AP BIO Unit 3 Study Guide PDF

Topic 1: Metabolism Metabolism: The totality of an organisms chemical reactions ➔​ All of the chemical reactions in an organism Metabolic pathways: A series of chemical reactions that either build complex molecules or break down complex molecules ➔​ Each step of the pathway is catalyzed by a...

Topic 1: Metabolism Metabolism: The totality of an organisms chemical reactions ➔​ All of the chemical reactions in an organism Metabolic pathways: A series of chemical reactions that either build complex molecules or break down complex molecules ➔​ Each step of the pathway is catalyzed by a specific enzyme Catabolic pathway: Pathways that release energy by breaking down complex molecules ➔​ Leads to the release of energy by the breakdown of complex molecules to simpler ones ➔​ Ex: digestive enzymes breaking down food to release energy ➔​ Cellular respiration Anabolic pathway: pathways that consume energy to build complicated molecules from simpler ones. ➔​ Ex: photosynthesis ➔​ Ex: your body linking together amino acids to form muscle protein Energy: the capacity/ability to do work Kinetic energy: energy associated with motion ➔​ Anything that is moving is said to possess kinetic energy Thermal energy: kinetic energy associated with the random movement of atoms or molecules Potential energy: stored energy ➔​ Energy that objects possess because of their structure or position Chemical energy: potential energy available for release in a chemical reaction ➔​ Complex molecules like glucose are high in chemical energy Laws of Thermodynamics Thermodynamics: The study of energy transformations that occur in matter First law of thermodynamics: Energy cannot be created or destroyed, but only transferred and transofrmed ➔​ The principle of conservation of energy ➔​ The electric company doesnt make energy but merely converts it to a form of energy that is convenient Second law of thermodynamics: every energy transfer or transformation increases the entropy in the universe ➔​ Entropy: a measure of molecular disorder, or randomness ➔​ During energy transformatoon, some energy is unstable and lost as heat Free Energy Free energy: the part of a systems energy that is available to preform work at a uniform temperature ➔​ ΔG is the symbol for a change free energy ➔​ The free energy change determines whether or not the reaction occurs spontanelousy Spontaneous process: A process that occurs without an overall input of energy ➔​ A process that is energetically favorable Exergonic reaction: Reactions that release energy ➔​ I.e. cellular respiration ➔​ Exergonic reactions are spontaneous, energetically favorable ➔​ ΔG < 0 Endergonic reactions: reactions that absorb energy ➔​ I.e photosynthesis ➔​ Endergonic reactions are not spontaneous, they absorb free energy ➔​ ΔG> 0 ATP Adenosine triphosphate (ATP): molecule that organisms use as a source of work ➔​ ATP couples exergonic reactions to endergonic reactions to power cellular work ➔​ ATP is made up out of 3 phosphate groups, a ribose sugar, and nitrogenous base adensine. ➔​ When a phosphate group is hydrolyzed, energy is released in an exergonic process. Energy coupling: the use of an exergonic process to drive an endergonic one. ➔​ The exergonic release of the phosphate group from ATP is used to do endergonic work. Phosphorylation: the released phosphate molecule from ATP moves to another molecule to give it energy Enzymes Catalysts: substances that can change the rate of a reaction without being altered in the process Enzymes: macromolecules that are biological catalysts ➔​ Enzymes are macromolecules that catalyze (speed up) reactions by lowering the activation energy ➔​ Enzymes are not consumed by the reaction, end in ase, and are a type or protein Activation energy: the amount of energy it takes to start a reaction ➔​ The amount of energy it takes to break the bonds of a reactant ➔​ Enzymes speed up reactions by lowering the activation energy, the amount of energy it takes to start a reaction Enzyme structure Substrate: the reactant an enzyme acts on Active site: area for substrate to bind Enzyme-substrate complex: A temporary complex formed when an enzyme binds to a substrate ➔​ While the enzyme and substrate are joined, the catalytic action of the enzyme converts the substrate to a product ➔​ The enzyme substrate complex is held together by weak interactions ➔​ The active site opens → substrates are held in the active site with weak interactions →the substrates are converted to products → the products are released Induced fit: enzymes will change the shape of their active site to allow the substrate to bind better Effects on enzymes: -​ Enzymes are proteins, which means their 3D shape can be affected by external factors -​ The efficiency of enzymes can be affected by pH, temperature, or chemicals -​ A change in shape means a change in function Optimal conditions: the conditions that allow enzymes to function optimally (at their best) -​ The rate of enzyme activity increases with temperature up to a certain point, after a certain point the enzyme will denature -​ Enzymes function best at a specific pH Cofactors: non-protein molecules that assist enzyme function -​ Inorganic cofactors consist of metals -​ Cofactors can be bound or loosely attacked -​ Holoenzymes: enzymes with the cofactor attached Coenzymes: organic factors -​ An example of a coenzyme is a vitamin Enzyme inhibitors: reduce the activity of a specific enzyme -​ Enzyme inhibition can be permanent or reversible -​ Permanent inhibition is usually done by poisons and toxins, it is when the inhibitor binds with covalent bonds -​ Reversible inhibition is usually held by weak interactions Competitve inhibitors: reversible inhibitors that compere with the substrate for the active site on the enzyme -​ Inhibition can be reversed by increasing the substrate concentration -​ Competitive inhibitors reduce enzyme activity by blocking subtsrtaes from binding to the active site Noncompetitive inhibitors: bind to an area other than the active site (allosteric site) which changes the shape of the active site, preventing the substrtate from binding Cells regulate their metabolic pathway by controlling when and where enzymes go off Allosteric regulation Allosteric enzymes have two binding sites -​ The active site -​ The allosteric site Allosteric site: a specific binding site but not the active site Allosteric regulation: when molecules bind to an allosteric site which can change the shape and function of the active site. -​ Once an regulator binds to an allosteric site it can either change the shape of the active site to inhibit or stimulate enzyme activity Allosteric activator: substrate binds to the allosteric site and the stabilizes the shape of the active site so that it remains open Allosteric inhibitor: substrate binds to the active site and stablizes the shape of the enzyme so that it closes Cooperativity: Substrate binds to one active site and the rest are stimulated in th process. -​ considered allosteric regulation since binding at one site changes the shape of other sites Feedback inhibition: the end product of an enzymatic pathway can switch off it's pathway by binding to the allosteric site of an early enzyme in the pathway -​ Feedback inhibition increases the efficiency of the pathway by turning it off when the end product accumulates in the cell Topic 2: Cellular respiration Cellular respiration: cells harvest chemical energy from organic molecules and use it to make ATP Catabolic pathways occur when molecules are broken down and their energy is released. Two catabolic pathways are fermentation and aerobic respiration The formula for cellular respiration is C6H12O6 + 6O2 → 6CO2 + 6H20 + energy -​ Starch is the major source of fuel for animals, it breaks down to glucose Energy harvest: Energy is released as electrons fall from organic molecules to O2 Glucose → NADH → ETC → O2 -​ The coenzyme NAD+ is an electron carrier -​ NAD+ picks up 2e- and 2H to make NADH which stores electrons -​ NADH carries electrons to the electron transport chain (ETC) -​ The electron transport chain transfers electrons to oxygen to make H20 which releases energy Substrate level phosphorylation: formation of ATP by direct transfer of a phosphate group to ADP. -​ Substrate level phosphorylation generates a small amount of ATP The three states of cellular respiration is glycolysis, pyruvate oxidation + the krebs cycle , and the electron transport chain. Glycolysis: degradation of glucose begins as it is broken down into two pyruvate molecyles. -​ Glycolysis occurs in the cytosol and splits glucose (6C) into 2 pyruvate (3C) -​ In glycolysis there are two steps, the energy investment phase and the energy pay off phase -​ In the energy investment phase, 2 ATP is used to detsablize glucose -​ In the energy pay off phase, 4 ATP are produced by substrate level phosphorylation -​ ATP generates a net 2 ATP, 2 NADH, and 2 pyruvate Stage 2: pyruvate oxidation + the citric acid cycle Pyruvate oxidation: pyruvate is reduced to Acetyl-coA in the mitochondrial matrix -​ A transport protein moves pyruvate from the cytosol to the mitochondrial matrix -​ In this process a Co2 molecule is removed from the pyruvate, electrons are stripped away to create NADH from NAD+, and CoenzymeA joins with the remaining two carbon to form Acetyl-Coa -​ Pyruvate oxidation creates Co2 and NADH Citric acid cycle: Acetyl-CoA enters and CO2, NADH, -​ The krebs cycle occurs in the mitochondrial matrix -​ In the citric acid cycle, the job of breaking down glucose is completed with co2 as a byproduct -​ Each turn of the citric acid cycle requires one acetyl coa, the cycle must turn twice to break down one glucose -​ The outputs of the citric acid cycle are 4 CO2, 2 ATP, 2 FADH2, and 6 NADH -​ ATP is produced by substrate level phosphorylation in the matrix Stage 3: Oxidative phosphorylation Oxidiative phosphorylation is combined with two parts. The electron transport chain + chemiosmosis -​ The electron transport chain occurs in the inner membrane of the mitochondria -​ It produces 26-28 ATP by oxidative phosphorylation -​ Chemiosmosis is when H+ ions are pumped across inner mitochondrial matrix -​ H+ diffuse through ATP synthase (ADP + P → ATP) -​ Oxidative phosphorylation is the term used because ADP is phosphorylated and oxygen is necessary to keep the electrons flowing Electron transport chain -​ The ETC is embedded in the inner mitochondrial membrane. -​ The ETC consists of 3 transmembrane proteins and non-protein complexes -​ The ETC is powdered by electrons from the electron carrier molecules NADH and FADH2. -​ Alternates between reduced/oxidized states as they accept/donate electrons -​ As electrons flow through the electron chain, the loss of energy by the electrons is used to power the pumping of protons across the inner membrane -​ At the end of the electron transport chain, the electrons combine with two hydrogen ions and oxygen to form water. -​ When O2 is not present the ETC comes to a halt and the production of ATP is not produced. Chemiosmis: Energy coupling mechanism -​ The hydrogen ions flow back down their gradient through transmembrane protein ATP synthase -​ ATP synthases uses the proton-motive force to phosphorylate ADP, forming ATP -​ The proton motive force is in place because the membrane is impermeable to hydrogen ions -​ Chemiosmosis is an energy coupling process that uses the energy stored in the form of an H+ gradient across a membrane to drive cellular wore -​ Chemiosmis is an H+ gradient across the membrane that drives cellular work -​ Proton motive-force: use the proton gradient to preform work -​ ATP synthase: an enzyme that makes ATP Anaerobic respiration: generates ATP without oxygen using the electron transport chain -​ Generate ATP using other electron acceptors that are not oxygen Obligate anaerobes: survive in the absence of oxygen -​ Cannot survive in the presence of oxygen Falculative anaerobes: can make ATP by aerobic respiration (with O2 present) or switch to fermentation without O2 present Fermentation: an expansion of glucose in which ATP is generated by substrate level phosphorylation -​ Fermentation consists of glycolysis and reactions that replenish NAD+ -​ NAD+ is the electron acceptor in glycolysis Alcholol fermentation: pyruvate is converted to ethanol, releasing carbon dioxide and oxiding NADH in the process to create more NAD+ Lactic acid fermentation: pyruvate is reduced by NADH and NAD+ is formed in the process, lactate is a waste product Phosphofrucktokinase: an allosteric enzyme that controls the rate of glycolysis and citric acid cycle. -​ PFK is inhibited by high levels of ATP Topic 3: Photosynthesis Photosynthesis: the conversion of light energy to chemical energy -​ Plants are autotrophs Autotrophs: Organisms that make their own food from simple substances in their surroundings -​ Autotrophs are producers Heterotrophs: Organisms that are unable to make their own food so they live off of other organisms -​ Heteroautotrophs are consumers Photosynthesis first evolved in prokaryotic organisms Cyanobacteria: early prokaryotes capable of photosynthesis -​ Cyanobacteria oxygneated the atmosphere of early earth Photosynthesis takes place in the chloroplasts of plants Chloroplasts: organelle for the location of photosynthesis -​ Chrloplasts are found in the mesophyll which is the cells that make up the interior tissue of the leaf  -​ Stomata: pores in leaves that allow CO2 to enter and O2 to leave -​ Stroma: liquid fluid in the cholorplast -​ Thykaloid: intermembrane sacs -​ Granum: stacks of thykaloids -​ Chrolophyll: green pigment in thykaloid membranes The formula for photosynthesis is 6H2O + 6CO2 → C6H12O6 + 6O2 -​ Photosynthesis splits H2O into H and O -​ In photosynthesis, the electrons are transferred with H+ to CO2, reducing it to sugar The two stages of photosynthesis are the light reactions and the calvin cycle Light: electromagnetic energy -​ Light is made up of particles called photons -​ Light travels in waves -​ Wavelength: the distance between one crest and another -​ A shorter wavelength means more energy and a longer wavelength means less energy -​ When light interacts with matter it can be reflected, absorbed, or transmitted Pigment: substances that absorb light -​ The color we see are the reflected wavelengths -​ Chlorophyll absorbs violet-blue and red and reflects green Chrolophyll a: primary pigment that is green/blue. -​ Chlorophyll a is involved in the light reactions Chrolophyll b: secondary/accessory yellow/green pigment Carotenoids: pigments that broaden the spectrum of energy absorbed by photosynthesis by picking up colors that photosynthetic pigments like chlorophyll usually wouldnt be able to absorb -​ Carotenoids are yellow/orange pigments Photoprotection: carotenoids offer photoprotection by absorbing and dissipating excess energy that could damage chlorophyll or interact with oxygen The light reactions occur in the thylakoid membrane and convert light energy to chemical energy -​ The net products of the light reactions are NADPH, ATP, and oxygen 1.​ Light energy is absorbed by the chlorophyll, which drives the transfer of electrons from water to NADP+ forming NADPH 2.​ Water is split during these reactions and O2 is released 3.​ ATP is generated using chemiosmosis to power the addition of a phosphate group to ADP Chrolophyll absorbs a photon of light -​ The electrons are excited and taken from ground state to an excited state -​ The electron is unstable so it falls back down to ground state  -​ As the electron falls to ground state it releases energy/heat and omits light as fluroersecne Photosystems: reaction centers and light capturing complexes. Light capturing complexes: Full of pigments associated with proteins that pass energy along -​ The pigments get excited and pass their energy on as they fall to their ground state -​ They keep passing their electrons on and on like a wave Reaction center: consists of chlorophyll a pair and a primary electron acceptor -​ The chlorophyll a pair doesnt pass the energy on but instead gives it to a primary electron acceptor. -​ The primary electron acceptor then donates electrons to the ETC Photosystem 2: reaction center P680 Photosystem 1: reaction center P700 In photosystem 2: -​ Light energy excites electrons and they pass on energy until they meet chlophyll a pair P680. -​ The electrons are passed to chlorophyll a pair P680 before P680 passes it to the primary electron acceptor -​ This creates P680+ which is reduced back to P680 through an electron from the splitting of water -​ H2O is split into 2e- which reduces P680+, the 2 Hydrogen are released into the thykaloid space, and the oxygen bonds to another oxygen and then is released as a byproduct Generation of ATP: -​ The fall of electrons from photosytem two to photosystem 1 provides energy to form ATP -​ The H+ gradient is a form of potential energy -​ ATP synthase couples the diffusion of H+ to the formation of ATP In photosystem 1: -​ The primary electron acceptor of photosystem 1 passes the excited electrons along the ETC, which transmits them to NADP+ which is reduced to NADPH. -​ The two important light reaction products are NADPH and ATP The inputs of the light reaction are H20, light energy, NADP+, and ADP + P The outputs are O2, ATP, NADPH Calvin Cycle The calvin cycle uses ATP and NADPH to reduce CO2 to sugar. -​ For net synthesis of one G3P molecule, the calvin cycle has to take place 3 times The three phases of the calvin cycle are fixation, reduction, and regeneration 1, Carbon Fixation -​ Co2 is fixed onto 5 carbon sugar RuBP, this process is facilitated by enzyme rubisco -​ A 6 carbon molecule is created that is highly unstable and has to be split into 2 3 carbon molecules named 3-phosphoglycerate 2. Reduction -​ 3 phosphoglycerate is phopsphorylated by ATP to becomes 1,3-biphosphoglycerate -​ 1,3-biphosphoglycerate is donated electrons from 6 NADPH to become G3P -​ 6 molecules of G3P are formed but only 1 is exited out the cycle while the remaining 5 remain to regenerate the cycle 3. Regeneration -​ The 5 remaining G3P molecules are rearranged to form 3 RuBP molecules -​ 3 ATP are used for regeneration -​ Cycle is now ready to take in Co2 again The production of one G3P molecules using 9 ATP molecules and 6 NADPH molecules. The inputs of the calvin cycle are 3 Co2, 6 NADPH, and 9 ATP. The outputs of the calvin cycle are 1 G3P, 6 NADP+, and 9 ADP C4, cam plants Photorespiration: -​ On hot sunny days the plants stomata closes to stop water loss -​ This means less co2 is present and more oxygen is available -​ Because more Oxygen is available this leads to photorespiration which is when rubisco fixes oxygen onto RuBP -​ Photorespiration is bad for the plant because no sugar is produced C4 plants: -​ Spatial separation of plants so that O2 isnt in close proximity with rubisco/RuBP -​ Mesophyll cells fix Co2 into 4-C molecule that is transferred to bundle sheath cells - they release CO2 to be used in the calvin cycle CAM plants -​ Open during the night and close during the day -​ Co2 is incorporated into organic acids and stored in vacuoles -​ During the day, light reactions occur and Co2 is released from organic acids and incorporated into the calvin cycle.