Catabolism and Electron Flow

catabolism

breakdown of larger molecules to obtain energy (ability to do work)

Gibbs Free Energy

energy available from a given reaction

-∆G

reaction favors the products (forward), spontaneous

+∆G

reaction favors the reactants (reverse), not spontaneous

∆H

enthalpy, the heat energy of a reaction (bonds being formed or broken)

∆S

entropy, disorder of a reaction

-∆H

exothermic

+∆H

endothermic

energy carriers

used to catabolize molecules in steps, rather than all at once

ATP

this molecule contains high energy phosphate bonds that release energy when hydrolyzed

NAD+ and FAD

store electrons (e-) on aromatic rings, movement of which releases energy; they must be recycled to be continually used

diversity

different electron carriers help catch more available energy

enzyme

helps to overcome the activation energy of a reaction, which speeds up reactions to biological rates; structures reactants in optimal way to facilitate reaction

sources for catabolism

different macromolecules feed into catabolic pathways at different points

fermentation

a process that puts the electron back on some organic compound in order to recycle the electron carrier; has a lower energy yield, but it’s easier

respiration

a process that uses the electron transport system to put electrons on an inorganic final acceptor (e.g. oxygen); has a higher energy yield, but requires specialized complexes

glycolysis

breakdown of glucose, yields 2 pyruvate, 2 ATP, and 2 NADH

ED pathway

breakdown of sugar acids into pyruvate, 1 ATP, 1 NADH, and 1 NADPH (less energetically favorable)

PPP pathway

begins like the other two pathways, yields 2 NADPH, and sugar intermediates for biosynthesis (or further catabolism)

investment and cleavage

What are the two stages of glycolysis?

lactic acid fermentation

just put electron back onto pyruvate

ethanolic fermentation

put electron on pyruvate and release CO2 from pyruvate

TCA cycle

• further breakdown of pyruvate to generate lots of electron carriers

• at least 10 different cycles in bacteria

• all are started by acetyl-CoA, so this is how diverse molecules are catabolized

syntrophy

• parter organism uses hydrogen gas, allows original organism catabolism to function

• without oxygen, put aromatic electrons on protons, make hydrogen gas

electron transport systems

• membrane soluble electron carriers, move e- and obtain energy in small bursts

  • yields small amounts of energy, so pump protons

cytochromes

basis of electron transport systems, part of larger oxireductase complexes (ORCs)

proton motive force

• movement of protons for energy generation

• energy of ETS is too small to make ATP directly, so pumps protons

  • dependent on charge difference and pH difference

organotrophs

organics are initial donor (e.g. NADH) in metabolism; can be aerobic or anaerobic

lithotrophs

inorganics are initial donor; can be aerobic or anaerobic

phototrophs

capture light to split H2O or H2S as initial donor

NADH dehydrogenase

NDH1: first ORC, takes electrons from NADH, bounces them down to a quinone and pumps 4 protons, quinones to move electrons between ORCs (small, planar molecules that are membrane permissible), recycles NAD+

cytochrome bo3

Cytochrome bo quinol oxidase complex: takes e- from quinol, bounces them down, pumps 4 protons, puts e- on oxygen to make water

overall ETS

pumps 8(ish) protons, makes water, and recycles NAD+

oxidative phosphorylation

using ETS energy to make ATP, through the proton motive force

ATP synthase

• Proton enters c subunit, causes rotation of gamma core, rotational energy in alpha and beta subunits can make ATP

• 3 protons cause enough rotation to make 1 ATP

bacteriorhodopsin

• In archaea, light causes conformational change in retinal that pumps a proton

• relaxes naturally when returned to ground state

• In bacteria, called proteorhodopsin

photolysis

• light energy is absorbed and used to split e- from a donor (usually H2O or H2S)

• e- is eventually put on an ETS (like before) to pump protons and make ATP

chlorophylls

absorb light energy in their chromophores (alters energy state), excites e-

antenna complexes

• photons can’t be moved, so they must arrange chlorophylls in best way to catch them

• bounce energy to reaction center, where e- is donated

thylakoids

membranous structures that maximize photon gathering

photosystem I

• How e- is replaced on chlorophyll depends on the photosystem used

• e- is replaced by cleavage of H2O or H2S

photosystem II

• e- is replaced by ETS

• pumps protons, makes NADH

• purple bacteria (proteobacteria)

oxygenic photolysis

• only by cyanobacteria and eukaryotes

• chromophores absorb higher energy light, so can split water and make oxygen

• pumps protons and makes NADPH