Term 2 Lecture 8: Thermodynamics Of Metabolism Flashcards
Schematics
Photosynthesis → glucose+O2→ respiration →H20+CO2+ATP → photosynthesis
General schematic for life:
High energy electrons used to convert ADP+Pi→ATP then via work ATP→ADP+Pi releasing energy.
Schematic for heterotrophs:
Foodstuff →waste+ high energy electrons
High energy electrons used to convert ADP+Pi → ATP. The low energy electrons produced then convert an oxidised receptor (O2) to a reduced acceptor (H2O). Via work ATP→ADP+Pi releasing energy for the heterotroph.
Thermodynamic basis of metabolism
Metabolism: the overall process through which living systems acquire/utilise free energy to carry out necessary functions
Living systems couple exergonic (energy producing) and endergonic (energy consuming) processes to maintain living state
Two main inputs for organisms are energy and carbon needed for biomolecule synthesis
Energy is generated by chemical reaction
In higher animals: oxidation of reduced carbon compounds e.g. fats and sugars
Or: absorption of light - photosynthesis (used by plants and some prokaryotes)
Carbon is derived from nutrients broken down into common intermediates:
Used as precursors in synthesis of other biomolecules
Or derived from CO2 by carbon fixation
Input/ output of nutrient oxidation and photosynthesis
Nutrient oxidation
Input (exergonic):
Organic compounds : O2, nitrate, sulphate, CO2 and oxidised compounds
Converted to: CO2, H2O, N, S, methane
and reduced compounds
Inorganic substances: such as sulphides and CO2
Converted to: oxidised compounds e.g. sulphur
Photosynthesis:
Input: CO2, H2O, light and inorganic compounds e.g. sulphides
Convert to: O2 and oxidised compounds e.g. sulphur
Nutrient ox. / Photosynth output (endergonic) :
Assimilation of N and other elements for growth
Transport to maintain cellular environment
Synthesis of biomolecules and growth
Movement and other processes requiring motility e.g. running and digestion
Organisms may be classified according to the basis of how they obtain carbon and energy
Phototrophs (light →ATP)
Chemotrophs: two types
Chemoorganotrophs (Org. Chem →ATP)
E.g. glucose+O2 → CO2+H2O(+ATP)
Chemolithotropes (inorg chem→ATP)
Inorg chem e.g. H2, H2S, Fe²+, NH4+
E.g. H2+O2 →H2O (+ATP)
Some organisms use “alternative” metabolic strategies to make life under very different to “normal” conditions possible - so far this has only been observed in microorganisms e.g. nitrogen fixing bacteria
Global classification of organisms
Nutritional category/ energy source/carbon source
Photoautotrophs
(Some bacteria and eukaryotes)
/Light/CO2
Photoheterotrophs
(Some bacteria)
/Light/ organic compounds
Chemoautotrophs
(Some bacteria and Archaea)
/Inorg substances
(Chemolithoautotrophs)
/ CO2
Chemohetetotrophs
(All domains)
/Org. Compounds
(Chemoorganoheterotrophs)
Inorg compounds
(Chemolithoheterotropes)
/ Org. Compounds
Trophic definitions
Autotroph- obtains carbon by fixation of CO2 (inorganic carbon)
Heterotroph - obtains carbon from organic sources
Phototrophs - obtain energy from light
Chemotroph - obtains energy from chemical reactions ( oxidation of org/inorg electron donors)
Alternative metabolism: Methanogens
Methanogens
Obtain energy from CO2+H2
CO2+4H2→CH4+2H2O
- this reaction is also used as a carbon source through CO2 assimilation
-methanogens are ancient organisms and may represent the beginnings of life
-they are a specific group of Archaea, distinct from other kingdoms - only survive in absence of O2 (anaerobic conditions)
- bacteria which metabolise org. Compounds in anaerobic conditions produce H2
Alternative metabolism: nitrogen fixation
Obtain energy by oxidising org compounds to CO2
When no O2 is available this is done by reducing N2 to ammonia:
N2+ org compound →CO2+NH3
(Org compound used as C source)
- large amounts of ATP are used to reduce N2 so organisms avoid N fixation where possible.
- N fixing bacteria are rare and often work in symbiosis partnerships where partner supplies nutrients and protects the bacteria from O2
E.g. legumes such as soy have N fixing bacteria in root nodules and the plant supplies org compounds in exchange for N - the N fixing bacteria convert N into a form usable for plants, the plant protects the bacteria from O2
History of O2 in the atmosphere
O2 is vital for most organisms extant today, used to oxidise food and produce energy. The atmosphere today is ~20% O2 but this was not always the case. It has changed dramatically over the billions of years since the origin of life.
3.8 billion years ago it was 0.01% of what it is now. This was when the first autotrophs evolved and they still exist today in anaerobic environments.
Then Methanogens evolved around 3 billion years ago.
Cyanobacteria evolved utilising light to photosynthesise producing O2 as a by-product leading to the global oxidation event killing off the majority of anaerobic life forms.
Approximately 1.5 billion years ago single cell eukaryotes evolved - a mix of aerobes and anaerobes.
600 mya land plants and animals appeared and O2 increased from 10% of current level to the current ~20% O2 atmosphere of today
Oxygen
If you convert O2→H2O and thermodynamically couple this conversion to an endergonic reaction you can drive the endergonic reaction to produce the molecules essential for life.
Organisms that cannot utilise O2 are far more limited in terms of energy available
O2+4H+ + 4e- →2H2O+0.816 V
( A favourable neg ∆G)
→ see a reduction potential table
Gibbs free energy explained
Energy in biochem systems is measured in Gibbs free energy (G) including energy and entropy terms G indicates spontaneity of a process change in free energy (∆G) must be neg for a process to occur naturally
∆G of reaction depends on reactant/product concentration
Metabolic pathways
Stage 1: Glycolysis aka fermentation, thought to be the oldest metabolic pathway in existence and produces very little energy.
Involves both soluble and glycolytic enzymes forming complexes that allow local concentrations of intermediates to differ from bulk cellular concentrations (accounts for thermodynamics)
Stage 2&3: pyruvate oxidation, TCA cycle and respiratory chain. Occurs in cytoplasmic compartment of aerobic prokaryotes and in specialised organelles in eukaryotes (mitochondria and chloroplasts in plants)
> As mitochondria have a double membrane system import/export via transport systems is necessary to get energy source in and ATP out
Cellular locations for energy pathways in pro and eukaryotes
Eukaryotes:
external to mitochondria
- glycolysis
Internal “ “ -
- On inner membrane - resp chain and - In matrix - citric acid cycle and pyruvate oxidation
Prokaryotes:
-In cytoplasm: glycolysis and citric acid cycle
- On plasma membrane: pyruvate oxidation and resp chain
Catabolic routes aka pathways
Exist for all classes of biological molecules
Core catabolic route is our focus pathway
Glycolysis ( in cytoplasm)
Polysaccharide
↓
Glucose
↓
Pyruvate
+ Co A
↓
Acetyl CoA (which can cross mitochondrial membrane)
↓
In mitochondrial matrix
↓
TCA cycle (citric acid cycle) - reversible
↓
NADH+QH2
↓ oxidative phosphorylation
H2O
Then
Glucose → CO2 + H2O (+ATP)
ATP is then used to drive anabolic processes to form biological molecules necessary for life.
