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At the end of the citric acid cycle, the reduced electron carriers contain the majority of the energy from glucose. Through oxidative phosphorylation, energy released by redox reactions is coupled indirectly to ATP synthesis. There are two coupled processes. First, in the electron transport chain, redox reactions transfer electrons from the reduced electron carriers to oxygen, and energy released is used to form a proton gradient by pumping protons from the mitochondrial matrix into the intermembrane space. Four multienzyme complexes catalyze the redox reactions. Complex I receives electrons from NADH and pumps protons while complex II receives electrons from FADH2 but does not pump protons. Coenzyme Q then receives electrons from complex I and II and donates electrons to complex III. Complex III then donates electrons to cytochrome C, a water-soluble protein. Complex IV then receives electrons from cytochrome C. Throughout this process, electrons are moving from molecules with low affinity to those with high affinity. Oxygen is the final electron acceptor at the end of the transport chain. The energy stored in the proton gradient is then released as protons flow back to the matrix through the ATP synthase proton channel. The flow from higher to lower concentrations releases energy. ATP synthase uses the energy released to form ATP.

Once pyruvate is formed from glucose it can be used in multiple pathways. Gluconeogenesis is the anabolic synthesis of glucose from pyruvate, but it is not the exact reverse of glycolysis. Pyruvate can also participate in two different catabolic processes: fermentation and slow cellular respiration. Fermentation happens when oxygen is low or energy is needed quickly, and there are two kinds: homolactic fermentation, which occurs in muscle cells, red blood cells, and some bacteria, and alcoholic fermentation, which occurs in yeast and some bacteria. The purpose of this fast anaerobic respiration is to regenerate NAD+ so that glycolysis can continue, and it does not generate additional ATP. Slow cellular respiration occurs when there is enough oxygen and the need for energy is not urgent. In slow respiration, pyruvate is used to synthesize acetyl-CoA to be further oxidized. Acetyl-CoA is an acetyl group attached to coenzyme A and is the central molecule in metabolism of fuel molecules. Formation of acetyl-CoA from pyruvate by a pyruvate dehydrogenase complex is the “point of no return” in carbohydrate metabolism. It cannot be converted back to pyruvate.

The metabolism includes both anabolic and catabolic processes. Catabolic processes are exergonic and spontaneous while anabolic processes are endergonic and non-spontaneous; however, metabolic coupling between biochemical pathways allows endergonic reactions to still occur. In metabolic coupling, energy released from an exergonic reaction is used to provide energy needed for an endergonic reaction. This energy is often exchanged through phosphate groups. Molecules with phosphate groups tend to have high free energies, so the removal of a phosphate group by hydrolysis results in a largely negative change is free energy. Phosphorylation, on the other hand, requires energy input. The magnitude of free energy available in the bond is the phosphoryl group transfer potential, and molecules with larger phosphoryl group transfer potentials can phosphorylate molecules with lower potential. In other words, energy released through the hydrolysis of a phosphoryl group is used to power the phosphorylation of another mloecule. An example is the coupling that occurs to power muscle contractions. Creatine phosphate is hydrolyzed to form creatine, and this energy is used to phosphorylate ADP to ATP. ATP is the main energy currency molecule in nearly all cells.

A polysaccharide called glycogen plays a key function in energy storage in animals. It is a homoglycan of glucose and is highly branched for efficient storage and release of glucose. Glycogen is mainly stored in the liver and muscle cells, the liver being the regulator of blood glucose levels and the muscle requiring the breakdown of glucose for energy for muscle contractions. Glycogen is synthesized through three main enzymes. Glycogenin forms glucose primers of at least four monomers, catalyzing the addition of glucose chains to its aspartic acid R-groups. Glycogenin is required to start all new glycogen molecules. Then, glycogen synthase catalyzes the addition of glucose to the primer one at a time through alpha (1,4) bonds. Next, the branching enzyme forms the branches of glycogen. It transfers a minimum of seven-unit chains of glucose, breaking an alpha (1,4) bond, and connects them to another chain through an alpha (1,6) bond. On the other hand, glycogen degradation occurs using two main enzymes. Glycogen phosphorylase removes monomers from non-reducing ends up until four units away from a branch point. Then, the debranching enzyme removes the three-unit chunk from the branch and attaches it to the main chain. It can then break the alpha (1,6) bond to remove the branch point glucose. This allows for glycogen phosphorylase to continue to degrade the chains of glucose.

Carbohydrates are one of the main biomolecules in organisms. They are made up of monosaccharides, the monomer units of carbohydrates. Monosaccharides share a common chemical formula consisting of carbons, hydrogens, and oxygens, and there are two types based on the different functional groups. An aldose such as glucose contains an aldehyde at the end of the carbon chain, while a ketose such as fructose has a ketone group within the chain. These monosaccharides have different properties because of these differing structures. Monosaccharides with four or more carbons are mainly rings. A ring forms through a reaction between a hydroxyl group and carbonyl carbon, resulting in a chiral anomeric carbon. Depending on the orientation of the hydrogen in the produced ring, the ring has either an alpha or beta conformation. Monosaccharides are then connected by glycosidic bonds, which form through the dehydration reaction between the anomeric carbon and a hydroxyl group. Since they are formed through dehydration, glycosidic bonds are also broken through hydrolysis. Longer chains of monosaccharides are referred to as polysaccharides.

Metabolic pathways are connected indirectly so that energy released by catabolic pathways is transferred to anabolic pathways. There are two main forms of transfer, and one of them is electrons. Oxidation-reduction, or redox, reactions transfer electrons between molecules. To be oxidized means to lose electrons, and to be reduced means to gain electrons. For every oxidation, there must be a reduction since there are no free electrons in cells. In order to distinguish which molecules will be reduced while another is oxidized, the reduction potential is determined. The reduction potential is the affinity for electrons, or the likelihood of being reduced. It is determined experimentally by comparing the molecule’s reactivity to hydrogen under standard conditions. If its oxidized form has a higher affinity for electrons than hydrogen, it accepts electrons and becomes reduced. On the other hand, if its oxidized form has a lower affinity than hydrogen, its reduced form donates electrons and becomes oxidized. The reduction potential is measured in volts, and a positive potential indicates spontaneity. There is an equation developed that relates the reduction potential to change in free energy, and the presence of a negative sign on one side indicates that a positive reduction potential means a negative change in free energy. This is parallel with the fact that a positive reduction potential means a spontaneous reaction.

The metabolism is made up of anabolic and catabolic processes. Anabolic processes are endergonic, meaning they are not spontaneous, while catabolic processes are exergonic and spontaneous. So how do endergonic reactions occur then? There is metabolic coupling between biochemical pathways so that energy released from an exergonic reaction is used to provide energy needed for an endergonic reaction. This exchange of energy happens in two forms: phosphate groups and electrons. Certain molecules with phosphate groups have high free energies, so the removal of a phosphate group by hydrolysis has a largely negative change is free energy. Phosphorylation, on the other hand, requires energy input. The magnitude of free energy available in the bond is the phosphoryl group transfer potential, and molecules with larger phosphoryl group transfer potentials can phosphorylate molecules with lower potential. In other words, energy released by hydrolysis is used to power other reactions. An example is the coupling that occurs to power muscle contractions. Creatine phosphate is hydrolyzed to form creatine, and this energy is used to phosphorylate ADP to ATP. ATP is the main energy currency molecule in nearly all cells. 

The ability to control enzyme activity is essential in cells in order to produce molecules when needed and to conserve energy/resources. One way to regulate enzymes is through activators and inhibitors. These molecules alter the enzyme's conformation or block the active site, but they are not involved in the reaction in any way. Enzymes can also be regulated through covalent modification by phosphorylation. The reversible addition of a phosphate group alters the conformation of the enzyme, increasing or decreasing its activity by affecting substrate binding and/or its ability to produce products. In phosphorylation, kinases add phosphate groups while phosphatases remove them. Another form of enzyme regulation is the cleavage of an inactive enzyme, where catalytically inactive precursors are cut to create the active enzyme. The activation of chymotrypsinogen to alpha-chymotrypsin is an example of this.

Irreversible inhibitors also regulate enzymes by permanently impairing enzyme activity, typically via covalent modification. Irreversible inhibitor usually, but not always, result in the complete loss of enzyme activity. On the other hand, reversible inhibitors are not permanent, and they come in three forms: competitive, uncompetitive, and noncompetitive/mixed. Competitive inhibitors bind to the active site and prevent substrate binding while uncompetitive inhibitors only bind to the enzyme-substrate complex at a location other than the active site; however, noncompetitive/mixed inhibitors are able to bind to the free enzyme and the enzyme-substrate complex at a location other than the active site, although not at the same time.

The ability to control enzyme activity is essential in cels in order to produce molecules when needed and conserve energy/resources. One way to reulate enzymes is through activators and inhibitors. These are molecules that alter the enzyme's conformation or block the active site, and they are not involved in the reaction in any way. Heteroallosteric effectors are molecules that interact with allosteric enzymes and alter their activity. Enzymes can also be regulated through covalent modification by phosphorylation. The reversible addition of a phosphate group alters the conformation of the enzyme, increasing or decreasing activity by affecting substrate binding and/or ability to produce products. Kinases are proteins that add phosphate groups, and phosphatases are proteins that remove phosphate groups. The cleavage of an inactive enzyme is another form of regulation. Catalytically inactive precursors are cut to create the active enzyme. The activation of chymotrypsinogen to alpha-chymotrypsin is an example of this. Another form of enzyme regulation is through irreversible inhibitors. These molecules permanently impair enzyme activity, typically via covalent modification. Irreversible inhibitor usually, but not always, result in the complete loss of enzyme activity. On the other hand, reversible inhibitors are not permanent, and they come in three forms: competitive, uncompetitive, and noncompetitive/mixed. Competitive inhibitors bind to the active site and prevent substrate binding, but uncompetitive inhibitors only bind to the enzyme-substrate complex at a location other than the active site. Noncompetitive/mixed inhibitors are able to bind to the free enyme and the enzyme-subtrate complex at a location other than the active site, but not at the same time. 

Although the FGENESH predicted 15 exons, the missing portion that was output by Phytozome suggests that there may be 16 exons. The Nucleotide BLAST matches to only eukaryotic green plants suggests that this gene plays a role in plant development that is not present in animals. Based on the UniProt description of the gene as involved in the cell membrane, the gene seems to be involved in the membrane and cell wall, which is only present in plants. This was also supported by the fact that only the kinase domain was conserved in species outside of plants. The whole of almost whole protein was only found in plants.

I hypothesize that the unknown gene codes for a transmembrane protein spanning the plasma membrane or cell wall of B. distachyon cells. The extracellular leucine-rich repeats are used to communicate with surrounding cells, activating the intracellular kinase domain to bind ATP and phosphorylate a protein