steroisomers.
- Sugars: Simple molecules. In 2019, ribose was found in a meteorite. Conceivable pathways for abiotic generation exist using simple molecules like formaldehyde as start point.
Major problem: Combination of C2 and C3 molecules. Selection of ribose and deoxyribose.
- Nucleic acids: Complex molecules: Uracil, thymine and cytosine can be made from pyrimidine in the lab under early Earth conditions. Pyrimidine has been found in meteorites.
Major Problems: How can nucleotides be made; solution of the chicken-egg problem.
- Lipids: Complex molecules. Not found so far, but fatty acids can form membrane-like layers.
Major Problems: Stability of lipid molecules.
What are the 3 major planets
- Europa (Jupiter)
- Enceladus (Saturn)
- Mars
What are some ideas about bacterial metabolism on Mars
Microbial oxidation of Fe and S: Martian soils are rich in Fe2+ which could be used as an electron donor with O2 or NO3 as terminal electron acceptor (as on Earth). However, O2 is rare and the presence of NO3 is not yet confirmed therefore perchlorate could be used as electron acceptor.
Many iron-oxidizer can use CO2 as the sole carbon source, which is abundant in the atmosphere of Mars. This would be a lithoautothrophic way of energy generation and carbon assimilation.
Molecular H2 could be used as an electron donor with iron or sulphur as electron acceptors while CO2 again could be used as carbon source.
