Thermodynamics Flashcards
Redox
Redox = oxidation-reduction. In this type of chemical reaction electrons are gained and lost by molecules, altering the net charge, the chemical valency, or the ionisation state of the molecules involved in the reaction. Electrons are often picked up by enzyme co-factors.
Oxidation
Loss of electrons
Reduction
Gain of electrons
Where do we see redox reactions
Molecules typically don’t just form free radicals or liberate electrons. We typically only see this in gas plasmas (fluorescent lights or the sun), and in electrochemistry (a metal wire absorbs and shields the free electron).
Electron acceptors
In biology they can act like metal wires to absorb and hold free electrons, effectively transporting these to other uses where their ground state can be regenerated and they can be recycled.
Fermentation
Glucose taken in from surroundings Products are Expelled to surroundings. So it have function fast it
puts electrons on other organic material (reducing equivalents). The problem for the cell is how to recycle the reducing equivalents it generates.
Rules of catabolic metabolism
Entropy of the Organism + its Surroundings must be increasing. Life is more organised (lower entropy) than its surroundings; therefore, it must be consuming something at lower entropy in its surroundings and expelling wastes at higher entropy. delta Gr <0
Entropic death
“heat death” To avoid entropic death on a planet isolated in space, there must be an abiotic input that keeps supplying a fresh source of Free Energy to the system.
- Gravity (geothermal heat and pressure)
- Sunlight
where did life evolve
Life evolved close to hydrothermal vents. molecular oxygen was not present = all anaerobic reactions. diagenesis occurred turning inorganic molecules into organic molecules. Exergonic= - Gibbs energy using hydrogen as energy source.
Exergonic
-Gr, Gibbs energy doesn’t need energy input (spontaneous)
Endergonic
+Gr, requires ATP (energy) input (non-spontaneous)
Photosynthesis
Anoxygenic Photosynthesis (not making O2): couples the reduction of CO2 with hydrogen as energy source and light to drive process.
Oxygenic Photosynthesis (makes O2): splits water to make electron available and drive the reduction of CO2 into organic carbon. Needs light to drive.
Oxygenic Photosynthesis Revolution
Early Anaerobes created a world of: H2, H2S, NH3 and hydrocarbons. The oxygenic cyanobacteria then started filling the atmosphere with O2. Nitrate was then produce to oxidise environment.
catabolic metabolism
The cell, therefore, is really an electrochemical cell. Selectively abstracting H+ and e- from one molecule and moving it to another. Every step of that process must be an equilibrium (driven forward by mass action) or an exergonic process.
Denitrifying Bacteria
respire nitrate, No ATP involved Net H+ transport
through membrane.
PMF - Protonmotive Force
bY localising the oxidation and reducing equivalents to the inner membrane, H+ can be pumped across to produce an electrochemical gradient. H+ accumulation in the periplasm creates a chemical potential across the cell membrane
This chemical potential can be used to:
• Drive molecular motors.
• Exchange hard (Na+ and Ca2+) through the membrane for cytoplasm pH and osmotic pressure control.
• Balance reducing equivalents between catabolic & anabolic metabolism.
• Active transport of nutrients.
• Create more ~P through oxidative phosphorylation
Evolution
Early earth was an anaerobic environment with geological processes generating early reduced organic molecules. early sources of reducing energy included H2 and H2S. prior to O2 microbes disposed of electrons onto CO2 or SO4 producing CH4 and acetate.
Oxygen cycle
Aerobic bioprocess - oxygen being used as term electron acceptor = result is water.
Oxygen photosynthesis - uses light energy to split water and produce O2 for the first time.
Carbon cycle
Abiotic geothermal process:
carbon source = CO2
Reducing energy = hydrogen
Source of electrons = Hydrogen
Nitrogen cycle - nitrification
Nitrification is the biological oxidation of ammonia to nitrate by the oxidation of nitrites to nitrates, energy yielding reactions. used to reduced NAD+. Term Electron Acceptor = oxygen anaerobic process
Elemental cycles
are mediated by biotic and abiotic processes… and make use of the continuous input of solar energy into the system. In this way the essential nutrients of life (C,H,O,N,P,S) are continuously recycled by microorganisms.
media design
When designing growth media for a bioprocess you must consider nutrient requirements for growth and production. Biomass exhibits a characteristic ratio of C:H:O:N:P:S… but only under balanced growth conditions.
2nd law thermodynamics
that the total S of the universe must be ≥ 0. Therefore, Cells must be consuming lower entropy materials from their environment and refilling the environment with materials at higher entropy for the whole system to have DS ≥ 0.
Nutrients
Primary Energy Substrate Plus (C, N, O, S, P,
and trace metals) (Low entropy chemicals).
Metabolic Products
Necessary for redox shuffle and to change the entropy of the environment. (High entropy chemicals)
Aerobic glucose conversion
life is capturing the energy released from oxidising glucose by compartmentalising the series of discrete redox reactions which create reduced electron carries to make PMF and ATP. Electrons are extracted from glucose and pushed onto reducing equivalents (NADH), they are then oxidised at the membrane and passes the electrons along the electron transport chain till they meet oxygen as there term electron acceptor, and during that process electrons are pumped out into the preplasim which creates PMF which is then used to make ATP
Biomass production
is exergonic - releases heat, therefore heat is generated during microbial growth
why is life so efficient
Because it is able to break down the oxidation in these discrete redox reactions
