Cell Biology Exam 4 Study Guide Fall 2024 PDF

EXAM 4 STUDY GUIDE CELL BIOLOGY Fall 2024 Note: this study guide contains many of the key concepts we have discussed in class. However, it does not necessarily contain everything that may be on the exam. Therefore, it is still very important that you are also reading the assigned textbook chapters...

EXAM 4 STUDY GUIDE CELL BIOLOGY Fall 2024 Note: this study guide contains many of the key concepts we have discussed in class. However, it does not necessarily contain everything that may be on the exam. Therefore, it is still very important that you are also reading the assigned textbook chapters in addition to studying the lecture slides. Chapter 13 Cellular Respiration is process by which cells harvest energy stored in food molecules. Energy released from food is captured in form of high-energy chemical bonds in activated carriers such as ATP & NADH. Activated carriers are small molecules that store energy in a high-energy linkage. Redox or Oxidation-reduction reaction: Reaction in which electrons are transferred from one chemical species (atoms, ions, molecules) to another. Depends on free-energy change (ΔG) for electron transfer. Redox pairs: Pairs of compounds such as NADH & NAD+ that can be interconverted by gain or loss of an electron. NADH is a strong electron donor à ΔG is highly favorable The breakdown of food molecules or catabolism occurs in 3 stages: 1. Digestion: breakdown of large food molecules by enzymes in mouth & gut. enzymes convert large polymeric molecules in food into simpler monomeric subunits. For example, proteins into amino acids, polysaccharides into sugars, fats into fatty acids. 2. Glycolysis: anaerobic process used to split each molecule of glucose into 2 smaller molecules of pyruvate. Anaerobic means that no oxygen is required for glycolysis. Generates ATP & NADH. Takes place in cytosol. Pyruvate is converted into acetyl CoA. 3. Citric acid cycle: produces NADH. Site of oxidative phosphorylation that produces ATP. Takes place in mitochondria. Glycolysis: Be familiar with each step of glycolysis including the molecules used at step, the molecules produced at each step & the enzymes involved in each step. o Energy investment occurs in steps 1-3 o The cleavage of the 6-carbon sugar to two 3-carbon sugars occurs in steps 4 & 5 o Energy generation occurs in steps 6-10 Glycolysis takes place in the cytosol. For each molecule of glucose that enters glycolysis, two molecules of ATP are initially consumed to prepare the sugar to be split. The net number of activated carrier molecules produced in glycolysis from one molecule of glucose (number and type of molecules produced minus the number of those molecules used as input) is 2 molecules of ATP and 2 molecules of NADH For each molecule of glucose that enters glycolysis, two molecules of pyruvate are produced In the presence of oxygen (aerobic cell respiration), pyruvate is pumped into mitochondrial matrix. Pyruvate dehydrogenase complex removes CO2 from pyruvate & generates NADH & acetyl CoA. In the absence of oxygen (fermentation), pyruvate is converted to lactate in the cytosol of active muscle cells. In yeast, pyruvate is converted into CO2 & ethanol. Both processes restore NAD+ which is necessary for glycolysis. Citric Acid Cycle:  Be familiar with each step of the citric acid cycle including the molecules used at step, the molecules produced at each step & the enzymes involved in each step. Citric acid cycle is series of reactions that take place in mitochondrial matrix of eukaryotic cells & the cytosol of prokaryotic cells. Catalyzes complete oxidation of carbon atoms in acetyl groups of acetyl CoA. Acetyl groups are transferred from acetyl CoA to a larger four- carbon molecule, oxaloacetate, to form six-carbon tricarboxylic acid, citric acid. The citric acid molecule (also called citrate) is then progressively oxidized, and the energy of this oxidation is harnessed to produce activated carriers, including NADH. Also called Krebs cycle or TCA cycle. The net result of one turn of the cycle is 3 molecules of NADH, 1 molecule of GTP, 1 molecule of FADH2, & 2 molecules of CO2. Many of intermediates formed in glycolysis & citric acid cycle are siphoned off by anabolic pathways in which intermediates are converted by a series of enzyme-catalyzed reactions into amino acids, nucleotides, lipids, & other small organic molecules that cell needs. Oxidative Phosphorylation: Final step in oxidation of food molecules is oxidative phosphorylation. In oxidative phosphorylation a phosphate group is added to ADP to produce ATP. In oxidative phosphorylation, molecular oxygen serves as a final electron acceptor. FADH2 and NADH become oxidized as they transfer a pair of electrons to the electron- transport chain (series of electron carriers embedded in inner mitochondrial membrane). The electron carriers in the electron-transport chain toggle between reduced and oxidized states as electrons are passed along. At specific sites in chain, the energy released is used to drive protons (H+) across inner membrane, from mitochondrial matrix to intermembrane space. Movement of electrons generates a proton gradient across inner membrane, which serves as a source of energy. The complete oxidation of 1 glucose molecule results in 30 molecules of ATP. Gluconeogenesis synthesizes glucose from pyruvate. For example, phosphofructokinase catalyzes phosphorylation of fructose-6-phosphate to form fructose 1,6-bisphophate in step 3 of glycolysis. To perform reverse reaction, enzyme fructose 1,6-bisphosphate removes phosphate from fructose 1,6- bisphophate in a simple hydrolysis reaction. Activity of enzyme is allosterically regulated by binding of a variety of metabolites providing positive & negative feedback regulation. Phosphofructokinase is turn on when ATP is depleted. When ATP is abundant, enzyme is turned off & glycolysis shuts down. Gluconeogenesis is a costly process, requiring substantial amts of energy from hydrolysis of ATP & GTP. So, fasting cells mobilize glucose that has been stored in form of glycogen—branched polymer of glucose. Glycogen is stored as small granules in cytoplasm of many animal cells, mainly the liver & muscle. The enzyme, glycogen phosphorylase, breaks down glycogen when cells need more glucose. Chapter 14 Cells obtain most of their energy by a membrane-based mechanism. Energy from food is broken down in process of oxidative phosphorylation in mitochondria. Plants use energy from sunlight in process of photosynthesis. Both processes result in generation of proton (H+) gradient across a membrane. Proton gradient is used to drive ATP synthesis. Mitochondria & chloroplasts are thought to have evolved from bacteria. As evidence of their bacterial ancestry, both chloroplasts & mitochondria reproduce or divide like bacteria. They undergo a fission process that is conceptually similar to bacterial division. Both contain their own DNA-based genome & machinery to replicate this DNA & make RNA/protein. Inner compartments (matrix & stroma) contain DNA & a special set of ribosomes. Membranes in both organelles (inner membrane & thylakoid membrane) contain protein complexes involved in ATP production. Be familiar with general organization of mitochondria & chloroplasts including where different processes of oxidative phosphorylation & photosynthesis occur. Mitochondria produce bulk of the cell’s ATP. Mitochondria are dynamic in shape, location, number, & function. In some cell types, mitochondria remain fixed in one location, where they supply ATP directly to a site of high energy consumption. Be familiar with the components & location of the electron transport chain. The electron transport chain contains over 40 proteins grouped into 3 large respiratory complexes. The three respiratory enzyme complexes, in the order in which they receive electrons, are (1) the NADH dehydrogenase complex, (2) the cytochrome c reductase complex, and (3) the cytochrome c oxidase complex. NADH dehydrogenase accepts electrons from NADH. Electrons are then passed to electron-carrier ubiquinone. Ubiquinone transports electrons to cytochrome c reductase complex.  Electrons are then passed to cytochrome c. Cytochrome c transports electrons to cytochrome c oxidase complex. NADH dehydrogenase, cytochrome c reductase and cytochrome c oxidase act as proton pumps by pumping protons from matrix into intermembrane space. Redox potentials increase along the mitochondrial electron-transport chain. Redox potentials serve as a measure of electron affinity, with a lower redox potential indicating a lower affinity for electrons. Molecules with a low redox potential donate electrons to molecules with a higher redox potential. The pumping of protons generates an electrochemical proton gradient across the inner mitochondrial membrane. This gradient is used to drive synthesis of ATP from ADP & phosphate. ATP synthase embedded in inner mitochondrial membrane catalyzes formation of ATP from ADP/phosphate. ATP synthase is composed of a stationary head, called the F1 ATPase, and a rotating portion called F0. Driven by the electrochemical proton gradient, the F0 part of the protein—which consists of the transmembrane H+ carrier plus a central stalk—spins rapidly within the stationary head of the F1 ATPase, causing it to generate ATP from ADP and phosphate. Be familiar with stages of photosynthesis. Photosynthesis takes places in specialized intracellular organelles called chloroplasts. Stage 1: Light Reactions. Electron-transport chain in thylakoid membrane harnesses energy of electron transport to pump protons into thylakoid space. Chlorophyll absorbs energy from sunlight & supplies high-energy electrons. Produces ATP & NADPH. Light energy is captured through actions of photosystems in thylakoid membrane. Each photosystem consists of a set of antenna complexes, which capture light energy, and a reaction center, which converts that light energy into chemical energy. Plant cells use 2 different photosystems. The 2 photosystems absorb different wavelengths of light with Photosystem I absorbing longer wavelengths & Photosystem II absorbing shorter wavelengths. When light energy is captured by photosystem II, a high-energy electron is transferred to a mobile electron carrier called plastoquinone (Q). This carrier transfers its electrons to a proton pump called the cytochrome b6-f complex. Results in pumping of protons into thylakoid space generating an electrochemical gradient. ATP synthase embedded in thylakoid membrane then uses energy of electrochemical proton gradient to produce ATP. At the same time, a second photosystem—called photosystem I—also captures the energy from sunlight. The reaction center of this photosystem passes its high-energy electrons to a different mobile electron carrier, called ferredoxin, which brings them to an enzyme that uses the electrons to reduce NADP+ to NADPH. Stage 2: Light-Independent Reactions or Carbon Fixation Cycle or Calvin Cycle. Occurs in chloroplast stroma. ATP & NADPH are used to produce 3-carbon sugars that can be exported to cytosol. Ribulose 1,5-bisphosphate or Rubisco catalyzes attachment of CO2 to 5-carbon sugar derivative, ribulose 1,5-bisphosphate, to yield 2 molecules of 3-carbon compound 3- phosphoglycerate. For every 3 molecules of CO2, 1 molecule of glyceraldehyde 3-phosphate is produced & 3 moles of ribulose 1,5-bisphosphate are regenerated. Carbon Fixation Cycle uses a total of 9 ATP + 6 NADPH Carbon Fixation Cycle occurs in 3 stages: In the first stage of the cycle, CO2 is added to ribulose 1,5-bisphosphate. In the second stage, ATP and NADPH are consumed to convert 3-phosphoglycerate to glyceraldehyde 3-phosphate. In the final stage, most of the glyceraldehyde 3-phosphate produced is used to regenerate ribulose 1,5- bisphosphate; the rest is transported out of the chloroplast stroma into the cytosol. Sugars generated by carbon fixation can either be stored as starch or used to produce ATP & other organic molecules. Starch & fat stored in stroma can be broken down to sugars & fatty acids, which are exported to cytosol. Some of exported sugars enters glycolysis, where it is converted to pyruvate. Most of that pyruvate enters plant cell mitochondria & is fed into citric acid cycle, leading to production of ATP by oxidative phosphorylation. The first living cells on Earth may have consumed geochemically produced organic molecules and generated ATP by fermentation. Because oxygen was not yet present in the atmosphere, such anaerobic fermentation reactions would have dumped organic acids—such as lactic or formic acids, for example—into the environment. Resulted in oxidative phosphorylation evolving in stages. Stage 1: evolution of ATPase that pumps H+ out of cytosol, preventing cell from become too acidic Stage 2: evolution of electron-transport driven pump Stage 3: Linking of systems to generate ATP synthase that uses protons pumped by electron-transport chain to synthesize ATP