Chapter 11: Catabolism – How Microbes Release & Conserve Energy

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Welcome back to the Deep Dive.

Today we're really getting into the nuts and bolts of how microbes stay alive.

Yeah, we're talking about energy, how they capture it, how they use it, where they get their basic building materials.

Exactly.

We're using Chapter 11 from Prescott's Microbiology as our guide, focusing on those core fueling reactions.

And you know, instead of just starting with diagrams, let's picture this place, the Berkeley Pit Lake in Butte, Montana.

Yeah, not exactly a tourist spot.

No, definitely not.

It's this huge old copper mine filled up with water that's incredibly acidic, like pH 2 .5, and it's just loaded with toxic heavy metals.

That's where all those snow geese landed back in 95 and, well,

didn't leave.

Such a harsh environment.

You'd think nothing could live there, right?

Chemically sterile, basically.

But that's the amazing part.

It's actually teeming with life, really unique microbes, fungi, even some algae.

Wow, surviving in that.

And not just surviving, some are making these really interesting chemicals, metabolites that scientists are looking out for, like new medicines, cancer treatments, things like that.

So that extreme resilience, that's kind of our entry point today into understanding microbial metabolism, its sheer flexibility.

Precisely.

It highlights just how adaptable these tiny organisms are.

Okay, so let's define the mission here.

What are we trying to understand?

It seems like it all comes down to getting three key things, right?

That's it.

First, ATP.

That's the cell's immediate energy currency, like cash.

Then you need reducing power, the NADH and NADPH, like rechargeable batteries.

Exactly, like rechargeable batteries, yeah.

They carry energy in the form of electrons for all sorts of reactions.

And third, you need the building blocks themselves.

Precursor metabolites, the basic carbon skeleton to build everything else.

ATP, reducing power and precursors.

Get those three and you're in business.

So how do we start classifying microbes based on how they get these?

It begins with the big picture needs.

Right.

Energy, electrons and carbon, where do they get each one?

For energy, it's either light, phototrophs or chemical reaction.

Cavitrophs.

Then electrons, either from inorganic stuff, rocks basically.

Lithotrophs, the rock heaters.

Or from organic molecules.

Organotrophs, like us.

And finally, carbon,

either fixing CO2 from the air.

Autotrophs, sulfeters.

Or eating ready -made organic molecules.

Heterotrophs, that's us again.

So when you mix and match these, you get the different nutritional lifestyles.

Exactly.

You get the major nutritional types.

And this shows the incredible diversity out there.

We and lots of pathogens are umorganoheterotrophs, organic chemicals for energy, electrons and carbon.

Kind of all in one package.

Yeah, that's a common strategy.

But some of the most biochemically interesting microbes are things like the chemolithoautotrophs.

The rock eating cell feeders.

Right.

They oxidize things like iron or sulfur compounds, maybe ammonia, that's their energy and electrons.

And then they grab CO2 from the environment for their carbon.

No sun, no sugar needed.

They're like the primary producers in places without light deep underground or maybe in the Berkeley pit.

Absolutely.

They're foundational in those kinds of extreme ecosystems.

Okay, let's zoom back in on the chemorganotrophs for a bit.

The ones using organic fuel like glucose.

They seem to have two main strategies to break it down.

Respiration and fermentation.

What's the electrons end up?

In respiration, the electrons get passed down a whole chain of carriers.

The electron transport chain or ETC.

Right.

And eventually they're handed off to an external molecule, something from outside the cell.

We call that an exogenous electron acceptor.

And moving electrons down that chain, that's what generates the proton motive force, the PMF.

Yes, that PMF is then used to make tons of ATP through oxidative phosphorylation.

That's the big energy payoff in respiration.

If that final acceptor is oxygen, O2, we call it aerobic respiration.

Simple enough.

Yep.

But if it's something else, maybe nitrate or sulfate, even CO2 and some microbes, then it's anaerobic respiration.

Still uses an ETC, still uses an external acceptor, just not oxygen.

Okay, so what about fermentation then?

Fermentation is different.

It's sort of the quick and dirty option.

There's no ETC, no external electron acceptor.

So where do the electrons go?

They get dumped onto an internal molecule, something generated inside the cell.

Often it's pyruvate or something derived from pyruvate.

We call that an endogenous acceptor.

And without the ETC and oxfos,

the ATP yield must be way lower.

Way lower.

Almost all the ATP you get from fermentation comes from substrate level phosphorylation, SLP.

That's just where an enzyme directly transfers a phosphate from a high energy intermediate onto ATP.

Much less efficient.

But microbes are so efficient, usually, it feels like these pathways aren't just one -way streets.

I remember reading about amphibolic pathways.

Ah, yes, that's a really crucial concept.

Amphibolic means dual function.

Think about glycolysis, the breakdown of glucose.

The Emden -Meierhoff pathway is the classic example, right?

Exactly.

That pathway doesn't just run one way to break down glucose for energy, which is catabolism.

It can also essentially run in reverse, or parts of it can, to beat things up.

That's anabolism.

So the cell uses the same set of

Pretty much.

It can pull intermediates off the pathway to use as precursor metabolites for building amino acids or lipids or whatever.

It's incredibly efficient.

Why build two separate systems when one flexible one can do both jobs?

That makes sense.

Okay, so focusing on breaking down glucose to pyruvate.

Prescott highlights three main routes for this first stage.

Right.

Three central pathways.

The first and most common is the one you mentioned.

The Emden -Meierhoff pathway, or EMP.

Found pretty much everywhere.

Bacteria, archaea, eukaryotes.

Yep.

It's the workhorse.

You put in two ATP to get it started, but you get four back out, plus two NADH molecules.

So the net gain is two ATP via SLP and two NADH per glucose.

It's good for maximizing that immediate ATP.

Okay.

What's the second one?

The Entner -Deuterhoff ED pathway.

The Entner -Deuterhoff.

Yeah.

If you find this one in certain gram -negative bacteria, especially soil microbes like pseudomonas, it takes a slightly different chemical route.

There's a key intermediate called KDPG that's unique to it.

And the yield is different too.

It is.

Per glucose, the ED pathway only nets you one ATP.

But importantly, it produces one NADH and one NADPH.

Ah, so it makes both kinds of reducing power.

Maybe it's less about raw ATP and more about balancing those electron carriers for different jobs.

That seems to be the case.

Yeah, it offers a different balance of products compared to EMP.

And the third route, the pentose phosphate pathway, PPP.

Right.

The PPP is maybe the most versatile.

It can operate aerobically or anaerobically, but its main role isn't really ATP production at all.

What's its primary job then?

Biosynthesis.

Construction.

Its major output is reducing power in the form of NADPH.

Okay, wait.

NADH goes to the ETC for ATP mostly.

What's NADPH used for?

NADPH is the main electron donor for anabolic reactions.

Building things up, like fatty acids or nucleotides, requires electrons, and NADPH is the cell's go -to supplier for that.

So PPP is about getting building blocks and the specific reducing power needed to assemble them.

Exactly.

It also generates crucial precursor metabolites like ribose 5 -phosphate, which you need for DNA and RNA, and erythrose 4 -phosphate for aromatic amino acids.

Very important pathway.

Okay, so let's say the What happens next?

Pyruvate doesn't enter the next big stage directly.

First, it gets converted, oxidized actually, into a molecule called acetyl -CoA.

This step also releases a molecule of CO2 and generates an NADH.

And that acetyl -CoA, that's the fuel for the next cycle.

That's the entry ticket to the tricarboxylic acid cycle, the TCA cycle, also called the Krebs cycle or citric acid cycle.

Right.

And what does the cell get out of the TCA cycle?

A huge haul of energy carriers.

For each acetyl -CoA that goes in, the cycle turns and spits out.

Two molecules of CO2, three NADH, one FADH2, another electron carrier, and one GTP, which is basically the same as an ATP.

So lots more reducing power generated.

And it's a cycle.

So it regenerates the starting molecule to accept the next acetyl -CoA.

Precisely.

And just like glycolysis, the TCA cycle is also amphibolic.

It's constantly spinning off intermediates that are used as precursors for biosynthesis.

Hugely important hub.

Okay.

Now we have all this NADH and FADH2 from glycolysis and the TCA cycle.

Where do they finally cash them in for ATP?

That happens at the electron transport chain and through oxidative phosphorylation.

This is where the vast majority of ATP is made during respiration.

And this is where we see some differences between, say, our mitochondria and bacterial systems.

Definitely.

The mitochondrial ETC is typically a set of four large protein complexes, very well defined.

In bacteria and archaea, the EPC is embedded in their plasma membrane and it can be much more varied.

How so?

Often shorter chains, sometimes branched pathways, they might use different types of cytochromes.

This variability means their efficiency can differ.

The PO ratio, the amount of ATP made per oxygen atom reduced, is often lower in bacteria than in mitochondria.

But the basic principle is the same.

Peter Mittal's chemiosmotic hypothesis.

Yes, absolutely.

As electrons move through the ETC complexes, energy is released and that energy is used to pump protons, hydrogen ions, H plus out of the cytoplasm across the membrane.

Creating a gradient.

More protons outside than inside?

Exactly.

You get both a charge difference, positive outside, negative inside, that's delta

concentration difference, higher H plus outside, that's delta pH, EPH.

Together, that electrochemical potential energy is the proton motive force, the PMF.

Like building up water behind a dam.

Stored energy.

Perfect analogy.

And the way the cell taps that energy is with this incredible molecular machine.

ATP synthase.

ATP synthase.

It acts like a tiny turbine or rotary engine.

The PMF provides the energy, forcing protons to flow back into the cell through a channel in the enzyme, the F0 part.

And that flow causes rotation.

It does.

It makes the central stalk, the gamma subunit, spin around inside the stationary headpiece, the F1 part.

And that spinning causes conformational changes in F1, literally forcing ADP and phosphate together to make ATP and then releasing it.

It's beautiful molecular machinery.

It really is.

So when you add it all up, the SLP from glycolysis TCA and the oxfos from the ETC, you get these textbook numbers, like maybe 32 ATP per glucose for eukaryotes.

But you always hear the actual yield is lower.

Why?

Because that PMF, that proton gradient, it's too valuable to only use for making ATP.

Ah, the cell uses it for other things too.

Oh yeah.

Bacteria use the PMF directly to power the rotation of their flagella so they can swim.

They also use it to drive active transport systems, pulling nutrients into the cell against their concentration gradient.

So there's a constant demand on that PMF, meaning not all of it can go towards making ATP.

Exactly.

Plus, remember those amphibolic pathways.

If the cell is actively growing, it's pulling precursor metabolites out of glycolysis and the TCA cycle.

That means less stuff going all the way through to generate the maximum reducing power.

So the theoretical yield is just that theoretical.

Real life is messier and involves tradeoffs.

Okay, that makes sense.

So that covers aerobic respiration, the high efficiency pathway.

What if oxygen isn't available?

What's Plan B?

Plan B is usually anaerobic respiration.

The cell still uses an ETC, still pumps protons, still makes ATP via ox -phos, but the final electron acceptor is something other than oxygen.

Like nitrate or sulfate.

Exactly.

Nitrate, NO3, sulfate, SO42, even CO2 or ferric iron, FA3 +, can be used by different microbes.

The only catch is these alternative acceptors generally have a less positive reduction potential than oxygen.

Meaning the energy drop for the electrons is smaller.

Right.

So less energy is released as electrons move down the chain, fewer protons get pumped, and ultimately you make less ATP compared to aerobic respiration.

Still better than nothing though.

And this has big environmental consequences, right?

Like denitrification.

Huge.

Denitrification is when bacteria use nitrate as their electron acceptor and reduce it all the way down to nitrogen gas N2.

This happens a lot in waterlogged soils.

Which is bad for farmers because it removes usable nitrogen from the soil.

Correct.

It means more fertilizer is needed.

But on the flip side, we actually harness denitrification in wastewater treatment plants to remove excess nitrogen compounds from sewage.

So it's ecologically important and useful biotechnologically.

Okay.

So anaerobic respiration is Plan B.

What if there are no suitable external electron acceptors at all?

No oxygen, no nitrate, nothing.

What then?

Then the microbe is forced into Plan C fermentation.

And the main goal here isn't really maximizing ATP, is it?

No, not at all.

Fermentation makes very little ATP, only through SLP during glycolysis.

The critical function of fermentation is to regenerate NAD plus from the NADH produced during glycolysis.

Why is regenerating NAD plus so important?

Because glycolysis needs NAD plus to accept electrons in one of its key steps.

If all the NAD plus gets converted to NADH and there's no ETC to take those electrons away, glycolysis grinds to a halt.

No glycolysis, no ATP,

cell dies.

So fermentation is basically a way to dump the electrons from NADH back onto an internal organic molecule just to get NAD plus back so glycolysis can keep running.

Precisely.

It allows the cell to keep making some ATP via SLP, even without respiration.

Common examples are lactic acid fermentation, like in yogurt production, or alcoholic fermentation in making beer and wine.

But wait, if fermenting organisms make so little ATP and they don't have an ETC pumping protons,

how do they generate the PMF they still need for things like nutrient transport and flagellar motility?

Ah, this is where it gets really tough for them energetically.

They have to essentially run their ATP synthase backwards.

Backwards?

What does that mean?

Instead of using PMF to make ATP, they use ATP to make PMF.

They hydrolyze, break down the precious little ATP they made via SLP, and use the energy released from that hydrolysis to actively pump protons out of the cell.

They spend ATP just to create the proton gradient.

That sounds incredibly wasteful.

It is incredibly costly.

It's like an energetic overdraft.

But they have no choice.

They absolutely need that PMF to bring in food and to move around, so they sacrifice some of their meager ATP earnings just to maintain those essential functions.

It shows how critical PMF is and why fermentation is really a low -yield, often temporary,

survival strategy.

Okay, that really highlights the desperation involved.

Let's shift gears slightly.

We've focused on glucose, but microbes eat lots of other things.

What about fats, lipids?

Lipids are great fuel sources.

They're first broken down into glycerol and fatty acids.

The fatty acids then enter a pathway called beta -oxidation.

Beta -oxidation?

What does that do?

It chops the long fatty acid chain down two carbons at a time, releasing acetyl -CoA in each cycle.

And that acetyl -CoA feeds straight into the TCA cycle.

Plus beta -oxidation itself generates NADH and FADH2.

So lipids yield a lot of energy via respiration.

Makes sense.

And proteins, how are they used for fuel?

Proteins first get hydrolyzed into their individual amino acids.

Then the amino group, NADRSH -NH2, has to be removed.

This is called deamination.

Often by transferring it to another molecule,

right?

Transamination?

Exactly.

Transamination is a common way.

Once the amino group is gone, you're left with an organic acid skeleton.

And depending on what the original amino acid was, that skeleton can be fed into the TCA cycle directly or into pyruvate processing or even into glycolysis at various points.

Very flexible.

Okay, now let's go back to those really extreme metabolisms we touched on earlier.

The chemolithotrophs, the rug eaters.

Right, the ones oxidizing inorganic compounds like hydrogen gas or sulfur compounds or ferrous iron,

Fe2+.

You mentioned they face a thermodynamic problem because their electron donors often aren't strong enough to donate electrons directly to NAD plus to make NADH.

That's the challenge.

The reduction potential of, say, the F2 plus Fe2 couple is much more positive than the NAD plus NADH couple.

Electrons naturally want to flow from more negative to more positive potentials downhill, thermodynamically speaking.

So how do they make the NADH or NADPH they absolutely need for fixing CO2 and building cell parts?

They have to use reverse electron flow.

Reverse flow.

Sounds difficult.

It is.

They essentially have to use some of the PMF they generate from oxidizing their inorganic donor energy that could have been used to make ATP to instead force electrons backwards uphill thermodynamically from the donor onto NADP plus say.

So they sacrifice potential ATP production to get the reducing power needed for biosynthesis.

Another major trade off.

A huge one.

It shows that sometimes for these autotrophs, building biomass is just as or even more critical than maximizing immediate ATP yield.

And wasn't there a newer mechanism mentioned?

Something about electron bifurcation?

Ah yes.

Flavin -based electron bifurcation or FBEB.

This is a really elegant mechanism, particularly important in anaerobic environments.

How does it work?

Does it still need PMF?

No, that's the beauty of it.

FBEB allows the cell to perform an energetically unfavorable reaction, like reducing NAD plus with a weak donor by tightly coupling it simultaneously with a separate, highly favorable electron transfer reaction.

So the energy released from the easy reaction drives the hard one.

Essentially, yes.

It's like using one reaction to pull the other one along, bypassing the need to spend PMF or ATP, a very clever thermodynamic trick used by many anaerobes.

Fascinating.

Okay, last major category.

Phototrophy.

Getting energy from light.

We know about the kind plants and cyanobacteria do.

Right.

Oxygenic photosynthesis.

Uses chlorophyll, has two distinct photosystems, photosystem II and I.

Critically, it uses water, H2O, as the electron donor.

Which why it releases oxygen O2 as a byproduct, and it makes both ATP and NADPH needed for CO2 fixation.

Correct.

It uses a non -cyclic flow of electrons for that.

But it can also do cyclic flow using only photosystem I just to generate extra ATP when needed.

But there are other kinds of phototrophy in bacteria.

Oh yes, an oxygenic phototrophy.

Found in groups like the purple and green bacteria.

They use different pigments called bacterioclorophils, and they typically only have one type of photosystem.

And crucially, they don't use water as the electron donor.

Right.

They use things like hydrogen sulfide, H2S, or sulfur, or hydrogen gas.

Because they don't split water, they don't produce oxygen, hence anoxygenic.

How do they make ATP in reducing power?

They often use cyclic electron flow around their single photosystem, primarily to generate PMF for ATP synthesis.

To get the reducing power the NADPH needed for CO2 fixation, they often have to rely on.

Reverse electron flow again.

Often, yes.

They use PMF generated by light to push electrons uphill onto NAD plus boat.

Seems like reverse electron flow is a common strategy when thermodynamics aren't quite cooperating.

It really is.

And there's one more really distinct type of phototrophy.

Rodopsin -based.

Yeah.

Like in halobacterium.

Exactly.

This isn't based on chlorophyll at all.

Organisms like halobacterium use a protein called bacteriodopsin, or arcoridopsin.

It's basically a light -driven proton pump.

So light hits the rodopsin, and it just directly pumps a proton across the membrane.

That's it.

No ETC involved at all.

Light energy is directly converted into a proton mode of force.

Wow.

So they can make ATP using ATP synthase powered by this light -driven PMF without needing complex electron transport chains.

Correct.

And this is a huge advantage for organisms, often chemogrynotrophs, living in nutrient -poor environments like the open ocean.

They can supplement their energy budget using light, making ATP without having to burn precious organic carbon compounds, saving those carbons for growth instead.

It's just another layer of metabolic flexibility.

Yeah.

Amazing.

It really is.

So if we try to wrap this all up, bring this deep dive home,

the overwhelming theme from Chapter 11 seems to be this incredible metabolic flexibility.

It's not one single way of doing things.

Not at all.

You've got the three different glycolytic pathways providing different balances of products.

You've got the fundamental choice between respiration and fermentation.

Respiration itself can be aerobic or anaerobic using a whole range of acceptors.

Then there's chemolithotrophy, eating rocks, and multiple kinds of photography.

Overlying all of that is the amphibolic nature of the central pathways, the constant juggling act between breaking things down for energy, catabolism, and building things up for growth, animalism.

It really drives home the success of microbes, their ability to thrive everywhere, from soil to our guts, to places like the Berkeley pit.

It all stems from this unparalleled adaptability.

Their genius lies in managing that core budget ATP, reducing power and precursor metabolites using whatever resources are available, whether chemical or physical.

They are the ultimate metabolic strategists.

Absolutely incredible.

Okay, let's leave our listeners with a final thought then.

Considering this immense versatility we've discussed, the constant need to acquire and balance ATP, reducing power and precursor metabolites.

Imagine we discover life on another world based on completely different chemistry.

Which of those three fundamental requirements do you think would be the hardest for that alien life form to consistently secure?

Something to ponder.

A great question to think about.

Thank you for joining us for this deep dive.