User:Arman Saied/sandbox

An electrochemical gradient is a gradient of electrochemical potential, usually for an ion that can move across a membrane. The gradient consists of two parts, the chemical gradient, or difference in solute concentration across a membrane, and the electrical gradient, or membrane potential (Vm). The ions move across the membrane to achieve the greatest amount of entropy in conformity with the second law of thermodynamics. When there are unequal concentrations of an ion across a permeable membrane, the ion will move across the membrane from the area of higher concentration to the area of lower concentration through simple diffusion. Ions also carry an electric charge that forms an electric potential across a membrane. If there is an unequal distribution of charges across the membrane, then the difference in electric potential generates a force that drives ion diffusion until the charges are balanced on both sides of the membrane.

Biological context
Electrochemical gradients play a role in cellular respiration in mitochondria and photosynthesis in chloroplasts.

The final step of cellular respiration is the electron transport chain. Four complexes embedded in inner membrane of the mitochondrion make up the electron transport chain. Complex I (CI) catalyzes the reduction of ubiquinone (UQ) to ubiquinol (UQH2) by the transfer of two electrons from reduced nicotinamide adenine dinucleotide (NADH) which translocates four protons from the mitochondrial matrix to the intermembrane space (IMS):

$$NADH + H^+ + UQ + 4H^+ (matrix) \longrightarrow NAD^+ + UQH_2 + 4H^+ (IMS)$$

Complex III (CIII) catalyzes the Q-cycle. The first step involving the transfer of two electrons from the UQH2 reduced by CI to two molecules of oxidized cytochrome c at the Qo site. In the second step, two more electrons reduce UQ to UQH2 at the Qi site. The total reaction is shown:

$$2\ cytochrome\ c\ (oxidized)\ +\ UQH_2\ +\ 2H^+\ (matrix) \longrightarrow 2\ cytochrome\ c\ (reduced)\ +\ UQ\ +\ 4H^+\ (IMS)$$

Complex IV (CIV) catalyzes the transfer of four electrons from the cytochrome c reduced by CIII to oxygen. The oxygen will then consume four protons from the matrix to form water while another four protons are pumped into the IMS. The total reaction is shown:

$$4\ cytochrome\ c\ (reduced)\ +\ 8H^+\ (matrix)\ +\ O_2 \longrightarrow 4\ cytochrome\ c\ (oxidized)\ +\ 4H^+\ (IMS)\ +\ 2H_2O$$

In total, there are twelve protons translocated from the matrix to the IMS which generates an electrochemical potential of more than 200mV. This drives the flux of protons back into the matrix through ATP synthase which produces ATP by adding an inorganic phosphate to ADP. Thus, generation of a proton electrochemical gradient is crucial for energy production in mitochondria.

Similar to the electron transport chain, the light-dependent reactions of photosynthesis pump protons into the thylakoid lumen of chloroplasts to drive the synthesis of ATP by ATP synthase. However, several other transporters and ion channels play a role in generating a proton electrochemical gradient. One is TPK3, a potassium channel that is activated by Ca2+ and conducts K+ from the thylakoid lumen to the stroma which helps establish the pH gradient. On the other hand, the electro-neutral K+ efflux antiporter (KEA3) transports K+ into the thylakoid lumen and H+ into the stroma which helps establish the electric field.

Ion gradients
The generation of a transmembrane electrical potential through ion movement across a cell membrane drives biological processes like nerve conduction, muscle contraction, hormone secretion, and sensory processes. By convention, a typical animal cell has a transmembrane electrical potential between -50mV and -70mV inside the cell.

Since the ions are charged, they cannot pass through the membrane via simple diffusion. Two different mechanisms can transport the ions across the membrane: active or passive transport. An example of active transport of ions is the Na+-K+-ATPase (NKA). NKA catalyzes the hydrolysis of ATP into ADP and an inorganic phosphate and for every molecule of ATP hydrolized, three Na+ are transported outside and two K+ are transported inside the cell. This makes the inside of the cell more negative than the outside and more specifically generates a Vm of about -60mV. An example of passive transport is ion fluxes through Na+, K+, Ca2+, and Cl- channels. These ions tend to move down there concentration gradient. For example, since there is a high concentration of Na+ outside the cell, Na+ will flow through the Na+ channel into the cell. Since the electric potential inside the cell is negative, the influx of a positive ion depolarizes the membrane which brings the transmembrane electric potential closer to zero. However, Na+ will continue moving down its concentration gradient as long as the effect of the chemical gradient is greater than the effect of the electrical gradient. Once the effect of both gradients are equal (for Na+ this at a Vm of about +70mV), the influx of Na+ stops because the driving force (ΔG) is zero. The equation for driving force is:

$$\Delta G=RTln(C_{in}/C_{out})+ZFV_m$$

In this equation, R represents the gas constant, T represents absolute temperature, Z is the ionic charge, and F represents the Faraday constant.

While the membrane potential changes with ion influx/efflux, ion concentration does not change because the ion concentration in cells is so large (>10M) that the change in concentration is negligible. This is not the case with Ca2+because the intracellular concentration (10-7M) is so low that an influx of Ca2+ can actually change the Ca2+ concentration.

Proton gradients
Proton gradients in particular are important in many different types of cells as a form of energy storage. The gradient is usually used to drive ATP synthase, flagellar rotation, or transport of metabolites. This section will focus on three membrane proteins that help establish proton gradients in their respective cells: bacteriorhodopsin, photosystem II (PSII), and cytochrome c oxidase (CcO).

The way bacteriorhodopsin generates a proton gradient in Archaea is through a proton pump. The proton pump relies on proton carriers to drive protons from the side of the membrane with a low H+ concentration to the side of the membrane with a high H+ concentration. In bacteriorhodopsin, the proton pump is activated by absorption of photons of 568nm wavelength which leads to isomerization of the Schiff base (SB). This moves SB away from Asp85 and Asp212, causing H+ transfer from SB to Asp85 forming the M1 state. The protein then shifts to the M2 state by separating Glu204 from Glu194 which releases a proton from Glu204 into the side of the membrane with a low H+ concentration. Then electrostatic interactions between the two Asp and Glu residues form the N state where the protein holds two protons. It is important that the second proton comes from Asp96 since its deprotonated state is unstable and rapidly reprotonated to form the N' state. In the N' state, SB returns to its original conformation causing Asp85 to release a second proton into the extracellular environment.

PSII also relies on light to drive the formation of proton gradients in chloroplasts, however PSII utilizes vectorial redox chemistry to achieve this goal. Rather than physically transporting protons through the protein, reactions requiring the binding of protons will occur on the intracellular side while reactions requiring the release of protons will occur on the extracellular side. Absorption of photons of 680nm wavelength is used to excite electrons in P680 to a higher energy level. These higher energy electrons are transferred to protein-bound plastoquinone (PQA) and then to unbound plastoquinone (PQB). This reduces plastoquinone (PQ) to plastoquinol (PQH2) which is released from PSII after absorbing two photons. The electrons in P680 are replenished by oxidizing water through the oxygen-evolving complex (OEC). This results in release of O2 and H+ into the stroma. The total reaction is shown:

$$4\ photons(680nm)\ +\ 2H_2O\ +\ 2PQ\ +\ 4H^+(lumen)\longrightarrow O_2\ +\ 2PQH_2\ +\ 4H^+(stroma)$$