Chapter 6 Central Metabolic Pathways summary notes
From 6.1-6.5
Energy= the capacity to do work
The purpose of the central metabolic pathways is to transfer energy from substrates (i.e. glucose
(food)) to a form that can do work for the cell in many different reactions and parts of the cell.
Adenosine triphosphate (ATP) is an example of stored energy. This is a common energy
currency in the cell. ATP donates energy, ADP accepts energy in for form of a high energy
phosphate bond.
Chemoorganotrophs make ATP two ways.
1. Substrate level phosphorylation = exergonic release of energy is used to add Pi to ADP.
2. Oxidative phosphorylation using energy of the Proton Motive Force (PMF).
Photosynthetic generation of ATP is called photophosphorylation, but also uses a PMF.
The metabolic pathways Glycolysis, TCA cycle and Pentose Phosphate pathway generate ATP
by substrate level phosphorylation.
These pathways also generate NADH, FADH2, and NADPH (reducing power—electron
carriers). Reducing power is the ability to donate an electron.
NADH and FADH2 are used to move protons across the membrane to generate a proton motive
force. This is used to make ATP. The metabolic pathways are linked to the PMF by NADH and
FADH2. The energy is still ultimately originating from the organic molecules (i.e. glucose).
NOTE that NADPH is used in biosynthetic pathways, and not used to generate ATP.
There are two main types of metabolic pathways for energy.
Catabolic and Anabolic.
Catabolism takes an energy source and converts it to ATP and precursor metabolites.
Anabolism takes the ATP and precursors to make cell components (also uses nutrients, nitrogen,
sulfur, iron, phosphate, to incorporate into the parts of the cell)
Precursor metabolites are carbon skeletons used to make other compounds. Example: Glucose to
Pyruvate then made into amino acids.
There are two forms of energy reactions:
Exergonic (releases energy= products lower ∆ G) and
Endergonic (stores energy= products higher ∆ G)
There are different ways to harvest energy. Two common energy sources are sunlight and
organic compounds (carbon bonds).
Harvesting light energy=photosynthesis; Using organic compounds = Chemooranotrophy
We will deal mainly with chemoorganotrophs for the purposes of this class.
Metabolic pathways can be linear (one way from start to finish), branched (products can be
diverted to different end products), and cyclic (a starting compound is regenerated through the
reactions).
Each step in these pathways is mediated by an enzyme.
Linear
Branched
Cyclic
What is reducing power? This was a question in the last lecture. Here is a brief explanation of
electron movement among atoms and why this is important.
Reduction is transfer of an electron to another compound (along with the proton H+).
The compound or element giving up the electron becomes oxidized.
The electron acceptor becomes reduced.
Oxidation – Reduction reactions drive energy and metabolism in cells.
See Figure 6.7 in Chapter 6. Chemical energy sources and terminal electron acceptors.
Electronegativity of atoms varies. Some hold onto the electrons more tightly.
Some give them up easily, and others take them easily. The ability to give up an electron can be
coupled with a reaction that generates energy. The larger the difference in the ability for the
atoms to hang onto their electrons, the greater the energy yield. It’s like falling down a potential
energy slope. (see Fig. 6.7) For this reason the terminal electron acceptor of reactions can affect
how much energy (ATP) is yielded from organic molecules like glucose.
The most energy yield generally comes from transfer of electrons to Oxygen as a terminal
electron acceptor (i.e. from Glucose). (On the chart, Oxygen is at the bottom).
These definitions and explanations were made to help you understand the processes described
next. All of them involve oxidation-reduction and electron transfer to generate ATP.
Central Metabolic pathways, Respiration and Fermentation:
2 main processes for catabolism of glucose:
1) Oxidize glucose to generate ATP, reducing power and precursor metabolites (central
metabolic pathways)
2) Transfer of electrons carried by NADH and FADH2 to terminal electron acceptors (respiration
and fermentation)
Central metabolic pathways: 3 key metabolic pathways oxidize glucose to CO2
These are catabolic, but precursor metabolites and reducing power are also generated and used
for biosynthesis (anabolic). Together these pathways are amphibolic. Fig. 6.10./Table 6.2
1.Glycolysis
2. Pentose phosphate pathway
3. TCA cycle (Tryicarboxylic acid cycle because oxaloacetate is regenerated)
Fermentation: pyruvate is the terminal electron acceptor. Inefficient. Generates acids,
alcohols, and gases. Used for generating many tasty foods for humans.
Cells that cannot respire, ferment. They have limited ability to regenerate their electron carriers.
Fermentation uses glycolysis only. Glucose is transformed to pyruvate (terminal electron
acceptor) yielding ATP and NAD+ (NADH donated electron to pyruvate.)
The full TCA cycle is not used, but elements of it are to generate specific precursor metabolites.
Glucose is not fully oxidized, and the ATP yield is less than if the TCA cycle was also used.
PRODUCTS OF fermentation (many are things we use). (Fig. 6.23)
Lactic acid (from lactate)
Ethanol: pyruvate to acetaldehyde to ethanol. (more detail in the food microbiology section
later).
Butyric acid (Clostridium)
Propionic acid, mixed acids, 2,3 Butanediol.
The reducing power generated is used to move electrons through an electron transport chain,
generate a PMF and make ATP.
Respiration: Electrons from Glucose are fed into electron transport chain to generate PMF.
Aerobic respiration: Oxygen is terminal electron acceptor.
Anaerobic respiration: similar but no oxygen. system uses other electron acceptors so the energy
yield is not as high.
Glycolysis: Glucose into 2 pyruvates, yields 2 ATP; 2NADH
and precursors
Two phases of glycolysis: 1) 5 steps consume energy. First group translocation into the cell (2
ATP); then 6 C transformed to 2 3C molecules with a phosphate.
2) the next five steps generate energy, Oxidizes and rearranges the 3-C molecules to generate 1
NADH, and 2ATP for each. So, 2 NADH, and 2 ATP net total.
(details figure 6.16)
Pentose Phoshate pathway.
Important pathway generates NADPH and 2 intermediates that are important biosynthetic
percursors
1)ribose 5-phosphate
2) erythrose 4-phosphate.
It also generates glyceraldehyde 3-phosphate (G3P) which can enter the Glycolysis pathway to
be broken down.
How are the glycolysis and PPP pathways linked?
TCA cycle
Transition step: Glycolysis feeds pyruvate into the TCA cycle after it is transformed to AcetylCoA by a large multi-enzyme complex.
A caron dioxide is removed from pyruvate and CoEnzyme A is added. This reaction generates
NADH.
TCA: Generates ATP, FADH2, NADH, and regenerates the starting molecule Oxaloacetate.
Cycles twice to make: 2 ATP, 6NADH, 2 FADH2, two different precursors.
Respiration:
Uses the reducing power from central metabolism pathway to create a proton gradient, then
makes ATP using oxidative phosphorylation.
The process that links the electron transport chain to ATP synthesis was proposed by Peter
Mitchell in 1961. Chemiosmotic theory. Nobel prize in 1978.
The electron transport chain is a group of membrane embedded electron carriers that pass
electrons sequentially, and eject protons. The protons are released on one side, thereby creating
a proton gradient. In prokaryotes, these are in the cytoplasmic membrane.
In mitochondria of eukaryotes, the e transport chain is in the inner membrane.
Energy is gradually released as the electrons are passed. Electrons go from higher to lower
energy states.
What are other actions that prokaryotes use their PMF for? (from earlier chapter 3)
Electron carriers are grouped into several protein complexes that function as proton pumps with
smaller proteins that can shuttle electrons from one complex to the next.
Three general groups of electron carriers:
Quinones, Cytochromes, and Flavoproteins
Quinones are lipid soluble and move within the membrane between protein complexes. Several
kinds exist.
Menaquinone-vitamin K, we get from our gut bacteria.
Cytochromes contain a heme group with an iron.
Some cytochromes are diagnostic for certain bacteria (cyt c in Neisseria).pg 143.
Flavoproteins contain a flavin group. FAD is a flavin. Riboflavin is needed from synthesis.
Proton Ejection! How does this work?
There are proteins in the e- transport chain that will accept only a hydrogen (e- + H+ together),
and others that only accept an electron. Because of the arrangement of the proteins in the
membrane, hydrogen carriers receiving an electron, must pick up a proton from the cytoplasm
(net – 1H+ in cytoplasm), a hydrogen carrier.
When the hydrogen carrier passes electrons to an electron carrier that takes only electrons, a
proton is ejected to the outside (+ 1 H+ to the outside). The net effect being fewer protons on the
inside of the cell.
Mitochondria: 4 different proton pumps, two electron carriers (ubiquinone and cytochrome c)
Complex I, II, III and IV. See page. 143
Complex I: NADH dehydrogenase complex—accepts electrons from NADH, transferring them
to ubiquinone, 4 H+ transfer
Complex II: succinate dehydrogenase complex—accepts electrons from the TCA cycle, when
FADH2 is formed during oxidation of succinate. (fig. 6.17, step 6) FADH2 transfer happens
down stream of the NADH . fewer protons are expelled
Complex III: cytochrome bc1 oxidase complex. Accepts electrons from ubiquinone—4 H+ then
transfers electrons to cytochrome c.
Complex IV: cytochrome c oxidase complex. 2 protons across the membrane
Terminal oxidoreductase. End of the chain, transfers eletrons to the terminal electron acceptor
which is Oxygen.
E-transport Chain in Prokaryotes:
Vary greatly and are versatile. A single species may have several alternative e- carriers. The
ability to vary the electron transport chain enables them to adapt to changing environmental
conditions that offer different terminal electron acceptors such as sulfate, and nitrate.
Here we use E. coli as an example (growing on glucose). Both aerobic and anaerobic respiration
is possible.
Aerobic respiration:
Two different NADH dehydrogenases, one is a proton pump equivalent to complex 1 in
Mitochondria.
E. coli has a succinate dehydrogenase equivalent to complex II of mitochondria.
In addition E. coli has several alternative complexes in order to take advantage of different
energy sources. Hydrogen is one. (No complex III or cytochrome c equivalents though).
Instead quinones shuttle electrons to one of two ubiquinol oxidases (like complex IV of mt).
One variation works well with high oxygen, the other with low oxygen (able to scavenge
oxygen).
Anaerobic respiration: Harvests less energy than aerobic. Why is that?
Some components of the anaerobic e- transport chain are different than the aerobic so that other
terminal electron acceptors can be used. For example, E. coli has a terminal oxidoreductase that
uses nitrate as the terminal electron acceptor. The product is nitrite, which is then converted to
ammonia (detoxified) because nitrite is toxic to the cell. Some bacteria can reduce the nitrite
even further to N2O or N2. Sulfate is another important terminal electron acceptor (not in E. coli,
but other bacteria). Sulfate reducers are important members of environmental bacterial
communities.
ATP synthase: This complex spans the membrane and electrons pass through it coupled with
synthesis of ATP. ~3 protons flow down the gradient to synthesize 1 ATP.
Using the mouse mitochondria as model a theoretical yield of ATP is 34 ATP for oxidative
phosphorylation. That is taking into account the reducing power (NADH and FADH2 ) from the
glycolysis, transitions step and TCA cycle.
Figure 6.21: theoretical yield of aerobic respiration in prokaryotes. 38 total. ATP from
substrate level phosphorylation= 4 and 34 from oxidative phosphorylation=38.
Fermentation: Fermentation is used by organisms that cannot respire, either because a suitable
terminal electron acceptor is not available, or because they lack an electron transport chain.
E.coli can do anaerobic and aerobic respiration, and fermentation. Streptococcus pneumoniae
can only ferment because it lacks an electron transport chain.
The only ATP generating pathway is glycolysis and involve substrate level phosphorylation.
The other additional steps oxidize NADH to regenerate NAD+ needed for additional rounds of
glycolysis. This is not as efficient as linking to respiration.
Products of fermentation depend on the pathway used. These products are significant for several
reasons. They are diagnostic for the pathway, which helps to identify certain organisms (like
lactic acid bacteria (Gr+)). Butyric acid (anaerobic Clostridium species).
The products of fermentation are also important for human uses.
These include: lactic acid in cheeses and ethanol.
Propionic acid made in swiss cheese process by Propionibacterium, which also gives of CO2
producing the holes in the cheese.
Mixed acids are produced through a multistep branching pathway. In Enterobacteriaceae used to
distinguish different genera.
Butanediol: uses two pyruvates in a multistep pathway that generates acetoin and CO2.
Detection of the acetoin is diagnostic for certain members of Enterobacteriaceae.
Extra credit. How does the ATP synthase work?