Thermodynamics

Question 1

Redox

Answer 1

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.

Question 2

Oxidation

Answer 2

Loss of electrons

Question 3

Reduction

Answer 3

Gain of electrons

Question 4

Where do we see redox reactions

Answer 4

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).

Question 5

Electron acceptors

Answer 5

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.

Question 6

Fermentation

Answer 6

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.

Question 7

Rules of catabolic metabolism

Answer 7

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

Question 8

Entropic death

Answer 8

“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

Question 9

where did life evolve

Answer 9

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.

Question 10

Exergonic

Answer 10

-Gr, Gibbs energy doesn’t need energy input (spontaneous)

Question 11

Endergonic

Answer 11

+Gr, requires ATP (energy) input (non-spontaneous)

Question 12

Photosynthesis

Answer 12

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.

Question 13

Oxygenic Photosynthesis Revolution

Answer 13

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.

Question 14

catabolic metabolism

Answer 14

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.

Question 15

Denitrifying Bacteria

Answer 15

respire nitrate, No ATP involved Net H+ transport

through membrane.

Question 16

PMF - Protonmotive Force

Answer 16

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

Question 17

Evolution

Answer 17

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.

Question 18

Oxygen cycle

Answer 18

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.

Question 19

Carbon cycle

Answer 19

Abiotic geothermal process:
carbon source = CO2
Reducing energy = hydrogen
Source of electrons = Hydrogen

Question 20

Nitrogen cycle - nitrification

Answer 20

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

Question 21

Elemental cycles

Answer 21

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.

Question 22

media design

Answer 22

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.

Question 23

2nd law thermodynamics

Answer 23

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.

Question 24

Nutrients

Answer 24

Primary Energy Substrate Plus (C, N, O, S, P,

and trace metals) (Low entropy chemicals).

Question 25

Metabolic Products

Answer 25

Necessary for redox shuffle and to change the entropy of the environment. (High entropy chemicals)

Question 26

Aerobic glucose conversion

Answer 26

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

Question 27

Biomass production

Answer 27

is exergonic - releases heat, therefore heat is generated during microbial growth

Question 28

why is life so efficient

Answer 28

Because it is able to break down the oxidation in these discrete redox reactions