American University of Beirut

Biol 201

Chapter 7: How Cells

Harvest Energy
I. Overview of Respiration
II. Glycolysis: Splitting Glucose
III. The Oxidation of Pyruvate to Produce
Acetyl-CoA
IV. The Krebs Cycle
V. The Electron Transport Chain
VI. Energy Yield of Aerobic Respiration
VII. Regulation of Aerobic Respiration
VIII. Oxidation without O2
IX. Catabolism of Proteins and Fats
X. Evolution of Metabolism

Marita E. Yaghi

American University of Beirut

Biol 201

I. Overview of Respiration:
Plant, algae and some Bacteria harvest energy of sunlight through
photosynthesis and convert this radiant energy into chemical one. These
organisms are called Autotrophs.
Other organisms use the organic compounds that autotrophs produce as
food. They are called Heterotrophs and form 95% of the population on Earth.
Autotrophs also extract energy from organic compounds but they have the
additional capacity to use the energy from sunlight to synthetize these
compounds.
The process of oxidation of organic compounds to extract energy from
chemical bonds is called Cellular Respiration.
Oxidation of Organic Compounds by Cells:
Most food contains a lot of carbs, fats and proteins rich in the very energetic
C-H bonds.
Stages are required to extract the energy from food. First, enzymes break
large molecules to small one; this is digestion. Second, other enzymes
dismantle these fragments a bit at a time to harvest the energy from them
at each stage; these reactions are called oxidation.
These oxidations state that energy metabolism is concerned with redox
reactions, but not only, as protons are also lost. So, hydrogen atoms are lost
in these dehydrogenations.
Cellular Respiration and Redox Reactions:
An atom that loses an electron is oxidized through oxidations while an
atom that gains an electron is reduced through reduction.
Cells utilize enzymes to facilitate the redox reactions to take energy from
food sources and convert it to ATP, the energy currency of the cell.
The redox reactions that occur through biological systems transport
energy-rich electrons that will carry this energy with them while going
from a molecule to another. The energy of the atom depends on its
orbital or energy level.
Enzymes catalyze redox reactions with the help of a cofactor, NAD+,
Nicotinamide Adenosine Dinucleotide, that accepts 2 electrons and a
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proton from the substrate to form NADH, which will be released from
the enzymes active site. This reaction is reversible.

During cellular respiration dozens of redox reactions happen using several

molecules such as NAD+ and releasing energy that will be used synthesize
ATP or be lost as heat.
At the end, the electrons have lost most of their energy and will then be
taken to the final electron acceptor. If the acceptor is:
- Oxygen aerobic respiration.
- Inorganic molecule (that is not oxygen) anaerobic respiration
- Organic molecule fermentation
Burning Carbs:
Both catabolism of Carbohydrates and wood combustion have the same
formula:
C6H12O6 + 6O2 6CO2 + 6H2O + Energy (Heat and ATP)
Under standard conditions, this reaction releases 686kcal/mol. In contrast,
in the cell, the change in free energy is G = -720 kcal/mol. This means the
cell releases more energy by making the same reaction in small steps.

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American University of Beirut

Biol 201

Metabolism and Electron Carriers:

During cellular respiration, glucose is oxidized to CO2 but not directly given
to O2, or it would be combustion. Instead using intermediate electron
acceptors permit the cell to gain more energy.
Many forms or electron carriers are used:
1. Soluble carriers move electrons from a molecule to another
2. Membrane bounded carriers form a redox chain
3. Carriers that move in the membrane
These carriers can all be oxidized then reduced multiple times.
Some carriers carry only electrons, like Iron-Containing Cytochromes, while
others carry both electrons and protons, like ubiquinone.
NAD+ is the most important electron carrier. It is made of two parts:
- Adenosine MonoPhosphate; AMP act as a core and give the NAD+ its
shape that is recognized by enzymes
- Nicotinamide MonoPhosphate; MNP active part of the molecule
that is readily reduced and accepts electrons

When NAD+ acquires 2 electrons and proton from the active site of an
enzyme, it becomes NADH. NADH can carry these energetic electrons and
supply them to other molecules, reducing them.
This ability to supply high-energy electrons is very important for energy
metabolism and biosynthesis of organic molecules. In animals, when ATP is
plentiful, the reducing power of the accumulated NADH can be used to

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Biol 201

supply fatty acids precursors with the electrons, converting them to

storable high-energy fats.
Metabolism harvest energy in stages:
The more energy release in one single step, the less energy is channeled to
useful paths as more is lost to heat. For this reason, if electrons are
transferred to oxygen in one step, releasing a lot of free energy at once, cells
would harvest very little energy.
The electrons from the C-H bonds of glucose are stripped down in stages,
called glycolysis and Krebs Cycle, and transferred to NAD+.
The electrons are also passed into the electron transport chain, located in
the inner membrane of the mitochondria before they are released to the
final electron acceptor, oxygen.
The movement of electrons in this transport chain creates a proton
gradient across the inner membrane of the mitochondria and the intermembrane space.
ATP role in metabolism:
Cells use ATP to power most of their activities that require an input of
energy like movement:
IG: contraction of muscles by movement of tiny fibers
IG: movement of mitochondria in the nerve cells
IG: pulling apart of chromosomes during division
Cells use ATP to drive endergonic reactions. In fact, enzymes have two
binding sites, one for ATP and one for the reactant. The ATP site splits the
ATP liberating G= -7.3kcal/mol of chemical energy, that will push the
reactant up to its activation energy, driving the now-favorable endergonic
reaction.
The many steps of cellular respiration have one goal: ATP synthesis.
ATP synthesis is an endergonic reaction itself and requires energy.

Mechanisms to make ATP:

1. Substrate-level phosphorylation:
A phosphate group is directly added to an ADP molecule, from a phosphatebearing intermediate, using an enzyme. During glycolysis, the energy
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Biol 201

provided by splitting the glucose molecules provides enough energy for this
mechanism.

2. Oxidative phosphorylation:
ATP is synthesized by the enzyme ATP Synthase that uses the proton
gradient to power this synthesis. The proton gradient is created by the
electron transport chain, where the electron will be donated to oxygen. The
catalyzed reaction by ATP synthase is:
ADP + Pi ATP
Most organisms combine the two methods to synthesize their ATP. The energy is
harvested by the oxidation reactions that remove highly energetic electrons from
glucose and transport them to their final electron acceptor creating a proton
gradient that will power ATP Synthase.

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American University of Beirut

Biol 201

II. Glycolysis: Splitting Glucose

Glucose can be split in many ways, but the best one is the glucose-catabolizing
process that liberates enough free energy to synthesize ATP.
Glycolysis occurs in the cytoplasm and converts glucose to two 3-Carbon
molecules called pyruvate.
It is made of 10 reactions that can be divided to two sets: during the first,
glucose is split to 2 3GP molecules and uses 2 ATP, and during the second, the 2
3GP molecules give 2 pyruvate molecules and 4 ATP.
The net formation of ATP is two.
Priming: change glucose to a compound that can be cleaved to two
phosphorylated molecules. It requires two ATP molecules.
1. Glucose is phosphorylated
Glucose + ATP Hexokinase Glucose 6-Phosphate + ADP
2. The phosphated glucose is rearranged to phosphated fructose.
Glucose 6-Phosphate phosphoglucose isomerase Fructose 6-Phosphate
3. The phosphated fructose is phosphorylated again.
Fructose 6-Phosphate + ATP phosphofructokinaseFructose 1,6-biphosphate + ADP

Cleavage: the 6-Carbon diphosphate sugar is split into 2 3-Carbon

monophosphate sugars. One is G3P and the other is converted to G3P.
4. The fructose 1,6-biphosphate is split to one Glyceraldehyde 3-Phosphate
and one Dihydroxyacetone molecules, each with one phosphate group:
Fructose 1, 6-biphosphate aldolase G3P + Dihydroxyacetone
5. The Dihydroxyacetone is converted to G3P.
Dihydroxyacetone isomerase G3P

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American University of Beirut

Biol 201

Oxidation and ATP formation: Each 3P molecule is oxidized, transferring two

electrons and a proton to NAD+ making NADH. Four molecules of ATP are formed.
6. The 2 G3P molecules are oxidized and phosphorylated to form BPG,
1,3-BiPhosphoGlycerate, that have one high-energy phosphate bond each
G3P + NAD+ + Pi glyceraldehyde 3-phosphate Dehydrogenase NADH + BPG
7. The BPG, 1,3-BiPhosphoGlycerate, molecules lose their high-energy
phosphate group to ADP becoming 3PG, 3-PhosphoGlycerate,

and

producing two ATP molecules

BPG + ATP phosphoglycerate kinase 3PG + ATP
8. The 2 3-PhosphoGlycerate, 3GP, are rearranged into 2GP : their phosphate
group is moved from the third to the second carbon:
3-PhosphoGylcerate phosphoglyceratemutase 2-phosphoglycerate
9. A water molecule is removed from each 2GP giving phosphated pyruvate
called PhosphoEnolPyruvate or PEP:
2-PhosphoGlycerate enolase PhosphoEnolPyruvate
10. The 2 phosphoenolpyruvate molecules are de-phosphorylated forming
two more ATP molecules and 2 pyruvate:
Phosphoenolpyruvate + ADP pyruvate kinase Pyruvate + ATP
Net Formation out of 1 glucose molecule:

2 ATP
2 NADH
2 H+
2 Pyruvate
2 H2O

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American University of Beirut

Biol 201

History of glycolysis:
Although the ATP yield from glycolysis is low, it is very efficient as it traps
up to 40% of the energy released.
Before, billion years ago, glycolysis was the primary way that heterotrophic
organisms used to make ATP from organic molecules.
Glycolysis has evolved backwards: the second part that converts 3GP to
pyruvate might be the original process. The synthesis of 3GP from glucose
might have happened later when other sources of 3GP ceased to exist.
Why does glycolysis still happen despite its low ATP yield>
i. Better than the alternative no ATP
ii. Evolution happens by improving on past successes and glycolysis
satisfied the evolution criteria in catabolic metabolism, meaning that
cells that could carry out glycolysis had an advantage over those who
couldnt, and thus, survived. So later improvement, to improve the
yield of ATP, was added to glycolysis, like layers. Glycolysis still
happens as a metabolic memory of the evolution past.
Net sequence of glycolysis:
Glucose + 2 ADP + 2 NAD+ + 2 Pi 2 pyruvate + 2 ATP + 2 NADH + 2 H2O + 2H+
- How is NADH recycled?
- What happens to pyruvate?
Recycling NADH:
When the cell carries out glycolysis, it converts NAD+ to NADH and accumulating
the second and depleting the 1st. Since the cell does not contain much NAD+, it
must recycle NADH to continue glycolysis. So other acceptors must take the
electrons from NADH, through two processes:
1. Aerobic respiration:
Oxygen takes the electrons transported by the NADH from G3P by a series of
electron transfers that happen in the mitochondria. This process also makes a
lot of ATP.
2. Fermentation:
If oxygen is unavailable, an organic molecule accepts the electrons; like
acetaldehyde in ethanolic fermentation or pyruvate in lactic acid fermentation.
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American University of Beirut

Biol 201

Fate of pyruvate:
It depends on what processes take place:
1. Aerobic respiration
Pyruvate is oxidized to produce Acetyl CoA and it goes in the Krebs Cycle.
2. Fermentation:
Pyruvate is reduced so NADH is recycled to NAD+

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III.

Biol 201

The Oxidation of Pyruvate to produce Acetyl-CoA

In the presence of oxygen, the oxidation of glucose that transformed it into
two pyruvate molecules must continue.
In eukaryotes, the extraction of additional energy from pyruvate happens
inside the mitochondria. In prokaryotes, it happens in the cytoplasm and in
the plasma membrane.
The oxidation of pyruvate happens in two steps:
i. Oxidation of pyruvate to a 2-carbon compound and CO2 molecule
ii. Oxidation of the 2-carbon compound in the Krebs Cycle to give two
CO2 molecules
The
first
oxidation
is
a
decarboxylation
1. A CO2 molecule leaves the pyruvate
that will become a 2-Carbon
compound, named acetyl
2. A pair of electrons and a proton
also detaches from the pyruvate
molecule, reducing NAD+ to NADH,
as well as another proton donated
to the solution
3. The acetyl molecules gets attached
to a coenzyme A, giving a
compound called Acetyl-CoA
This reaction that involves 3 intermediate stages is catalyzed by a
multienzyme complex called Pyruvate Dehydrogenase. This complex
contains 60 subunits and is one of the largest known.
The net reaction is:
Pyruvate + NAD+ + CoA Pyruvate DehydrogenaseAcetyl-CoA + NADH + CO +
2

H+
The molecule of NADH produced will be used to make ATP; the acetyl group
is fed into the Krebs cycle that will complete the oxidation.
Net formation out of the two pyruvate molecules:
2 NADH
2 CO2
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2 H+
2 Acetyl-CoA
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IV. The Krebs cycle:

The Acetyl group from the pyruvate is oxidized again in a series of 9 reactions
that happen in the matrix of the mitochondria and that will transfer electrons and
protons to NAD+ and FAD, making NADH and FADH2 this is the Krebs cycle.
In brief, the 2-Carbon acetyl combines with a 4-Carbon compound called
oxaloacetate forming a 6-Carbon compound called citrate.
Then, citrate will then go in multiple redox reactions; 5 steps that will convert the
citrate to a 5-Carbon then a 4-Carbon compound, called succinate, producing two
NADH and one ATP.
Succinate will go into 3 more reactions that will restore the oxaloacetate,
producing one NADH and one FADH2 from FAD, Flavin Adenosine Dinucleotide.
Both are electron carriers.
The electrons will be transferred to the electron carriers in the inner
membrane of mitochondria, and their movement will create a proton gradient.
The Steps of the Krebs cycle:

1. Condensation
- Citrate is formed from Acetyl-CoA and Oxaloacetate
- This condensation is irreversible, and once it happens it commits the
molecule to the rest of the cycle; so the cell usually inhibits it when the
concentration of ATP is high enough and stimulates it when it is low
- When the cell has a lot of ATP and inhibits the Krebs cycle, Acetyl-CoA is
channeled into fats synthesis
Acetyl-CoA + Oxaloacetate Citrate Synthetase Citrate + CoA-SH
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2. Isomerization
- The hydroxyl group of citrate must be repositioned so the oxidations can
happen
- An H2O molecule is removed from the citrate, in form of an H and an
OH
3. Isomerization
- Another water molecule is added to the intermediate compound, in form
of an H and an OH
- What really happens is exchanging the places of the H, on C#2, and the
OH on C#3
Citrate aconitase Isocitrate
4. The First Oxidation
- The Isocitrate goes into an oxidative decarboxylation reaction
- A pair of electrons and a proton are lost, reducing NAD+
- A CO2 molecule is also lost, forming a 5-Carbon compound called
-KetoGlutarate
Isocitrate + NAD+ Isocitrate dehydrogenase -KetoGlutarate+ CO2 + NADH
5. The Second Oxidation
- The 5-Carbon compound -KetoGlutarate will also go through an
oxidative decarboxylation reaction
- 2 electrons and a proton are lost and reduce NAD+ to NADH
- A CO2 molecule is lost, forming a 4-carbon compound that will bind to
CoA-SH, forming Succinyl-CoA
-KetoGlutarate + NAD+ + CoA-SH -KetoGlutarate Dehydrogenase Succinyl-CoA + NADH +
CO2

6. Substrate-Level Phosphorylation
- The bond between succinate and CoA is a high energy bond
- In reactions like those in glycolysis, the bond is broken down, driving
enough energy to phosphorylate a GDP, Guanine DiPhosphate, to GTP,
Guanine Triphosphate
- The GTP will then go to an enzyme that will take the Pi and bind it to
ADP forming an ATP
Succinyl-CoA + GDP + Pi Succinyl-CoA Synthetase Succinate + GTP + CoASH
GTP + ADP GDP + ATP
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7. The Third Oxidation

- The succinate will lose a pair of electrons due an enzyme located in the
inner membrane of the mitochondria and become fumarate
- The energy is just enough to reduce a FAD molecule to FADH2 one, also
located in the inner membrane; this molecule cannot diffuse from the
membrane nor can it carry protons it just carries electrons,
contributing with them to the electron transport chain
Succinate + FAD succinate dehydrogenase Fumarate + FADH2
8. Hydrolysis Fumarate receives a water molecule forming Malate
Fumarate + H2O fumarase Malate
9. Regeneration of Oxaloacetate
- Malate is oxidized forming Oxaloacetate
- A pair of electrons a and proton reduce NAD+ to NADH
Malate + NAD+ malate dehydrogenase Oxaloacetate + NADH

Net formation out of 1 Acetyl-CoA Molecule: (2 are formed for 1 glucose molecule)
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1 ATP
2 CO2
Fate of Glucose:

Biol 201

3 NADH
1 FADH2

In this process of aerobic respiration, glucose was split to two pyruvate

molecules. The two pyruvate molecules were then oxidized to two AcetylCoA molecules, losing two CO2. Then, the Acetyl-CoA went into the Krebs
cycle by binding to two oxaloacetate molecules, and each was split to two
CO2 molecules.
So all that is left are six CO2 molecules, and the energy that was in the
glucose.
Some of the energy is not in the 4 ATP molecules formed, while the rest is in
the electrons pairs present in the12 carriers: 10 NADH and 2 FADH2
molecules.
The path of the electrons:
To follow the path of the transfers that happen, it is important to follow the
electrons.
In glycolysis, the enzymes extracts two hydrogen atoms from glucose
one proton and two electrons reduce NAD+ to NADH and one proton is
released in the surrounding solution.
The energy captured by NADH is not released all at once: instead, the
electrons are transferred to a chain of electron carriers, called the electron
transport chain, embedded in the inner membrane of the mitochondria. At
each step, the electron is moved to a slightly more electronegative carrier,
down its energy gradient.
Oxygen captures these electrons at the end. It also binds with a proton to
form a water molecule.
The entire process of electron transfer releases 53kcal/mol under standard
conditions gradually, as it moves along the chain. This energy will be used
to make ATP.

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V. The
Electron
Chemiosmosis

Biol 201

Transport

Chain

and

The 10 NADH and the 2 FADH2 each contain a pair of electrons, from the
reduction of the NAD+ and FAD.
These 12 molecules will carry the electrons to the inner mitochondria membrane,
where the electrons are transferred to the electrons transport chain, a series of
membrane bounded proteins.
The Electron Chain produces a Proton Gradient:
The first protein in the series is called NADH Dehydrogenase; it receives
electrons directly from NADH, and emits a proton in the intermembrane
space of the mitochondria.
A carrier called ubiquinone passes the electrons from NADH
dehydrogenase to the second protein: BC1 Complex. FADH2 also directly
pass their electrons to ubiquinone.
BC1 complex receives the electrons transported by ubiquinone, and emits a
proton in the intermembrane space.
Another carrier called Cytochrome C takes the electrons from the BC1
Complex and passes them to the final protein: Cytochrome Oxidase
Complex.
The Cytochrome Oxidase Complex uses four electrons and four protons to
oxidize a molecule of oxygen, giving two water molecules. It also releases a
proton in the intermembrane space.
O2 + 4e- + 4H+ 2H2O

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The release of the protons in the intermembrane space is powered by the

energy released by the movement of electrons through the electron
transport chain. In fact, the flow of the highly-energetic electrons inside the
three transmembrane proteins induces a change in these pumps, causing
them to transport protons across the membrane. A proton gradient is then
formed.
NADH activates three of these proteins whereas FADH2 only activates two
of them.
Chemiosmosis and ATP production:
Because protons have been transferred to the intermembrane space (IMS),
the matrix now is negatively charged relatively to the IMS. Protons are of
course attracted to the matrix, area of low concentration, and they will
want to diffuse.
But the membrane is permeable to ions, so this process is very slow. Most
of the protons, though, re-enter the matrix via a transmembrane protein:
ATP Synthase, an enzyme that will use the energy in the gradient of proton,
an electrochemical gradient, to drive the synthesis of ATP. The movement
of the protons is like osmosis; thus, the ATP formation is called
chemiosmosis.
The newly formed ATP molecules will be transported to many places in the
cell via facilitated diffusion, to couple with endergonic reactions.
It is the cellular respiration that ultimately drives the proton pump, and
thus contributes to the formation of ATP.
ATP Synthase Mechanism:
This enzyme has a complex structure that can be
distorted to 2 major parts:
1.
The F0 membrane bounded complex:
It contains a channel in which protons pass down
their concentration gradient, causing F0 and the
stalk to rotate relatively to the Knob.
2.
The F1 complex made of a stalk and a headdomain (knob):
The rotation of F0 and the stalk changes the
conformation of the head-domain, catalyzing the
binding of ADP and Pi, and forming ATP.
Thus, the formation of ATP is made by a tiny rotary
motor powered by the electrochemical proton
gradient
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VI. Energy Yield of Aerobic Respiration:

The number of ATP molecule produces depends on the number of protons
transported to the electron transport chain. We know that, at the end of
aerobic respiration, 10 NADH and 2 FADH2 molecules are formed for each
glucose molecule, each of them transporting 10 and 6 H+ respectively.
We know that each ATP molecule requires 4 H+, thus:
- 10/4 = 2.5 ATP molecules for 1 NADH
- 6/4 = 1.5 ATP molecules for 1 FADH2
So we have:
- Glycolysis
2 ATP
2 NADH 2 x 2.5 = 5 ATP
- The oxidation of pyruvate to Acetyl-CoA 2 NADH 2 x 2.5 = 5 ATP
- The Krebs cycle :
2 ATP
6 NADH 6 x 2.5 = 15 ATP
2 FADH2 2 x 1.5 = 3 ATP
In sum, this is 32 ATP for respiration in prokaryotes, and 30 in eukaryotes,
as 2 ATP molecules are required to move the NADH of glycolysis from the
cytoplasm to the mitochondria by active transport.
The calculation of the P/O ratio (Phosphate to Oxygen ratio) has changed
over time:
- Before since there was redox reactions at three sites for NADH and at
two sites for FADH2, it was thought that NADH produced 3 ATP
molecules whereas FADH2 produced 2.
- The nature of the calculation changed when the link between the proton
gradient and the ATP production was established, as we needed to know
the # of protons pumped during electron transport. It was found out
that NADH caused the pump of 10H+ while FADH2 led to the pump of
6H+. Also we needed to know the number of protons needed for a
rotation. The ATP synthase, who has 3 sites to bind ATP, uses 12H+ per
cycle, thus 4H+ per ATP. This led to a P/O ration 2.5 approx.
Glucose provides 686 kcal/mol, and ATP stores 7.3 kcal/mol of free energy.
For 30 ATP per glucose molecule in eukaryotes, 32% of the energy is
captured. This high energy storage promoted the development of
heterotrophs, extracting more energy over time and feeding on autotrophs.
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VII. Regulation of Aerobic Respiration:

When cells possess a lot of ATP, the key reactions of glycolysis, the Krebs cycle
and fatty acids breakdown are inhibited. The regulation of these biochemical
pathways is an example of feedback inhibition.
Control of the catabolic pathways can
happen at two key points:
1. In glycolysis:
The enzyme phosphofructokinase,
that changes fructose 6-phosphate to
fructose 1,6-biphosphate, irreversible
reaction that commits the molecule to
glycolytic sequence, has ATP for
allosteric inhibitor, as well as citrate
from the Krebs cycle. High levels of
both ATP and citrate inhibit
phosphofructokinase; so when the cell
has an excess of ATP or when more
citrate than used is being produced,
glycolysis is slowed.
2. In the pyruvate oxidation:
Another control point is the enzyme
pyruvate dehydrogenase, which
converts pyruvate to Acetyl-CoA,
another irreversible reaction that
commits the molecule to the Krebs
cycle. High levels of NADH inhibit
pyruvate dehydrogenase.
3. In the Krebs cycle:
Another control point is the enzyme Citrate Synthetase, which catalyzes the
conversion of oxaloacetate and Acetyl-CoA to citrate. High levels of ATP
inhibit this enzyme, also inhibiting two other Krebs cycle enzymes.

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VIII. Oxidation Without O2:

In the presence of oxygen, large amounts of ATP are produced. But even with
no oxygen, ATP can be produced and electrons can be accepted by other electrons
acceptors.
If the final electron acceptor is an inorganic molecule, we have Anaerobic
Respiration while if it is organic, it is called Fermentation.
The free energy released is not as great as using oxygen because of the
lower affinity for electrons; thus, less ATP is produced.
Anaerobic Respiration:
Methanogens:
- Use CO2 as the final electron acceptor and reduce it to CH4
- Archaea
- The hydrogen molecules are derived from inorganic molecules
produced by other organisms.
- Found in diverse environments: IG: soil, digestive track of ruminants
(cows)
Sulfur bacteria
- Evidence for these Bacteria was found in a groups of rocks that are 2.7
BYA old and known as Woman River iron formation
- Organic materials in these rocks contain the light sulfur isotope: 32S
compared to the heavy one 34S; this enrichment comes from biological
sulfur reduction only. It is carried by some prokaryotes.
- The Bacteria reduces inorganic sulfate SO4 to Hydrogen Sulfide H2S,
using protons provided by other organisms.
- The early sulfate reducers set the stage for evolution of photosynthesis,
creating an environment rich in H2S. The first form of photosynthesis
obtained hydrogen molecules from H2S using the energy of the sunlight.
Fermentation:
Organisms that cannot use O2 as a final electron acceptor rely only on
glycolysis to make ATP. So another process, called fermentation, recycles
NADH, oxidizing it to NAD+, allowing glycolysis to continue.

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Biol 201

Bacteria uses more than a dozen fermentation reactions, using pyruvate or

one of its derivatives to accept electrons from NADH, regenerating NAD+.
Organic molecule + NADH
reduced organic molecule + NAD+
The reduced organic compound might be and acid or an alcohol.
Two important types:
i. Ethanol Fermentation:
- Yeast and animals
- Pyruvate
accepts
the
electrons from NADH:
Pyruvate loses 2 CO2
molecules,
becoming
acetaldehyde.
Then,
acetaldehyde accepts a pair
of electrons from NADH,
oxidizing it to NAD+ and
becoming ethanol.
- Source of wine and beer.
- Ethanol kills yeast when it reaches 12% approximately real wine
has only 12% approximately

ii.

Lactic fermentation
- Animal cells like muscle cells
regenerate ATP without
decarboxylation
- Lactate
dehydrogenase
transfers electrons from
NADH back to pyruvate to
regenerate NAD+, making
lactic acid on the way.
- It closes the cycle, allowing
metabolism and glycolysis to
continue as long as glucose is
available.
- Blood circulation removes excess lactate, ionized lactic acid, from
muscles. But if the removal is slower than the production, this leads
to accumulate lactate and interfere with muscle function leading to
fatigue.

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IX. Catabolism of proteins and fats

Aerobic respiration is the catabolism of glucose, which organisms obtain
from the digestion food such as carbs or photosynthesis.
Organic molecules, other than glucose, are important sources of
energy, like proteins and fats.
Catabolism of proteins:

The catabolism of proteins leads to

remove amino groups.
At first, proteins are broken down to
amino acids. Then, an amino group
is removed from each amino acid:
this is deamination. The remaining
carbon
chains
are
usually
intermediates of the cellular
respiration:
- Alanine pyruvate
- Glutamate -KetoGlutarate (Glutamic Acid)
- Aspartate oxaloacetate (Aspartic Acid)
The reactions of glycolysis and Krebs cycle will then go on and remove high
energy electrons from these molecules to produce ATP.
Catabolism of fatty acids:
Usually produces acetyl groups.
Fats fatty acids + glycerol many C-H bonds are rich in energy
Fatty acids are oxidized in the matrix of the mitochondrion and enzymes
remove acetyl group, a 2-carbon compound, at each cycle of this process,
then each acetyl group is combined with an Enzyme-CoA to make AcetylCoA, just like from the oxidation of pyruvate. This process is called
oxidation and it is used to make ATP.
Catabolism of fats is very dependent of O2, and cannot therefore happen
without it

Marita E. Yaghi

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American University of Beirut

Biol 201

How much ATP?

If a 6-C molecule is considered, we know
that two rounds of -oxidation will make 3
Acetyl-CoA, with one ATP molecule used at
each round, but 1 NADH and 1 FADH2 are
made, thus the needed amount to make 4
ATP. 2-4x2=6 ATP
Then, the Acetyl-CoA molecules go in the
Krebs cycle, producing 10 ATP. So, in brief,
we have:
8 (from oxidation) 2 (for the -oxidation
rounds) + 3 x 10 (for Krebs cycle) = 36 ATP
molecules for one 6 carbon fatty acid.

For the same number of carbons as

glucose, a fatty acid has provided 20%
more energy.
Also, a 6-C fatty acid weighs 2/3 of a
glucose molecule, meaning a gram of fatty
acids contains twice more calories than a
gram of carbohydrates. This is why fat is a
storage molecule for energy in animals:
less space and more energy.
Key intermediates connect metabolic pathways:
Oxidation of different food particles are interrelated by a number of key
intermediates, like pyruvate and Acetyl-CoA, that link the breakdown of different
starting point of the respiration process.
These key intermediates also link the inter-conversion of different types of
molecules, like sugars ad amino acids.
The first stage of extracting energy is breaking down big molecules to
smaller ones, yielding little energy. Then, oxidative respiration takes place and
extracts energy, primarily in the form of highly energetic electrons, producing
water and carbon dioxide. Some key intermediates are also used for the reverse
pathways, which would be the biosynthetic pathways.
Marita E. Yaghi

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American University of Beirut

Biol 201

The cell can make amino acids, fats and glucose or get them from external
sources. They use reactions similar to the biochemical breakdown to go through
the biochemical synthesis of these compounds. The two reverse reactions can
even share enzymes if the free energy changes are small.
Gluconeogenesis uses all but three enzymes of the glycolytic pathways. It
is like glycolysis is running backwards. So glycolysis can go forward or backward
depending on the concentration of the intermediates, with only 3 enzymes that
differ for making and breaking.
Acetyl-CoA roles:
Can be generated from the oxidation of pyruvate, but also fat, protein and
lipids breakdown almost all catabolized molecules give Acetyl-CoA.
Can be used in synthesis of fatty acids units of two carbons derived from
Acetyl-CoA build up hydrocarbon chains in fatty acids.
Acetyl-CoA can also be channeled into ATP synthesis.
The pathway taken by Acetyl-CoA depends on the level of ATP in the cell:
- High ATP level Acetyl-CoA is channeled to fat synthesis are there is
excessive energy in the body (explains the presence of fat in the body,
which are reserves made when people took in too much energy)
- Low ATP level Acetyl-CoA is directed to ATP production
Marita E. Yaghi

24

American University of Beirut

Biol 201

X. Evolution of metabolism:
Both catabolic and anabolic process evolved together, and the timeline we have is
only based on geochemical evidence and is only a hypothesis. These would be the
steps:
1. Harness chemical bond energy ability to store energy in ATP
- Earliest forms of life got energy by degrading organic molecules
produced abiotically, by the inorganic processes on early earth
- Harnessing energy and storing it in the bonds of ATP was the first step
of metabolic evolution
2. Evolution of Glycolysis
- Second major event of metabolism, that accompanied the evolution of
divert catalytic functions in proteins
- The proteins could, in more than one step, harness a larger fraction of
energy by breaking chemical bonds
- This pathway has evolved early in life as it is present in all organisms
and hasnt changed for more than 2 BY.
3. Anoxygenic photosynthesis (anaerobic) using H2S
- Different way of generating ATP in organisms: instead of obtaining
energy by shuffling bonds, these organisms used light to pump protons
out of their cells, making a proton gradient used to power the synthesis
of ATP through chemiosmosis.
- Photosynthesis evolved in the absence of oxygen using H2S dissolved
H2S in the oceans of early earth was the source of free hydrogen atoms.
- The hydrogen atoms were used to build organic molecules and free
sulfur was a by-product of this reaction
- Green Sulfur Bacteria and Heliobacteria
4. Oxygen-forming photosynthesis not using H2S
- H2O was used to provide the hydrogen atoms and Oxygen became the
final electron acceptor, making then oxygen gas O2.
- 2BYA, cells capable of carrying this process became dominant on Earth
and oxygen began to accumulate in the atmosphere, changing the
conditions on earth permanently.
Marita E. Yaghi

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American University of Beirut

Biol 201

- Our atmosphere today, made of 20.9% oxygen gas, has every molecule
derived from an oxygen-forming photosynthetic reaction
- Cyanobacteria
5. Nitrogen fixation
- Available from dead organic matter and chemical reactions that made
the Nitrogen molecule.
- Nitrogen was needed for life to expand as it is on the basis of proteins
and nucleic acids
- Nitrogen can obtained by breaking the triple bond from N2 gas : NN; so
NH3 can be made
- Evolved in the nitrogen rich environment of the Earth where no Oxygen
was present as oxygen is a poison to it.
- Today, nitrogen fixation happens either in oxygen-free environments or
compartments in prokaryotes, called diazotrophs
6. Aerobic respiration
- Employs the same proton pump as photosynthesis but is powered by
ATP made from the breakdown of big organic molecule
- First non-H2S photosynthesis evolved with Purple Non-Sulfur Bacteria;
later on, some developed the ability to respire using only energy and
electrons from the breakdown of organic molecules
- Mitochondria is descendant of these Purple Non-Sulfur Bacteria
- Aerobic metabolism developed over time and became favored by natural
selection, as a very efficient way of obtaining energy from organic
molecules.

Marita E. Yaghi

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