Unit 3 Exam Study Guide PDF

Unit 3: Transformations of Energy and Matter Overview of Energy and Metabolism (Chapter 3) 3.a Define metabolism, catabolism, and anabolism. Metabolism: All the chemical and physical activities in your body that use or convert energy. Catabolism: Breaks molecules down into smaller units to p...

Unit 3: Transformations of Energy and Matter Overview of Energy and Metabolism (Chapter 3) 3.a Define metabolism, catabolism, and anabolism. Metabolism: All the chemical and physical activities in your body that use or convert energy. Catabolism: Breaks molecules down into smaller units to produce energy Anabolism: Process that builds up body tissues and energy stores. 3.b Define energy and list the types of work performed by cells. Energy is the ability to do work Chemical Work: Synthesis of molecules Mechanical Work: Movement Transport Work: Moving molecules across membranes 3.c Compare and contrast biological oxidation and reduction reactions. Identify the relative “oxidation state” of carbon atoms in an organic molecule. In biological systems, oxidation refers to a reaction where a molecule loses electrons (or gains oxygen atoms), increasing its oxidation state, while reduction is where a molecule gains electrons (or loses oxygen atoms), decreasing its oxidation state 3.d Describe the role of activated carrier molecules in energy transformations. Activated carrier molecules store and transfer energy in cells. They capture energy from processes like food breakdown and release it to power other activities, such as muscle contraction or molecule synthesis. Enzymes and Other Protein Functions (Chapters 3 and 4) 4.j Define activation energy and describe the relationship between activation energy and the rate of a reaction. Activation energy is the minimum energy needed to start a chemical reaction. The higher the activation energy, the slower the reaction rate. Lowering activation energy makes reactions happen faster. 4.k Explain how enzymes increase the rate of chemical reactions. Define transition state and explain how activation energy is changed in enzyme-catalyzed reactions. Enzymes speed up chemical reactions by lowering the activation energy. They stabilize the transition state, which is the high-energy state between reactants and products, making the reaction easier to proceed. 4.l Define active site and substrate and explain how the active site of an enzyme determines its substrate specificity. Active site: The region on an enzyme where the substrate binds and the reaction occurs. Substrate: The specific molecule upon which an enzyme acts. The active site's shape and chemical properties are specific to the substrate, like a "lock and key," ensuring only the correct substrate binds. 4.m State the relationship between substrate concentration and rate of reaction (i.e. Michaelis-Menten equation) As substrate concentration increases, the reaction rate increases until it plateaus (saturation). The Michaelis-Menten equation models this relationship: Where v= reaction rate, Vmax= max rate, [S] = substrate concentration, Km​= substrate concentration at half Vmax 4.n Define Vmax and Km. Be able to determine the values of Vmax and Km given a graph of rate of reaction vs. substrate concentration. Vmax: The maximum reaction rate when the enzyme is fully saturated with substrate. Km: The substrate concentration at which the reaction rate is half of Vmax. 4.o Distinguish between reversible and irreversible enzyme inhibition. Reversible inhibition: Inhibitors bind non-covalently and can detach, restoring enzyme activity. Irreversible inhibition: Inhibitors bind covalently, permanently inactivating the enzyme. 4.p Compare and contrast competitive and non-competitive enzyme inhibition. Competitive inhibition: Inhibitor resembles the substrate and binds to the active site, blocking the substrate. Can be overcome by increasing substrate concentration. Non-competitive inhibition: Inhibitor binds to a site other than the active site, changing the enzyme’s shape and reducing its activity. Cannot be overcome by increasing substrate concentration. 4.q Describe how cofactors and coenzymes assist enzymes in catalyzing reactions. Cofactors: Inorganic molecules (e.g., metal ions) that help stabilize the enzyme or assist in the reaction. Coenzymes: Organic molecules (e.g., vitamins) that transfer chemical groups between molecules during the reaction. 4.r Explain how changes in temperature and pH affect enzyme activity. Temperature: Increasing temperature speeds up reactions to an optimal point, but extreme heat denatures enzymes, reducing activity. pH: Enzymes work best at an optimal pH. Too acidic or basic environments can alter the enzyme's structure, reducing activity. Getting Energy from Food (Chapter 13) 13.a Summarize the three major stages in which food molecules (proteins, polysaccharides, and fats) are broken down within cells. Digestion: Proteins, polysaccharides, and fats are broken down into amino acids, sugars, and fatty acids outside cells or in lysosomes. Glycolysis: Glucose is partially broken down in the cytoplasm to form pyruvate, generating a small amount of ATP and NADH. Oxidative Phosphorylation: Addition of inorganic phosphate to ADP, forming ATP, using the energy from oxidation of nutrient molecules 13.b Explain the purpose of glycolysis from a cellular perspective. Glycolysis breaks down glucose to produce ATP and NADH, providing cells with quick energy and molecules needed for further energy production. 13.c Name the overall inputs and outputs of glycolysis. Inputs: Glucose, 2 NAD+, 2 ADP, and 2 Pi Outputs: 2 Pyruvate, 2 NADH, 2 ATP (net gain) 13.d Describe, in general, what happens during the three major stages of glycolysis. Stage 1: Phosphorylation and Isomerization: glucose is activated by adding phosphate groups Stage 2: Cleavage: splits the molecule into two identical 3-carbon molecules Stage 3: Oxidation and ATP Generation: produces energy in the form of ATP by converting these 3-carbon molecules into pyruvate while also generating NADH 13.e Explain why cells need to regenerate NAD+ after glycolysis and describe how cells regenerate the NAD+ needed for glycolysis in the absence of oxygen (fermentation) and presence of oxygen (aerobic respiration). Cells need to regenerate NAD+ after glycolysis because NAD+ acts as an electron carrier that is essential for the process to continue. In the Absence of Oxygen (Fermentation): Cells regenerate NAD+ by converting pyruvate into lactic acid (in animals) or ethanol and CO2 (in yeast and plants). This allows glycolysis to continue even without oxygen. In the Presence of Oxygen (Aerobic Respiration): Pyruvate enters the mitochondria, where it’s further processed in the citric acid cycle, ultimately allowing NADH to transfer electrons to the electron transport chain, regenerating NAD+ and producing more ATP. 13.f Explain the role of acetyl CoA in the catabolism of sugars, fats, and proteins. Acetyl CoA carries small energy-rich pieces from broken-down sugars, fats, and proteins into a process called the citric acid cycle, where more energy can be extracted. (It’s like a delivery truck for energy molecules.) 13.g Describe the overall process of the citric acid cycle and oxidative phosphorylation. Citric Acid Cycle: A series of chemical reactions that take Acetyl CoA and produce energy carriers (like NADH and FADH2) and carbon dioxide as waste. Oxidative Phosphorylation: The energy carriers (NADH, FADH2) go to the electron transport chain, creating a "battery" to power ATP production, the energy currency of cells. Cell Signaling (Chapter 16) 16.a Describe the general components of signal transduction, including signals, receptors, effectors, second messengers, and cellular response. Signal transduction is like a relay race: 1. Signal: The "start" (e.g., hormones). 2. Receptor: The "receiver" on a cell's surface or inside it. 3. Effector: The "worker" inside the cell that makes changes. 4. Second messengers: Molecules that carry the message inside the cell. 5. Response: The final "action," like turning a gene on or off. 16.b Explain, using specific examples, how cell signaling leads to changes incell physiology or behavior. Example: Adrenaline signaling 1. Adrenaline binds to receptors on muscle cells. 2. This activates a cascade inside the cell. 3. The result: muscle cells break down glycogen into glucose for energy, preparing the body for action. 16.c Define ligand and list examples of extracellular signaling molecules. Ligand: A molecule that binds to a receptor to start signaling. **Examples: hormones like insulin, neurotransmitters like dopamine.** 16.d Define and distinguish between autocrine, paracrine, endocrine, and contact-dependent signaling. Autocrine: A cell signals itself (like writing yourself a note). Paracrine: A cell signals nearby cells (like talking to a neighbor). Endocrine: A cell sends signals through the bloodstream to far-away cells (like sending mail). Contact-dependent: A cell signals another by touching it (like a handshake). 16.e Compare and contrast between the following types of receptors: ion channel receptors, G-Protein Coupled Receptors (GCPRs), Receptor Tyrosine Kinases (RTKs), and nuclear receptors. Ion channel receptors: Open doors for ions like calcium when a signal comes. G-Protein Coupled Receptors (GPCRs): Start a cascade inside the cell using G proteins. Receptor Tyrosine Kinases (RTKs): Activate multiple pathways by adding "tags" (phosphate groups). Nuclear receptors: Work inside the cell and turn genes on/off 16.f Describe the general mechanism of signal transduction through G-Protein Coupled Receptors, including the activation of G Proteins and the specific downstream signaling molecules. 1) A signal binds to the GPCR. 2) The GPCR activates a G protein inside the cell. 3) The G protein turns on other molecules (like enzymes) to create a response. 16.g Describe the general mechanism of signal transduction through Receptor Tyrosine Kinases, including the activation of RTKs and the specific downstream signaling molecules. 1) A signal binds to the RTK, making it pair up with another RTK. 2) The RTK adds phosphate "tags" to itself. 3) These tags recruit other molecules to start signaling. 16.h Define second messenger and give specific examples of second messengers and their effects on cell signaling pathways. Second messengers: Molecules like cAMP or calcium that spread the message inside the cell. **Example: cAMP activates enzymes that help cells respond to adrenaline.** 16.i Compare and contrast the molecular mechanisms of membrane receptor-mediated and nuclear receptor-mediated signal transduction. Membrane receptors: Signals start at the surface and are relayed inside. Nuclear receptors: Signals pass through the membrane and directly control DNA. Energy Generation in Mitochondria and Chloroplasts (Chapter 14) Mitochondria and Aerobic Respiration 14.b Describe the electron transport chain in detail, including the flow of electrons through the electron transport chain, and the establishment of the electrochemical proton gradient. Electron Transport Chain (ETC): Electrons from NADH/FADH₂ flow through protein complexes (I-IV). Energy from electrons pumps protons into the intermembrane space, creating an electrochemical gradient. 14.c Describe chemiosmotic coupling, the proton motive force, and how the FoF1 ATP synthase complex synthesizes ATP, including the role of each of its subunits, and the conformational changes of the β subunits. Chemiosmotic coupling: Protons flow back into the mitochondria through ATP synthase, like water through a turbine. FoF1 ATP synthase: Fo part: Lets protons flow through. F1 part: Spins and makes ATP by changing the shape of its β subunits. β subunits: Rotate and change shape to bind ADP, synthesize ATP, and release it.