Mitochondria are rod-shaped structures that are enclosed within two membranes - the outer membrane and the inner membrane. The membranes are made up of phospholipids and proteins. The space in between the two membranes is called the inter-membrane space. The structure of the various components of mitochondria are as follows: The outer membrane is a relatively simple phospholipid bilayer, containing protein structures called porins. Ions, nutrient molecules, ATP, ADP, etc. can pass through the outer membrane with ease. The inner membrane is freely permeable only to oxygen, carbon dioxide, and water. Its structure is highly complex, including all of the complexes of the electron transport system, the ATP synthetase complex, and transport proteins. There are folds present which are organized into lamillae (layers), called the cristae. The cristae greatly increase the total surface area of the inner membrane which makes room for many more of the above-named structures than if the inner membrane were shaped like the outer membrane. The membranes create two compartments. The intermembrane space is the region between the inner and outer membranes. It has an important role in the primary function of mitochondria, which is oxidative phosphorylation. The matrix is a complex mixture of enzymes that are important for the synthesis of ATP molecules, special mitochondrial ribosomes, tRNAs and the mitochondrial DNA. Besides these, it has oxygen, carbon dioxide and other recyclable intermediates.
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)?
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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 a glycolytic enzyme that catalyzes the irreversible transfer of a phosphate from ATP to fructose-6-phosphate. Because this reaction is irreversible, PFK is the key regulatory enzyme for glycolysis. When ATP levels are high in the cell, the cell no longer needs metabolic energy production to occur. In this case, PFK's activity is inhibited by allosteric regulation by ATP itself, closing the valve on the flow of carbohydrates through glycolysis.
3. In general, how are fats and proteins utilized during cellular metabolism? Use Figure 5.8 as an initial guide (1 pt).
Proteins contain carbon, hydrogen, oxygen, nitrogen , and sometimes other atoms. They form the cellular structural elements, are biochemical catalysts, and are important regulators of gene expression . Digestion breaks protein down to amino acids. If amino acids are in excess of the body's biological requirements, they are metabolized to glycogen or fat and subsequently used for energy metabolism. If amino acids are to be used for energy their carbon skeletons are converted to acetyl CoA, which enters the Krebs cycle for oxidation, producing ATP. The final products of protein catabolism include carbon dioxide, water, ATP, urea, and ammonia.
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 is a complex of three enzymes that transform pyruvate into acetyl-CoA by a process called pyruvate decarboxylation which involves 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).
7. Why are the electron transport chain complexes referred to as proton pumps (1 pt)?
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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)?
NADH+H+ arrives from Stage II of carbohydrate metabolism or Stage III (TCA cycle) to the ETC and immediately oxidizes to NAD+ with its protons (hydrogen ions) going into the matrix and its electrons (e-) going to cytochrome complex 1. As the electrons arrive on cyctrochrome complex 1 the complex immediately goes through redox (reduction and oxidation). This reaction creates a proton pump within the cytochrome, pumping some protons from the matrix through the cytochrome into the intermembrane space. The electrons now transfer to mobile carrier Q and NAD+ returns to its original source.
FADH2 arrives from the TCA cycle to the ETC and goes directly to cytochrome mobile carrier Q. FADH2 oxidizes to FAD with its protons going into the matrix and its electrons going to mobile carrier Q. Mobile carrier Q shuttles the electrons from FADH2 (and from cytochrome 1) to cytochrome complex 2. The electrons are transferred to cytochrome complex 2 and it immediately goes through redox (reduction and oxidation). This creates a proton pump, pumping protons from the matrix through cytochrome complex 2 directly into the intermembrane space of the mitochondrion. FAD returns to the TCA cycle.
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 above the membrane, inside the matrix of the mitochondria.
The binding change mechanism involves the active site of a Î² subunit cycling between three states. In the "open" state, ADP and phosphate enter the active site. The protein then closes up around the molecules and binds them loosely - the "loose" state. The enzyme then undergoes another change in shape and forces these molecules together, with the active site in the resulting "tight" state binding the newly-produced ATP molecule with very high affinity. Finally, the active site cycles back to the open state, releasing ATP and binding more ADP and phosphate, ready for the next cycle of ATP production.
11. Describe the structure of a chloroplast and give a brief summary of its evolutionary origin (1.5 pts).
The chloroplast is the organelle where photosynthesis occurs in photosynthetic eukaryotes. The organelle is surrounded by a double membrane. Inside the inner membrane is a complex mix of enzymes and water. This is called stroma and is important as the site of the dark reactions, more properly called the Calvin cycle. Within in the stroma is a network of stacked sacs. Each stack is called a granum and each of the flattened sacs which make up the granum is called a thylakoid. Each thylakoid has a series of photosystems and associated proteins. The photosystems contain chlorophyll and other pigments and all these associated structures in the thylakoid membrane are the site for the light reactions in which light energy is converted to chemical energy needed for the Calvin cycle in the dark reaction.
Chloroplasts are believed to have arisen 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)?
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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 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.