HARNESSING ENERGY
A few people are fascinated when they are told how cells
harness and utilize the energy in the universe by such processes as
photosynthesis, metabolism, and biosynthesis. Some people go on
to study these processes as scientists. But most people are bored
and/or confused by such accounts. Indeed, if the topic of energy
transduction were left out of introductory courses, there might well
be far more biologically literate persons in our midst. Yet to tell
the story of life and not tell of energy transduction would be like
telling the story of the earth and leaving out heat convection. No
energy transduction, no life.
In this brief and most incomplete account, we will do our
best to transcend the tedium and lift up what is intriguing about
these vital activities. As we explain how these processes work,
moreover, we will also be looking at the evolution of life since, in
a very important sense, the evolution of life has entailed the
evolution of energy-transduction systems. And finally, an
understanding of these matters is essential to any grasp of
planetary ecology, a topic that we trust to be of keen interest to our
readers.
Overview
Everything that a cell does, and hence an organism does,
depends on biochemistry, and chemistry, as we noted in the
previous chapter, depends on the flow of energy, from a source (a
“higher” energy state) to a sink (a “lower” energy state).
To get into our topic, we can start with an animal that has just
eaten some sucrose (table sugar). Sucrose consists of two stable
molecules, glucose and fructose, that are joined together by a
chemical bond. In the animal’s gut, sucrose snuggles into the
pocket of an enzyme called sucrase, and sucrase catalyzes the
disruption of the bond between them, generating free glucose and
fructose. Energy, in the form of heat, is also released. Because
sucrose, by virtue of its bond, has a higher energy than glucose and
fructose, the chemical reaction – the bond-breaking reaction – can
occur spontaneously. So far so good.
So the next question is, how are glucose and fructose joined
together in the first place? Glucose and fructose are themselves
very stable molecules, with their atoms in stable configurations.
Even if they were brought close together by an enzyme, they
would very rarely, on their own, join together to form a chemical
bond. Therefore, they need to be activated. Plant cells take
molecules of glucose and fructose and, in reactions that require
energy input, convert them into new shapes that we can call
glucose* and fructose*. Glucose* and fructose* molecules have a
higher energy alone than when they are bonded together.
Therefore, when glucose* and fructose* are brought together in an
enzyme pocket, the sucrose bond forms spontaneously, with much
of the “activation energy” becoming stored in the bond. It is this
energy that is then released as heat when the bond is broken in the
gut.
So we have pushed back the question one more step: Where
does the energy come from to activate the glucose and fructose?
The answer is that it comes from photons spewed out from the sun
as it burns its hydrogen fuel. The electromagnetic energy in the
photons gets converted into high-energy chemical bonds in
molecules called ATP. The energy in ATP is then transferred into
creating glucose* and fructose*, and the rest is easy.
The crux of the matter, then, is the formation of the highenergy bonds in ATP. If photons could somehow just blast
themselves into ATP to form high-energy molecules, then this
would be the end of our story and we could move on to the next
chapter. But it’s not that simple. Instead, an elegant sequence of
steps, collectively known as photosynthesis, is required to form the
ATP that activates the glucose and fructose. During the course of
photosynthesis, moreover, a second kind of high-energy molecule,
NADPH, is also formed, and although NADPH is not directly
involved in making the sucrose bonds, it collaborates with ATP in
the formation of glucose, fructose, and most of the other building
blocks of the cell. Therefore, what we need to understand is the
way ATP and NADPH are generated by photosynthesis.
The Essence of Photosynthesis
In Chapter 3 we had our first encounter with the activation of
molecules so that they could engage in chemistry. In our scenario
for the origin of life, carbon monoxide was activated by brute
force: the enormous temperatures and pressures in hydrothermal
vents provided the energy to change the configuration of CO
molecules such that they went on to produce formic acid, pyruvate,
and related “building-block” products, molecules that were then
stabilized when they moved into the cooler oceans. But such deepearth chemistry cannot underlie the bioenergetics of a cell itself.
Life needs to carry out its biochemistry under moderate and
circumscribed temperatures and pressures and in tiny volumes.
Therefore, it needs to find an energy source compatible with these
constraints.
By far the most ubiquitous solution has been to use the
electromagnetic energy coming from the sun in the form of
photons in the visible portion of the spectrum (c.f. Chapter **).
These photons are absorbed by pigments, the most important being
chlorophyll. A pigment can be thought of as a molecule with a
cloud of electrons swarming about within it, rather like a swarm of
gnats on a summer’s day. When a photon hits one of these
electrons, the electron momentarily acquires extra energy – it
becomes “activated.” Chlorophyll’s swarming electrons are poised
to become activated by light in the red and blue range.
Photosynthesis basically entails transferring the energy of these
activated electrons into the high-energy chemical bonds in ATP
and NADPH.
First let’s make NADPH. The principle here is the same as
always: energy flows downhill. The activated electron in
chlrophyll, left to its own devices, would, moments later, fall back
down to its original energy level, releasing heat and accomplishing
nothing. But, before that happens, the electron is “captured” by a
molecule we can call Q, converting Q into an activated Q*
configuration. The chlorophyll, we say, serves as an electron
donor and Q as an electron acceptor. Sitting right next to Q is
another molecule that we can call R. Q* is favorably disposed to
donating its electron to R – energy flows downhill in the process -the result being that Q* becomes Q again and R becomes R*. R*
then donates its electron to S, generating R and S*, and so on. At
the end of this electron transfer chain, NADPH is the final electron
acceptor: it stores the energy of the activated electron in the form
of a chemical bond, energy that can later be donated to drive
biosynthetic reactions.
And now, a core concept. Electrons are not usually donated
by themselves, for the simple reason that they are not soluble in
water, making their transfer very difficult in the aqueous
environment of the cell. Instead, they are donated in the form of
water-soluble hydrogen atoms which, as we have seen in Chapter
**, consist of one electron and one proton. Electrons are still
donated – nothing has changed in this respect -- but protons (H+)
are associated with them. So, the electron-hungry molecule at the
end of the chain is called NADP+, and after it has accepted both an
electron and a proton it is called NADPH.
We can now respond to the obvious question: why does the
cell “bother” to transfer electrons from Q to R to S? Why doesn’t
the excited electron from chlophyll just drop down and form
NADPH in one swoop? The answer is that the fact that there are
protons moving along the chain is of critical importance for
making ATP. Alas, the way ATP is made is so bizarre that no
useful analogies come to mind, so we will simply state, without
further comment, that the moving protons generate a concentration
gradient across a membrane, then flow back across that gradient
through a channel, and a channel-associated enzyme called ATP
synthase catalyzes the conversion of the energy associated with
that flow into what is called a phosphoanhydride bond. More
specifically, a phosphate group is added to a molecule called ADP,
and the resultant phosphoanhydride bond in ATP contains energy
that can later be released in biosynthetic reactions.
But before we move on to biosynthesis, we need to take care
of one other matter. The electrons (and accompanying protons)
released from the chlorophyll and used to make NADPH need to
be replaced; otherwise the chlorophyll will not be able to keep
performing its electron donations and the whole process will
quickly grind to a halt. In early versions of photosynthesis, these
so-called “primary electrons” were donated by molecules like H2S
and methane (CH4), and certain kinds of modern photosynthetic
bacteria continue this practice. But most modern photosynthetic
organisms use water, which is conveniently ubiquitous, as the
primary electron donor, in the following reaction
2 H20  4 electrons + 4 protons + O2
where we need to start with two molecules of water to get the two
oxygen atoms needed to form molecular oxygen, O2. The
electrons and the protons replace those lost by the chlorophyll, and
the O2 bubbles off into the atmosphere. We will return to the
consequences of this release of oxygen shortly, but first we will
look at what photosynthetic organisms do with the ATP and
NADPH that they have generated as the consequence of photon
absorption.
Fixation of Carbon Dioxide into Sugar
Our atmosphere doesn’t contain much CO2 (Chapter **), but
there’s enough available for photosynthetic organisms to do the job
of converting it into sugars, sugars having the generic structure
CH2O (glucose, for example, is C6H12O6). An enzyme called
Rubisco, the most abundant enzyme on earth, catalyzes a reaction
wherein a molecule of CO2 is added to a 5-carbon sugar, creating a
6-carbon sugar. The 5-carbon sugar has been activated by ATP –
it is in a high-energy configuration – and the addition of the CO2
converts it into a lower-energy configuration. Moreover, in order
for the 5-carbon sugar to be activated by ATP, it first has to accept
electrons and protons from NADPH.
So we can think of CO2 fixation as starting with a low-energy
sugar that gets activated first by NADPH and then by ATP,
reaching the state where it will spontaneously (in the presence of
Rubisco) form a bond with CO2. Some of the resultant 6-carbon
sugars go on to transform into glucose and fructose; others get
converted back into activated 5-carbon sugars that pick up more
CO2 in a continuously cycling process. The overall result is that,
as long as ATP and NADPH are available, carbon in the air is
continuously being added to organic sugars.
We are just about there. The glucose and fructose produced
by photosynthesis have many possible biosynthetic fates. Some
molecules become activated, in ATP-dependent reactions, to form
glucose* and fructose* which, as we have seen, combine to form
sucrose. Others serve as building blocks for enzyme-catalyzed
reactions, dependent on ATP and NADPH, that result in the
biosynthesis of amino acids, nucleotides, and such macromolecules
as lipids, proteins, and DNA and RNA. All of these biosynthetic
products, be they small sucrose molecules or enormous protein
molecules, are chock-full of chemical bonds whose energy derives
proximately from ATP and NADPH and ultimately from the red
and blue photons released by the Sun.
The Oxygen Connection
We can now trun our attention to oxygen. O2 is a very
reactive molecule, eager to accept electrons and thereby achieve a
lower-energy status. When photosynthetic bacteria first came up
with the wonderful trick of “splitting” water, the O2 that was
released into the atmosphere combined with electron-donating
atoms in the environment – for example, all of the exposed iron on
the planet was converted to iron oxide (rust). But as oxygenevolving bacteria became more and more abundant, surface iron
could no longer “mop up” the O2 and it became an increasingly
abundant component of the Earth’s atmosphere. An anaerobic
(oxygen-free) planet became an aerobic (oxygen-containing)
planet.
Life up until that time had evolved in an anaerobic
environment, and the rising levels of oxygen presented organisms
with enormous difficulties: the O2 entered their cells and pulled
electrons out of essential molecules, with lethal consequences.
Some of these organisms retreated into the increasingly rare
anaerobic niches on the planet -- deep crevices beneath the earth,
for example – and similar anaerobic bacteria continue to flourish in
these habitats today, albeit they usually die if exposed to even a
whiff of air. Most of the remaining organisms were probably
killed off: the build-up of molecular oxygen is thought to have
produced one of the first major planet-wide extinctions. Indeed,
the early oxygen-evolving bacteria themselves would have been
vulnerable to the very O2 they were producing. The whole watersplitting experiment might well have resulted in a near-sterilization
the earth.
But as often happens during the evolution of life, some of the
organisms at that time figured out ways to make lemonade from
the oxygen lemon. From our perspective on bioenergetics, the
most significant of these was the evolution of a process known as
respiration in which the reactive properties of oxygen are used as
the basis for making ATP and, in the process, its toxic properties
are neutralized.
To think about how this works, let’s return to our original
glucose molecules that were cleaved from sucrose in an animal’s
gut. Once this happens, they are absorbed into the blood and then
enter the cells of the body, where they are commonly metabolized:
in a series of reactions catalyzed by enzymes, they are broken
down, bit by bit, into molecules of CO2, the released energy being
transferred either into the phosphoanhydride bonds of ATP or else
to NADH (an NADPH equivalent) in the form of electrons and
protons. The ATP and NADH go on to participate in biosynthetic
reactions, generating proteins and lipids and so on, just as we saw
for plant cells. However, in cells that are engaging in respiration,
NADH has a second possible fate: it can donate its electrons and
protons to oxygen.
The strategy here is one that we saw earlier when we
considered photosynthesis. In photosynthesis, we saw that when
high-energy electrons/protons from chlorophyll are donated to
NADP+, the donation is gradual, through a Q, then R, then S series,
allowing the flowing protons to engage in the bizarre process of
ATP formation. In respiration it is the same. The high-energy
electrons/protons from NADH are donated through a similar Q, R,
S series, called the respiratory electron transfer chain, before they
reach oxygen, with the proton flow again allowing ATP systhesis.
Finally, at the end of the chain, S* donates its electron and proton
to oxygen in the following reaction:
O2 + 4 protons + 4electrons  2 H2O
So, during respiration, when protons and electrons flow from
NADH to oxygen to form water, a great deal of additional ATP is
generated. This ATP, along with the ATP and NADH derived
from the metabolism of glucose, is then used to drive the
biosynthesis of amino acids, nucleotides, and macromolecules.
Standing back, then, here is what we see.
 Atmospheric CO2 is converted into carbohydrates, with
ATP and NADPH powering the reactions.
 Carbohydrates are metabolized to CO2, with ATP and
NADH being formed in the process.
 The ATP and NADPH needed for CO2 fixation are
generated during photosynthetic electron transport, the
electrons and protons ultimately deriving from water
and energized by photons.
 Much of the ATP formed during the course of
carbohydrate metabolism is generated during
respiratory electron transport, the electrons and protons
deriving from NADH and flowing into oxygen to form
water
Putting Bioenergetics Back into Organisms
Our account, with its necessary focus on atoms and electrons,
has been somewhat disembodied. Where does all this
biochemistry take place, and how did it evolve? We will move
back and forth in evolutionary history as we respond to these
questions.
Let’s begin with a cell in the leaf of a tulip. Its chlorophylls,
water-splitting enzymes, photosynthetic electron transport chains,
ATP synthases, and Rubisco enzymes are all located in tiny
membrane-rich organelles called chloroplasts that float about in the
cell’s interior (also called its cytoplasm). Floating about as well in
the cytoplasm are even tinier organelles called mitochondria.
Located in the mitochondria are many of the enzymes involved in
carbohydrate metabolism, plus the respiratory electron transport
chain and the associated ATP synthases. And finally, in the
cytoplasm itself are the rest of the enzymes involved in
carbohydrate metabolism. When a glucose molecule enters the
leaf cell from the sap, or when the leaf cell makes its own glucose
via CO2 fixation, the cell then makes a choice: the glucose either
enters a biosynthetic pathway or else it is metabolized, partially
broken down in the cytoplasm and finished off in the
mitochondrion.
Now we can move to an animal cell, where we discover that
it’s basically the same as the tulip leaf cell – glucose is
metabolized first in the cytoplasm and then in mitochondria by the
same enzymes and cofactors – the obvious difference being that it
doesn’t have chloroplasts. Therefore, animals are totally dependent
on photosynthetic organisms as primary sources of fixed carbon,
carbon that may be eaten directly, as by an herbivore or, in the case
of a carnivore, carbon that has first been eaten by another animal
and converted to animal tissue.
When we move to aerobic bacteria, we find that they are also
of two kinds: cells that possess pigments and carry out
photosynthesis as well as respiration, and cells that carry out
respiration alone and require external sources of food.
We are now in a position to take in a remarkable fact about
evolution: mitochondra and chloroplasts were once free-living
aerobic bacteria that came to take up residency in what are now
plant and animal cells. We will use the occasion of telling this
story to set out the larger picture of how life evolved on this planet.
Evolution of Bacteria
In the previous chapter on the origins of life, our chemical
focus was on the formation of organic building blocks, such as
formic acid, in hydrothermal vents. This was germane in that the
earliest cells are thought to have used these building blocks as a
source of food, extracting energy from their chemical bonds.
So, let us imagine this primordial cell. Its DNA-based
genome would encode genes that specify uptake proteins that
allow the formic acid to cross the lipid membrane and enter the
cell. It would also encode genes that specify metabolic enzymes
that catalyze the breakdown of the formic acid into smaller
molecules, with the released electrons and protons generating highenergy “currency” molecules like ATP and NADH. These would
then be used by the cell to mediate the synthesis of the proteins,
lipids, and DNA/RNA essential to being a cell at all.
To cells in this lineage we can add the first electron transport
chains, wherein electrons and protons are transferred from electron
donors like NADH to electron acceptors like Q, R, and S, making
additional ATP along the way. The final acceptor for the electrons
was not, however, O2 since, as we have seen, there was at that time
no O2 available. Instead, acceptors such as sulfate (SO4-) were
used, yielding H2S as the product rather than H2O.
Creatures resembling these cells are alive today: they are
called anaerobic bacteria, and they often inhabit extraordinary
niches using extraordinary adaptations. For example, bacteria that
live in the anaerobic guts of cattle and other ruminants use CO2 as
their terminal electron acceptors, producing gaseous methane
(CH4) which is then released in flatulence. Since methane is a
significant greenhouse gas in the atmosphere, these bacteria (and
their hosts) are potential contributors to global warming.
With the advent of O2 came the aerobic bacteria, using O2 as
the terminal electron acceptor. Collectively, the anaerobic and
aerobic bacteria are capable of utilizing just about every kind of
organic compound on the planet as a source of carbon and energy,
and it is impossible to exaggerate their importance in the presentday food chain: they degrade the organic material of dead plants,
animals, and other bacteria, recycling the end products to the
environment, and serve themselves as a food source for countless
organisms. Nor should we neglect to mention a subset of aerobic
and anaerobic bacteria that produce enzymes capable of nitrogen
fixation. Using ATP as energy currency, these bacteria transform
the inert N2 gas in the atmosphere into ammonium (NH4+) ions that
are used to donate nitrogen to amino acids and nucleotides. No
nitrogen fixation, no DNA, RNA, or proteins.
Bacteria that utilize organic molecules from the environment,
be they components of the primal soup or products of dying
organsisms, are to be contrasted with bacteria that make organic
molecules on their own, the major players here being those that
carry out photosynthesis. Again there are two general classes,
those that carry out photosynthesis anaerobically, extracting,
electrons from e.g. H2S and producing sulfur as a byproduct, and
those that extract electrons from water and generate O2 as a
byproduct.
So, as a generalization with many fascinating footnotes, we
can say that modern bacteria are of 4 kinds: anaerobic and aerobic
consumers of organic molecules, and anaerobic and aerobic
photosynthesizers. If we now ratchet back and ask what is known
about the appearance of these organisms on the planet, what we
can say is that fossils of tiny organisms of the size of bacteria have
been found in rocks dated to ~3.8 billion years ago. Although we
have no idea how they carried out their energy transduction, it is
safe to say that they did so anaerobically since evidence for a
significant amount of O2 in the atmosphere is not evident
geologically until ~2.5 billion years ago. Therefore, we can posit
the following bacterial sequence:
 anaerobic consumers (originally, of “primal soup”
molecules)
 anaerobic photosynthesizers
 oxygen-liberating photosynthesizers
 aerobic, respiring consumers and photosynthesizers
So, this is all very well for bacteria, and bacteria are without
question the most abundant and, by many criteria, the most
important organisms on the earth. But still, how about the likes of
us? Where do we fit in?
Evolution of Eukaryotes
Bacteria are called prokaryotes because their genomes are not
contained within an organelle called a nucleus (karyon); organisms
that possess such a nucleus, like us, are called eukaryotes. It turns
out that there are in fact two kinds of prokaryotes: the bacteria and
the archea. As diagramed in Figure 1, the bacteria and the archea
share a common ancestor and then, later, the archea and the
eukaryotes share a common ancestor. This means, of course, that
all three groups are related to the common ancestor that gave rise
to the prokaryotes; it also means that to understand who we are, we
need to think about the archea.
The archea are tiny single-celled organisms like bacteria, and
were only recently recognized as a distinct kind of organism.
Moreover, until recently they were thought to be constrained to
extreme environments like hot sulfur springs, but it is now clear
that they are more widely dispersed and indeed represent ~20% of
the marine picoplankton biomass. What is fascinating about
modern archea is that whereas their metabolic enzymes are similar
to bacteria, their enzymes involved in DNA replication,
transcription, and translation are more like the eukaryotic versions.
This generates the notion that the common ancestor to eukaryotes
and archea also had these enzymes and that the diverging protoeukaryotes went on to develop a true nucleus and other features
characteristic of the eukaryotic cell.
One of these features, absent in prokaryotes, is the capacity
to engulf (“endocytose”) large particles, including whole bacteria,
bringing them into the cytoplasm and digesting them as a food
source (Figure 2). It is here that we can finally circle back to our
story of the origins of chloroplasts and mitochondria.
It is now clear that early in the evolution of eukaryotes,
perhaps 1.5 billion years ago, a eukaryotic cell endocytosed an
aerobic bacterium but did not digest it. Instead, over the ensuing
millennia, its descendants “tamed” their bacteria such that they
became mitochondria, dutifully producing abundant ATP for their
host cells. In a second event, and about that same time, a
mitochondria-harboring eukaryote endocytosed an aerobic
photosynthetic bacterium and, over the ensuing millennia, the
ensuing lineage “tamed” these such that they became chloroplasts,
dutifully capturing energy from photons and fixing CO2 for their
host cells.
The taming process was challenging since it involved gaining
control of the bacterium’s capacity to divide and overwhelm the
host with daughter bacteria, but this was eventually successful:
modern mitochondria and chloroplasts can no longer survive on
their own. As a result, eukaryotic cells now possess cooperative
mitochondria and, in photosynthetic lineages, cooperative
chloroplasts, dividing just often enough to supply the cells with
now-essential supplies of ATP, NAD(P)H, and, for algae and
plants, fixed carbon.
This puts us in a position to trace the evolution of eukaryotes.
For hundreds of millions of years after they acquired their essential
features – a nucleus, endocytosis, and mitochondria and
chloroplasts – eukaryotes populated the planet as single-celled
organisms, the descendants of whom continue to thrive today as
single-celled algae, yeasts, and protozoa. They also came up with
the remarkable invention of sex, fusing in pairs with one another,
recombining their genomes, and emerging again as single cells via
a special kind of cell division called meiosis (cf Chapter **). Most
of the present-day single-celled eukaryotes continue to be sexual.
And then, perhaps a million years ago, some of these sexual
organisms began to experiment with multicellularity, wherein a
single organism is composed of many cells, with multiple cell
types engaging in specialized sets of activities but cooperating to
generate a functional whole. The first cell specializations were
doubtless very simple, but over time they have become stunningly
complex: muscles for movement, flowers for sex, nervous systems
for coordination, and so on. We are, of course, such multicellular
eukaryotes, as are all the organisms we call animals and plants.
But deep inside, each one of the cells in a multicellular organism
functions pretty much like a yeast cell, taking up carbohydrates for
energy, making ATP in mitochondria, and carrying out DNA
replication and gene expression in very much the same way. Yeast
cells, in turn, presumably resemble the first mitochondriacontaining eukaryotes that arose 1.5 billion years ago, and these
proto-eukaryotes, in turn, conserved most of the “good ideas”
encoded in the genomes of their prokaryotic forebears.
In the next chapter we will consider how these “good ideas”
arise and how they become preserved by the process called natural
selection.