Chapter 6: Metabolism Presentation PDF

Chapter 6: An Introduction to Metabolism Andrea Zeebe QR Code: Please sign in :) A helpful way to study  Energy - Defined: - Capacity of a system to do work/create change - Can be transformed from one type to another type, can be transferred from one system to another...

Chapter 6: An Introduction to Metabolism Andrea Zeebe QR Code: Please sign in :) A helpful way to study  Energy - Defined: - Capacity of a system to do work/create change - Can be transformed from one type to another type, can be transferred from one system to another system - Bioenergetics: study of energy flow through living systems - Cellular processes occur via chemical reactions - Some require energy - Some release energy - Metabolism: sum total of all chemical reactions in a cell - Fate of these chemical reactions are governed by direction (concentration, energy) and rate (catalysts) - Cells must continually obtain energy to replenish the constant energy- requiring chemical reactions  Types of Energy 1. Free energy - a measure of the capacity of the system to do work 2. Lost energy - energy lost to disorder, can't be transformed into free energy - All energy transfers involve losing some energy in an unusable form such as heat, resulting in entropy 3. Kinetic - energy of movement a. Thermal - energy of movement of atoms and molecules - Heat is thermal energy in transfer from one system to another - Thermodynamics - changes in heat 4. Potential - stored energy due to location and structure a. Chemical Energy - stored energy of chemical bonds, location of atoms and their valence electrons - Responsible for providing living cells with energy from food  Kinetic and Potential Energy in a Cell Kinetic Energy - Movement in/out of cell (ex. motor proteins in/out = mechanical) - Heat moves around freely Potential Energy - Elastic energy in folding of protein (stored) - Storing energy across plasma membrane in electrochemical gradients Enthalpy - sum of kinetic and potential Question 1: Which of the following best describes the difference between kinetic and potential energy within a cell? a. Kinetic energy refers to the energy stored in molecules like ATP, while potential energy is the energy used for cellular movement. b. Kinetic energy is the energy associated with molecules in motion, such as ions moving across a membrane, while potential energy is stored energy, like the energy in chemical bonds of glucose or ATP. c. Kinetic energy is the energy released during cellular respiration, while potential energy is only found in heat energy produced by the cell d. Kinetic energy refers to the energy needed for muscle contraction, while potential energy refers to energy stored in the cell membrane.  Metabolic pathways - A series of interconnected biochemical reactions that convert a substrate molecule or molecules, step-by-step, through a series of metabolic intermediates, eventually yielding a final product or products - Each step is catalyzed by a specific enzyme  Metabolism 1) Anabolism: require energy to synthesize complex molecules from simpler ones - Endergonic - nonspontaneous - Examples: - Synthesizing sugar from CO2 - Proteins from amino acids - DNA from nucleic acids 2) Catabolism - release energy when complex molecules break down into simpler ones - Exergonic - spontaneous - Examples: - Breakdown of sugar: single glucose molecule = enough energy to make Question 2: Which of the following statements describes anabolism and catabolism correctly? A) Anabolism is exergonic and releases energy, while catabolism is endergonic and requires energy input B) Anabolism involves synthesizing complex molecules and requires energy (endergonic), while catabolism breaks down complex molecules and releases energy (exergonic) C) Catabolism is the process of synthesizing complex molecules like DNA and proteins, while anabolism breaks down molecules like glucose to release energy D) Both anabolism and catabolism are exergonic processes, releasing energy during chemical reactions in the cell  Gibbs Free Energy - Usable energy: energy that is available to do work - Energy that takes place with a chemical reaction that is available after we account for entropy Note: - Delta G < 0 is spontaneous; Delta G > 0 is non-spontaneous  Temperature: Always positive in Kelvin Delta H = Delta S = negative positive [decrease in Anabolism [energy disorder] absorbed]  Temperature: Always positive in Kelvin Delta H = Delta S = positive negative [increase in Catabolism [energy released] disorder] Endergonic Reactions Exergonic Reactions Delta G > 0 Delta G < 0 - Requires an energy input - Reactions that release energy rather than releasing energy - Reactions products have less energy than - Products have more energy reactants than reactants Spontaneous: can occur without adding energy EX. ANABOLISM **Not one that suddenly or quickly occurs - Ex. rusting of iron is an example of a spontaneous reaction that occurs slowly over time Question 3: Which of the following correctly states the relationship between anabolic and catabolic pathways? a. Catabolic pathways produce usable cellular energy by synthesizing more complex organic molecules. b. Degradation of organic molecules by anabolic pathways provides the energy to drive catabolic pathways. c. Energy derived from catabolic pathways is used to drive the breakdown of organic molecules in anabolic pathways. d. Anabolic pathways synthesize more complex organic molecules using the energy derived from catabolic pathways. e. The flow of energy between catabolic and anabolic pathways is reversible.  Carbohydrate metabolism Sugar (simple carb) has a lot of energy stored in its bonds, so living things consume it as a major energy source 1. Cellular respiration (catabolic) - A single glucose molecule can store enough energy to make a great deal of ATP - 36 to 38 molecules 2. Photosynthesis (anabolic) - The amount of energy needed to make one glucose molecule from six carbon dioxide molecules is 18 ATP molecules and 12 NADPH molecules  Equilibrium In a closed system, reactions will proceed until they reach a state of equilibrium - One of lowest possible free energy and state of maximal entropy - All reactions are reversible - Energy is required to push reactions away from equilibrium Cells are open systems, would die if they were closed systems because they would reach equilibrium and run out of free energy to do work - Living organisms are in a constant energy-requiring, uphill battle against equilibrium and entropy Thermodynamics Thermodynamics: the study of energy and energy transfer involving physical matter Open and closed system - Open = one in which energy and matter can transfer between the system and its surroundings - Closed = one that can transfer energy but not matter to its surroundings - Biological organism - Open system  Laws of Thermodynamics 0: Definition of Temperature - If two objects are at thermal equilibrium with each Question: which other, and a third object is at thermal equilibrium laws do not with one, it has to be at thermal equilibrium with apply to living both systems? - Thermal equilibrium - equal amount of thermal energy be transferred and transferred back between objects, heat is constant (at same temperature) 1: Law of conservation - Energy can neither be created nor be destroyed Laws of Thermodynamics 2: Law of entropy - Every energy transfer increases the entropy of the universe - Entropy can never decrease in a closed, isolated system 3: Concept of absolute zero - There is some temperature at which a system can be lowered to at which entropy can no longer change - Absolute zero - 0K Question 4: Which of the thermodynamics law(s) do not apply to living systems?  Question: what type of energy ATP do you think ATP stores? - Adenosine triphosphate (ribonucleotide) - Structure: adenosine bound to three phosphate groups - Adenosine: nucleoside of the nitrogenous base adenine and 5 carbon sugar (ribose) - Primary energy currency of all cells - high energy molecule that stores energy within its bonds (not the only one though) - ATP hydrolysis (catabolic, exergonic) releases energy (-7.3 kcal/mol) that cells can use to do work  Question: which type of metabolic reaction requires energy Energy coupling coupling? - Occurs when the energy produced by one reaction or system is used to drive another reaction or system - Converts an endergonic reaction to a net exergonic reaction - how our cells use ATP  Energy coupling - Cells couple the ATP hydrolysis exergonic reaction allowing them to proceed - Example: Na + and K+ ion pump - Sodium out the cell and potassium into the cell - 1 ATP = 3 Na+ and 2 K+ - Large percentage of cells’ ATP powers this pump - Na+/K+ in phosphorylated state = has more free energy; triggered to undergo a conformational change  Activation energy - Defined: amount of energy input necessary for all chemical reactions to occur - comes from energy of heat - Even exergonic reactions require a small amount of energy input before they can proceed - Higher the activation energy, the slower the chemical reaction - Enzymes lower activation energy - Transition state - max energy, unstable - EA is always positive Question 5: Below is a diagram of ________ which is an _______ reaction in which energy is _________. a. Catabolism, endergonic, absorbed b. Anabolism, exergonic, released c. Catabolism, exergonic, released d. Anabolism, endergonic, absorbed How are chemical reactions regulated? Speed up the rate of the reaction by: 1. Adding heat 2. Using enzymes to lower activation energy  Heat Thermal energy is produced when a rise in temperature causes atoms and molecules to move faster and collide with each other The hotter it is, the faster the molecules are moving, the more likely they will collide and react  Enzymes - Enzyme - Protein that speeds up the rate of a chemical reaction by lowering the activation energy necessary for a chemical reaction to occur - Substrate - reactant that binds to enzyme - Function: - Lowers activation energy by orienting substrate in such a way that Question: does destabilizes/strains their bonds to initiate a the substrate chemical reaction bind to the - Do NOT change the reactions delta G active site - Ex. don’t change whether a reaction is covalently or exergonic (spontaneous) or endergonic noncovalently?  Substrates - Substrate: the chemical reactant to which an enzyme binds to - Active site: the location within the enzyme where the substrate binds - Unique combo of amino acid residues - Characteristics: large, small, acidic, basic, hydrophilic/hydrophobic, positively or negatively charged, neutral - “Best fit” = the shape and the amino acid functional group attraction to the substrate - Environmental influences: - Environmental temperature increases reaction rates - Outside of optimal range can affect chemical bonds within the active site - Denature: high temperature Question 6: Do the substrates bind to the active site covalently or noncovalently? Environmental influences  Induced fit - Expands on “lock and key model” - As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that confirms an ideal binding arrangement between the enzyme and the substrate transition state - Maximizes enzyme’s catalytic function - Lowers Ea - Orients substrate in correct way - Optimal environment for reaction to occur - Participate in chemical reaction itself - Can provide certain ions or chemical groups that actually form covalent bonds with substrate molecules as a necessary step of the reaction process - Enzyme will always return to its original state at the reaction’s completion  Regulating enzymes - Competitive inhibition: an inhibitor molecule competes with the substrate for active site binding - Noncompetitive (allosteric) inhibition: an inhibitor molecule binds to the enzyme in a location other than the active site (allosteric site) but still manages to prevent substrate binding to the active site 1. Allosteric inhibition: Bind to enzymes in a location where their binding induces a conformational change that reduces the enzyme’s affinity for the substrate 2. Allosteric activators: bind to locations on an enzyme away from the active site, including a conformational change that increases the affinity for the enzyme’s active site for its substrate Question 7: Which of the following statements about allosteric binding is true? A) Allosteric binding leads to the formation of a covalent bond between the enzyme and the effector. B) Allosteric binding can only activate the enzyme, never inhibit it. C) Allosteric binding alters the enzyme's shape, which can enhance or reduce its activity. D) Allosteric binding occurs exclusively at the active site of the enzyme. Nonprotein helper molecules - Binding to these molecules promotes optimal conformation and function for their respective enzymes - Types: - Prosthetic groups: small molecules that are permanently attached to enzyme - Cofactors: inorganic ions - Ex: metal ions (Fe2+, Mg2+, Zn2+) - Ex. zinc binding to a DNA polymerase - Coenzymes: organic molecules - Ex: vitamins - Ex. vitamin C is a coenzyme for multiple enzymes that take part in building collagen  Feedback inhibition - End product of a pathway regulates the pathway itself - Using a reaction product to regulate its own further production - Ex: ATP is an allosteric regulator of some of the enzymes involved in sugar's catabolic breakdown - When relative ADP levels are high compared to ATP = the cell is triggered to produce  Organization of enzymes in a cell - Enzymes are present in specific parts of the cell based on function - Location depends on function - Some enzymes act as structural components of membranes - In eukaryotic cells, some enzymes reside in specific organelles - Enzymes for cellular respiration = in mitochondria - Enzymes for digesting cellular debris = in lysosomes  Practice Quiz: 3. In general, the hydrolysis of ATP drives cellular work by __________. 1. Which of the following reactions would be endergonic? a. Lowering the activation energy of the a. glucose + fructose → sucrose reaction b. HCl → H+ + Cl- b. Releasing heat c. C6H12O6 + 6 O2 → 6 CO2 + 6 H2O c. Changing to ADP and phosphate d. ATP → ADP + Pi d. Releasing free energy that can be e. All of the listed responses are coupled to other reactions correct. e. Acting as a catalyst 2. Consider the growth of a farmer's crop over a 4. How do enzymes lower activation season. Which of the following correctly states a energy? limitation imposed by the first or second law of a. by increasing reactivity of products thermodynamics? b. by locally concentrating the a. The process of photosynthesis produces energy that the reactants plant uses to grow. c. by harnessing heat energy to drive b. Growth of the crops must occur spontaneously. the breakage of bonds between c. To obey the first law, the crops must represent an open atoms system.