User talk:Simpsons contributor/Oxidative phosphorylation

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1 The electron-transport chain
2 Proton gradient across the membrane
3 ATP Synthase
- 3.1 The mechanism of action of ATP synthase
- 3.2 ATP synthase and G proteins
4 Reactive oxygen species
5 References

[edit] The electron-transport chain

As mentioned at the start of the article, during the Krebs cycle NADH and FADH₂ are produced. NADH and FADH₂, each contain two electrons which have a high transfer potential; in other words, they are highly reduced and hence energy-rich molecules. The electrons travel through an electron transport chain which results in the pumping of protons across the inner membrane and the production of a pH gradient across this membrane.

[edit] Complex I

Complex I

Complex I, also known as NADH-Q oxidoreductase, is the first protein in the electron-transport chain. Complex 1 is a giant enzyme with a molecular mass of 880 kd. The structure hasn’t been fully elucidated yet, but the enzyme consists of at least 34 polypeptide chains, resembles a boot with a large “ball” poking out past the membrane. The genes that encode the individual proteins are contained in the cells nucleus and the mitochondrion; this is the case for many enzymes present in the mitochondrion.

The overall reaction which is catalyzed by this enzyme is:

$\mbox{NADH + Q + 5H}^{+}_{matrix} \rightarrow \mbox{NAD}^+ + \mbox{QH}_2 + \mbox{4H}^+_{cytosol}$

The start of the reaction, and indeed the entire electron chain, is the binding of a NADH molecule to complex 1, which subsequently donates its two high transfer potential electrons. The electrons enter complex 1 via a prosthetic group attached to the complex, flavin mononucleotide (FMN). The addition of electrons to FMN converts it to its reduced form, FMNH₂. The reduction of the FMN molecule, due to the acceptance of two electrons, causes it to bind two protons. This contributes to the production of the pH gradient by removing two protons from inside the mitochondrial matrix; but it doesn’t pump any protons across the membrane. The resulting FMNH₂ molecule is subsequently oxidized back to FMN and donates the two electrons which originally reduced it.

Here are the equations of the reactions:

$\mbox{NADH + H}^+ + \mbox{FMN} \rightarrow \mbox{NAD}^+ + \mbox{FMNH}_2$

$\mbox{FMNH}_2 \rightarrow \mbox{FMN} + \mbox{2e}^- + \mbox{2H}^+$

The electrons formed from the oxidation FMNH₂ are transferred through a series of iron-sulphur clusters; the second kind of prosthetic group present in the complex. Iron-sulphur clusters are often present in enzymes which involve a transfer of electrons. There are several types of iron-sulphur clusters. The simplest kind consists of a single iron ion is tetrahedrally coordinated to the sulfhydral groups of four cystein (an amino acid) molecules present in the polypeptide chain. The second kind, denoted by 2Fe – 2S, contains 2 iron ions and two inorganic sulfides. Several others are shown in this image^[1]. Iron-sulphur clusters usually undergo redox reactions without binding or releasing protons, so serve solely to transport electrons through the protein, rather then contribute to the production of the pH gradient.

The electrons that pass through the iron-sulphur clusters are transferred to a coenzyme Q group present in the complex. There are three 4Fe-4S clusters present between the FMNH₂ and Q groups. The electrons flow through all three on their way from FMNH₂ to Q. The exact details of this process are not fully understood by biochemists yet. The basic mechanism involves the uptake of two protons as Q is reduced to QH₂ due to the transfer of 2 electrons from the aforementioned iron-sulphur cluster. Here is the equation of the reaction (the two electrons are the ones which were released during the oxidation of FMNH₂. They are passed to the Q molecule from the third iron-sulphur cluster):

$\mbox{Q} + \mbox{2H}^+ + \mbox{2e}^- \rightarrow \mbox{QH}_2$

The two high transfer potential electrons present in the QH₂ molecule are transferred to another 4Fe-4S complex and the two hydrogen ions are released into the cytosolic side; which contributes to the production of the pH gradient. Finally, these two electrons are transferred to a mobile Q molecule which accepts the electrons and is reduced to QH₂ (as before), but is then released from the protein complex into the hydrophobic core of the membrane. This QH₂ molecule reattaches to complex II where it is oxidized to release its two high transfer potential electrons.

[edit] Complex II

Complex II

Complex II, also known as succinate-Q reductase, is the second protein in the electron-transport chain.

[edit] Complex III

Complex III

Complex III, also known as Q-cytochrome c oxidoreductase or simply cytochrome reductase, is the third protein in the electron-transport chain. A cytochrome is a kind of electron-transferring protein which contains at least one heme group. The iron ion inside complex II’s heme groups alternate between a reduced ferrous (+2) and oxidized ferric (+3) state as the electrons are transferred through the protein.

The overall reaction catalyzed by complex III is:

$\mbox{QH}_2 + \mbox{2Cyt c}_{ox} + \mbox{2H}^+_{matrix} \rightarrow \mbox{Q} + \mbox{2Cyt c}_{red} + \mbox{4H}^+_{cytosol}$

The enzyme contains 3 heme groups which participate in transferring the electron through it. The electron originates from the mobile coenzyme Q which was released from complex I. It terminates at cytochrome c; an electron carrying protein containing a heme group. Unlike coenzyme Q, which carriers 2 electrons, cytochrome c only carries 1.

The reduced coenzyme Q binds to a site inside complex III. The reduced coenzyme Q molecule transfers its electrons one at a time. The electron travels first through a 2Fe-2S cluster and then to a heme group held inside complex III. The electron travels from this immobile heme molecule to the heme group inside the cytochrome c protein bound to complex III. The heme group within the cytochrome c protein is now in its reduced form and the enzyme is free to diffuse away from complex III. The hydrogen ions released during the oxidation of QH₂ are transferred to the cytosolic side of the membrane and hence serve to create the proton gradient.

[edit] Complex IV

Complex IV

Complex IV, also known as cytochrome c oxidase, is the fourth and final protein in the electron transport chain.

[edit] Proton gradient across the membrane

The electron transport chain is the flow of electrons from NADH to O₂. This is an exergonic process (work is done during the process). The process of oxidative phosphorylation terminates at the synthesis of ATP from ADP and orthophosphate; an endogonic process (work is required to drive the reaction). The work that drives the reaction is the net flow of protons across the membrane in which the ATP synthase is embedded in.

The reactions and the work released are shown below:

The first reaction creates a net difference of proton concentration across the membrane and hence an increase in entropy. The decrease in entropy across the membrane drives the endogonic process of ATP synthesis. This reaction is carried out by one single protein complex known originally as the mitochondrial ATPase, which is misleading since it implies the reaction is carried out the other way round (which it can be, though this is not its function in this case); today it most often known as ATP synthase.

[edit] ATP Synthase

ATP synthase is the final protein in the metabolic pathway. Most of the ATP in any prokaryote or eukaryote comes from the process the ATP synthase catalyses. ATP is synthesized from ADP and orthophosphate:

ATP synthase is a massive protein complex which resembles a ball on a stick. The “ball” shaped head contains six proteins of two different kinds (three α subunits and three β subunits). The “stick” consists of one protein: the γ subunit, which is long and extends throughout the α and β subunits. Both the α and β subunits bind nucleotides, but only the β subunits participate in the ADP phosphorylation reaction. ATP synthase is part of the P-loop NTPase family.

[edit] The mechanism of action of ATP synthase

As protons cross the membrane through the base of ATP synthase the central stem (the subunit) rotates inside the α and β subunits. The in and out movement of the α and β subunits cause the necessary movement of the active sites leading to the production of ATP.

[edit] ATP synthase and G proteins

[edit] Reactive oxygen species

Molecular oxygen is ideal as a terminal electron acceptor due to its high affinity for electrons. However, the reduction of molecular oxygen yields potentially harmful intermediates. The transfer of four electrons results in the production of water, which is not harmful. The transfer of one or two electrons produces superoxide anion and peroxide as shown below:

$\begin{matrix} \quad & {e^-} & \quad & {e^-} \\ {\mbox{O}_{2}} & \longrightarrow & \mbox{O}_2^{\underline{\bullet}} & \longrightarrow & \mbox{O}_2^{2-} \\ \quad & \quad & \mbox{Superoxide} & \quad & \mbox{Peroxide} \\ \quad & \quad & \mbox{anion} & \quad & \quad \end{matrix}$

These compounds and, particularly, their reaction products such as hydrogen peroxide are very harmful to many cellular components.

Due to the efficiency of the cytochrome c oxidase complex very few partly reduced intermediates are released. Inevitable small amounts of superoxide anion and peroxide are released though.Species which can be produced from these such as Hydrogen peroxide (H₂O₂) and the hydroxyl radical (•OH) are collectively referred to as reactive oxygen species or ROS. There are many enzymes whose task is to convert ROS into less reactive species. Chief among theses enzymes is superoxide dismutase. This enzyme converts superoxide radicals into molecular oxygen and hydrogen peroxide as shown below:

$\begin{matrix} \quad & \quad & \quad & \mbox{Superoxide} & \quad & \quad & \quad \\ \quad & \quad & \quad & \mbox{dismatase} & \quad & \quad & \quad \\ \mbox{2O}_2^{\underline{\bullet}} & + & \mbox{2H}^+ & \longleftarrow \! \longrightarrow & \mbox{O}_2 & + & 2\mbox{H}_2 \mbox{O}_2 \\ \end{matrix}$

There are two varieties of the enzyme within eukaryotes. The hydrogen peroxide released from the cytochrome c oxidase complex and by superoxide dismutase is scavenged by the enzyme catalase. Catalase converts hydrogen peroxide into molecular oxygen and water as shown below:

$\begin{matrix} \quad & \mbox{Catalase} & \quad & \quad & \quad \\ 2\mbox{H}_2 \mbox{O} & \longleftarrow \! \longrightarrow & \mbox{O}_2 & + & 2\mbox{H}_2 \mbox{O} \\ \end{matrix}$

Superoxide dismutase and catalase are both remarkably efficient and carry out their reactions at or near the diffusion-limited rate.

Antioxidant vitamins C and E also serve to convert ROS to less harmful compounds. Vitamin E cannot exist in the mitochondrial matrix sine it will not mix with water; it is hydrophobic. It instead exists in the inner membrane of the mitochondrion and protects the membrane from being harmed by ROS. Vitamin C is hydrophilic and carries out its reactions in the mitochondrial matrix.