AP Biology Unit 3 Study Guide 2022-23 PDF

AP Biology Unit 3 Study Guide Chapter 6 – Terms to know: metabolic pathway​ ​ ​ enzyme​ ​ ​ ​ anabolism catabolism​ ​ ​ ​ kinetic energy​​ ​ ​ potential energy entropy​...

AP Biology Unit 3 Study Guide Chapter 6 – Terms to know: metabolic pathway​ ​ ​ enzyme​ ​ ​ ​ anabolism catabolism​ ​ ​ ​ kinetic energy​​ ​ ​ potential energy entropy​ ​ ​ ​ spontaneous process​ ​ ​ free energy equilibrium​ ​ ​ ​ exergonic​ ​ ​ ​ endergonic ATP​ ​ ​ ​ ​ energy coupling​ ​ ​ phosphorylation substrate​ ​ ​ ​ enzyme-substrate complex​ ​ active site cofactors (types)​ ​ ​ noncompetitive inhibitor​ ​ competitive inhibitor allosteric regulation​ ​ ​ Concepts to know: ​ The forms of energy and the way one type of energy can be converted to another o​ Kinetic energy: energy an object possesses due to its motion – amount of KE an object has depends on its mass and velocity → can be converted into PE (object being lifted), heat (due to friction), or electrical energy (turbines in power plants) o​ Potential energy: energy stored in an object due to its position, shape, or state → can be converted into KE when an object is allowed to fall or move, or other forms like heat or electrical energy (water in a dam has PE, when it starts flowing, that water is now KE, then it is converted into electricity by turbines) o​ Thermal energy: internal energy of an object due to the random motion of its molecules – faster the molecules move, the higher the temp, vice versa → can be converted into mechanical energy, electrical energy, or even light o​ Chemical energy: stored in the bonds of atoms and molecules – energy released in a chemical reaction → can be converted into thermal energy, KE, electrical energy o​ Electrical energy: associated with the movement of electrons through a conductor → can be converted into light, heat, or mechanical energy ​ In general, know the implications of the first and second laws of thermodynamics in relation to energy transfer in organisms. o​ 1st law: energy cannot be created nor destroyed, it can only be changed from one form into another ▪​ for organisms: energy expenditure (organisms must obtain energy from external sources and convert it into various forms to carry out metabolic processes), metabolism (chemical energy is broken down during digestion and cellular respiration, being converted into ATP for cellular work), energy balance (organisms must balance the energy they intake with the energy they expend) o​ 2nd law: in any energy conversion or transfer, the total entropy (disorder) of an isolated system with always increase over time → means that energy transformations are not perfectly efficient, and some energy is always lost as heat, which increases the system’s disorder ▪​ for organisms: not all energy from food or sunlight is converted into useful work (like growth, movement or reproduction) → this is why organisms need a constant input of energy from their environment to maintain order and function. organisms produce heat  as a byproduct of energy conversion, which is not useful for doing work but plays an important role in maintaining body temperature (the heat produced by metabolic processes is also a key reason why living systems are not perfectly efficient). Lastly, all biochemical reactions in organisms increase entropy to some degree (the breakdown of glucose in cellular respiration releases energy in the form of ATP but also produces waste products like CO2 and H2O and some energy is released as heat, both increasing the overall entropy of the system) ​ The usefulness of ΔG in relation to metabolism (endergonic, exergonic). o​ changeG is a crucial concept that helps us understand the energy dynamics of chemical reactions, mainly those involved in metabolism o​ changeG tells us whether a reaction can occur spontaneously and whether it will release or consume energy o​ In metabolism: ▪​ exergonic reactions: release of energy – associated with catabolic processes (ex. cellular respiration) (changeG < 0) ▪​ endergonic reactions: require energy input – associated with anabolic processes (ex. protein synthesis, DNA replication, muscle contraction) (changeG > 0) ▪​ Organisms rely on coupling exergonic and endergonic reactions to ensure that necessary biochemical processes can proceed efficiently ​ The structure of ATP and the way we explain energy storage in the bonds between phosphates. o​ ATP = adenosine triphosphate ▪​ contains: adenine (nitrogenous base), ribose (5 carbon sugar), phosphate groups o​ The energy in ATP is stored primarily in the high-energy bonds between the phosphate groups – there is a significant amount of energy released when they are broken o​ The bonds between phosphates are broken when ATP is hydrolyzed (water added) into ADP and an inorganic phosphate + energy o​ ATP is an efficient energy carrier because it provides a moderate energy yield per hydrolysis event. Also, ATP can be quickly regenerated through processes like cellular respiration or photosynthesis o​ ATP is often coupled with endergonic (energy-requiring) reactions which allows cells to perform work ​ Have an understanding of energy coupling combining an endergonic process with hydrolysis of ATP o​ involves linking an endergonic reaction with an exergonic reaction o​ ATP hydrolysis is exergonic (releases energy), while many essential biological processes are endergonic, meaning they require energy input. By coupling these two types of reactions, cells can harness energy is a controlled manner to carry out functions that would otherwise be impossible o​ How it works: ▪​ ATP is hydrolyzed, releasing energy → this energy is now available for cellular work ▪​ An endergonic reaction (like protein synthesis, muscle contraction, active transport, or DNA replication) is now coupled with the exergonic reaction → ATP energy is transferred to one of these reactions (through the process of phosphorylation – phosphate group of ATP is transferred to a molecule in the endergonic reaction)  ▪​ So, the energy released by the exergonic hydrolysis of ATP is used to power endergonic reactions, letting the cell perform necessary biochemical tasks ​ Types of “work.” o​ “work” refers to the energy used to perform tasks or drive processes → the energy for all types of work in living organisms comes from chemical energy, usually in the form of ATP o​ Types of work: ▪​ Chemical work: the energy required to drive endergonic reactions (protein synthesis, DNA replication, metabolic pathways ▪​ Transport work: the movement of molecules or ions across membranes, typically against their concentration gradient (requiring energy) (ex. active transport, vesicular transport, endocytosis or exocytosis – process of taking in materials or expelling materials) ▪​ Mechanical work: involves physical movement or changes in the shape of a structure (ex. muscle contraction, cell division, ciliary and flagellar movement, intracellular transport) ▪​ Electrical work: most commonly seen in excitable cells (like neurons and muscle cells) (ex. action potentials in neurons, cardiac muscle contraction, electrochemical gradient maintenance) ​ The ADP – ATP cycle. o​ the continuous conversion of ADP to ATP o​ ​ How phosphorylation is related to the concept of conformational change in proteins (hint: think about the conditions that determine tertiary structure). o​ Phosphorylation: the addition of a phosphate group to a molecule, resulting in a change in the proteins structure, which in turn, affects its function o​ When the phosphate group (negatively charged), attaches to a protein, it can push apart or attract other parts of the protein, causing the protein to fold differently (conformational change) o​ the addition of a phosphate group can disrupt or create new interactions between the protein’s parts, causing it to change shape o​ phosphorylation can also make parts of the protein more hydrophilic or hydrophobic, which can push the protein to fold differently, exposing or hiding certain areas of the protein o​ In most cases, phosphorylation helps proteins act like switches in pathways that send signals inside cells, telling them what to do ​ The role of activation energy in chemical reactions and how (structurally, etc.) enzymes serve to lower this. o​ in a chemical reaction, a certain amount of energy is needed to start the reaction, called the activation energy (Ea) o​ Enzymes help speed up chemical reactions by lowering the activation energy o​ How they do this: ▪​ enzymes bring the molecules that need to react close together, making it easier for them to interact ▪​ Enzymes can change the shape of the molecules (substrates) so that bonds are weaker and easier to break ▪​ enzymes can create a special area (called active site) where the reaction can happen more easily ▪​ enzymes can also use “helpers” like vitamins or metal ions (coenzymes) to assist in the reaction and lower the energy needed ​ The induced-fit modification to the lock and key hypothesis for enzyme function. o​ Lock and key model suggests that the enzyme’s active site (lock) has a perfectly shaped spot that fits exactly with the substrate (key) o​ Induced-fit model shows that the enzyme’s active site changes shape slightly when the substrate binds to it ▪​ instead of the enzyme’s active site being a perfect fit from the start, the enzyme adapts to better fit the substrate once it binds → helps the enzyme hold the substrate in the best position for the reaction to occur ​ How temperature, pH, and substrate concentration affect the rate of enzyme function. o​ Temperature: ▪​ in low temps, enzymes work slowly because molecules move less and have less energy ▪​ enzymes work best at a certain temperature (around body temp) ▪​ If it gets too hot, enzymes can denature (lose their shape) and they will not work at all o​ pH: ▪​ enzymes have an optimal pH where they work best (each is different depending on where it is working) ▪​ if the pH is too low or high, the enzyme’s shape can change, and it might stop working because it can’t bind to the substrate properly o​ Substrate concentration: ▪​ if there is a low substrate concentration, the enzyme has less to work on, so the reaction happens slowly ▪​ As more substrate is added, the rate of reaction increases because there’s more for the enzyme to act on ▪​ if there’s too much substrate, all the enzyme’s active sites get filled up, and the reaction rate levels off ​ Allosteric regulation of enzymes and the two basic methods of enzyme inhibition. o​ Allosteric regulation happens when a molecule binds to a part of an enzyme called the “allosteric site” (a site other than the active site where the substrate binds) → when this molecule binds, it changes the shape of the enzyme, which can either activate or inhibit the enzyme’s activity ▪​ Activation: when the activator binds to the allosteric site, it changes the enzyme’s shape so that the active site fits better with the substrate, increasing the enzyme’s activity ▪​ Inhibition: when an inhibitor binds to the allosteric site, it changes the enzyme’s shape in a way that prevents the substrate from fitting properly, decreasing the enzyme’s activity o​ Competitive inhibition: ▪​ an inhibitor molecule competes with the substrate for the same active site on the enzyme ▪​ If the inhibitor binds to the active site, the substrate can’t bind, so the reaction is blocked ▪​ Adding more substrate can outcompete the inhibitor o​ Non-competitive inhibition: ▪​ the inhibitor binds to a different site on the enzyme (not the active site) ▪​ This changes the enzyme’s shape so the active site no longer works properly, and the substrate can’t bind effectively ▪​ cannot be overcome by adding more substrate ​ How feedback inhibition is used to regulate enzyme activity. o​ feedback inhibition is a way for cells to regulate enzyme activity and prevent overproduction of a product o​ a self regulating mechanism that helps maintain balance in biochemical pathways o​ How it works: ▪​ 1. in a metabolic pathway, the final product of the pathway can act as an inhibitor for the first enzyme in the pathway ▪​ 2. when the cell has enough of the end product, it binds to the first enzyme and stops it from working ▪​ 3. this prevents the cells from making more of the product than it needs o​ Example: when a heater is on, it has to get to a certain degree before it turns off, then when it gets too cold, it turns on again ​ Why ΔG cannot be equal to zero. o​ at changeG = 0, the state is in equilibrium, meaning that no net work can be done, and no energy is available for useful work o​ Reactions must be able to proceed in a way that provides energy for processes like muscle movement, protein synthesis, and other essential activities o​ if deltaG were exactly 0, it would mean no energy is available to drive these processes ▪​ deltaG is negative, it means a spontaneous process is taking place  ▪​ deltaG is positive, it means energy input is required Chapter 7 – Terms to know: glycolysis​ ​ ​ ​ ​ ADP oxidation​ ​ ​ ​ reduction​ ​ ​ ​ respiration aerobic​​ ​ ​ ​ anaerobic​ ​ ​ ​ fermentation alcohol fermentation​ ​ ​ lactic acid​ ​ ​ ​ acetyl coenzyme Kreb’s (citric) cycle​ ​ ​ electron transport chain​ ​ matrix hydrogen acceptor​ ​ ​ ​ ​ ​ NAD+ electrochemical gradient​ ​ proton pump​ ​ ​ ​ cristae ​ ​ chemical energy​ ​ ​ ​ ​ dehydrogenase​​ ​ ​ chemiosmosis​ ATP synthase​ ​ ​ ​ electronegativity​ ​ ​ facultative anaerobe deamination​ ​ ​ ​ oxidizing agent​ ​ ​ reducing agent proton motive force​ ​ ​ cytochromes​ ​ ​ ​ acetyl CoA glyceraldehyde-3-phosphate​ ​ pyruvate​ ​ ​ ​ obligate anaerobe Concepts to know: ​ ADP – ATP cycle ​ Energy coupling mechanisms (i.e. proton motive force) ​ How energy (potential) is stored in food ​ The molecular components of ATP ​ The role of coenzymes as hydrogen/electron acceptors (such as NAD+ and FAD) ​ Know what happens in each of the three phases of respiration ​ Detail both types of anaerobic pathways and why pyruvate must be modified during anaerobic respiration. ​ Be able to explain what is actually happening in the inner membrane of the mitochondria as energy from electrons is used to pump protons to an area of high concentration ​ What causes electrons to move through an electron transport chain. (and the consideration of oxygen as the final electron acceptor.) ​ The chemical reaction for respiration  ​ Be able to contrast types of phosphorylation (substrate-level and oxidative versions). ​ What happens when oxygen concentrations are low (alternatives to aerobic res.) ​ Facultative vs. obligate anaerobes. ​ Alternate metabolic pathways for proteins and fats, etc. ​ Redox reactions in covalent compounds (relationship to electronegativity changes) Chapter 8 - Terms to know: autotroph​ ​ ​ ​ heterotroph​ ​ ​ mesophyll stroma​ ​ ​ ​ grana​ ​ ​ ​ thylakoid membrane stomata​ ​ ​ ​ chlorophyll​ ​ ​ photophosphorylation carbon fixation​ ​ ​ NADPH​ ​ ​ antioxidant photosystems I and II​ ​ primary electron acceptor​ reaction center photon​ ​ ​ ​ ground state​ ​ ​ excited state cyclic photophosphorylation​ photorespiration​ ​ RuBisCO G3P​ ​ ​ ​ 3-PGA​​ ​ ​ PEP PEP carboxylase​ ​ ​ CAM plants​ ​ ​ pigment noncyclic photophosphorylation oxaloacetate​ ​ ​ malate Concepts to know: ​ The nature of light as a form of energy and the concept of energy transfer in photosynthesis. (endergonic, +∆G, nonspontaneous, etc.) ​ Origin of oxygenated atmosphere using prokaryotic cyanobacteria (hypothesis) ​ How the structure of common leaves represents a good adaptation for carrying out photosynthesis. (See pg 157) ​ The relationship between wavelengths of light, their frequencies and the energy associated with them. Then recall how chlorophyll absorbs this light energy. ​ The structure of chloroplasts, especially internal membranes that produce ATP ​ What an absorption spectrum communicates and why these are important. ​ The two main stages of photosynthesis and the way in which they are related. ​ Be able to describe the operation of photosystems and the function of water in the light-dependent reactions. Knowledge of the coordinated pathway that serves to capture light. ​ The phases of the Calvin cycle. ​ The similarities in the way chemiosmosis functions in both mitochondria and chloroplasts. ​ Adaptations to excess radiant energy, heat and photorespiration (including vitamin production/antioxidants, cyclic photophosphorylation and the differences between C3 and C4 photosynthesis). ​ Different leaf structures for C-3 and C-4 plants.