Metabolism and Energy Chapters 8.

Metabolism and Energy Chapters 8

Organisms are energy transformers!
Metabolism and Energy Organisms are energy transformers! Metabolism Catabolism Anabolism Bioenergetics Energy Kinetic Heat/Thermal Light Energy Potential Chemical Catabolism- cellular respiration- sugar put in to the body is broken down to do work in the cell (movement, active transport, etc). Energy released (helps to drive anabolic pathways). Anabolic- sometimes called biosynthetic pathways- synthesis of a protein from amino acids. Energy required/absorbed. Bioenergetics- the study of how energy flows through living systems. Energy- the capacity to cause change. Some forms of energy can be used to do work- or move matter against opposing forces (friction and gravity) Kinetic Energy- moving objects can perform work by imparting motion to other matter. Moving water through a dam turns turbines, moving bowling ball knocks over pins Heat/Thermal Energy- comes from the movement of atoms or molecules associated with kinetic energy Potential Energy- because of location or structure, height, chemical bonds, etc. Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Metabolism and Energy Organisms are energy transformers! Metabolism Metabolic pathway begins with a specific molecule, which is then altered in a series of defined steps leading to a specific product Each step is catalyzed by a specific enzyme Catabolism- cellular respiration- sugar put in to the body is broken down to do work in the cell (movement, active transport, etc). Energy released (helps to drive anabolic pathways). Anabolic- sometimes called biosynthetic pathways- synthesis of a protein from amino acids. Energy required/absorbed. Bioenergetics- the study of how energy flows through living systems. Energy- the capacity to cause change. Some forms of energy can be used to do work- or move matter against opposing forces (friction and gravity) Kinetic Energy- moving objects can perform work by imparting motion to other matter. Moving water through a dam turns turbines, moving bowling ball knocks over pins Heat/Thermal Energy- comes from the movement of atoms or molecules associated with kinetic energy Potential Energy- because of location or structure, height, chemical bonds, etc. Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Metabolism and Energy Organisms are energy transformers! Metabolism Catabolism Energy released (helps to drive anabolic pathways). Ex: cellular respiration sugar put in to the body is broken down to do work in the cell (movement, active transport, etc). Catabolism- cellular respiration- sugar put in to the body is broken down to do work in the cell (movement, active transport, etc). Energy released (helps to drive anabolic pathways). Anabolic- sometimes called biosynthetic pathways- synthesis of a protein from amino acids. Energy required/absorbed. Bioenergetics- the study of how energy flows through living systems. Energy- the capacity to cause change. Some forms of energy can be used to do work- or move matter against opposing forces (friction and gravity) Kinetic Energy- moving objects can perform work by imparting motion to other matter. Moving water through a dam turns turbines, moving bowling ball knocks over pins Heat/Thermal Energy- comes from the movement of atoms or molecules associated with kinetic energy Potential Energy- because of location or structure, height, chemical bonds, etc. Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Metabolism and Energy Organisms are energy transformers! Metabolism Catabolism Anabolism sometimes called biosynthetic pathways- Ex: synthesis of a protein from amino acids. Energy required/absorbed. Anabolic- sometimes called biosynthetic pathways- synthesis of a protein from amino acids. Energy required/absorbed. Bioenergetics- the study of how energy flows through living systems. Energy- the capacity to cause change. Some forms of energy can be used to do work- or move matter against opposing forces (friction and gravity) Kinetic Energy- moving objects can perform work by imparting motion to other matter. Moving water through a dam turns turbines, moving bowling ball knocks over pins Heat/Thermal Energy- comes from the movement of atoms or molecules associated with kinetic energy Potential Energy- because of location or structure, height, chemical bonds, etc. Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Metabolism and Energy Organisms are energy transformers! Metabolism Catabolism Anabolism Bioenergetics the study of how energy flows through living systems. These processes also apply to bioenergetics: Bioenergetics- the study of how energy flows through living systems. Energy- the capacity to cause change. Some forms of energy can be used to do work- or move matter against opposing forces (friction and gravity) Kinetic Energy- moving objects can perform work by imparting motion to other matter. Moving water through a dam turns turbines, moving bowling ball knocks over pins Heat/Thermal Energy- comes from the movement of atoms or molecules associated with kinetic energy Potential Energy- because of location or structure, height, chemical bonds, etc. Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Metabolism and Energy Metabolism Catabolism Anabolism Bioenergetics Energy the capacity to cause change. Some forms of energy can be used to do work- or move matter against opposing forces Ex: (friction and gravity) Ability to rearrange a collection of matter Organisms are energy transformers! Energy- the capacity to cause change. Some forms of energy can be used to do work- or move matter against opposing forces (friction and gravity) Kinetic Energy- moving objects can perform work by imparting motion to other matter. Moving water through a dam turns turbines, moving bowling ball knocks over pins Heat/Thermal Energy- comes from the movement of atoms or molecules associated with kinetic energy Potential Energy- because of location or structure, height, chemical bonds, etc. Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Metabolism and Energy Organisms are energy transformers! Energy Kinetic Relative motion of objects moving objects can perform work by imparting motion to other matter. Ex: Moving water through a dam turns turbines, moving bowling ball knocks over pins Kinetic Energy- moving objects can perform work by imparting motion to other matter. Moving water through a dam turns turbines, moving bowling ball knocks over pins Heat/Thermal Energy- comes from the movement of atoms or molecules associated with kinetic energy Potential Energy- because of location or structure, height, chemical bonds, etc. Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Metabolism and Energy Organisms are energy transformers! Energy Kinetic Heat/Thermal comes from the movement of atoms or molecules associated with kinetic energy Heat/Thermal Energy- comes from the movement of atoms or molecules associated with kinetic energy Potential Energy- because of location or structure, height, chemical bonds, etc. Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Metabolism and Energy Organisms are energy transformers! Energy Kinetic Heat/Thermal Light Energy Type of energy that can be harnessed to perform work Ex. Powering Photosynthesis Potential Energy- because of location or structure, height, chemical bonds, etc. Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Metabolism and Energy Organisms are energy transformers! Kinetic Heat/Thermal Light Energy Potential Non-kinetic energy because of location or structure, height, chemical bonds, etc. Potential Energy- because of location or structure, height, chemical bonds, etc. Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Metabolism and Energy Kinetic Heat/Thermal Light Energy Potential Chemical the potential energy available for release by a reaction. Ex: Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Organisms are energy transformers! Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Metabolism and Energy Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal. Chemical- the potential energy available for release by a reaction. Glucose is high in chemical energy and the process of glycolysis breaks it down. As bonds are broken, energy is released, but bonds also reform to make new molecules, thus it uses some energy. Net release, thus ANABOLIC OR CATABOLIC??? Organisms are energy transformers! All original energy comes from light. (photosynthesis- primary producer- consumer- who changes it from chemical to kinetic and releases thermal.

Thermodynamics What is Thermodynamics? Let’s go back to the beginning…

Thermodynamics The energy transformations that occur in a collection of matter Thermodynamics- the energy transformations that occur in a collection of matter. Matter is divided into system- what is under study, or surroundings- everything else. The total of the system plus the surroundings is the universe. Isolated systems are unable to exchange matter/energy with the surroundings, open systems can. *Which system are we? Open- we exchange matter 1st Law of Thermodynamics- energy cannot be created or destroy- only transferred or transformed. This is known as conservation of energy. Electric company doesn’t make energy, but converts it into a form we can use. *Do plants make their own energy? Not really, they transform energy from the sun. 2nd Law of Thermodynamics- every energy transfer increases the entropy of the universe Entropy- measure of randomness or disorder (Increasing temperature increases entropy) Image: bear is converting chemical energy (potential) into kinetic energy so he move- picture B- as a result, he is exchanging energy and materials with the environment. When he releases heat that increases entropy. Image-

Thermodynamics Thermodynamics First Law of Thermodynamics
System vs. Surroundings Isolated System vs. Open System First Law of Thermodynamics Thermodynamics- the energy transformations that occur in a collection of matter. Matter is divided into system- what is under study- or surroundings- everything else. The total of the system plus the surroundings is the universe. Isolated systems are unable to exchange matter/energy with the surroundings, open systems can. *Which system are we? Open- we exchange matter 1st Law of Thermodynamics- energy cannot be created or destroy- only transferred or transformed. This is known as conservation of energy. Electric company doesn’t make energy, but converts it into a form we can use. *Do plants make their own energy? Not really, they transform energy from the sun. 2nd Law of Thermodynamics- every energy transfer increases the entropy of the universe Entropy- measure of randomness or disorder (Increasing temperature increases entropy) Image: bear is converting chemical energy (potential) into kinetic energy so he move- picture B- as a result, he is exchanging energy and materials with the environment. When he releases heat that increases entropy. Image-

Thermodynamics Two Laws of Thermodynamics govern energy exchange:
First Law of Thermodynamics Second Law of Thermodynamics Thermodynamics- the energy transformations that occur in a collection of matter. Matter is divided into system- what is under study- or surroundings- everything else. The total of the system plus the surroundings is the universe. Isolated systems are unable to exchange matter/energy with the surroundings, open systems can. *Which system are we? Open- we exchange matter 1st Law of Thermodynamics- energy cannot be created or destroy- only transferred or transformed. This is known as conservation of energy. Electric company doesn’t make energy, but converts it into a form we can use. *Do plants make their own energy? Not really, they transform energy from the sun. 2nd Law of Thermodynamics- every energy transfer increases the entropy of the universe Entropy- measure of randomness or disorder (Increasing temperature increases entropy) Image: bear is converting chemical energy (potential) into kinetic energy so he move- picture B- as a result, he is exchanging energy and materials with the environment. When he releases heat that increases entropy. Image-

Thermodynamics Two Laws of Thermodynamics govern energy exchange:
First Law of Thermodynamics energy cannot be created or destroy- Only transferred or transformed Known as Principle of conservation of energy Thermodynamics- the energy transformations that occur in a collection of matter. Matter is divided into system- what is under study- or surroundings- everything else. The total of the system plus the surroundings is the universe. Isolated systems are unable to exchange matter/energy with the surroundings, open systems can. *Which system are we? Open- we exchange matter 1st Law of Thermodynamics- energy cannot be created or destroy- only transferred or transformed. This is known as conservation of energy. Electric company doesn’t make energy, but converts it into a form we can use. *Do plants make their own energy? Not really, they transform energy from the sun. 2nd Law of Thermodynamics- every energy transfer increases the entropy of the universe Entropy- measure of randomness or disorder (Increasing temperature increases entropy) Image: bear is converting chemical energy (potential) into kinetic energy so he move- picture B- as a result, he is exchanging energy and materials with the environment. When he releases heat that increases entropy. Image-

Thermodynamics Second Law of Thermodynamics
During energy transfer, some energy become unusable energy (unavailable to do work) Entropy (S) – Measure of disorder or randomness Energy is generally lost at every step, this is generally due to loss of energy as heat This constant losing of heat / energy makes the universe disordered We describe this using the term: entropy In order for a process to be spontaneous it must increase the entropy of the universe, and would have a positive delta S. Spontaneous doesn’t necessarily mean quickly, but rather energetically favorable. Rusting is spontaneous, but happens over a long period of time. Nonspontaneous processes cannot occur on their own. Energy must be added to the system to make it occur. Less ordered amino acids make up proteins that are more ordered. This does not happen spontaneously, requires net energy input.

Thermodynamics So, What is the Second Law of Thermodynamics?
Every energy transfer or transformation increases the entropy of the universe Energy is generally lost at every step, this is generally due to loss of energy as heat This constant losing of heat / energy makes the universe disordered We describe this using the term: entropy In order for a process to be spontaneous it must increase the entropy of the universe, and would have a positive delta S. Spontaneous doesn’t necessarily mean quickly, but rather energetically favorable. Rusting is spontaneous, but happens over a long period of time. Nonspontaneous processes cannot occur on their own. Energy must be added to the system to make it occur. Less ordered amino acids make up proteins that are more ordered. This does not happen spontaneously, requires net energy input.

Thermodynamics Spontaneous (Energetically Favorable) vs. Nonspontaneous Processes Leads to the second way we state the 2nd Law of Thermodynamics: For a process to occur spontaneously, it must increase the entropy of the universe Energy is generally lost at every step, this is generally due to loss of energy as heat This constant losing of heat / energy makes the universe disordered We describe this using the term: entropy In order for a process to be spontaneous it must increase the entropy of the universe, and would have a positive delta S. Spontaneous processes occur on their own /without input of energy Spontaneous doesn’t necessarily mean quickly, but rather energetically favorable. Rusting is spontaneous, but happens over a long period of time. Nonspontaneous processes cannot occur on their own. Energy must be added to the system to make it occur. Less ordered amino acids make up proteins that are more ordered. This does not happen spontaneously, requires net energy input.

Think-Pair-Share How does the second law of thermodynamics help explain the diffusion of a substance across a membrane? If you place a teaspoon of sugar in the bottom of a glass of water, it will dissolve completely over time. Left longer, eventually the water will disappear and the sugar crystals will reappear. Explain these observations in terms of entropy. When substances move from high to low, they go from high entropy to low entropy- which increases the total entropy of the system. This is spontaneous. When substances move from low to high, they go from low entropy to high entropy- this may increase the entropy of this system, but not the total entropy of the universe- thus this is nonspontaneous. *Book says when molecules are equal on both sides of the membrane, they are more random than when they are different on both sides. A highly concentrated area has less entropy than a low concentrated area, because there is less space for molecules to move about. Potential Energy- Kinetic Energy-Chemical Energy held in bonds then converted to thermal energy released as heat and kinetic energy for activity. Dissolves completely because going from less entropy (a clump) to more entropy when dissolved in water. Water will evaporate where it goes from less entropy inside the glass to vapor molecules spread out in the air. Crystals will precipitate out.

ΔG = ΔGfinal – ΔGinitial
Gibbs Free Energy Free Energy Portion of system’s energy that can perform work when temp and pressure are uniform throughout system ΔG = free energy of a system -ΔG = spontaneous reaction +ΔG = nonspontaneous reaction ΔG = 0 = Dead Cell (can do no work) ΔG = ΔH – TΔS ΔG = ΔGfinal – ΔGinitial Enthalpy Free energy – the portion of a system’s energy that can do work. – Delta G Enthalpy- total energy – Delta H Temperature is in Kelvin Once we know delta G we can predict whether the reaction will be spontaneous or not. Processes with negative delta G are spontaneous. **For delta G to be negative, either delta H is negative (meaning the system gives up enthalpy or energy) and H decreases, or delta S must be positive (the system gives up order and S increases). Or both. In other words, every spontaneous reaction decreases the system’s free energy. Relevance to Biology: gives us the power to predict which kinds of change can happen without help – can be harnessed to perform work Thus if there is more energy at the end of the reaction, then it absorbed energy, so it is not spontaneous If there is more energy at the beginning of the reaction, that makes delta G negative, thus it occurs spontaneously. (and loses energy over the course of a reaction) A process is spontaneous when it is moving toward equilibrium- diffusion is spontaneous but active transport is not. *Would they have a positive or negative delta G? Diffusion- negative, active transport- positive Enthalpy is a measure of the total energy of a thermodynamic system. It includes the system's internal energy or thermodynamic potential (a state function), as well as its volume and pressure (the energy required to "make room for it" by displacing its environment, which is an extensive quantity). ***GO back to previous slide and rediscuss

Gibbs Free Energy ΔG = ΔH – TΔS ΔG = ΔGfinal – ΔGinitial ΔH = he change in the system’s enthalpy What is enthalpy? Total energy ΔS = change in system’s entropy T = absolute Temperature in Kelvin Free energy – the portion of a system’s energy that can do work. Enthalpy- total energy Temperature is in Kelvin Once we know delta G we can predict whether the reaction will be spontaneous or not. Processes with negative delta G are spontaneous. **For delta G to be negative, either delta H is negative (meaning the system gives up enthalpy or energy) and H decreases, or delta S must be positive (the system gives up order and S increases). Or both.

Gibbs Free Energy ΔG = ΔH – TΔS ΔG = ΔGfinal – ΔGinitial Can think of this as difference in final state and initial state In other words, every spontaneous reaction decreases the system’s free energy. Thus if there is more energy at the end of the reaction, then it absorbed energy, so it is not spontaneous If there is more energy at the beginning of the reaction, that makes delta G negative, thus it occurs spontaneously. (and loses energy over the course of a reaction) Negative if loss of energy because has less free energy… system is less likely to change and is therefore more stable than it was previously Positive if gain of energy because has more free energy… system is more likely to change and is therefore less stable than it was previously Systems like to move towards greater stability – to equilibrium As reaction proceeds toward equilibrium, free energy of the mixture of reactants and products decreases Increases when pushed away from equilibrium Systems never spontaneously move away from equilibrium A process is spontaneous when it is moving toward equilibrium- diffusion is spontaneous but active transport is not. *Would they have a positive or negative delta G? Diffusion- negative, active transport- positive ***GO back to previous slide and rediscuss

Gibbs Free Energy Endergonic vs. Exergonic Reactions +ΔG -ΔG
Non-Spontaneous Spontaneous Which would have a positive or negative delta S? Exergonic - Loses free energy, thus negative delta G, occur spontaneously, greater work can be done Example: cell respiration – delta G = -686 kcal/ mol This is under standard conditions: Endergonic- gains free energy, thus positive delta G, not spontaneous Example: photosynthesis – delta G = +686 kcal/ mol This is under standard conditions. Well, where do plants get the energy?

Gibbs Free Energy Reactions in isolates system eventually reach equilibrium and then cannot do work Metabolism reactions are reversible and eventually will reach equilibrium Living cell is not in equilibrium Some reactions are constantly pulled in one direction and this keeps them from reaching equilibrium In other words, every spontaneous reaction decreases the system’s free energy. Thus if there is more energy at the end of the reaction, then it absorbed energy, so it is not spontaneous If there is more energy at the beginning of the reaction, that makes delta G negative, thus it occurs spontaneously. (and loses energy over the course of a reaction) Negative if loss of energy because has less free energy… system is less likely to change and is therefore more stable than it was previously Positive if gain of energy because has more free energy… system is more likely to change and is therefore less stable than it was previously Systems like to move towards greater stability – to equilibrium As reaction proceeds toward equilibrium, free energy of the mixture of reactants and products decreases Increases when pushed away from equilibrium Systems never spontaneously move away from equilibrium A process is spontaneous when it is moving toward equilibrium- diffusion is spontaneous but active transport is not. *Would they have a positive or negative delta G? Diffusion- negative, active transport- positive ***GO back to previous slide and rediscuss

Warm Up Exercise Glow in the dark necklaces are snapped in a way that allows two chemicals to mix and they glow. Is this an endergonic or exergonic reaction? Explain. In simple diffusion, H+ ions move to an equal concentration on both sides of a cell membrane. In cotransport, H+ ions are pumped across a membrane to create a concentration gradient. Which situation allows the H+ ions to perform work in the system? When things are the same on both sides, it is at equilibrium and can do no work. Exergonic- a similar reaction happens in fireflies- discuss transforming bacteria with firefly gene

ATP and Cellular Work Three Types of Work Energy Coupling Chemical
Transport Mechanical Energy Coupling Phosphorylated Intermediate Chemical- pushing of endergonic reactions (exergonic drives endergonic) Transport- pumping across membranes Mechanical- beating of cilia, muscle contraction, movement of chromosomes, etc Energy Coupling- using an exergonic process to drive an endergonic one. Relies on ATP. *Is the hydrolysis of ATP endergonic or exergonic? Anabolic or Catabolic? (exergonic, catabolic) Why is ATP such a good energy molecule? *It isnt because the phosphate bonds have a lot of energy, but he reactants (water and ATP) have a high free energy compared to the products (P and ADP) which has very low free energy, so the difference in them is a lot more than most molecules. ATP molecule is under a lot of pressure because of the three negative phosphate groups (3 like charges, crowded together), which gives it a lot of potential energy. Transport, Mechanical, and Chemical work are all powered by ATP The process of shivering uses ATP hydrolysis during muscle contraction to generate heat and warm the body. More productively, ATP released from exergonic processes can drive endergonic processes. If the delta G is less than what is released by ATP hydrolysis, then 2 reactions are coupled, and overall they are still endergonic. Usually the phosphate during ATP hydrolysis is transferred to another molecule called the phosphorylated intermediate. This makes this intermediate more reactive than when it was unphosphorylated. (Activates it, like protein kinase)

Why is ATP such a good energy molecule?
What is ATP? Contains ribose sugar, nitrogenous base adenine, and chain of 3 phosphate groups bonded to it. Bonds can be broken by hydrolysis Chemical- pushing of endergonic reactions (exergonic drives endergonic) Transport- pumping across membranes Mechanical- beating of cilia, muscle contraction, movement of chromosomes, etc Energy Coupling- using an exergonic process to drive an endergonic one. Relies on ATP. *Is the hydrolysis of ATP endergonic or exergonic? Anabolic or Catabolic? (exergonic, catabolic) Why is ATP such a good energy molecule? *It isnt because the phosphate bonds have a lot of energy, but he reactants (water and ATP) have a high free energy compared to the products (P and ADP) which has very low free energy, so the difference in them is a lot more than most molecules. ATP molecule is under a lot of pressure because of the three negative phosphate groups (3 like charges, crowded together), which gives it a lot of potential energy. Transport, Mechanical, and Chemical work are all powered by ATP The process of shivering uses ATP hydrolysis during muscle contraction to generate heat and warm the body. More productively, ATP released from exergonic processes can drive endergonic processes. If the delta G is less than what is released by ATP hydrolysis, then 2 reactions are coupled, and overall they are still endergonic. Usually the phosphate during ATP hydrolysis is transferred to another molecule called the phosphorylated intermediate. This makes this intermediate more reactive than when it was unphosphorylated. (Activates it, like protein kinase)

Why is ATP such a good energy molecule?
When bond is broken , a molecule of inorganic phosphate leaves the ATP It become adenosine diphosphate (ADP) Chemical- pushing of endergonic reactions (exergonic drives endergonic) Transport- pumping across membranes Mechanical- beating of cilia, muscle contraction, movement of chromosomes, etc Energy Coupling- using an exergonic process to drive an endergonic one. Relies on ATP. *Is the hydrolysis of ATP endergonic or exergonic? Anabolic or Catabolic? (exergonic, catabolic) Why is ATP such a good energy molecule? *It isnt because the phosphate bonds have a lot of energy, but he reactants (water and ATP) have a high free energy compared to the products (P and ADP) which has very low free energy, so the difference in them is a lot more than most molecules. ATP molecule is under a lot of pressure because of the three negative phosphate groups (3 like charges, crowded together), which gives it a lot of potential energy. The energy release is generally greater than theenergy most other molecules could deliver 3 phosphate groups are negative and crowded together, very instable Similar to compressed spring Transport, Mechanical, and Chemical work are all powered by ATP The process of shivering uses ATP hydrolysis during muscle contraction to generate heat and warm the body. More productively, ATP released from exergonic processes can drive endergonic processes. If the delta G is less than what is released by ATP hydrolysis, then 2 reactions are coupled, and overall they are still endergonic. Usually the phosphate during ATP hydrolysis is transferred to another molecule called the phosphorylated intermediate. This makes this intermediate more reactive than when it was unphosphorylated. (Activates it, like protein kinase)

Is Hydrolysis of ATP endergonic and exergonic? Anabolic or catabolic?
Chemical- pushing of endergonic reactions (exergonic drives endergonic) Transport- pumping across membranes Mechanical- beating of cilia, muscle contraction, movement of chromosomes, etc Energy Coupling- using an exergonic process to drive an endergonic one. Relies on ATP. *Is the hydrolysis of ATP endergonic or exergonic? Anabolic or Catabolic? (exergonic, catabolic) Why is ATP such a good energy molecule? *It isnt because the phosphate bonds have a lot of energy, but he reactants (water and ATP) have a high free energy compared to the products (P and ADP) which has very low free energy, so the difference in them is a lot more than most molecules. ATP molecule is under a lot of pressure because of the three negative phosphate groups (3 like charges, crowded together), which gives it a lot of potential energy. Transport, Mechanical, and Chemical work are all powered by ATP The process of shivering uses ATP hydrolysis during muscle contraction to generate heat and warm the body. More productively, ATP released from exergonic processes can drive endergonic processes. If the delta G is less than what is released by ATP hydrolysis, then 2 reactions are coupled, and overall they are still endergonic. Usually the phosphate during ATP hydrolysis is transferred to another molecule called the phosphorylated intermediate. This makes this intermediate more reactive than when it was unphosphorylated. (Activates it, like protein kinase)

Does it release -7.3 kcal / mol in the cell?
No, it’s about -13 kcal / mol Transport, Mechanical, and Chemical work are all powered by ATP The process of shivering uses ATP hydrolysis during muscle contraction to generate heat and warm the body. More productively, ATP released from exergonic processes can drive endergonic processes. If the delta G is less than what is released by ATP hydrolysis, then 2 reactions are coupled, and overall they are still endergonic. Usually the phosphate during ATP hydrolysis is transferred to another molecule called the phosphorylated intermediate. This makes this intermediate more reactive than when it was unphosphorylated. (Activates it, like protein kinase)

ATP Hydrolysis kh Is A spontaneous? Is ATP breakdown spontaneous?
When you couple them is it spontaneous? This is an example of ATP driving chemical work With specific enzymes help, cell is able to energy couple and drive process with the energy released by hydrolysis of ATP Usually involves the transfer of a Phosphate group from ATP to some other molecule

ATP and Cellular Work The recipient of the phosphate is said to be phosphorylated This phosphorylated intermediate ist he key to coupling exergonic and endergonic reactiosn … is is more reactive And less stable When phosphate binds, (from ATP) it changes protein’s shape and activates it, like in the transport proteins ATP also drives the motor protein to help vesicles move along microtubules. These motor proteins and microtubules also help sister chromatids separate during anaphase of mitosis. (Requires many ATP molecules- each time Phosphate binds it changes the shape of the protein causing it to be able to move)

ATP Cycle The body regenerates 10 million molecules of ATP per second per cell! A muscle cell recycles its entire pool of ATP in less than a minute. If it were not regenerated, we would use nearly our body weight in ATP each day. The ATP cycle is an energy coupling reaction, creating ATP requires 7.3 kcal/mol of energy. Breaking down ATP releases -7.3. The endergonic formation of ATP must be coupled with other processes to be carried out. Namely, cellular respiration- which provides energy from the endergonic process of making ATP.

Enzymes Enzymes- biological catalyst
Substrates – reactants that bind to the enzyme, usually in the active site *What type of reactions are spontaneous? (Exergonic) *Which means what? (they require no energy to happen) But we don’t know how fast they happen. Without enzymes, all reactions occur very slowly. Enzyme- macromolecule that acts as a catalyst- speeds up a reaction without being consumed by the reaction. Most enzymes are proteins, although some are made of RNA (to be discussed later) Enzymes sound like what they act on: Sucrase on sucrose, lactase on lactose, protease on proteins *What are the elements of the left and right sides of the reactants called? (reactants and products) The reactants of an enzyme catalyzed reaction are more specifically called SUBSTRATES

Enzymes Activation Energy (EA)
the energy required to get a reaction started. Many times this energy is absorbed as thermal energy from the environment Many times room temperature may be enough, but most reactants need more energy than that to get started. AKA = free energy of activation Reactants go from a stable state, to the unstable transition state- which requires energy. This contorts the molecules so bonds can be broken and rearranged. The formation of new bonds releases more energy than was required for the original bonds to be broken. Activation Energy- the energy required to get a reaction started. Many times this energy is absorbed as thermal energy from the environment. Occasionally room temperature may be enough, but most reactants need more energy than that to get started. AKA = free energy of activation Heat speeds a reaction by allowing reactants to attain the transition state more often, but this solution is inappropriate for biological systems because it would denature proteins and kill cells. Additionally, it would speed up all reactions, not just those that are needed. Instead of heat, organisms use enzymes to speed up reactions. Is the delta G positive or negative here? (negative, thus spontaneous, exergonic)

Enzymes Activation Energy (EA)
the energy required to get a reaction started. Reactants go from a stable state, to the unstable transition state- which requires energy. This contorts the molecules so bonds can be broken and rearranged. The formation of new bonds releases more energy than was required for the original bonds to be broken. Activation Energy- the energy required to get a reaction started. Many times this energy is absorbed as thermal energy from the environment. Occasionally room temperature may be enough, but most reactants need more energy than that to get started. AKA = free energy of activation Heat speeds a reaction by allowing reactants to attain the transition state more often, but this solution is inappropriate for biological systems because it would denature proteins and kill cells. Additionally, it would speed up all reactions, not just those that are needed. Instead of heat, organisms use enzymes to speed up reactions. Is the delta G positive or negative here? (negative, thus spontaneous, exergonic)

How does heat effect an enzyme?
Heat speeds a reaction by allowing reactants to attain the transition state more often This solution is inappropriate for biological systems because it would denature proteins and kill cells. Additionally, it would speed up all reactions, not just those that are needed. Reactants go from a stable state, to the unstable transition state- which requires energy. This contorts the molecules so bonds can be broken and rearranged. The formation of new bonds releases more energy than was required for the original bonds to be broken. Activation Energy- the energy required to get a reaction started. Many times this energy is absorbed as thermal energy from the environment. Occasionally room temperature may be enough, but most reactants need more energy than that to get started. AKA = free energy of activation Heat speeds a reaction by allowing reactants to attain the transition state more often, but this solution is inappropriate for biological systems because it would denature proteins and kill cells. Additionally, it would speed up all reactions, not just those that are needed. Instead of heat, organisms use enzymes to speed up reactions. Is the delta G positive or negative here? (negative, thus spontaneous, exergonic)

Enzymes Enzymes catalyze reactions by lowering the activation energy.
The Law of thermodynamics favors the break down of the proteins, DNA, and other molecules in the cell. They are rich in energy and have potential to decompose spontaneously This makes it easier to reach the transition state, even at moderate temperatures. It cannot change delta G though and make an endergonic reaction exergonic. This makes metabolism more fluid and dynamic and processes able to proceed rapidly.

Enzymes Enzyme + Substrate = Enzyme-Substrate Complex
Enzyme Enzyme Enzyme + Substrate Substrate(s) Complex Product(s) Enzyme is sucrase, substrate is sucrose, enzyme substrate complex = sucrase+sucrose, produce is glucose + fructose + sucrase (left over, recycled) Sucrose+sucrease+H2O yields Sucrase-sucrose-H2O complex yields Sucrase + glucose + fructose The reaction catalyzed by each enzyme is very specific. Remember most of them are proteins, so they have a unique shape 3D (as a result of their amino acid sequence), and they are unable to bind with others unless their shapes are complementary. Reactant that an enzyme acts on is referred to as the enzyme’s substrate. Forms a enzyme – substrate complex Bind to the active site on a enzymatic protein Only restricted regions of the enzyme molecule atually bind to the substrate… generally a groove where catalysis occurs

Enzymes Active Site pocket or groove on the surface of the enzyme where the substrate binds and catalysis occurs. A pocket or groove on the surface of the enzyme where the substrate binds and catalysis occurs. When the substrate enters the active site, it forms weak bonds with the enzyme, inducing a change in the shape of the protein. This change allows additional weak bond (ie: hydrogen bonds) to form, causing the active site to fit around the substrate snugly- this is called the induced fit. As it enters, reactions between the chemical groups and those on the R groups of the AA that form active site, cause the enzyme to change its shape slightly to that the active site fits more snugly – induced fit Once together in the active site, the reactants are converted into products, and then they depart from the active site, the enzyme an then take in another substrate molecule into its active site. This cycle happens very quickly such that a single enzyme molecule can act on about a thousand substrate molecules per second. Some enzymes are even faster. Enzymes emerge from the reaction in their original form and are available to be recycled. Therefore, very small amounts of enzyme can have a large metabolic impact by cycling over and over again. Most reactions are reversible and enzymes can catalyze the forward or reverse reaction Enzymes lower activation energy and speed up reaction by providing a place for substrates to come together and orient. As the enzyme snugly binds to them, it also may promote movement toward transition state, lowering the activation energy needed to reach this transitional state. A particular R group on the amino acids in the active site may also provide a favorable environment for the reaction (may raise or lower pH that the substrates need to proceed) The rate at which a reaction occurs depends on the amount of enzymes and substrate.

Enzymes Induced Fit When the substrate enters the active site, it forms weak bonds with the enzyme, inducing a change in the shape of the protein. This change allows additional weak bond (ie: hydrogen bonds) to form, causing the active site to fit around the substrate snugly- A pocket or groove on the surface of the enzyme where the substrate binds and catalysis occurs. When the substrate enters the active site, it forms weak bonds with the enzyme, inducing a change in the shape of the protein. This change allows additional weak bond (ie: hydrogen bonds) to form, causing the active site to fit around the substrate snugly- this is called the induced fit. As it enters, reactions between the chemical groups and those on the R groups of the AA that form active site, cause the enzyme to change its shape slightly to that the active site fits more snugly – induced fit Once together in the active site, the reactants are converted into products, and then they depart from the active site, the enzyme an then take in another substrate molecule into its active site. This cycle happens very quickly such that a single enzyme molecule can act on about a thousand substrate molecules per second. Some enzymes are even faster. Enzymes emerge from the reaction in their original form and are available to be recycled. Therefore, very small amounts of enzyme can have a large metabolic impact by cycling over and over again. Most reactions are reversible and enzymes can catalyze the forward or reverse reaction Enzymes lower activation energy and speed up reaction by providing a place for substrates to come together and orient. As the enzyme snugly binds to them, it also may promote movement toward transition state, lowering the activation energy needed to reach this transitional state. A particular R group on the amino acids in the active site may also provide a favorable environment for the reaction (may raise or lower pH that the substrates need to proceed) The rate at which a reaction occurs depends on the amount of enzymes and substrate.

Effects of Environment
Changes in the environment of the enzyme can cause inefficiencies or denaturation of the enzyme: Temperature pH Concentration of Enzyme Concentration of Substrate The rate at which a particular amount of enzyme converts substrate to product depends on the amount of enzyme and substrate. If there is a lot of substrate, all of the active sites will be occupied. When this happens, the enzyme is said to be saturated, and the rate is determined by how fast the enzyme converts reactants to products. Cells usually increase the rate of a reaction by producing more enzymes. There also exist optimal conditions that favor the most active shape for the enzyme molecule To a point a higher temp increases rate of reaction because causes substrate to collide with active site of enzyme more often. Too high, disrupts hydrogen bonds and proteins denature. Each enzyme has ideal temperature. Hot spring bacteria are higher. Most enzymes have optimal pH of Exceptions: pepsin a digestive enzyme works best in stomach acid- pH of 2

Enzymes Cofactors Coenzyme
nonprotein components that help in catalytic activity. Usually bound to enzyme (sometimes permanently, sometimes loosely) Coenzyme If cofactor is organic Many vitamins are important because they are coenzymes or make up coenzymes Cofactors are nonprotein components that help in catalytic activity. Usually bound to enzyme – sometimes permanently, sometimes loosly. Ex: zinc, iron, copper. Organic molecule cofactors are called coenzyme. Most vitamins are important because they are coenzymes or make up coenzymes.

Enzyme Action Competitive Inhibitors
Resembles normal substrate molecule Reduce productivity of enzyme by blocking substrates from entering active sites Certain chemicals selectively inhibit the action of specific enzymes. If they bind to the enzyme covalently, their effects are usually irreversible. If they bind via weak interactions, then it is usually reversible. A competitive inhibitor resembles the normal substrate molecule and competes for admission into the active site. They reduce the productivity of enzymes by blocking substrates from entering the active site. This is overcome by increases concentration of substrate so when an active site becomes available, there is more substrate than the competitor to gain entry to the active site. Noncompetitive inhibitors bind to the enzyme in a place other than the active site which changes its shape making the active site less efficient at catalyzing the conversion of reactant to product. Example inhibitors: penicillin- blocks the active site of an enzyme that many bacterial cells use to make their cell walls. Pesticide, DDT and Sarin, a nerve gas (used in Tokyo subway terrorist action in 1995 that killed many people) effect enzymes important in the nervous system. Sometimes inhibition is good and serves as a regulator of metabolism, turning off chemical pathways using naturally occurring molecules in the cell.

Enzyme Action Noncompetitive Inhibitors
Don’t directly compete with substrate Impede enzymatic reactions by binding to another part of the enzyme Certain chemicals selectively inhibit the action of specific enzymes. If they bind to the enzyme covalently, their effects are usually irreversible. If they bind via weak interactions, then it is usually reversible. A competitive inhibitor resembles the normal substrate molecule and competes for admission into the active site. They reduce the productivity of enzymes by blocking substrates from entering the active site. This is overcome by increases concentration of substrate so when an active site becomes available, there is more substrate than the competitor to gain entry to the active site. Noncompetitive inhibitors bind to the enzyme in a place other than the active site which changes its shape making the active site less efficient at catalyzing the conversion of reactant to product. Example inhibitors: penicillin- blocks the active site of an enzyme that many bacterial cells use to make their cell walls. Pesticide, DDT and Sarin, a nerve gas (used in Tokyo subway terrorist action in 1995 that killed many people) effect enzymes important in the nervous system. Sometimes inhibition is good and serves as a regulator of metabolism, turning off chemical pathways using naturally occurring molecules in the cell.

Allosteric Regulation
If all enzymes were working at the same time, metabolism would be chaos. So it is important for cell to regulate this (discussed later) by either turning on or off genes that code for specific enzymes are regulating enzyme activity once they are made. Allosteric Regulation- when a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site. (Basically reversible noncompetitive inhibitors) Regulatory molecule binds to regulatory site (or allosteric site). Activator stabilizes functional active site and inhibitors stabilizes inactive form. *At low concentrations, activators and inhibitors dissociate from the enzyme. The enzyme can then oscillate again. *Most enzymes that are known to be allosterically regulated are composed of 2 or more subunits. The subunits fit together in such a way that the binding of an activator or inhibitor affects them all. ADP activates many enzymes which causes generation of ATP. ATP on the other hand binds to the same enzymes inhibiting their activity. If ATP is used and more needed, ADP is present which causes the enzymes to be activated. When ATP backs up, the enzymes are inhibited.

Allosteric Regulation
Term used to describe any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site Can be inhibition or stimulation Generally constructed from two or more subunits If all enzymes were working at the same time, metabolism would be chaos. So it is important for cell to regulate this (discussed later) by either turning on or off genes that code for specific enzymes are regulating enzyme activity once they are made. Allosteric Regulation- when a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site. (Basically reversible noncompetitive inhibitors) Regulatory molecule binds to regulatory site (or allosteric site). Activator stabilizes functional active site and inhibitors stabilizes inactive form. *At low concentrations, activators and inhibitors dissociate from the enzyme. The enzyme can then oscillate again. *Most enzymes that are known to be allosterically regulated are composed of 2 or more subunits. The subunits fit together in such a way that the binding of an activator or inhibitor affects them all. ADP activates many enzymes which causes generation of ATP. ATP on the other hand binds to the same enzymes inhibiting their activity. If ATP is used and more needed, ADP is present which causes the enzymes to be activated. When ATP backs up, the enzymes are inhibited.

Allosteric Site regulatory site
Both activators and inhibitors can bind to these sites: Activator stabilizes functional active site Inhibitors stabilizes inactive form Shape change in one subunit affects shape of other subunit Allosteric Regulation- when a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site. (Basically reversible noncompetitive inhibitors) Regulatory molecule binds to regulatory site (or allosteric site). Activator stabilizes functional active site and inhibitors stabilizes inactive form. *At low concentrations, activators and inhibitors dissociate from the enzyme. The enzyme can then oscillate again. *Most enzymes that are known to be allosterically regulated are composed of 2 or more subunits. The subunits fit together in such a way that the binding of an activator or inhibitor affects them all. ADP functions as an activator and activates many enzymes which causes generation of ATP. ATP on the other hand functions as an inhibitor and binds to the same enzymes inhibiting their activity. If ATP is used and more needed, ADP is present which causes the enzymes to be activated. When ATP backs up, the enzymes are inhibited.

Cooperativity A different type of allosteric activation in which a substrate binds to an active site stimulating the catallytic powers of a multisubunit enzyme by affecting other active sites Another type of allosteric activation. (Because binding at one site affects another site) Cooperativity- Substrate molecule binding to one active site in a multisubunit enzyme, triggers a shape change in all of the subunits. This increases activity of other active sites. Hemoglobin (a protein with four units) in blood- although not an enzyme, displays cooperativity, bc when oxygen binds at one site, it increases the affinity for oxygen to bind at the other 3 sites.

Cooperativity Amplifies the response of enzymes to substrates
An induced fit in one subunit can trigger the same favorable shape change in other subunits Another type of allosteric activation. (Because binding at one site affects another site) Cooperativity- Substrate molecule binding to one active site in a multisubunit enzyme, triggers a shape change in all of the subunits. This increases activity of other active sites. Hemoglobin (a protein with four units) in blood- although not an enzyme, displays cooperativity, bc when oxygen binds at one site, it increases the affinity for oxygen to bind at the other 3 sites.

Feedback Inhibition Metabolic pathway switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway When ATP inhibits enzyme in ATP generating pathway, this is feedback inhibition. Negative feedback. As isoleucine accumulates, it binds to active site, slowing its own synthesis. This prevents cell from wasting chemical energy by making more product than necessary.

Feedback Inhibition When ATP inhibits enzyme in ATP generating pathway, this is feedback inhibition. Negative feedback. As isoleucine accumulates, it binds to active site, slowing its own synthesis. This prevents cell from wasting chemical energy by making more product than necessary.

Metabolism and Energy Chapters 8.

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Metabolism and Energy Chapters 8.

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