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In the late 1800s, Hans Christian Gram developed the gram staining procedure. Gram staining is a valuable diagnostic tool used in the clinical and research world. The gram stain is a method used to determine the identification of unknown bacteria. (BIO215, 2017)
According to Healthline.com, typically when you’re sick, you go to the doctors. If your doctor happens to suspect that you may have an infection, he or she may order to have a culture, and/or a gram stain done to check for bacteria. If it happens to be that you do have a bacterial infection, your doctor can then have a gram stain done on the bacteria to see if the bacteria in your infection are gram negative or gram positive bacteria. A gram stain can be performed on various types of specimens such as blood, tissue, stool, urine, and sputum. Determining whether the bacteria is gram negative or gram positive bacteria can play a huge role in what treatment your doctor may or may not recommended for you take to fight the infection and what type of bacterial infection you may have. Having a gram stain done can help your doctor decide if the bacteria is responsible for your symptoms and to see what type of bacteria is present. (Healthline, 2016)
Gram negative bacteria are more resistance to antibiotics, while gram positive bacteria are more susceptible to antibiotics. Gram negative bacteria is more resistant to antibiotics because of the outer membrane of lipopolysaccharide. The Lipid portion of the lipopolysaccharide acts as an endotoxin. (Diffen, 2018) Knowing what antibiotic to use when having an infection is very important when trying to overcome the bacterial infection to get better and not let the bacterial infection get out of hand.
According to Diffen.com, the six-gram positive genera of bacteria are known to cause disease in humans are Streptococcus, Staphylococcus, Corynebacterium, Listeria, Bacillus, and Clostridium. A few that fall under gram negative would be Pseudomonas aeruginosa, Neisseria gonorrhoeae, Chlamydia trachomatis, and Yersinia pestis. (Diffen, 2018)
There are a few steps you must follow to do a gram stain. According to BIO215 Lab Book, first the gram negative or gram positive cells are stained by a primary stain, crystal violet, for 30 seconds and then rinsed with water. Then, iodine is added to the smear for one minute and then rinsed. Iodine is a mordant the combines with crystal violet which forms an insoluble complex in gram positive cells. Both, gram negative and gram positive bacteria will appear purple as of now. Then you’ll drip decolorizer with alcohol to the smear for no more than 20 seconds and rinse. Gram positive still appears purple under the microscope because it’s cell wall retains the crystal violet, but the decolorizer removes the mordant complex in gram negative cells, letting them appear colorless. Then, safranin is added to the smear for a minute and then rinsed. Safranin is the counterstain that colors the gram negative cells pink. Safranin sticks to gram positive cells as well but their appearance isn’t changed because the crystal violet is more intense than the safranin. (BIO215, 2017)
Also, after determining if the bacteria present is gram negative or gram positive bacteria, the size, shape, and quantity of the bacteria can also provide more information about your infection you may have. (Healthline, 2016)

Question 4: Oxidative vs substrate level phosphorylation
First, I’ll start off with a few differences between oxidative phosphorylation and substrate level phosphorylation from the Differencebetween.com website. Oxidative phosphorylation is a process by which energy released by chemical oxidation of nutrients is used for the synthesis of ATP, Adenosine Triphosphate. In Substrate level phosphorylation transfers a phosphate group directly from the substrate, a phosphorylated compound, to ADP, Adenosine Diphosphate, to produce ATP. In substrate level phosphorylation, the energy is generated from a handful of reactions for this process. In oxidative phosphorylation, the energy that is generated from the reaction of the electron transport chain is used for this process. (Difference Between, 2017) I will further explain the electron transport chain in detail later. During substrate level phosphorylation, a small difference of redox potential is generated, whereas in oxidative phosphorylation, there is larger difference in redox potential that is generated to power this. Substrate level phosphorylation occurs under both aerobic and anaerobic conditions. (Difference Between, 2017) Aerobic means that oxygen is present or needed. Anaerobic is meaning when little or no oxygen is present or needed. (Anderson, D. G., et al., 2016) Substrates are partially oxidized and in oxidative phosphorylation, electron donors are completely oxidized. Substrate level phosphorylation occurs in the cytosol and mitochondria. Oxidative phosphorylation occurs in the inner membrane of mitochondria. Substrate level phosphorylation can be seen in the Krebs cycle and glycolysis. Oxidative phosphorylation can only be seen during the electron transport chain. Substrate level phosphorylation is not associated with the electron transport chain or ATP synthase. Oxidative phosphorylation is associated with both, the electron transport chain and ATP synthase. (Difference Between, 2017) The enzyme ATP synthase uses the energy of the proton motive force to drive the synthesis of ATP. (Anderson, D. G., et al, 2016) In substrate level phosphorylation, it does not use O2 or NADH for the formation of ATP. In oxidative phosphorylation, this uses O2 and NADH to produce ATP. (Difference Between, 2017) In substrate level phosphorylation the net ATP production is four ATP. In oxidative phosphorylation the net ATP production is thirty four ATP. (PEDIAA, 2017)
Now, what energizes oxidative phosphorylation? The electron transport chain is what energizes oxidative phosphorylation. But where does all of this occur? According to Science Prof Online, electron transport chain requires a membrane in order to work. In the prokaryotic cells, such as bacteria and archaea’s, the electron transport takes place in the cell’s plasma membrane, in folded areas called the mesosomes. In eukaryotic cells, such as plants, animals, and fungi, the electron transport chain occurs in cellular organelles, such as the mitochondria. This is where eukaryotic power factories break down food to make ATP. Also, having a mitochondria to turn food into ATP, plant cells have organelles called chloroplasts with an internal thylakoid membrane, where the electron transport chain uses sunlight to make ATP. (Science Prof Online, 2016)
The electron transport chain is so important because it creates ATP. ATP is a big form of energy. If we don’t have any energy, how can anything get done? We just wouldn’t be able to. According to DBriers.com, the electron transport chain is where the majority of the ATP is created. Thirty-four ATP molecules are made from the products of one molecule of glucose. This is the movement of electrons from high energy to low energy that makes the proton gradient. The electron transport chain can only occur when oxygen is available. (DBriers, 2012)
Question 5: Oxygenic vs. Anoxygenic
First, I’ll start off with some differences between oxygenic photosynthesis and anoxygenic photosynthesis. According to PEDIAA.com, oxygenic photosynthesis occurs in algae, plants, and cyanobacteria. The final electron acceptor is water in oxygenic photosynthesis. Anoxygenic photosynthesis is used by certain bacteria, in which oxygen is not produced. It occurs in green sulfur and nonsulfur bacteria, purple bacteria, heliobacteria, and acidobacteria. In oxygenic photosynthesis, photosystems I and II are used, whereas in anoxygenic photosynthesis only photosystem I is used. Water is the electron source in oxygenic photosynthesis and hydrogen, hydrogen sulfide or ferrous ions serves as the electron donor in anoxygenic photosynthesis. As figured by the name, oxygenic photosynthesis, oxygen is produced during the light reaction. In anoxygenic photosynthesis, oxygen is not produced during the light reaction. In oxygenic photosynthesis, chlorophylls are used and in anoxygenic photosynthesis, bacteriochlorophylls or chlorophylls are used. ADP serves as the terminal electron acceptor, producing NADPH, in oxygenic photosynthesis. NADPH is not produced as the electrons are cycled back to the system in anoxygenic photosynthesis. In oxygenic photosynthesis, ATP is produced by noncyclic photophosphorylation. In anoxygenic photosynthesis, ATP is produced by cyclic photophosphorylation. Oxygenic photosynthesis is shown as 6CO2 + 6H2O ?Light C6H12O6 + 6O2. (A) Anoxygenic photosynthesis is shown as 6CO2 + 12H2S + Light ? C6H12O6 + 12S + 6H2O. (PEDIAA, 2018)
According to our text book, in light reactions in cyanobacteria and photosynthetic eukaryotic cells, photosystem I and photosystem II work together as part of the light reactions. The energy that is absorbed by photosystem I and photosystem II raise the energy of electrons stripped from water to a high enough level that it can be used to generate a proton motive force and produce reducing power. This is why it is considered oxygenic photosynthesis because it does just that, it generates oxygen. (Anderson, D. G., et al., 2016) According to News.net, all living and breathing organisms inhale oxygen from the air to produce energy and exhale carbon dioxide into the atmosphere. In our text book, the Tandem Photosystems of Cyanobacteria and Chloroplasts, energy that is captured by antennae pigments excites a reaction center chlorophyll. This causes it to emit a high energy electron, which is passed to an electron transport chain. In cyclic photophosphorylation, electrons emitted by photosystem I are returned to that photosystem. In non-cyclic photophosphorylation, the electrons used to replenish photosystems I are donated by radiant energy, excited photosystem II. Then, photosystem II replenishes its own electrons by stripping them from water, in return, producing oxygen. (Anderson, D. G., et al., 2016) On News.net, I found in the absence of oxygenic photosynthesis, atmospheric oxygen would eventually be depleted. In a complete reaction of oxygenic photosynthesis, six carbon dioxide molecules combine with twelve molecules of water in the presence of sunlight, which makes the energy for the reaction to happen. As a result of the reaction, a single glucose molecule, six oxygen molecules, and six water molecules are formed. (News, 2017)
According to Anderson, D. G. et al., anoxygenic photosynthetic bacteria have only a single photosystem. It cannot use water as an electron donor for reducing power. This is exactly why it is considered anoxygenic, it does not generate oxygen. Hydrogen gas, hydrogen sulfide, and organic compounds is what anoxygenic photosynthetic bacteria use as electron donors. (Anderson, D. G., et al., 2016) The way anoxygenic photosynthesize bacteria with the use of light energy is similar in the way plants use light energy. Both plants and anoxygenic photosynthesis bacteria, use carbon dioxide to create energy. But aside from having that in common they differ from how anoxygenic photosynthesis use only the use photosystem I for collecting energy from light and plants use both photosystems. (Study) According to our text book, there are two groups of anoxygenic photosynthetic bacteria. They are purple bacteria and green bacteria. The purple bacteria synthesize ATP using a photosystem similar to photosystem II in oxygenic photosynthesis of cyanobacteria and eukaryotes. Although this photosystem does not raise the electrons to an energy level that is high enough to reduce NAD+, so the cells must use an alternative mechanism to generate reducing power. They use a process called the reverse electron transport. In doing so, using ATP to run the electron transport chain in the reverse direction. Green bacteria have a photosystem that is similar to the photosystem I in oxygenic photosynthesis of cyanobacteria and eukaryotes. The electrons that are emitted can either reduce NAD+, or generate a proton motive force. (Anderson, D. G., et al., 2016)

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