Fermentation

Fermentation is another anaerobic (non-oxygen-requiring) pathway for breaking down

glucose, one that's performed by many types of organisms and cells. In fermentation, the
only energy extraction pathway is glycolysis, with one or two extra reactions tacked on at
the end.

Fermentation and cellular respiration begin the same way, with glycolysis. In
fermentation, however, the pyruvate made in glycolysis does not continue through
oxidation and the citric acid cycle, and the electron transport chain does not run. Because
the electron transport chain isn't functional, the \text{NADH}NADHN, A, D, Hmade in
glycolysis cannot drop its electrons off there to turn back into \text {NAD}^+NAD+N, A,
D, start superscript, plus, end superscript

The purpose of the extra reactions in fermentation, then, is to regenerate the electron
carrier \text{NAD}^+NAD+N, A, D, start superscript, plus, end superscript from
the \text{NADH}NADHN, A, D, H produced in glycolysis. The extra reactions
accomplish this by letting \text{NADH}NADHN, A, D, H drop its electrons off with an
organic molecule (such as pyruvate, the end product of glycolysis). This drop-off allows
glycolysis to keep running by ensuring a steady supply of \text{NAD}^+NAD+N, A, D,
start superscript, plus, end superscript.

Steps in the Citric Acid Cycle

Step 1. The first step is a condensation step, combining the two-carbon acetyl group (from acetyl
CoA) with a four-carbon oxaloacetate molecule to form a six-carbon molecule of citrate. CoA is bound
to a sulfhydryl group (-SH) and diffuses away to eventually combine with another acetyl group. This
step is irreversible because it is highly exergonic. The rate of this reaction is controlled by negative
feedback and the amount of ATP available. If ATP levels increase, the rate of this reaction decreases.
If ATP is in short supply, the rate increases.

Step 2. Citrate loses one water molecule and gains another as citrate is converted into its isomer,
isocitrate.
Steps 3 and 4. In step three, isocitrate is oxidized, producing a five-carbon molecule, α-ketoglutarate,
together with a molecule of CO2 and two electrons, which reduce NAD+ to NADH. This step is also
regulated by negative feedback from ATP and NADH and by a positive effect of ADP. Steps three
and four are both oxidation and decarboxylation steps, which release electrons that reduce NAD+ to
NADH and release carboxyl groups that form CO2 molecules. α-Ketoglutarate is the product of step
three, and a succinyl group is the product of step four. CoA binds the succinyl group to form succinyl
CoA. The enzyme that catalyzes step four is regulated by feedback inhibition of ATP, succinyl CoA,
and NADH.

Step 5. A phosphate group is substituted for coenzyme A, and a high- energy bond is formed. This
energy is used in substrate-level phosphorylation (during the conversion of the succinyl group to
succinate) to form either guanine triphosphate (GTP) or ATP. There are two forms of the enzyme,
called isoenzymes, for this step, depending upon the type of animal tissue in which they are found.
One form is found in tissues that use large amounts of ATP, such as heart and skeletal muscle. This
form produces ATP. The second form of the enzyme is found in tissues that have a high number of
anabolic pathways, such as liver. This form produces GTP. GTP is energetically equivalent to ATP;
however, its use is more restricted. In particular, protein synthesis primarily uses GTP.

Step 6. Step six is a dehydration process that converts succinate into fumarate. Two hydrogen atoms
are transferred to FAD, producing FADH2. The energy contained in the electrons of these atoms is
insufficient to reduce NAD+ but adequate to reduce FAD. Unlike NADH, this carrier remains attached
to the enzyme and transfers the electrons to the electron transport chain directly. This process is
made possible by the localization of the enzyme catalyzing this step inside the inner membrane of the
mitochondrion.

Step 7. Water is added to fumarate during step seven, and malate is produced. The last step in the
citric acid cycle regenerates oxaloacetate by oxidizing malate. Another molecule of NADH is
produced.

Steps of Glycolysis
Glycolysis is an extramitochondrial pathway and is carried by a group of eleven enzymes.
Glucose is converted to pyruvate in 10 steps by glycolysis. The glycolytic patway can be
divided into two phases:

Preparatory Phase :
This phase is also called glucose activation phase. In the preparatory phase of glycolysis,
two molecules of ATP are invested and the hexose chain is cleaved into two triose
phosphates. During this, phosphorylation of glucose and it’s conversion to glyceraldehyde-
3-phosphate take place. The steps 1, 2, 3, 4 and 5 together are called as the preparatory
phase.

Payoff Phase :
This phase is also called energy extraction phase. During this phase, conversion of
glyceraldehyde-3-phophate to pyruvate and the coupled formation of ATP take
place. Because Glucose is split to yield two molecules of D-Glyceraldehyde-3-phosphate,
each step in the payoff phase occurs twice per molecule of glucose. The steps after 5
constitute payoff phase.

Steps of Glycolysis
1. The first step in glycolysis is the conversion of D-glucose into glucose-6-phosphate.
The enzyme that catalyzes this reaction is hexokinase.
2. The second reaction of glycolysis is the rearrangement of glucose 6-phosphate
(G6P) into fructose 6-phosphate (F6P) by glucose phosphate isomerase
(Phosphoglucose Isomerase).
3. Phosphofructokinase, with magnesium as a cofactor, changes fructose 6-phosphate
into fructose 1,6-bisphosphate.
4. The enzyme Aldolase splits fructose 1, 6-bisphosphate into two sugars that are
isomers of each other. These two sugars are dihydroxyacetone phosphate (DHAP)
and glyceraldehyde 3-phosphate (GAP).
5. The enzyme triophosphate isomerase rapidly inter- converts the molecules
dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GAP).
Glyceraldehyde phosphate is removed / used in next step of Glycolysis.
6. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) dehydrogenates and adds an
inorganic phosphate to glyceraldehyde 3-phosphate, producing 1,3-
bisphosphoglycerate.
7. Phosphoglycerate kinase transfers a phosphate group from 1,3-bisphosphoglycerate
to ADP to form ATP and 3-phosphoglycerate.
8. The enzyme phosphoglycero mutase relocates the P from 3- phosphoglycerate from
the 3rd carbon to the 2nd carbon to form 2-phosphoglycerate.
9. The enzyme enolase removes a molecule of water from 2-phosphoglycerate to form
phosphoenolpyruvic acid (PEP).
10. The enzyme pyruvate kinase transfers a P from phosphoenolpyruvate (PEP) to ADP
to form pyruvic acid and ATP Result in step 10.

Although 2 ATP molecules are used in steps 1-3, 2 ATP molecules are generated in step
7 and 2 more in step 10. This gives a total of 4 ATP molecules produced. If you subtract
the 2 ATP molecules used in steps 1-3 from the 4 generated at the end of step 10, you
end up with a net total of 2 ATP molecules produced.
ETC CYCLE

The electron transport chain is made up of a series of spatially separated enzyme complexes that transfer

electrons from electron donors to electron receptors via sets of redox reactions. This is also accompanied by a

transfer of protons (H+ ions) across the membrane. This leads to the development of an electrochemical proton

gradient across the membrane that activates the ATP synthase proton pump, thereby, driving the generation of

ATP molecules (energy). The cycle ends by the absorption of electrons by oxygen molecules.

In eukaryotic organisms, the electron transport chain is found embedded in the inner membrane of the

mitochondria, in bacteria it is found in the cell membrane, and in case of plant cells, it is present in the

thylakoid membrane of the chloroplasts.

In chloroplasts, photons from light are used produce the proton gradient; whereas, in the mitochondria and

bacterial cells, the conversions occurring in the enzyme complexes, generate the proton gradient.

This pathway is the most efficient method of producing energy. The initial substrates for this cycle are the end

products obtained from other pathways. Pyruvate, obtained from glycolysis, is taken up by the mitochondria,

where it is oxidized via the Krebs/citric acid cycle. The substrates required for the pathway are NADH

(nicotinamide adenine dinucleotide), succinate, and molecular oxygen.

NADH acts as the first electron donor, and gets oxidized to NAD+ by enzyme complex I, accompanied by the

release of a proton out of the matrix. The electron is then transported to complex II, which brings about the

conversion of succinate to fumarate. Molecular oxygen (O2) acts as an electron acceptor in complex IV, and

gets converted to a water molecule (H2O). Each enzyme complex carries out the transport of electrons

accompanied by the release of protons in the intermembrane space.

The accumulation of protons outside the membrane gives rise to a proton gradient. This high concentration of

protons initiates the process of chemiosmosis, and activates the ATP synthase complex. Chemiosmosis refers

to the generation of an electrical as well as a pH potential across a membrane due to large difference in proton

concentrations. The activated ATP synthase utilizes this potential, and acts as a proton pump to restore
concentration balance. While pumping the proton back into the matrix, it also conducts the phosphorylation of

ADP (Adenosine Diphosphate) to yield ATP molecules.

 Complex I - NADH-coenzyme Q oxidoreductase

The reduced coenzyme NADH binds to this complex, and functions to reduce coenzyme Q10.
This reaction donates electrons, which are then transferred through this complex using FMN
(Flavin mononucleotide) and a series of Fe-S (Iron-sulpur) clusters. The transport of these
electrons brings about the transfer of protons across the membrane into the intermembrane
space.

 Complex II - Succinate-Q oxidoreductase

This complex acts on the succinate produced by the citric acid cycle, and converts it to
fumarate. This reaction is driven by the reduction and oxidation of FAD (Flavin adenine
dinucleotide) along with the help of a series of Fe-S clusters. These reactions also drive the
redox reactions of quinone. These sets of reactions help in transporting the electrons to the
third enzyme complex.

 Complex III - Q-cytochrome c oxidoreductase

This complex oxidizes ubiquinol and also reduces two molecules of cytochrome-c. The
electron is transported via these reactions onto complex IV accompanied by the release of
protons.

 Complex IV - ytochrome c oxidase

The received electron is received by a molecular oxygen to yield a water molecule. This
conversion occurs in the presence of Copper (Cu) ions, and drives the oxidation of the reduced
cytochrome-c. Protons are pumped out during the course of this reaction.

 ATP Synthase
The protons produced from the initial oxidation of the NADH molecule, and their presence in
the intermembrane space gives rise to a potential gradient. It is utilized by this complex to
transport the protons back into the matrix. The transport itself also generates energy that is
used to achieve phosphorylation of the ADP molecules to form ATP.

Any anomalies or defects in any of the components that constitute the electron transport chain
leads to the development of a vast array of developmental, neurological, and physical disorders.