Metabolic Processes Flashcards
Identify and describe the two components of metabolism.
Anabolic reactions are when smaller molecules are made into larger molecules.
Catabolic reactions are when larger molecules are broken down into smaller molecules.
Identify and describe different forms of kinetic and potential energy.
Kinetic energy is the energy of motion. Ions and molecules are in a constant state of motion in living things. This includes electric, thermal, mechanical, and electromagnetic.
Potential energy is energy stored in the bond of molecules. It includes chemical, gravitational, and elastic.
Explain how the Laws of Thermodynamics apply to living things.
The first law of thermodynamics is energy cannot be created or destroyed. This applies to living things because it is not consumed but changes forms. Plants take energy from the sun and change it into a usable form of energy for them. The energy is then broken down by animals to be used for energy.
The second law of thermodynamics states that the transfer of energy is not always 100% efficient. This is due to entropy. This is a measure of disorder in a closed system. All of the available energy is not useful to all organisms. Plants are a good example of this. Not 100% of light is absorbed by plants, some is lost as heat energy and to the surroundings.
Distinguish between endothermic and exothermic reactions and draw diagrams that show the changes in potential energy associated with each reaction type.
Endothermic reactions absorb more energy when chemical bonds are straining and breaking than released during formation.
Exothermic reactions release more energy when reactant bonds are straining and breaking than they release during bond formation.
Distinguish between endergonic and exergonic reactions and draw diagrams that show the changes in free energy associated with each reaction type.
Endergonic reactions have positive free energy and absorb free energy.
Exergonic reactions have negative free energy and release free energy.
Explain why reactions in the living world are coupled and give at least one specific example of reaction coupling from the living world.
Reactants couple because organisms appear to obey the Second Law of Thermodynamics as they move, grow, repair, and reproduce. The free energy required for living things is often produced by exergonic reactions that are coupled with an endergonic reaction. Synthesizing glutamine requires free energy and breaking down ATP gives off energy. They are coupled together to balance each other out. 
Describe the structure and function of ATP.
ATP consists of the nitrogen-containing base adenine, a five-carbon ribose sugar, and three phosphate groups. The negative charges of the phosphate groups create a high-energy bond between the terminal phosphate and the rest of the molecule. When this bond is hydrolyzed energy is released to support life processes. ATP is the energy currency of cells. It can be earned, spent, and saved. ATP captures chemical energy obtained from the breakdown of food molecules.
Identify and describe the four phases of aerobic cellular respiration in terms of their reactants, products and the locations where they occur.
Glycolysis~ The breakdown of glucose by hexokinase and two ATP into glucose-Pi, then into fructose-Pi, and then into the highly unstable fructose 1,6-bisphosphate. It is then broken down by aldose into 2 G3P and DHAP. The G3P turns into 1,3-BPGA. During this 2 NAD and 2 NADH are released. Finally, the 1,3-BPGA is broken down into 4 ATP and 2 pyruvates. The products are? This occurs in the cytoplasm.
Transition Reaction~ The pyruvate has its carboxyl group removed and this leaves behind a 2-carbon molecule and 2 CO2. The two-carbon molecule is oxidized using NAD+ to pick up the lost electrons. The oxidized two carbon molecules then attach to Coenzyme A to create Acetyl CoA. The products are? This occurs in the inner mitochondrial matrix.
Krebs Cycle~ Acetyl CoA enters the cycle. NADH is turned into NAD+, and CO2 is released. This happens twice. ADP and Pi are then turned into ATP. FAD+ is turned into FADH. Finally, NAD+ is turned into NADH and no CO2 is released. The products are? This occurs in the mitochondrial matrix.
Electron Transport Chain and Chemiosmosis~ This is the final step. NADH becomes NAD+, and the lost electrons travel through the electron transport chain. Later down the line, electrons from FADH become FAD+ will also join. The products at the end, ½ O2, 2 electrons, and 2H+ molecules, will form water. The extra energy will help move H+ molecules from the matrix into the intermembrane space along their electrochemical gradient. In the end, the high concentration of H+ molecules will go through ATP synthase, which spins a protein-made rotor that squishes ADP and Pi together to form ATP. The products are? This occurs in the mitochondrial matrix and intermembrane space.
Describe the investment, cleavage and energy harvest phases of glycolysis.
Investment~ The breakdown of glucose by hexokinase and two ATP into glucose-Pi, then into fructose-Pi, and then into the highly unstable fructose 1,6-bisphosphate.
Cleavage~ It is then broken down by aldose into 2 G3P and DHAP. The G3P turns into 1,3-BPGA. During this 2 NAD and 2 NADH are released.
Energy Harvest~ Finally, the 1,3-BPGA is broken down into 4 ATP and 2 pyruvates.
Explain the relationship between glycolysis and two types of anaerobic fermentation and draw diagrams to illustrate each type of fermentation.
Fermentation occurs at the end of glycolysis when oxygen is lacking.
Lactic Acid Fermentation~ This is when pyruvate is converted into lactic acid using the enzyme lactate dehydrogenase. This supports the production of ATP despite the lack of oxygen in the system. An increase in lactic acid can cause a change in pH that results in lactic acidosis. To avoid this lactic acid is sent back to the liver where it is converted back to glucose in the Cori Cycle. This costs 6 ATP, a debt to the body that must be repaid.
Ethanol Fermentation~ This is when pyruvate is converted to acetaldehyde and then into ethanol. This is a form of alcohol. It uses alcohol dehydrogenase to catalyze the reaction.
Explain how electron transport chains are used to create electrochemical gradients of hydrogen ions that support ATP synthesis in cellular respiration and photosynthesis and identify the similarities and differences between the two types of electron transport chains.
Cellular Respiration~ As electrons go across the electron transport chain, they give off free energy that can be used by H+ ions to travel from the matrix into the intermembrane space. This creates a large amount of H+ ions giving it a positive charge on one side creating an electrochemical gradient. Because they are so highly concentrated, they want to move to a place of lesser concentration so they move through ATP synthase to spin a rotor that then compresses ADP and Pi together to form ADP. It occurs in the mitochondria. It comes from the breakdown of organic molecules.
Photosynthesis~ Electrons enter the chain from light energy. The photons then excite and break the bonds in the Mg molecule in the center of the activation center. These electrons are excited and are then passed to an acceptor molecule. It is then replaced by an electron from water. When water is broken down it releases electrons, ½ O2 molecule, and 2 H+ molecules. It takes place in the mitochondria and is from light energy and water.
Oxidative phosphorylation has two parts: the electron transport chain (ETC) and chemiosmosis. The ETC is a collection of proteins bound to the inner mitochondrial membrane and organic molecules, which electrons pass through in a series of redox reactions, and release energy. The energy released forms a proton gradient, which is used in chemiosmosis to make a large amount of ATP by the protein ATP-synthase.
Photosynthesis is a metabolic process that converts light energy into chemical energy to build sugars. In the light-dependent reactions, light energy and water are used to make ATP, NADPH, and oxygen (O2). The proton gradient used to make the ATP forms via an electron transport chain. In the light-independent reactions, sugar is made from the ATP and NADPH from the previous reactions.
Identify the components required for the light dependent reactions, where they are located in the chloroplast and how these components support a transfer of light energy to chemical energy by photoexcitation of electrons.
Light-dependent reactions occur in the thylakoid membrane of the chloroplasts. Here light and water are both required. This process does not produce glucose, but the ATP and NADPH that support the dark reactions in producing glucose. The light goes into the pigmentation receptors, here the photons break the bond of Mg in the middle of the activation center. This releases electrons that then get excited in the P680 and get accepted by an acceptor molecule, it is then replaced by the electrons given off by the breakdown of water. Water goes into the P680, it is broken down into electrons, 2 H+ molecules, and ½ an O2 molecule. Then it goes through the membrane. When it gets through the membrane it will enter the P700 it will join with a special pair of chlorophyll molecules in the reaction center. When light energy is absorbed by pigments and passed inward to the reaction center, the electron in P700 is boosted to a very high energy level and transferred to an acceptor molecule. The special pair’s missing electron is replaced by a new electron from P680, arriving via the electron transport chain. NADPH formation, the high energy electron travels down a short second leg of the electron transport chain. At the end of the chain, the electron is passed to NADP+ along with a second electron from the same pathway, to make NADPH. The net effect of these steps is to convert light energy into chemical energy in the form of ATP and NADPH. The ATP and NADPH from the light-dependent reactions are used to make sugars in the next stage of photosynthesis, the Calvin Cycle.
Compare non-cyclic photophosphorylation and cyclic photophosphorylation in terms of the structures involved in these processes and what they produce.
Non-cyclic phosphorylation is the primary pathway, it involves both photosystems, NADPH, and ATP. Water is split by photosystem 2 on the side of the membrane facing the thylakoid space. The diffusion of H+ from the thylakoid space back to the stroma powers ATP synthase. ATP and NADPH are produced on the side facing the stroma, where the Calvin cycle takes place.
Cyclic photophosphorylation uses only photosystem 1 and produces only ATP. Cyclic photophosphorylation generates surplus ATP satisfying the higher demand in the Calvin cycle.
Explain how the light-dependent and light-independent reactions are interdependent.
Without the NADPH and ATP produced in the light-dependent reactions, the Calvin cycle couldn’t happen. The 3-PGA could not be broken down without ATP and NADPH and make it into G3P which will produce glucose and continue the cycle with RuBP. The light independent reactions will then supply NADP+ and ADP to the light-independent reactions, it uses these to synthesize further into NADPH and ATP.
Describe the three phases of the light-independent reactions in terms of carbon fixation and the rearrangement of organic molecules required to produce glucose.
Phase One Carbon Fixation~ RuBP and CO2 bind to the active site of the RuBisCO enzyme. The reaction is catalyzed by RuBisCO and produces an unstable six carbon intermediate. The six carbon intermediate is easily hydrolysed to form 2 of 3-PGA.
Phase Two The Reduction Reactions~ PO4 is transferred from ATP to the 3PGA forming 1,3 BPGA. H+ and electrons are transferred from NADPH to the 1,3 BPGA forming G3P. One G3P leaves the cycle to become glucose and the other five are recycled.
Phase Three Regeneration of RuBP~ The recycled G3P are used to regenerate the RuBP. It becomes 3 RuBP using 3 ATP.
Define photorespiration and explain why it is a problem for a plant.
Early photoautotrophs evolved RuBisCO at a time when oxygen concentration was low. As oxygen concentration in the oceans and atmosphere increased, a problem developed, O2 inhibits the active site on the RuBisCO enzyme. Because the light independent reactions are cyclical, plants had to process phosphoglycolate to keep the rest of the reaction pathway going. We call this process photorespiration because the plant produces CO2 rather than consuming it during the light independent reactions. Because no G3P leaves the cycle during photorespiration it does not produce any sugar. The degree to which RuBisCO is inhibited by O2 is proportional to temperature. This means that plants living in warm environments had to evolve strategies to subvert photorespiration.
Alternative Mechanisms of Carbon Fixation.
The enzyme RuBisCO evolved in the low oxygen environment of ancient Earth. Photorespiration occurs when RuBisCo acts as an oxygenase enzyme. It catalyzes a reaction between oxygen and RuBP that consumes ATP and releases organic carbon from the plant. Some plants that survive in warm environments demonstrate structural solutions to the problem of photorespiration. C4 plants, like corn and sugarcane, fix CO2 as malate in their mesophyll cells. The mesophyll cells isolate cells closer to the vascular bundle, called bundle sheath cells, from the air spaces of the spongy mesophyll. The malate produced in the mesophyll cells is hydrolysed to pyruvate and CO2 in the bundle sheath cells providing an input of carbon to the RuBisCo sequestered there. Some plants that survive in warm environments demonstrate temporal solutions to the problem of photorespiration. CAM plants, like cacti and aloe, fix CO2, as malate but rather than using a separate cell they carry out carbon fixation at night when temperatures are typically lower. The malate is stored in the large vacuoles of the cactus cells. The malate produced at night is hydrolysed to pyruvate and CO2 during the day providing a CO2 input to the light independent reactions. A key enzyme in both C4 and CAM plants is PEP carboxylase.
