chapter 8 Introduction to metabolism
Overview
This chapter focuses on how matter and energy are transformed by an organism's metabolism and what role enzymes play in the process. The chemistry of life is organized into metabolic pathways that can be catabolic or anabolic, releasing or consuming energy. These pathways are subject to the laws of thermodynamics, meaning energy can not be destroyed and every energy transfer increases the entropy (disorder) of the universe. Organisms can increase their order as long as the order around them decreases when, for example, spontaneous processes that do not require an input of energy occur.
Free energy is the portion of a system's energy that is available to perform work and spontaneous processes decrease the amount of free energy (-delta G). Systems are more stable with less free energy, so spontaneous processes are considered energetically favorable. Exergonic reactions occur spontaneously and release free energy, while endergonic reactions are non spontaneous and absorb free energy.
Cellular work is powered by the coupling of exergonic reactions to endergonic reactions by ATP, which is called energy coupling. The energy released by ATP hydrolysis can be harnessed to drive reactions that are endergonic. ATP is especially useful since it can constantly be regenerated in ATP synthesis and hydrolysis.
Enzymes act as biological catalysts that speed up reactions without being consumed. Enzymes must lower the activation energy (energy needed to contort reactant molecules so bonds can break) for the reaction to speed up. They are very specific to certain reactions and do not affect the change in free energy of a reaction. They are also specific to the substrate they bind to at the active site. The R groups of amino acids that make up the active site catalyze the conversion of the substrate to product.
Local conditions will affect enzyme activity: temperature, pH, salinity, cofactors, and inhibitors. Enzymes have optimal temperature, pH, and salinity, and may denature if environmental conditions are not favorable. Cofactors are non protein helpers that activate catalytic activities. Inhibitors impede enzymatic reactions by blocking the substrate from the active site (competitive) or changing the enzyme's shape by binding to another part of the enzyme (noncompetitive).
Lastly, the regulation of enzyme activity is necessary to control metabolism. Allosteric regulation affects protein's function at one site by the binding of a regulatory molecule to a separate site. An allosteric activator binds to regulatory site and stabilizes the active shape of an enzyme, while the allosteric inhibitor stabilizes the inactive form. The interaction of the subunits of an enzyme allows only one regulator to be necessary (called cooperativity). Feedback inhibition regulates enzyme activity by the inhibitory binding of the end product to the enzyme that acts earlier on in the pathway.
Big Ideas
2.A.1 All living systems require constant input of free energy.
4.B.1 Interactions between molecules affect their structure and function.
Artifact
Click here to view the laboratory report on AP Lab #13: Enzymes.
Reflection
I picked this lab because it was a straightforward and hands-on way to show students how enzyme activity can be affected by numerous factors. Students acted as enzymes using everyday materials like toothpicks and tape, which contributed to my understanding of enzyme function and provided a simple way to master the concept. As one of the first labs performed in class, this activity offered a simple learning process in regard to the function of enzymes as well as
Study Tool
Videos are my favorite study tools and help to visualize small, and at times complex, processes on the cellular level. Here is one about enzyme function:
This chapter focuses on how matter and energy are transformed by an organism's metabolism and what role enzymes play in the process. The chemistry of life is organized into metabolic pathways that can be catabolic or anabolic, releasing or consuming energy. These pathways are subject to the laws of thermodynamics, meaning energy can not be destroyed and every energy transfer increases the entropy (disorder) of the universe. Organisms can increase their order as long as the order around them decreases when, for example, spontaneous processes that do not require an input of energy occur.
Free energy is the portion of a system's energy that is available to perform work and spontaneous processes decrease the amount of free energy (-delta G). Systems are more stable with less free energy, so spontaneous processes are considered energetically favorable. Exergonic reactions occur spontaneously and release free energy, while endergonic reactions are non spontaneous and absorb free energy.
Cellular work is powered by the coupling of exergonic reactions to endergonic reactions by ATP, which is called energy coupling. The energy released by ATP hydrolysis can be harnessed to drive reactions that are endergonic. ATP is especially useful since it can constantly be regenerated in ATP synthesis and hydrolysis.
Enzymes act as biological catalysts that speed up reactions without being consumed. Enzymes must lower the activation energy (energy needed to contort reactant molecules so bonds can break) for the reaction to speed up. They are very specific to certain reactions and do not affect the change in free energy of a reaction. They are also specific to the substrate they bind to at the active site. The R groups of amino acids that make up the active site catalyze the conversion of the substrate to product.
Local conditions will affect enzyme activity: temperature, pH, salinity, cofactors, and inhibitors. Enzymes have optimal temperature, pH, and salinity, and may denature if environmental conditions are not favorable. Cofactors are non protein helpers that activate catalytic activities. Inhibitors impede enzymatic reactions by blocking the substrate from the active site (competitive) or changing the enzyme's shape by binding to another part of the enzyme (noncompetitive).
Lastly, the regulation of enzyme activity is necessary to control metabolism. Allosteric regulation affects protein's function at one site by the binding of a regulatory molecule to a separate site. An allosteric activator binds to regulatory site and stabilizes the active shape of an enzyme, while the allosteric inhibitor stabilizes the inactive form. The interaction of the subunits of an enzyme allows only one regulator to be necessary (called cooperativity). Feedback inhibition regulates enzyme activity by the inhibitory binding of the end product to the enzyme that acts earlier on in the pathway.
Big Ideas
2.A.1 All living systems require constant input of free energy.
4.B.1 Interactions between molecules affect their structure and function.
Artifact
Click here to view the laboratory report on AP Lab #13: Enzymes.
Reflection
I picked this lab because it was a straightforward and hands-on way to show students how enzyme activity can be affected by numerous factors. Students acted as enzymes using everyday materials like toothpicks and tape, which contributed to my understanding of enzyme function and provided a simple way to master the concept. As one of the first labs performed in class, this activity offered a simple learning process in regard to the function of enzymes as well as
Study Tool
Videos are my favorite study tools and help to visualize small, and at times complex, processes on the cellular level. Here is one about enzyme function:
chapter 9 Cellular respiration & fermentation
Overview
Chapter nine explains the steps of cellular respiration and fermentation. Cellular respiration refers to aerobic respiration, a catabolic pathway in which oxygen (and the organic fuel) is consumed with the reaction. Redox reactions transfer electrons and drive cellular respiration. Reduction is the addition of electrons to a substance and oxidation is the removal of electrons from a substance. The reducing agent acts as an electron donor and the oxidizing agent acts as the electron acceptor. The organic fuel broken down in cellular respiration is like a reservoir of electrons with hydrogen atoms that the coenzyme NAD+ accepts and transfers. The coenzyme cycles easily between NAD+ and NADH, its reduced form. Dehydrogenase is the enzyme that removes the H-atoms from the substrate and delivers the two electrons with one H-atom to NAD+. The electron transport chain is what breaks the fall of electrons to oxygen into several energy-releasing steps. It is found on the inner membrane of the mitochondrion and allows the electrons to move down the energy gradient from glucose to oxygen.
Glycolysis is the first step of respiration and yields 2 ATP and 2 NADH by splitting glucose into two 3-Carbon molecules of pyruvate. This process does not require oxygen and has two phases: the energy investment phase, in which the cell spends ATP and the energy payoff phase, in which ATP is made by substrate-level phosphorylation and NAD+ turning into NADH. Substrate-level phosphorylation is a mode of ATP synthesis when an enzyme transfers a phosphate group from a substrate to ADP.
After glycolysis, pyruvate is oxidized to acetyl CoA in the mitochondrion, linking glycolysis to the citric acid cycle. Pyruvate oxidation yields 2 NADH and releases 2 CO₂. The citric acid cycle, also called the Krebs cycle oxidizes the organic fuel from pyruvate and yields 1 ATP, 1 FADH₂, 3 NADH, 2 CO₂, and one C4 molecule per turn. A glucose molecule, however requires two turns of the cycle.
The next step is oxidative phosphorylation, in which chemiosmosis couples electron transport to ATP synthesis. Each component of the electron transport chain is reduced when electrons are accepted from the uphill neighbor and returns to the oxidized form after the electrons are passed on. With each electron transfer, H-atoms are pumped into the inter membrane space of the mitochondrion, which creates an H+ gradient. FADH₂ and NADH from earlier on supply the electrons for the chain. At the end of the chain, oxygen picks up the electrons and 2 H+, forming H20, which is released. Chemiosmosis is the process where energy stored as the H+ gradient across the membrane is harnessed to drive work, like ATP synthesis. ATP synthase is the enzyme that uses the gradient to make ATP from ADP and a phosphate group. The energy stored as the proton-motive force couples the redox reactions of the electron transport chain to ATP synthesis.
Glycolysis produces 2 ATP molecules for one glucose, as does the citric acid cycle. Oxidative phosphorylation, on the other hand, produces about 26-28 ATP, depending on the electron shuttle.
Fermentation is an extension of glycolysis, allowing the continuous generation of ATP without oxygen, when sufficient NAD+ is present and able to be regenerated. In alcohol fermentation, pyruvate is converted to ethanol when CO₂ is released and NADH reduces the product. In lactic acid fermentation, pyruvate is reduced by NADH to form lactate and no CO₂ is released. Fermentation, cellular respiration, and anaerobic respiration all use glycolysis to generate ATP with NAD+, but have different mechanisms and final electron acceptors to oxidize NADH back to NAD+. Obligate anaerobes are organisms that carry out only fermentation or anaerobic respiration and don't survive in the presence of oxygen. Facultative anaerobes are organisms that make enough ATP to survive using fermentation or respiration, like muscle cells.
Big Ideas
2.A.1 All living systems require constant input of free energy.
2.A.2 Organisms capture and store free energy for use in biological processes.
Artifact
Click here to see notes from class on the stages of cellular respiration:
Chapter nine explains the steps of cellular respiration and fermentation. Cellular respiration refers to aerobic respiration, a catabolic pathway in which oxygen (and the organic fuel) is consumed with the reaction. Redox reactions transfer electrons and drive cellular respiration. Reduction is the addition of electrons to a substance and oxidation is the removal of electrons from a substance. The reducing agent acts as an electron donor and the oxidizing agent acts as the electron acceptor. The organic fuel broken down in cellular respiration is like a reservoir of electrons with hydrogen atoms that the coenzyme NAD+ accepts and transfers. The coenzyme cycles easily between NAD+ and NADH, its reduced form. Dehydrogenase is the enzyme that removes the H-atoms from the substrate and delivers the two electrons with one H-atom to NAD+. The electron transport chain is what breaks the fall of electrons to oxygen into several energy-releasing steps. It is found on the inner membrane of the mitochondrion and allows the electrons to move down the energy gradient from glucose to oxygen.
Glycolysis is the first step of respiration and yields 2 ATP and 2 NADH by splitting glucose into two 3-Carbon molecules of pyruvate. This process does not require oxygen and has two phases: the energy investment phase, in which the cell spends ATP and the energy payoff phase, in which ATP is made by substrate-level phosphorylation and NAD+ turning into NADH. Substrate-level phosphorylation is a mode of ATP synthesis when an enzyme transfers a phosphate group from a substrate to ADP.
After glycolysis, pyruvate is oxidized to acetyl CoA in the mitochondrion, linking glycolysis to the citric acid cycle. Pyruvate oxidation yields 2 NADH and releases 2 CO₂. The citric acid cycle, also called the Krebs cycle oxidizes the organic fuel from pyruvate and yields 1 ATP, 1 FADH₂, 3 NADH, 2 CO₂, and one C4 molecule per turn. A glucose molecule, however requires two turns of the cycle.
The next step is oxidative phosphorylation, in which chemiosmosis couples electron transport to ATP synthesis. Each component of the electron transport chain is reduced when electrons are accepted from the uphill neighbor and returns to the oxidized form after the electrons are passed on. With each electron transfer, H-atoms are pumped into the inter membrane space of the mitochondrion, which creates an H+ gradient. FADH₂ and NADH from earlier on supply the electrons for the chain. At the end of the chain, oxygen picks up the electrons and 2 H+, forming H20, which is released. Chemiosmosis is the process where energy stored as the H+ gradient across the membrane is harnessed to drive work, like ATP synthesis. ATP synthase is the enzyme that uses the gradient to make ATP from ADP and a phosphate group. The energy stored as the proton-motive force couples the redox reactions of the electron transport chain to ATP synthesis.
Glycolysis produces 2 ATP molecules for one glucose, as does the citric acid cycle. Oxidative phosphorylation, on the other hand, produces about 26-28 ATP, depending on the electron shuttle.
Fermentation is an extension of glycolysis, allowing the continuous generation of ATP without oxygen, when sufficient NAD+ is present and able to be regenerated. In alcohol fermentation, pyruvate is converted to ethanol when CO₂ is released and NADH reduces the product. In lactic acid fermentation, pyruvate is reduced by NADH to form lactate and no CO₂ is released. Fermentation, cellular respiration, and anaerobic respiration all use glycolysis to generate ATP with NAD+, but have different mechanisms and final electron acceptors to oxidize NADH back to NAD+. Obligate anaerobes are organisms that carry out only fermentation or anaerobic respiration and don't survive in the presence of oxygen. Facultative anaerobes are organisms that make enough ATP to survive using fermentation or respiration, like muscle cells.
Big Ideas
2.A.1 All living systems require constant input of free energy.
2.A.2 Organisms capture and store free energy for use in biological processes.
Artifact
Click here to see notes from class on the stages of cellular respiration:
cellular_respiration.pdf | |
File Size: | 232 kb |
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Reflection
The drawing that was done in class especially helped me to understand cellular respiration because I drew the process on paper while it was being explained. The colors and organization of the picture were helpful in separating the different steps and components of the process. The charts summarized what was being used and produced for each step. This kind of visual learning helps many students to gain a more imaginable portrayal of the process.
Study Tool
The drawing that was done in class especially helped me to understand cellular respiration because I drew the process on paper while it was being explained. The colors and organization of the picture were helpful in separating the different steps and components of the process. The charts summarized what was being used and produced for each step. This kind of visual learning helps many students to gain a more imaginable portrayal of the process.
Study Tool
chapter 10 photosynthesis
Overview
Photosynthesis is the process that converts light energy into chemical energy, which is essential to all life. Autotrophs are the producers that sustain themselves without consuming other organisms. Heterotrophs (consumers) survive on the compounds made by other organisms and can not make their own food.
The process of photosynthesis takes place in the chloroplasts of plants, in the mesophyll tissue inside the leaf. The reaction is: 6 CO2 + 12 H2O + light energy -----> C6H12O6 + 6 O2 + 6 H2O
There are two main stages of this process: the light reactions and the dark reactions (Calvin cycle). Chloroplasts use the light energy to make sugar by coordinating the two stages
In the light reactions, pigments, like chlorophyll, absorb various wavelengths of visible light. A photon of light excites an electron, transferring it to a state of higher potential energy in a complex of chlorophyll and other small molecules called a photosystem. A photosystem is composed of a light-harvesting complex, which absorbs and transfers the light energy with pigments to the reaction-center complex, which holds a special pair of chlorophyll a molecules that transfer an electron to the primary electron acceptor. The acceptor gets the electrons and becomes reduced in photosystem II, which acts before photosystem I.
As the photoexcited electrons are passed to PS I via electron transport chain, an enzyme catalyzes the split of H2O into two electrons, two H+, and an oxygen atom. The electrons replace those electrons lost in the P680 chlorophyll a pair. The exergonic fall of electrons in the transport chain provides energy for ATP synthesis, allowing for chemiosmosis, as the created H+ gradient in the thylakoid space powers ATP synthase. Once the electron gets to PS I, it excites the P700 chlorophyll a molecules, is transferred to the primary electron acceptor, and gets passed down another electron transport chain that does not produce ATP. An enzyme then catalyzes the reduction of NADP+ to NADPH, which is then readily available for use in the Calvin cycle.
The dark reactions consume energy and build carbohydrates in three phases: carbon fixation, carbon reduction, and regeneration. In the process, 3 CO2 molecules, NADPH, and ATP are consumed. In carbon fixation, each CO2 molecule is attached to a 5-Carbon sugar (RuBP). The product is unstable and splits into two molecules of 3-phosphoglycerate (PGA). In phase 2, each PGA molecule gets a phosphate group from ATP and is reduced by NADPH, turning into the 3-Carbon sugar G3P. For every three CO2 molecules, 6 molecules of G3P form. One molecule of G3P exits to be used by the plant cell and the other 5 G3P go to phase 3, in which they are rearranged back into 3 RuBP molecules, which can again accept CO2 molecules. For regeneration, three ATP molecules are used. The Calvin cycle consumes 9 ATP and 6 NADPH to make one G3P, which becomes the starting material for glucose, meaning the Calvin cycle must go around twice for one molecule of glucose to be produced.
Big Ideas
2.A.1 All living systems require constant input of free energy.
2.A.2 Organisms capture and store free energy for use in biological processes.
Artifact/Study Tool
Photosynthesis is the process that converts light energy into chemical energy, which is essential to all life. Autotrophs are the producers that sustain themselves without consuming other organisms. Heterotrophs (consumers) survive on the compounds made by other organisms and can not make their own food.
The process of photosynthesis takes place in the chloroplasts of plants, in the mesophyll tissue inside the leaf. The reaction is: 6 CO2 + 12 H2O + light energy -----> C6H12O6 + 6 O2 + 6 H2O
There are two main stages of this process: the light reactions and the dark reactions (Calvin cycle). Chloroplasts use the light energy to make sugar by coordinating the two stages
In the light reactions, pigments, like chlorophyll, absorb various wavelengths of visible light. A photon of light excites an electron, transferring it to a state of higher potential energy in a complex of chlorophyll and other small molecules called a photosystem. A photosystem is composed of a light-harvesting complex, which absorbs and transfers the light energy with pigments to the reaction-center complex, which holds a special pair of chlorophyll a molecules that transfer an electron to the primary electron acceptor. The acceptor gets the electrons and becomes reduced in photosystem II, which acts before photosystem I.
As the photoexcited electrons are passed to PS I via electron transport chain, an enzyme catalyzes the split of H2O into two electrons, two H+, and an oxygen atom. The electrons replace those electrons lost in the P680 chlorophyll a pair. The exergonic fall of electrons in the transport chain provides energy for ATP synthesis, allowing for chemiosmosis, as the created H+ gradient in the thylakoid space powers ATP synthase. Once the electron gets to PS I, it excites the P700 chlorophyll a molecules, is transferred to the primary electron acceptor, and gets passed down another electron transport chain that does not produce ATP. An enzyme then catalyzes the reduction of NADP+ to NADPH, which is then readily available for use in the Calvin cycle.
The dark reactions consume energy and build carbohydrates in three phases: carbon fixation, carbon reduction, and regeneration. In the process, 3 CO2 molecules, NADPH, and ATP are consumed. In carbon fixation, each CO2 molecule is attached to a 5-Carbon sugar (RuBP). The product is unstable and splits into two molecules of 3-phosphoglycerate (PGA). In phase 2, each PGA molecule gets a phosphate group from ATP and is reduced by NADPH, turning into the 3-Carbon sugar G3P. For every three CO2 molecules, 6 molecules of G3P form. One molecule of G3P exits to be used by the plant cell and the other 5 G3P go to phase 3, in which they are rearranged back into 3 RuBP molecules, which can again accept CO2 molecules. For regeneration, three ATP molecules are used. The Calvin cycle consumes 9 ATP and 6 NADPH to make one G3P, which becomes the starting material for glucose, meaning the Calvin cycle must go around twice for one molecule of glucose to be produced.
Big Ideas
2.A.1 All living systems require constant input of free energy.
2.A.2 Organisms capture and store free energy for use in biological processes.
Artifact/Study Tool
Reflection
This artifact was very helpful to me for reviewing the light-dependent and light-independent reactions. Although Hank Green does not go into as great detail about the individual aspects of photosynthesis as the Campbell Biology textbook does, the video is very helpful when used in conjunction with notes, assignments, and the facts that were already committed to memory. The video provides a great source for visualizing and revising Chapter 10.
This artifact was very helpful to me for reviewing the light-dependent and light-independent reactions. Although Hank Green does not go into as great detail about the individual aspects of photosynthesis as the Campbell Biology textbook does, the video is very helpful when used in conjunction with notes, assignments, and the facts that were already committed to memory. The video provides a great source for visualizing and revising Chapter 10.