Structure Of The Mitochondria Biology Essay

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Describe the structure of the mitochondria. Compare and contrast the inner and outer membrane and the intermembrane space and the matrix.

Mitochondria are large organelles made of proteins and phospholipids, enclosed within the outer and inner membranes involved in the production of energy to the cell. The space between the inner and outer membranes is the inter-membrane space. The mitochondrion is capable of changing its dynamic shape such as in rod shape or sausage shape, as well as fusing or splitting with another. The outer membrane is comprised of lipids and enzymes that provide the mitochondrion as its outer boundary. The membrane contains porins, protein structures that aid in the bypass of ions, and molecules such as ATP and ADP. The mitochondrion membrane is divided into the a compartment in the interior of the mitochondrion called matrix and a compartment in the outer and inner membrane called intermembrane space. The matrix is vital to the synthesis of ATP molecules, the mitochondrial DNA, tRNA and special mitochondrial ribosomes. The inter-membrane space consists of a gel-like matrix and proteins in the space initiating cell suicide and oxidative phosphorylation. The inner membrane is highly permeable to about all molecules and ions a well as oxygen, CO2 and water. Its highly complex structure comprises of electron transport system, ATP synthetase complex and transport proteins. In the interior surface area of the membrane is cristae, inwardly folded sheets that contain the mechanism required for aerobic respiration and ATP formation.

2. In glycolysis, what type of reactions do hexokinase and phosphofructokinase catalyze? In general, what is the importance of these reactions - or in other words what makes them unique in the glycolysis pathway (see figures 3.25, 3.31 and 5.6; 1 pt)?

The first step in glycolysis is phosphorylation of glucose by a family of enzymes called hexokinases to form glucose 6-phosphate (G6P). This reaction consumes ATP, but it acts to keep the glucose concentration low, promoting continuous transport of glucose into the cell through the plasma membrane transporters. In addition, it blocks the glucose from leaking out because the cell lacks transporters for G6P. Phosphofructokinase (PFK) is an enzyme that permanently transfers phosphate from ATP to fructose-6-phosphate. Due to the permanent reaction, PFK is the regulatory enzyme for glycolysis. Production of metabolic energy is no longer needed when ATP levels are high in the cell. Therefore, PFK is delayed by allosteric regulation via ATP, preventing the flow of carbohydrates in glycosis in closing the valve.

3. In general, how are fats and proteins utilized during cellular metabolism? Use Figure 5.8 as an initial guide (1 pt).

Proteins are biochemical catalysts which form cellular structural elements such as hydrogen and nitrogen, and play a vital role in gene expression. Protein is broken down into amino acids by digestion. If there is excess amino acids in the body, they are metabolized into glycogen or fat, resulting to the the use of energy metabolism. Thus, if amino acids are used for energy, their carbon skeletons is then converted to acetyl CoA. Subsequently, it will enter into the Krebs cycle for oxidation, creating ATP. CO2, water, ATP, urea and ammonia will be the final products of the protein catabolism. On the contrary, fats are oxidized by hydrolysis to fatty acids and glycerol. Next, the glycerol enters glycolysis and the fatty acids are broken into acetyl-CoA, which is supplied into the citric acid cycle. In result, the fatty acids release energy via oxidation due to additional amounts of oxygen in carbohydrates.

4. What two molecules combine in the TCA cycle to form Citrate? Where did each 'precursor' molecule come from (1 pt)?

The Citric Acid cycle begins with acetyl-CoA transferring its two-carbon acetyl group to the four-carbon acceptor compound called oxaloacetate to form a six-carbon compound called citrate. Acetly-CoA is created when from the reaction of pyruvate dehydrogenase. Oxaloacetate is created from a combination of pyruvate carboxylase and Malate dehydrogenase.

5. Would you expect to find the pyruvate dehydrogenase complex in an anaerobic bacterium? Explain why or why not and explain what task this complex performs (1.5 pts).

Pyruvate dehydrogenase complex, three enzyme complex that alter pyruvate into acetyl-CoA via pyruvate decarboxylation, involved in the oxidation of pyruvate. Since anaerobic bacterium only exists in oxygen-free environments you would not expect them to contain this complex.

6. What are high energy electrons and what is represented by an oxidation-reduction potential? Using this knowledge briefly explain the importance of Figure 5.14 and the role of the high energy electrons carried by NADH and FADH2 in the creation of ATP (3 points).

NADH+H+ enters from Stage II of carbohydrate metabolism to the ETC and oxidized to NAD+ along with its protins (hydrogen ions) into the matrix and its electrons (e-) going to cytochrome complex I. Cytochrome c acts a carrier, transporting electrons between large complexes. As the electrons enter cytochrome complex I, the complex proceeds into redox (reduction and oxidation). The reaction produces a proton pump within the cytochrome, forcing some protons from the matrix through the cytochrome and into the inter-membrane space. Subsequnetly, the electrons are trasnfered to carriers Q and NAD+ returns to its original source.

7. Why are the electron transport chain complexes referred to as proton pumps (1 pt)?

Electron transport chains are biochemical reactions that produce ATP. ATP is made by an enzyme called ATP synthase. ATP synthase is powered by a transmembrane proton gradient, which conduct protons from high to low concentration across the membrane. In essence working to pump protons through a proton channel which temporarily opens in the inner membrane.

8. How are NADH and FADH2 different when it comes to interacting with the ETC (1 pt)?

FADH2 enters from the TCA cycle to the ETC and proceeds to the cytochrome carrier Q. FADH2 is then oxidized to FAD along with its protons into the matrix and its electrons going to carrier Q. Carrier Q transports the electrons from FADH2 from cytochrome 1 to cytochrome complex 2. Next, the electrons are moved to the cytochrome complex 2 and proceeds through redox (reduction and oxidation). In result, creating a proton pump, forcing protons from the matrix via cytochrome complex 2 into the intermembrane space of the mitochondrion. Finally, the FAD returns to the TCA cycle.

NADH+H+ enters from Stage II of carbohydrate metabolism to the ETC and oxidized to NAD+ along with its protins (hydrogen ions) into the matrix and its electrons (e-) going to cytochrome complex I. Cytochrome c acts a carrier, transporting electrons between large complexes. As the electrons enter cytochrome complex I, the complex proceeds into redox (reduction and oxidation). The reaction produces a proton pump within the cytochrome, forcing some protons from the matrix through the cytochrome and into the inter-membrane space. Subsequnetly, the electrons are trasnfered to carriers Q and NAD+ returns to its original source.

9. What does the proton-motive force represent (you don't need to explain the formula; 1 pt)?

A proton-motive force represents the energy that is generated by the transfer of protons or electrons across an energy-transducing membrane.

10. Describe the structure of ATP synthase and the binding change hypothesis of mitochondrial ATP production (2.5 points).

ATP synthase is made up of two portions, F1 and F0. The FO portion is within the membrane of the mitochnodria and the F1 portion is located inside the matrix of the mitochondria. In the biding change hypothesis of ATP formation, the binding mechanism change involves the active site of B subunit cycling between three states. In the "open" state, ADP and phosphate enter the active site. Next, the protein closes around the molecules and binds them loosely, entering the "loose" state. The enzyme proceeds into another change in shape and forces these molecules together with the active site resulting into the "tight" state. ATP molecule is tightly binded to the active site. Finally, the active site cycles returns to the open state, releasing ATP and binding more ADP and phosphate.

11. Describe the structure of a chloroplast and give a brief summary of its evolutionary origin (1.5 pts).

Chloroplast is an organelle found during photosynthesis in eukaryotes. The organelle is enclosed with a double membrane and a mixture of enzyme and water in the inner membrane. This is refered to as the stroma, as the site for dark reactions, also known as Calvin cycle. Within the stroma, are tightly packed sacs; each stack named granum and each flattened sacs composing of the granum is called thylakoid. Each thylakoid has associated proteins and photosystem sequence. The photosystem contain chlorophyll and other pigments associated in the thylakoid membrane are the site for the light reation in which light energy is converted into chemical energy for the Calvin cycle in the dark reaction. Chloroplasts are believed to have risen as free living bacteria that became endosymbiont with the ancestors of photosynthetic eukaryotes. An endosymbiont is any organism that lives within the body or cells of another organism.

12. Briefly describe the experiment performed by Ruben and Kamen and describe what this experiment helped to prove (this experiment can be found in the textbook; 1 pt).

Ruben and Kamen bombarded graphite in the cyclotron, a type of particle accelerator,in hopes of producing a radioactive isotope of carbon that could be used as a tracer in investigating chemical reactions in photosynthesis. Their experiment resulted in production of carbon-14.

13. What is the photosynthetic role of the light-harvesting antenna pigments (1 pt)?

In photosynthetic systems a variable number of pigments act as light-harvesting antenna to absorb and direct solar energy to photochemical reaction centers. The effectiveness of the reaction centers depends on the efficient transfer of excitation energy from these antenna molecules.

14. In plants, what are photosystems, what is the significance of the primary P680 and P700 pigments, and how do these fit into the Z scheme arrangement depicted in Figure 6.10 of your text (2 pts)?

Photosystems are protein complexes that are found in the thylakoid membranes of plants. They are involved in photosynthesis as enzymes which use light to reduce molecules. There are two families of photosystems. Within photosystem type 1 is the P700 reaction center. Its absorption spectrum peaks at 700 nm. When photosystem I absorbs light, an electron is excited to a higher energy level in the P700 chlorophyll. These electrons are moved in pairs in an oxidation/reduction process from P700 to electron acceptors. Within photosystem type II is the P680 reaction center. Its absorption spectrum peaks at 680nm.

15. What is photolysis and what is its significance during photosynthesis (1 pt)?

Photolysis is defind as the splitting or decomposition of a chemical compound by means of light energy or photons. Photolysis is the part of photosynthesis that occurs in the granum of a chloroplast where light is absorbed by chlorophyll, turned into chemical energy, and used to split apart the oxygen and hydrogen in water. The oxygen is released as a byproduct while the reduced hydrogen acceptor makes its way to the second stage of photosynthesis, the Calvin cycle.

16. What is photophosphorylation and how is this accomplished by PSII and PSI (1.5 pt)?

Photophosphorylation is the production of ATP using the energy of sunlight. In photophosphorylation, light energy is used to create a high-energy electron donor and a lower-energy electron acceptor. Electrons then move spontaneously from donor to acceptor through an electron transport chain.

When a special chlorophyll molecule of PSII absorbs a photon, an electron in this molecule attains a higher energy level. Because this state of an electron is very unstable, the electron is transferred from one to another molecule creating a chain of redox reactions, called an electron transport chain (ETC). The electron flow goes from PSII to cytochrome b6f to PSI. In PSI the electron gets the energy from another photon. The final electron acceptor is NADP. Cytochrome b6f and ATP synthase are working together to create ATP. This process is called photophosphorylation

17. What is the function of Rubisco (1 pt)?

In the Calvin Cycle of photosynthesis, the enzyme rubisco grabs CO2 and incorporates it into RuBP (commonly called carbon fixation). The cycle continues until one G3P is made; a precursor to glucose.

18. What is the usefulness or function of the 12 GAP molecules produced by the fixation of 6 CO2 molecules via the Calvin cycle (1 pt)?

The function is for the manufacturing of carbohydrates

19. Why it is believed that the increased levels of CO2 in our atmosphere over the last century have lead to an increase in crop yields? Explain (1 pt).

20. What is the function of phosphoenolpyruvate carboxylase and what advantage is given to plants that contain this enzyme? Explain why (1 pt)

Phosphoenolpyruvate carboxylase is an enzyme in the family of carboxy-lyases that catalyzes the addition of CO2 to phosphoenolpyruvate (PEP) to form the four-carbon compound oxaloacetate. Carbon fixation via PEP carboxylase assimilates the available CO2 into a four-carbon compound (oxaloacetate, which is further converted to malate) that can be stored or shuttled between plant cells. This allows for a separation of initial CO2 fixation by contact with air and secondary CO2 fixation into sugars by RuBisCO during the light-independent reactions of photosynthesis.

In succulent CAM plants adapted for growth in very dry conditions, PEP carboxylase fixes CO2 during the night when the plant opens its stomata to allow for gas exchange. During the day time, the plant closes the stomata to preserve water and releases CO2 inside the leaf from the storage compounds produced during the night. This allows the plants to thrive in dry climates by conducting photosynthesis without losing water through open stomata during the day.