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Where do the electrons and protons formed from biological reactions go?

Where do the electrons and protons formed from biological reactions go?


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In a reaction like disulphide bond formation protons and electrons are released. These particles are presumably damaging in high levels. What systems are in place to prevent a build up of electrons and protons?


I've reproduced the diagram that you linked to. It shows the oxidation of a pair of thiols to create a disulphide. What is missing from this scheme is the accompanying oxidising agent. So for example this could be carried out without catalysis in a reaction with molecular oxygen, in which case hydrogen peroxide would be formed. So the electrons and protons have ended up on the oxygen.

In a biological system this oxidation would usually be carried out by an enzyme, in which case the oxidising agent would probably be FAD (flavin adenine dinucleotide) or NAD+(nicotinamide adenine dinucleotide). These are by far the most commonly used redox cofactors. In a typical eukaryotic cell these would end up either (a) being reduced either by the mitochondrial electron transport chain (in which case the ultimate electron acceptor would again be oxygen); or (b) when they were used as a reducing agent in a metabolic reaction.


Using light to move electrons and protons

Photo-electron proton transfer with p-MeOH-ArOH and N-methyl-4,4'-bypyridinium. Credit: Thomas J. Meyer, David W. Thompson

(Phys.org)—In some chemical reactions both electrons and protons move together. When they transfer, they can move concertedly or in separate steps. Light-induced reactions of this sort are particularly relevant to biological systems, such as Photosystem II where plants use photons from the sun to convert water into oxygen.

To better understand how light can lead to the transfer of protons in a chemical reaction, a group of researchers from the University of North Carolina, Shanxi University in China, and Memorial University in Newfoundland have conducted adsorption studies on a new family of experiments to observe the transition that occurs when protons transfer between hydrogen-bonded complexes in solution . They provide evidence for new optical transitions characteristic of the direct transfer of a proton. This report recently appeared in the Proceedings of the National Academy of Sciences.

N-methyl-4,4'-bipyridinium cation (MQ + ) serves as proton acceptor, where a proton will add to the non-methylated pyridinium amine. If proton transfer occurs, then MQ+ will form a radical cation (MQH + • ) whose absorbance spectra in the UV/visible range can be compared to N, N'-dimethyl-4, 4'-bypyridinium (MV 2+ ).

By using ultrafast laser flash photolysis measurements, they found direct evidence for a low energy absorption band between p-methoxyphenyl and the mehylviologen acceptor, MQ + . It appears at 360 nm and as early as 250 fs after the laser pulse. Based on these properties, it is clearly the product of proton transfer from the phenol to give MeOPhO • —H-MQ + .

The appearance of this reaction involving the transfer of both an electron and proton after absorbing a single photon is supported by the vibrational coherence of the radical cation and by it characteristic spectral properties. By inference, related transitions, which are often at low intensities, could play an important role in the degradation of certain biological molecules, such as DNA.

The appearance of these absorption bands could have theoretical significance. They demonstrate a way to use simple spectroscopic measurements to explore the intimate details of how these reactions occur in nature. This provides new physical insight into processes that could be of broad biological and chemical relevance.

Abstract
The phenols 4-methylphenol, 4-methoxyphenol, and N-acetyl-tyrosine form hydrogen-bonded adducts with N-methyl-4, 4′-bipyridinium cation (MQ+) in aqueous solution as evidenced by the appearance of low-energy, low-absorptivity features in UV-visible spectra. They are assigned to the known examples of optically induced, concerted electron–proton transfer, photoEPT. The results of ultrafast transient absorption measurements on the assembly MeOPhO-H—-MQ+ are consistent with concerted EPT by the instantaneous appearance of spectral features for MeOPhO·—-H-MQ+ in the transient spectra at the first observation time of 0.1 ps. The transient decays to MeOPhO-H—-MQ+ in 2.5 ps, accompanied by the appearance of oscillations in the decay traces with a period of ∼1 ps, consistent with a vibrational coherence and relaxation from a higher υ(N-H) vibrational level or levels on the timescale for back EPT.


Oxidizing Agents: Dioxygen

O2, dioxygen, is one of the most potent oxidizing agents used in nature.

    Draw the Lewis structure of dioxygen, O2.

If dioxygen acts as an oxidizing agent, it can get fully reduced to water.

    As dioxygen is reduced, it (gives electrons/accepts electrons). Circle one.

This reaction really happens one electron at a time.

    Draw Lewis structures for the following series of oxygen species (superoxide, O2 - peroxide, O2 2- oxide, O 2- ).

Properties of Dioxygen

Chemically, cellular respiration is considered an exothermic redox reaction.

Technically, cellular respiration is a combustion reaction but it clearly does not resemble one when it occurs in a living cell.

    Balance the above reaction.

Nature must deal with these two properties of dioxygen so as to utilize oxygen in the oxidation of carbohydrates and lipids to CO2 &ndash without a combustion!

    How does an organism complete the oxidation of glucose without a fire?

As oxygen reacts as an oxidizing agent, it gets reduced to produce nasty, dangerous products (superoxide, peroxide).

    Could you imagine a situation when we would want to produce these species?

PUFA radical oxidation

Ground state triplet oxygen reacts readily with certain fats in the body.

Oxidation of PUFAs is mediated by free radicals such as the hydroxyl radical (HO&bull). Shown here is the proposed first step in the oxidation of linolenic acid, an w-3 fatty acid:

Although the reaction illustrated shows one of the hydrogens on C-14 being abstracted there are other hydrogen atoms that are susceptible to this kind of reaction.

    Draw resonance structures for radical intermediate 1.

Radical intermediate 1 reacts with molecular oxygen:

    How does this mechanism allow for propagation of this radical degradation process?


Researchers tap CRISPR technology to connect biology, electronics

Credit: CC0 Public Domain

In an effort to create first-of-kind microelectronic devices that connect with biological systems, University of Maryland (UMD) researchers are utilizing CRISPR technology in a novel way to electronically turn "on" and "off" several genes simultaneously. Their technique, published in Nature Communications, has the potential to further bridge the gap between the electronic and biological worlds, paving the way for new wearable and "smart" devices.

"Faced with the COVID-19 pandemic, we now have an even deeper understanding of how 'smart' devices could benefit the general population," said William E. Bentley, professor in UMD's Fischell Department of Bioengineering and Institute for Bioscience and Biotechnology Research (IBBR), and director of the Robert E. Fischell Institute for Biomedical Devices. "Imagine what the world would be like if we could wear a device and access an app on our smartphone capable of detecting whether the wearer has the active virus, generated immunity, or has not been infected. We don't have this yet, but it is increasingly clear that a suite of technologies enabling rapid transfer of information between biology and electronics is needed to make this a reality. "

With such a device, this information could be used, for example, to dynamically and autonomously conduct effective contact tracing, Bentley said.

In the past 60 years, microelectronics have greatly evolved from the first implantable pacemaker to personal wearables that harness the power of interrelated computing devices—better known as the Internet of things, or IoT. The next great wave of microelectronics could include devices that tap into and control molecules—such as glucose, hormones, or DNA—to better human health. But, a major roadblock remains.

Despite how advanced current smart devices might be, today's microelectronic devices process information using materials such as silicon, gold, or chemicals, and an energy source that provides electrons. But, free electrons do not exist in biological systems. As such, there remains a technology gap between microelectronics and the biological world.

Over two years ago, Bentley, his IBBR and Fischell Institute colleague, Gregory F,. Payne, and their teams published research on a loophole they discovered.

In biological systems, there already exists a small class of molecules capable of shuttling electrons. These molecules, known as "redox" molecules, can transport electrons to any location. To do this, redox molecules must first undergo a series of chemical reactions—oxidation or reduction reactions—to transport electrons to the intended target.

By engineering cells with synthetic biology components, Bentley's research team created a sophisticated synthetic "switching" system in bacterial cells that recognizes electrons instead of more traditional molecular signals and incorporates the biologically programmable genetic circuitry of CRISPR. Best known for gene editing, CRISPR control functions were modified to work with SoxR, a regulatory protein that is responsive to redox molecules and is found in E.coli. Instead of editing genes, the team is using CRISPR to focus a cell's metabolic machinery to carry out desired functions.

The group's process involves what is known as downregulation and upregulation, whereby, a cell either decreases (downregulation) or increases (upregulation) the quantity of a particular component—such as a protein—in response to an external stimulus. The team successfully demonstrated that, using CRISPR, they could electrically program the upregulation and downregulation of specific genes in E.coli as well as in Salmonella. In this way, the team proved that information programmed electrically can be transmitted to and within many strains of bacteria using the same medium of redox as a communication channel.

Even more, the group created and applied CRISPR technology to take advantage of the signal processing capabilities in electronics and telecommunications. They immobilized cells in a gel and used electronic signals to create a well-defined chemical gradient of the CRISPR-controlling extracellular signal. They showed that cells exposed to the most highly oxidized pyocyanin—a metabolite capable of participating in a redox reaction—showcased the highest level of CRISPR activity, while the cells exposed to minimally oxidized pyocyanin demonstrated the lowest level of CRISPR activity. In so doing, the team effectively supported their hypothesis that electrical signals could be used to spatially control CRISPR.

While CRISPR is universally considered an agile tool for biology, this work represents the first demonstration of how CRISPR can be used in bioelectronics to electronically target and control select genes, simultaneously.

"Our next steps involve ramping up our bioelectronics work so that the next generation communication devices can indeed incorporate biological information that is obtained locally," Bentley said.


Mechanism of Biological Nitrogen Fixation

The biological nitrogen fixation is carried out by some bacte­ria, cyanobacteria and symbiotic bacteria. In symbiotic association, the bacterium provides fixed nitrogen (NH3) to the host and derives carbohydrates and other nutrients from the latter.

Biological nitrogen fixation occurs in the presence of the enzyme nitrogenase which is found inside the nitrogen fixing prokaryote. In addition to this enzyme, a source of reducing equivalents (ferredoxin (Fd) or flavodoxin in vivo), ATP and protons are required.

The overall stoichiometry of biological nitrogen fixation is represented by the following equation:

N2 + 8H + + 8e – + 16 ATP → 2NH3 + H2 + 16 ADP + 16 Pi

The enzyme nitrogenase is in-fact an enzyme complex which consists of two metallo-proteins.

(i) Fe-protein or iron-protein component (previously called as azo ferredoxin) and

(ii) Fe Mo-protein or iron-molybdenum protein component (previously called as molybdoferredoxin). None of these two components alone can catalyse the reduction of N2 to NH3.

The Fe-protein component of nitrogenase is smaller than its other component and is an Fe-S protein which is extremely sensitive to O2 and is irreversibly inactivated by it. This Fe-S protein is a dimer of two similar peptide chains each with a molecular mass of 30-72 kDa (depending upon the micro-organism). This dimer contains four Fe atoms and four S atoms (which are labile and 12 titrable thiol groups).

The MoFe-protein component of nitrogenase is larger of the two components and consists of two different peptide chains which are associated as a mixed (α2β2 ) tetramer with a total molecular mass of 180 – 235 k Dalton (depending upon the micro-organism). This tetramer contains two Mo atoms, about 24 Fe atoms, about 24 labile S atoms and 30 titrable thiol groups probably in the form of three 24 Fe4 – S4 clusters. This component is also sensitive to O2.

i. Because nitrogenase enzyme complex is sensitive to O2, biological nitrogen fixation requires anaerobic conditions. If the nitrogen fixing organism is anaerobic than there is no such problem. But, even when the organism is aerobic, nitrogen fixation occurs only when conditions are made to maintain very low level of O2 or almost anaerobic conditions prevail inside them around the enzyme nitrogenease.

ii. Apart from N2, the enzyme nitrogenase can reduce a number of other substrates such as N2O (nitrous oxide), N3 – (azide), C2H2 (acetylene), protons (2H + ) and catalyse hydrolysis of ATP.

iii. Direct measurement of nitrogen fixation is done by mass spectroscopy. However, for comparative studies reduction of acetylene can be measured rather easily by gas chromatography method.

The electrons are transferred from reduced ferredoxin or flavodoxin or other effective reducing agents to Fe-protein component which gets reduced. From reduced Fe-protein, the elec­trons are given to MoFe-protein component which in turn gets reduced and is accompanied by hydrolysis of ATP into ADP and inorganic phosphate (Pi). Two Mg ++ and 2 ATP molecules are required per electron transferred during this process.

Binding of 2 ATPs to reduced Fe-protein and subsequent hydrolysis of 2 ATPs to 2 ADP + 2 Pi is believed to cause a conformatorial change of Fe-protein which facilitates redox (reduction-oxidation) reactions. From reduced MoFe-protein, the electrons are finally transferred to molecular nitrogen (N2) and 8 protons, so that two ammonia and one hydrogen molecule are produced (see the equa­tion and Fig. 9.4)

iv. At first glance, it might be expected that six electrons and six protons would be required for reduc­tion of one N2 molecule to two molecules of ammonia. But, the reduction of N2 is obligatorily linked to the reduction of two protons to form one H2 molecule also. It is believed that this is necessary for the binding of nitrogen at the active site.

v. The electrons for regeneration of reduced electron donors (ferredoxin, flavodoxin etc.) are provided by the cell metabolism e.g., pyruvate oxidation.

Substantial amount of energy is lost by the micro-organisms in the formation of H2 mol­ecule during nitrogen fixation. However, in some rhizobia, hydrogenase enzyme is found which splits H2 to electrons and protons (H2 → 2H + + 2e – ). These electrons may then be used again in reduction of nitrogen, thereby increasing the efficiency of nitrogen fixation.

Although scientists have tried to explain the mechanism of biological nitrogen fixation, but the precise pathway of electron transfer, substrate entry and product release and source of protons during biological nitrogen fixation have not yet been fully elucidated.

Formation of Root Nodules in Leguminous Plants:

The rhizobia occur as the free-living organisms in the soil before infecting their respec­tive host plants to form root nodules. The symbiosis between rhizobia and leguminous host plant is not always obligatory. However, under conditions of limited nitrogen supply in the soil, there is elaborate exchange of signals between the two symbionts for development of symbiotic relationship.

vi. There are separate host specific genes and rhizobial specific genes which are involved in nodule formation. The host plant genes are called as nodulin or Nod genes while rhizobial genes are called as nodulation or nod genes. Some Nod factors produced by rhizobia act as signals for symbiosis.

The rhizobia migrate and accumulate in the soil near the roots of the legume plant in response to the secretion of cer­tain chemicals such as flavonoids and be-taines by the roots. Root hairs of legume produce specific sugar binding proteins called as lectins. These lectins are activated by Nod factors to facilitate the attachment of rhizobia to the root hairs whose tips in turn become curved (Fig. 9.5 A).

Rhizobia now secrete enzymes which degrade the cell walls of root hairs at the point of their attachment for entry into the root hair. From root hairs, the rhizobia en­ter into the cells of inner layers of cortex through infection threads (tubular exten­sions of the in-folded plasma membrane pro­duced by fusion of Golgi-derived membrane vesicles).

The rhizobia continue to multiply inside infection thread and are released into cortical cells in large numbers, where they cause cortical cells to multiply and ulti­mately result in the formation of nodules on the upper surface of the roots (Fig. 9.5 A & B). After their release into cortical cells, the rhizobia stop dividing and enlarge.

Electron microscopic studies have shown groups of rhizobia to the surrounded by single membranes which originate from host cell plasma membrane. The enlarged and non motile groups of bacteria inside the membranes are called as bacteroids and the membrane surrounding them as peribacterioid membrane.

The space between bacteroids and peribacteroid membrane is called as peribacteroid space. These bacteroids are aerobic and the nitrogenase enzyme is found inside them. The bacteroides lack a firm wall and are osmotically labile. In root nodule cells of Glycine max, often groups of 4 – 6 bacteroids are enclosed in­side the peribacteroid membranes (Fig. 9.5 C)

The number of chromosomes in cortical cells infected by rhizobia which later develop into nodule is double the number of chromosome in other somatic cells of the legume (i.e., they are tetraploid) and seems to be pre-requisite for nodule formation. Apart from infected cells which are tetraploid, some unifected diploid cells are also found in nodule. The nodule has its own vascular system which is connected with vascular system of the root to facilitate transfer of fixed nitrogen i.e., NH3 to the host and carbohydrates and other nutrients from the host to the bacteroids.

In root nodules of leguminous plants, a red pigment- an oxygen binding heme protein which is very much similar to hemoglobin of red blood corpuscles is found. This pigment is called as leg-hemoglobin and occurs in cytosol of infected nodule cells. Leg-hemoglobin gives pinkish-red colour to the nodules. The globin part of this pigment is synthesized in host plant genome in response to the bacterial infection, while its heme portion is synthesized by bacte­rial genome.

Although a correlation has been found between the concentration of hemoglobin and the rate of nitrogen fixation, but this pigment does not play a direct role in nitrogen fixation. It (i) protects the nitrogenase inside the bacteroids from deterimental effect of oxygen and (ii) main­tains adequate supply of oxygen to the bacteroids, so that through respiration ATPs continue to be generated which are required for nitrogen fixation.

After its formation inside bacteroids, ammonia (or NH4 + ) is released into cytosol of infected nod­ule cells where it is converted into amides (chiefly asparagine and glutamine) or ureids (chiefly allantoic acid, allantoin and citrulline). These amides or ureids are then translocated to shoots of host plant through xylem, where they are rapidly catabolized to NH4 + for entry into mainstream of ammonium assimilation.


For Students & Teachers

For Teachers Only

ENDURING UNDERSTANDING
ENE-1
The highly complex organization of living systems requires constant input of energy and the exchange of macromolecules.

LEARNING OBJECTIVE
ENE-1.I
Describe the photosynthetic processes that allow organisms to capture and store energy.

ENE-1.J
Explain how cells capture energy from light and transfer it to biological molecules for storage and use.

ESSENTIAL KNOWLEDGE
ENE-1.I.1
Organisms capture and store energy for use in biological processes–

  1. Photosynthesis captures energy from the sun and produces sugars.
    1. Photosynthesis first evolved in prokaryotic organisms.
    2. Scientific evidence supports the claim that prokaryotic (cyanobacterial) photosynthesis was responsible for the production of an oxygenated atmosphere.
    3. Prokaryotic photosynthetic pathways were the foundation of eukaryotic photosynthesis.

    ENE-1.I.2
    The light-dependent reactions of photosynthesis in eukaryotes involve a series of coordinated reaction pathways that capture energy present in light to yield ATP and NADPH, which power the production of organic molecules.

    ENE-1.J.1
    During photosynthesis, chlorophylls absorb energy from light, boosting electrons to a higher energy level in photosystems I and II.

    ENE-1.J.2
    Photosystems I and II are embedded in the internal membranes of chloroplasts and are connected by the transfer of higher energy electrons through an electron transport chain (ETC).

    ENE-1.J.3
    When electrons are transferred between molecules in a sequence of reactions as they pass through the ETC, an electrochemical gradient of protons (hydrogen ions) is established across the internal membrane.

    ENE-1.J.4
    The formation of the proton gradient is linked to the synthesis of ATP from ADP and inorganic phosphate via ATP synthase.

    ENE-1.J.5
    The energy captured in the light reactions and transferred to ATP and NADPH powers the production of carbohydrates from carbon dioxide in the Calvin cycle, which occurs in the stroma of the chloroplast.

    EXCLUSION STATEMENT

    Memorization of the steps in the Calvin cycle, the structure of the molecules, and the names of enzymes (with the exception of ATP synthase) are beyond the scope of the course and the AP Exam.


    The Chemistry of Biology: Chemical Reactions: Ionic, Covalent, and Polar Covalent Bonds

    The Chemistry of Biology

    Chemical reactions are important to all levels of biology. In the simplest terms, a reaction requires reactants and products. Reactants are the atoms or molecules that are involved with the change, and products are the resulting changed atoms or molecules. In most biological reactions, enzymes act as catalysts to increase the rate of a reaction. A chemical reaction occurs when reactants are joined together to create a product that has different chemical properties than the original reactants. This always involves an energy change and a change in the electron configuration around the original atoms. When electrons redistribute their orbitals to include two or more atomic nuclei, as is the case in a covalent bond, or donate or accept electrons, as is the case in an ionic bond, a chemical reaction has occurred. Two general types of bonds form during chemical reactions: ionic and covalent.

    Ionic bonds form when the outermost, or valence, electrons of an atom are donated or received in association with a second atom. Because the electrons are now orbiting around the receiving atom and not their original atom, the receiving atom now has an imbalance between the number of protons and electrons and becomes a negatively charged ion. The donating atom also has a proton-electron imbalance and becomes a positively charged ion because it lost a negatively charged electron and the number of its protons remained the same. The resulting molecule has properties different from the original atoms. It is important to remember that because of the unequal electron distribution around the reacting atoms, the resulting ionic compounds have partial charges. This importance is developed in greater detail in Specialized Cell Structure and Function, but it explains the fact that water can dissolve any substance that has a partial charge on it. A typical example for an ionic bond is the joining of a sodium atom, which donates an electron, to a chlorine atom, which accepts the electron, to form sodium chloride, also known as table salt.

    Covalent bonds occur when two or more atoms share their electrons. The electrons are not donated/accepted instead, they incorporate their orbitals to create an electron cloud around all participating atoms. When the electrons are shared evenly around all reacting nuclei, there is no partial charge on the resulting molecule, as is the case when carbon covalently bonds with itself. However, in some cases, the electrons are not shared evenly and partial charges occur, as in the case of polar covalent bonds.

    In reality, many bonds are actually a hybridization of ionic and covalent and have characteristics of both types. Atoms with polar covalent bonds share their electrons (covalent characteristic) unevenly (ionic characteristic), giving a slight positive (+) charge to one end of the molecule and a slight negative (-) charge to the other end. Water is a polar covalent molecule because the electrons spend more of their time around the oxygen atom because the oxygen atom has more protons acting as electron-magnets. Because of this uneven sharing of electrons, the oxygen end of the molecule has a slight negative charge, and the hydrogen end has a partial positive charge because the electrons are spending more time orbiting around the oxygen atom. The overall molecule has a partial positive and a partial negative end. As a result, water molecules tend to align themselves so that the positive end of one molecule aligns with the negative end of another molecule (opposites attract).

    Notice also in the ionic model that the electrons are drawn away from the sending atom and accepted by the receiving atom. The covalent model shows the electrons being shared equally around all of the atoms, whereas the polar covalent shows the unequal sharing of the electrons.

    In all cases, the driving force for any chemical reaction is a move toward greater stability of the atoms. To increase stability, atoms tend to react so that they lower their energy and increase their entropy (randomness or lack of organization). In chemical terms, this means that they seek to have a stable number of electrons in their outermost orbital. The stable number means that the outermost energy level is either completely full or completely empty. Chemists call this the v because often eight valence electrons are required to reach stability. Atoms react to achieve this electron configuration by donating/accepting electrons (ionic) or sharing them (covalent). Biomolecules are considered organic because they contain the element carbon and are covalently bonded.


    Contents

    The core of PSII consists of a pseudo-symmetric heterodimer of two homologous proteins D1 and D2. [2] Unlike the reaction centers of all other photosystems in which the positive charge sitting on the chlorophyll dimer that undergoes the initial photoinduced charge separation is equally shared by the two monomers, in intact PSII the charge is mostly localized on one chlorophyll center (70−80%). [3] Because of this, P680 + is highly oxidizing and can take part in the splitting of water. [2]

    Photosystem II (of cyanobacteria and green plants) is composed of around 20 subunits (depending on the organism) as well as other accessory, light-harvesting proteins. Each photosystem II contains at least 99 cofactors: 35 chlorophyll a, 12 beta-carotene, two pheophytin, two plastoquinone, two heme, one bicarbonate, 20 lipids, the Mn
    4 CaO
    5 cluster (including two chloride ions), one non heme Fe 2+
    and two putative Ca 2+
    ions per monomer. [4] There are several crystal structures of photosystem II. [5] The PDB accession codes for this protein are 3WU2, 3BZ1, 3BZ2 (3BZ1 and 3BZ2 are monomeric structures of the Photosystem II dimer), [4] 2AXT, 1S5L, 1W5C, 1ILX, 1FE1, 1IZL.

    The oxygen-evolving complex is the site of water oxidation. It is a metallo-oxo cluster comprising four manganese ions (in oxidation states ranging from +3 to +4) [6] and one divalent calcium ion. When it oxidizes water, producing oxygen gas and protons, it sequentially delivers the four electrons from water to a tyrosine (D1-Y161) sidechain and then to P680 itself. It is composed of three protein subunits, OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ) a fourth PsbR peptide is associated nearby.

    The first structural model of the oxygen-evolving complex was solved using X-ray crystallography from frozen protein crystals with a resolution of 3.8Å in 2001. [7] Over the next years the resolution of the model was gradually increased to 2.9Å. [8] [9] [10] While obtaining these structures was in itself a great feat, they did not show the oxygen-evolving complex in full detail. In 2011 the OEC of PSII was resolved to a level of 1.9Å revealing five oxygen atoms serving as oxo bridges linking the five metal atoms and four water molecules bound to the Mn4CaO5 cluster more than 1,300 water molecules were found in each photosystem II monomer, some forming extensive hydrogen-bonding networks that may serve as channels for protons, water or oxygen molecules. [11] At this stage, it is suggested that the structures obtained by X-ray crystallography are biased, since there is evidence that the manganese atoms are reduced by the high-intensity X-rays used, altering the observed OEC structure. This incentivized researchers to take their crystals to a different X-ray facilities, called X-ray Free Electron Lasers, such as SLAC in the USA. In 2014 the structure observed in 2011 was confirmed. [12] Knowing the structure of Photosystem II did not suffice to reveal how it works exactly. So now the race has started to solve the structure of Photosystem II at different stages in the mechanistic cycle (discussed below). Currently structures of the S1 state and the S3 state's have been published almost simultaneously from two different groups, showing the addition of an oxygen molecule designated O6 between Mn1 and Mn4, [13] [14] suggesting that this may be the site on the oxygen evolving complex, where oxygen is produced.

    Photosynthetic water splitting (or oxygen evolution) is one of the most important reactions on the planet, since it is the source of nearly all the atmosphere's oxygen. Moreover, artificial photosynthetic water-splitting may contribute to the effective use of sunlight as an alternative energy-source.

    The mechanism of water oxidation is understood in substantial detail. [15] [16] [17] The oxidation of water to molecular oxygen requires extraction of four electrons and four protons from two molecules of water. The experimental evidence that oxygen is released through cyclic reaction of oxygen evolving complex (OEC) within one PSII was provided by Pierre Joliot et al. [18] They have shown that, if dark-adapted photosynthetic material (higher plants, algae, and cyanobacteria) is exposed to a series of single turnover flashes, oxygen evolution is detected with typical period-four damped oscillation with maxima on the third and the seventh flash and with minima on the first and the fifth flash (for review, see [19] ). Based on this experiment, Bessel Kok and co-workers [20] introduced a cycle of five flash-induced transitions of the so-called S-states, describing the four redox states of OEC: When four oxidizing equivalents have been stored (at the S4-state), OEC returns to its basic S0-state. In the absence of light, the OEC will "relax" to the S1 state the S1 state is often described as being "dark-stable". The S1 state is largely considered to consist of manganese ions with oxidation states of Mn 3+ , Mn 3+ , Mn 4+ , Mn 4+ . [21] Finally, the intermediate S-states [22] were proposed by Jablonsky and Lazar as a regulatory mechanism and link between S-states and tyrosine Z.

    In 2012, Renger expressed the idea of internal changes of water molecules into typical oxides in different S-states during water splitting. [23]

    Inhibitors of PSII are used as herbicides. There are two main chemical families, the triazines derived from cyanuric chloride [24] of which atrazine and simazine are the most commonly used and the aryl ureas which include chlortoluron and diuron (DCMU). [25] [26]


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    Section Summary

    Matter is anything that occupies space and has mass. It is made up of atoms of different elements. All of the 92 elements that occur naturally have unique qualities that allow them to combine in various ways to create compounds or molecules. Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can be donated or shared between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.

    Exercises

    Glossary

    anion: a negative ion formed by gaining electrons

    atomic number: the number of protons in an atom

    cation: a positive ion formed by losing electrons

    chemical bond: an interaction between two or more of the same or different elements that results in the formation of molecules

    covalent bond: a type of strong bond between two or more of the same or different elements forms when electrons are shared between elements

    electron: a negatively charged particle that resides outside of the nucleus in the electron orbital lacks functional mass and has a charge of –1

    electron transfer: the movement of electrons from one element to another

    element: one of 118 unique substances that cannot be broken down into smaller substances and retain the characteristic of that substance each element has a specified number of protons and unique properties

    hydrogen bond: a weak bond between partially positively charged hydrogen atoms and partially negatively charged elements or molecules

    ion: an atom or compound that does not contain equal numbers of protons and electrons, and therefore has a net charge

    ionic bond: a chemical bond that forms between ions of opposite charges

    isotope: one or more forms of an element that have different numbers of neutrons

    mass number: the number of protons plus neutrons in an atom

    matter: anything that has mass and occupies space

    neutron: a particle with no charge that resides in the nucleus of an atom has a mass of 1

    nonpolar covalent bond: a type of covalent bond that forms between atoms when electrons are shared equally between atoms, resulting in no regions with partial charges as in polar covalent bonds

    nucleus: (chemistry) the dense center of an atom made up of protons and (except in the case of a hydrogen atom) neutrons

    octet rule: states that the outermost shell of an element with a low atomic number can hold eight electrons

    periodic table of elements: an organizational chart of elements, indicating the atomic number and mass number of each element also provides key information about the properties of elements

    polar covalent bond:a type of covalent bond in which electrons are pulled toward one atom and away from another, resulting in slightly positive and slightly negative charged regions of the molecule

    proton: a positively charged particle that resides in the nucleus of an atom has a mass of 1 and a charge of +1

    radioactive isotope: an isotope that spontaneously emits particles or energy to form a more stable element

    van der Waals interaction: a weak attraction or interaction between molecules caused by slightly positively charged or slightly negatively charged atoms