Using your lecture notes, develop a narrative to accurately portray the amphibolic nature of cellular respiration. The narrative can be descriptive, analogous, or scientific, or another approach to your choosing. Whatever style you choose, the narrative must reflect the scope and sequence of your respiration understanding. This needs to be a maximum of four pages but a minimum of two pages.
Deep near the center of the local star there are protons that are flying around as deuterium and tritium both of which are radioactive isotopes of hydrogen. These single protons are smashed together to form one single nuclei with the larger proton count. This formation of the helium atom also releases tons of energy. The helium atom then tends to decay into one helium atom and a neutron. The excess energy resulting from the formation of the unstable helium atom then goes on to heat the nearby gases and other matter surrounding the reaction.
Eventually that heat-up of the matter (mostly gases) in the region tends to release many, many protons and eventually over the course of millions of years these photons pass through the sun and then fly outwards into outer space. These photons are quantified packets of energy that are also known as electromagnetic waves. Eventually they reach the atmosphere of Earth and many are `stuck' heating the atmosphere up making those particular gases heat up and so on.
The photons that do eventually get past the layers of atmosphere on Earth tend to reach down to the surface and heat up the water. Numerous things are scattered across the surface of the planet such as plants. The photons hit the surface of green leaves and enter the photosystems I and II in the chloroplasts. Through the process of photosynthesis the energy of the photons is practically locked into the bonds of glucose molecules. Other biological systems roam the face of the planet and live alongside the plant life. Heterotrophs tend to eat the autotrophic plants and in that way they are able to get the energy that was originally produced in the sun.
The question now comes to what exactly is done with this energy in the form of glucose that the heterotrophs have now obtained. Saying that they have already obtained the energy is rather fallacious as the sugar is not usable cellular energy directly and is so far only in the mouth of the heterotrophic animal. Suppose then that we follow the sugar through the human body to illustrate the process by which the energy of the local star is unlocked and used to keep the organism in homeostasis, reproducing, growing, and doing all of the many other things associated with living.
Ingestion, digestion, absorption, elimination are the four stages of food processing, whereby ingestion involves the mechanical and chemical breakdown of the food material into more manageable components much smaller in nature such that then the digestive process can begin to break down the components into their smaller forms (such as “pizza” into the fatty acids embedded in the cheese). The absorption stage is equivalent to the part where the food passes through the animal such as in the gastrointestinal system whereby the intestines begin to absorb the passing food materials. The elimination process is where the materials that have been unused and once the complex lipid molecules have been broken down and no longer used in the system it goes out and the organism is basically done with the materials. The gastrointestinal tracts usually run through the entire organism and the material is ingested in such a way in the abdomen such that the material can be distributed to the rest of the body (the intestines aren't at your toes or in your head!).
The digestive system includes the salivary glands, mouth, esophagus, stomach, liver, pancreas, gallbladder, small and large intestines, and rectum. The salivary glands produces a substance that begins the decomposition of food input materials. The mouth assists in mechanical decomposition of the food by breaking it apart into smaller and smaller components assisted by the chewing action of the jaw and structure of the teeth. The food particles travel down the esophagus and into the stomach, the liver secretes bile, stores the bile in the gallbladder, the bile is used to break down fat that has been taken in, the food travels to the small intestine where most of the food digestion and absorption takes place. The small intestine includes the duodenum, jejunum, and ileum. The pancreas, liver, and gallbladder all secrete digestive juices (such as bile) into the duodenum of the small intestine to break down food. The jejunum is the second part of the small intestine which digests the broken-down food materials. The jejunum is responsible for absorbing digested foods into the human system to distribute to other cells (etc.). The jejunum connects to the large intestine at the cecum (through the ileocecal valve) of the large intestine. The appendix is an offshoot of the cecum. The large intestine removes some liquids and electrolytes from the food materials being processed and eventually ends with the anal canal.
The brain triggers the release of gastrointestinal juices (gastric juices) when animals see, hear, or taste food. It is by this hormone-based triggering that the stomach and the intestines do not continuously release enzymes for the degradation of food for digestion when there is no more food remaining in the intestines. The hormone gastrin is released into the circulatory system when food stimulates the stomach wall. This release of gastrin goes through the blood stream and after it completely makes its way back it actually triggers the stomach to release even more gastric juices so that there is continued digestion as long as there are food stuffs still within the stomach which really turns into an example of negative feedback as the acidity of the stomach solution becomes too low. Other hormones called enterogastrones, secreted by the wall of the duodenum, tells the intestinal cells to secrete secretin, which signals the pancrease to release bicarbonate, which then proceeds to neutralize the acid. These hormones are used to stop food from being transferred down further, to secrete special enzymes to degrade food, and generally control the acidity of the digestive contents relative to the general presence of enzymes in the blood stream sort of as a messenger system to influence the intestinal system.
Bile assists in the digestion of fats in the duodenum (remember that bile is produced in the liver and stored in the gallbladder). Numerous digestive enzymes function in the small intestine as hydrolytic enzymes in order to break polysaccharides (in other words: complex carbohydrates) down to monosaccharides (the monomers). Also, numerous enzymes are in the duodenum that have polypeptide substrates meaning that they break apart proteins down into amino acids such as the enzymes trypsin and chymotrypsin. An enzyme called dipeptidase attaches to the lining of the intestine and splits small peptides, carboxypeptidase breaks one amino acid at a time (beginning at the carboxyl group end of some polypeptide chain), and aminopeptidase works in the opposite direction of carboxypeptidase (it starts at the head, not the carboxyl tail). Protein digestion could occur with only aminopeptidase or only carboxypeptidase and not the other, however, the rate of hydrolysis is greatly increased with both proteins present. Nucleases hydrolyze DNA and RNA into their component nucleotides. Lipase hydrolyzes fat molecules. The most complex of these processes is the protein digestion where enzymes specifically target `heads' or `tails' and start breaking off amino acids one by one and can even have some primitive sense of `team work' going on in the duodenum of the small intestine.
Eventually the materials in the small intestine are small enough to be absorbed and transported across the plasma membrane of cells. These materials are then carried by a series of enzymes to reach regions within the cytoplasm to undergo glycolysis. The first step of glycolysis involves the enzyme hexokinase phosphorylating the glucose molecule which means that one phosphate group is added to glucose from ATP. The result is glucose 6-phosphate and ADP. The second step of glycolysis has the enzyme phosphoglucoisomerase that takes the new glucose formation and reconfigures it into the isomer fructose 6-phosphate. Isomers have the same chemical formula but different configurations. Thirdly, the enzyme phosphofructokinase takes the fructose 6-phosphate and adds another phosphate group from another ATP molecule making fructose 1, 6 diphosphate. The enzyme aldolase then splits this fructose molecule into two sugars as the fourth step. The resulting molecules are dihydroxyacetone phosphate and glyceraldehyde phosphate (both are sugars). After the fifth step, in the system includes two molecules of Glyceraldehyde phosphate (C3H5O3P1) resulting from the nature of the enzyme triose phosphate isomerase. The sixth step gets rather complicated and functions for both glyceraldehydes phosphate molecules. First, it takes the enzyme triose phosphate dehydrogenase and the substrate glyceraldehyde phosphate and transfers one hydrogen atom to NAD+ to form NADH. Secondly, in step six, the enzyme triose phosphate dehydrogenase adds a phosphate to the oxidized molecule (the glyceraldehyde phosphate) resulting in 1, 3-diphoshoglyceric acid or C3H4O4P2. The seventh step involves the enzyme phosphoglycerokinase that takes one of the phosphates from each of the 1, 3-diphosphoglyceric acids and puts it back on ADP to form ATP (twice, because there are two of those acids). The process yields two 3-phosphoglyceric acid molecules and two ATP molecules. The eighth step involves an enzyme that takes the phosphate from the 3-phosphoglyceric acid and transfers it to the second carbon atom which makes 2-phosphoglyceric acid. Remember, that means that there are two of the 2-phosphoglyceric acids. In the ninth step, the enzyme enolase makes the 2-phosphoglyceric acid to undergo a condensation reaction (meaning that H2O is removed) and results in PEP. The tenth step involves the enzyme pyruvate kinase that transfers a phosphate from PEP and puts it on ADP to make ATP and also results in pyruvate acid.
The process of glycolysis thus produces four ATP molecules and two pyruvate acids. This is important to remember because it shows that glycolysis requires energy in order to begin the entire process and then results in two pyruvate acid molecules. The pyruvate acid is fed into the Kreb's citric acid cycle where eight NADH molecules and two FADH molecules are resulting.
In addition to catabolizing for energetic needs, the citric acid cycle uses pathways as precursor to synthesizing molecules. What we see here is this chain where the molecules and acids that are present within the citric acid cycle. We begin at the top and come into this chain working clockwise and we start with citric acid (citrate). Then it goes to isocitrate and then to alpha-ketoglutarate and then to succinly-CoA and then to succinate and then to fumarate and then to malarate and then to oxeoloacetate.
The citric acid cycle is catabolic: molecules are broken down to serve energy needs of the cell. Ketogluterrate breaks down with the action of succinly-Coa to produce a 4-carbon acid called succinate. Succinate reorganizes itself into fumarate (fumeric acid) and you may also see succinate as “succinal acid” and then the fumarate step is where FAD is produced. The fumarate step is also where the two molecules of ATP are phosphorylated from that particular enzyme. Fumeric acid is reorganized into malate acid which is then reorganized as oxaloacetate which then combines with the pyruvate from glycolysis and starts the whole thing over again.
The pyruvate connects to the citrate, isocitrate is an intermediate step, five-carbon acid ketogluterate wihich is an NAD step, where it connects to the hydrogen, and then we have succinyl-Coa, and then we have succinate and fumarate acids that are intermediates and at that point we get 2 ATP. When the citric acid cycle is done we have 2 ATP molecules from glycolysis and then 2 from the citric from the Kreb's citric acid cycle.
The FAD and NADH molecules travel to the membrane of the mitochondria and enter the electron transport chain where the hypothetical process of chemiosmosis occurs. The NADH is going to deposit its hydrogen in the membrane and the electrons are going to be sent to three different carriers and then produces a hydrogen concentration gradient and as it is passed through the ATP synthase the energy of the original electron causes ATP to form in that high-energy bond.
The purpose of the electron transport chain is to phosphorylate ADP into ATP. It is a collection of the electrons so that it may keep them around long enough to accumulate and make the ATP molecules
Hydrogen ions are also known as protons. They have this gradient because there is a low concentration of ions and then one of high concentration. ADP and inorganic phosphate is used to synthesize into ATP. This process requires ATP synthase. The eventual production of ATP occurs as a result of the hydrogen concentration gradient and those hydrogen ions passing through ATP synthase.
ATP synthase is an integral protein that stretches the length of the mitochondrial membrane and that protein acts as an enzyme for the final production of ATP. ATP synthase is near other membrane proteins. The energy associated with the gradient is used to synthesize ATP from ADP and inorganic phosphorus ions.
The energy associated with this gradient is used to synthesize ATP from ADP and this includes at the ATP synthase complex. One hydrogen ion enters from the intermembrane space and a second ion enters from the matrix space and then the ATP synthase rotates and once three protons enter through the matrix stpace there is enough in the complex to synthesize ATP. There is energy in the gradient that is used to make ATP.
The proton enters the ATP synthase and exits into the matrix space. The electron transport chain does this: it transfers the energy from hydrogen atoms (protons) that are from the FAD and NAD carriers from the original transporter protein across. The first one pumps the hydrogen atoms out from the inside to the outside which creates the concentration gradient. While it does that, the electrons from the hydrogen are removed to create a positive hydrogen ion, and as those positive hydrogen ions are built up, they are pumped, which requires energy from the electrons, are pumped into the ATP synthase, and then there are three protons per one molecule of ATP, and the energy present is used to phosphorylate one molecule of ATP.
NADH delivers the hydrogen atom to the first set of proteins which are dehydrogenase which is going to remove the hydrogen atoms and pump the hydrogen ions through the mitochondrial membrane and strip an electron from each hydrogen atom.
The energy released as electrons pass down the gradient from NADH to oxygen is harnessed by three enzyme complexes of the respiratory chain (I, III, and IV) to pump protons (H+) outwards. Hydrogen atoms have one proton and one electron.
The NADH dehydrogenase strips off the electron. The hydrogen with its single proton goes outside. The electron has to go somewhere. In order to go the molecule called Cytochrome C reductase picks up the electron. The electron then is passed down from cytochrome C reductase to the same thing except it's Cytochrome C oxidase.
Those three steps right there provide a concentration gradient of hydrogen in the intermembrane space which is the outer edge of the mitochondrial membrane. As their concentration increases there (which is the same as saying that the pH decreases), a strong diffusion gradient is set up. The only exit for these protons is through the ATP synthase complex. Hydrogen is not going to routinely diffuse across that membrane and that push comes from ATP synthase that it has to have to get back over and diffuse across that membrane. As in chlorplasts, the energy released as these proteins flow down their gradient is harnessed to the synthesis of ATP. This process is called chemiosmosis and is an example of facilitated diffusion.
Sources
http://biology.clc.uc.edu/Courses/bio104/cellresp.htm cellular respiration and fermentation (glycolysis and fermentation)
http://staff.jccc.net/PDECELL/cellresp/respintro.html introduction to cellular respiration
http://www.windows.ucar.edu/tour/link=/sun/Solar_interior/Nuclear_Reactions/Fusion/Fusion_in_stars/H_fusion.html the hydrogen fusion process
http://hyperphysics.phy-astr.gsu.edu/hbase/astro/procyc.html proton-proton fusion
http://zebu.uoregon.edu/~soper/Light/fusion.html nuclear fusion in the sun (interesting diagram, looks like a good read)
http://www.energyquest.ca.gov/story/chapter13.html the energy story
http://biology.about.com/od/cellularprocesses/a/aa082704a.htm steps of glycolysis
Bryan Bishop Respiration narrative December 4th, 02006
(done in class, one day) Due: Dec.8th