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BiO exam TwO
Ch 5- 9
| Question | Answer |
|---|---|
| Metabolism | the sum of all chemical reactions within a living organism. |
| Catabolism | the breakdown of complex organic compounds into simpler ones. Energy is released. |
| Anabolism | energy requiring reactions used to build complex organic molecules from simpler ones. |
| Energy | capacity to do work, cause change, etc. |
| Potential Energy | Built up energy. |
| Kinetic energy | Energy in motion |
| Redox reactions | A chemical reaction where one reactant loses electrons while the other reactant gins those electrons. |
| First Law of Thermodynamics | The total amount of energy in a closed system remains constant. More energy cannot be created, and existing energy cannot be destroyed. It can only be converted from one form to another. |
| Second Law of Thermodynamics | The spontaneous direction of energy flow is from high quality to low-quality forms. With each conversion, some energy is randomly dispersed in a form (usually heat) that is not as readily available to do work and entropy increases |
| What are the assumptions thermodynamics assume or don’t account for? | That the system is closed and does not account for energy |
| Activation energy | the amount of energy required to start a chemical reaction. |
| The physiological temperature and pressure of most living organisms is too low for what? | For chemical reactions to proceed quickly enough to maintain the life of the organism. |
| What would raising the temperature and/or pressure of living organisms do? | It would speed up the reactions, but would also probably kill the organism. |
| Catalyst | a substance that changes the rate of a chemical reaction without being altered itself. |
| Enzyme | biological catalyst; usually protein, but can be RNA (ribozymes). |
| What do Enzymes do? | reduce the activation energy of a reaction, or change the rate of a reaction |
| What is the molecular weight range in enzymes? | The molecular weights range from about 10,000 to over a million |
| How many reactions does each enzyme catalyze? | a single reaction or single group of related reactions. |
| What causes the specificity and activity of an enzyme? | It’s three-dimensional structure (tertiary and/or quaternary structure). |
| How are enzymes are named? | they are usually named for what they do, or for the substrate upon that they act, and usually end in -ase or -zyme. |
| What do enzymes consity of? | Some enzymes consist entirely of proteins. Most have protein and non-protein components. |
| Apoenzyme | the protein component of an enzyme. |
| Cofactor | the non-protein component of an enzyme. It may be a metal ion or a coenzyme |
| coenzyme | complex organic molecule. |
| Holoenzyme | the combination of apoenzyme and cofactor. If the cofactor is removed, the apoenzyme will not function. |
| NAD | nicotinaminde adenine dinucleotide |
| NADH | nicotinaminde adenine dinucleotide phosphate. |
| FMN | flavin mononumcleotide |
| FAD | Flavin adenine dinucleotide |
| CoA | Coenzyme A |
| nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) are derived from? | the B vitamin, nicotinic acid (niacin). |
| flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are derivatives of ? | the B vitamin, riboflavin. |
| Another important enzyme, coenzyme A (CoA) is derived from? | the B vitamin, pantothenic acid. |
| Active Site | where the substrate binds to the enzyme. |
| Enzyme- Substrate complex | What the enzyme is called when it has a substrate bound to it. |
| What is the catalytic cycle of an enzyme? | The substrate binds to the active site of the enzyme, forming an enzyme- substrate complex. The substrate molecule is transformed and the products are released and the unchanged enzyme reacts with more substrates. |
| The substrate | "induces the protein to alter its shape slightly and embrace the substrate more intimately." |
| The substrate molecule is transformed by? | rearrangement of existing atoms, breakdown of the substrate molecule, or the addition of another substrate molecule. |
| Turnover number | the number of substrate molecules that an enzyme converts to products in a second. Generally ranges from 1 to 10,000 and can be as high as 500,000 or more. |
| a) DNA polymerase I has a turnover number of? | 15. |
| b) Lactate dehydrogenase has a turnover number of ? | 1000. |
| c) Carbonic anhydrase has a turnover number of | 600,000. |
| d) Catalase has a turnover number of | >1,000,000. |
| Factors that influence enzyme activity are | temperature, pH, and substrate concentration |
| Temperature effect on enzyme activity | In general, activity increases with temperature until the enzyme starts to denature. |
| Heat denaturation is | usually not reversible. |
| pH | enzymes have pH optima at which their activities are maximized. Increases or decreases in pH generally cause decreased activity. |
| Extreme changes in pH can cause | denaturation that may or may not be reversible. |
| Substrate concentration | enzymatic activity increases with substrate concentration until the saturation point is reached |
| Saturation point | the active site is always occupied by substrate molecules. |
| Increases in substrate concentration beyond the saturation concentration | do not increase enzymatic activity. |
| Competitive inhibition | The inhibitor resembles substrate but no reaction occurs and substrate cannot bind. |
| competitive inhibitors | Inhibitors that structurally resemble substrate |
| Allosteric (noncompetitive) inhibition | Inhibitor bind someplace other than the active site, which changes the characteristics of the active site no longer reacts with the substrate |
| Biochemical pathway | a sequence of enzymatically catalyzed chemical reactions. |
| Feedback inhibition | this is a form of allosteric inhibition in which the products of an enzyme or an enzyme pathway inhibit one or more of the enzymes in the pathway. |
| ATP | adenosine triphosphate. |
| ATP | the cell's energy currency. |
| ATP is formed by | adding a phosphate group to ADP |
| Phosphorylation | the addition of a phosphate group to a compound |
| Substrate-level phosphorylation | generation of ATP by directly transferring a phosphate from one compound to ADP. |
| Electron transport chain | The transfer of electrons through the carriers generates proton gradients that power ATP synthetase to phosphorylate ADP. |
| Photophosphorylation | occurs only in photosynthetic cells. Light energy powers electron transport through an electron transport chain similar to that of respiration. |
| Where do the steps of aerobic respiration occur? | Glycolysis occurs in cytoplasm, respiration occurs in the inner membrane of the mitochondrion |
| What are the steps of aerobic respiration? | glycolysis, pyruvate oxidation, krebs cycle, electron transport chain, and chemiosmosis |
| Glycolysis | anaerobic oxidation of glucose to pyruvic acid. |
| One molecule of glucose produces | 2 NADH, 2 pyruvates, and 2 ATP |
| Glycolysis needs | NADH to be recycled to NAD or glycolysis will stop. |
| The fates of Pyruvate are | fermentation, oxidation, lipid metabolism, respiration, or other metabolism. |
| Fermentation | pathways that recycle NADH into NAD and have organic end products. |
| Animal fermentation | pyruvate produces lactate |
| Plant fermentation | pyruvate produces ethanol |
| Aerobic respiration | pyruvate from glycolysis is converted to acetyl CoA. Each acetyl CoA molecule undergoes oxidation in the Krebs cycle (TCA or citric acid cycle). |
| High-energy electrons are produced in the TCA cycle are used in? | Electron transport chain |
| Pyruvate Oxidation | Pyruvate is oxidized to form Acetyl CoA |
| Each Acetyl-CoA in the Krebs cycle produces | 3 NADH, 2 CO2, 1 FADH, 1 GTP (ATP equivalent) |
| Respiratory electron transport | Electrons from NADH and FADH are used to pump H+ across the inner mitochondrial membrane into the intermembrane space. |
| The electrons from each NADH cause | 6 H+ to be pumped across the inner membrane. |
| How many H+ are required for each ATP? | 2 |
| One NADH makes how many ATP? | 3 |
| The theoretical yield of aerobic respiration | 38~36 ATP |
| The actual yield of aerobic respiration | About 30 ATP per glucose |
| What happened to the missing ATP? | Some protons may leak or are used for something else |
| Anaerobic Respiration | Where substances other than oxygen are used as the final electron acceptor. |
| Why isn’t anaerobic respiration as efficient as aerobic respiration? | because only parts of the Krebs cycle are used in these pathways. |
| How are proteins catabolized? | Proteins are broken down into amino acids, which can be converted into pyruvate, acetyl CoA or Krebs cycle intermediates. |
| How are lipids catabolized? | Triglycerides are broken down into glycerol and fatty acids. Glycerol is converted into 3-PGAL and the fatty acids are converted into C2 units (beta-oxidation) that are converted into acetyl CoA. |
| How are nucleic acids catabolized? | They are broken down into nucleotides, which are converted to Krebs cycle intermediates. |
| How is glycogen catabolized? | Glycogen is broken down into glucose, which is then used in glycolysis and on forth. |
| What are alternate forms of energy? | glycogen, proteins, nucleic acids, and lipids. |
| Phagocytosis | “cell eating” The plasma membrane of a cell extends around the area of the target substance and forms a vacuole (phagosome). |
| Pinocytosis | “Cell drinking” dissolved material in the extracellular environment is incorporated into a vesicle and can be done by any cell (since solutes can diffuse through any cell wall) |
| Receptor- Mediated Endocytosis | A form of pinocytosis that have receptors (that are held in place by clathrin) that get specific molecules and closes into a clathrin ring when the receptors are full and delivers them, then go back and do the process over again. |
| Vacuole | Formed in phagocytosis |
| Vesicle | Formed in pinocytosis |
| Clathrin- Ring | Formed in Receptor- mediated endocytosis |
| Secretion/Exocytosis | Reverse of phagocytosis, where material is packaged into vesicles, which fuse with the plasma membrane and releases the continents outside the cell. |
| Cellular Junctions | Connect cells and allow communication |
| Direct contact | messenger molecule move directly between cells and is limited by rate of diffusion. |
| Paracrine Signalling | hormones are released into the local environment and only cells with the specific receptors can read the hormones |
| Endocrine Signaling | Hormones are released into the bloodstream, require specific receptors to be read |
| Synaptic Signaling | Specialized paracrine signaling in the nerve cells. Signal Transduction |
| Enzyme Cascades | linked series of reactions that amplifies chemical signals |
| Tight Junctions | Stiches adjacent cells together. Are physically weak but waterproof and allow cells to control where solutes go. |
| Anchoring Junctions | cells are joined together by proteins (desosomes and hemiesomes) and that distribute stress. They are very strong “ritz crackers” |
| Cadherin junction | Anchors to cytoskeleton. Are weaker but cheaper. |
| Communicating Junctions | Cytoplasmic connections between cells that allow direct communication. Gap Junctions |
| Plasmodesma(ta) Junctions | Communication junctions in plants |
| Autotrophs | use inorganic carbon as a carbon source for making complex organic molecules. Most also use inorganic N, P and S. |
| Photoautotrophs | use light as energy source for ATP generation (plants, algae, cyanobacteria, some eubacteria). |
| Chemoautotrophs | use inorganic chemicals as energy source for ATP generation (some prokaryotes). |
| Heterotrophs | use preformed organic molecules as a carbon source. |
| Photoheterotrophs | use light as energy source for ATP generation (some eubacteria). |
| Chemoheterotrophs | use organic molecules as energy source for ATP generation (most prokaryotes, fungi, protozoa, animals). |
| What are some types of autotrophs? | Photoautotrophs and Chemoautotrophs |
| What are some types of Heterotrophs? | Photoheterotrophs and Chemheterotrophs. |
| Photosynthetic pigments | embedded within the thylakoid membranes. |
| Chlorophylls | green pigment that absorbs light in the blue and red regions of the spectrum. |
| What are the types of chlorophylls? | Chlorophyll a., which is present in all plant-like organisms, and Chlorophyll b., which is present in plant, and there are other forms of chlorophyll |
| Accessory pigments | the carotenoids (carotenes and xanthophylls) are yellow-orange pigments that allow the utilization of other wavelengths of light. They also dissipate excess light energy in the form of heat. |
| Photosynthesis | Fixation of CO₂ into carbohydrates using ATP generated by light |
| What are the parts of photosynthesis? | Light harvesting, photosynthetic electron transport, carbon fixation. |
| Light dependent reactions | Reactions that take place in the thylakoid (Iight harvesting, linear and cyclic PET) are called light reactions because they require light. Light is used to drive redox reactions, which drive ATP and NADPH₂ |
| Dark Reactions | Reactions that take place in the Stoma ( Carbon Fixation and reducing carbohydrates) don’t require light. ATP and NADPH₂ drive carbohydrate formation |
| Photosystems | Made up of accessory pigments and proteins. The antenna absorbs light and the reaction center releases electrons. |
| Photosystem I | has reaction center P700 |
| Photosystem II | has reaction center P680 |
| Linear Photosynthetic Electron Transport | Uses light to energize photosystems and uses H₂O as a source of electrons in photosystem II, and attracts hydrogen ions to make ATP in ATP synthase and produces O₂ and NADPH₂. |
| What parts are used in Linear PET? | Photosystem II, PQ, Cytb₆f, PC, Photosystem I, Fd, FNR. |
| Cyclic Photosynthetic Electron Transport | Similar to linear PET, but only uses Photosystem I and recycles the same electron over and over, so all it needs is light to recharge the electron. It only produces ATP |
| What are the two pathways of Cyclic PET? | FQR pathway and NDH pathway |
| What are the parts used in FQR pathway | FQR, PQ, Cytb₆f, PC, PS I, Fd, and maybe FNR. |
| What are the parts used in NDH pathway | NDH, PQ, Cytb₆f, PC, PS I, Fd, FNR |
| What is the difference between Linear PET and Cyclic PET? | Cyclic PET has FQR or NDH but doesn’t have Photosystem II, while Linear PET does have Photosystem I. Also Cyclic PET does not split H₂O or produce NADPH. Both PET do make hydrogen gradient and need light Chemiosmotic ATP generation |
| Calvin –Benson (C₃) cycle | Converts CO₂ to PGAL. RuBP reacts with CO₂ (RuBicCO) and produces PGA, which goes through various oxidations of ATP to ADP and NADPH to NADP to produce PGAL. |
| How many turns of the Calvin-Benson cycle to release 1 ADP? | 1 turn |
| How many turns of the Calvin- Benson cycle to release the equivalent of 1 PGAL? | 3 turns |
| How many turns of the Calvin- Benson cycle to release the equivalent of 1 Glucose? | 6 turns |
| How many turns of the Calbvin- Benson cycle to release the equivalent of 1 sucrose? | 12 turns |
| RuBisCO | The enzyme that adds RuBP to CO₂ or to O₂ |
| Photorespiration | when O₂ is added to RuBP instead of CO₂, which releases CO₂ without producing ATP or NADPH, which is inefficient for the plant, because it reverses the work it has already done. |
| How often does photorespiration occur? | about 30% of the time and increases with temperature |
| How do plants prevent photorespiration? | By either increasing the amount of CO₂ or by decreasing the amount of O₂ |
| C₄ photosynthesis | the sites of O₂ production and CO₂ fixation are in different cells. This process uses more ATP because it transports Oxaloacetate in bundle sheath cells. While this process uses more ATP, it is more efficient in the long run. |
| Crassulacean Acid Metabolism (CAM) | Similar to C₄ except the light and dark reaction are separated by time. For instance, light reaction occur during the day and dark reactions occur during the night |
| Anoxygenic bacterial photosynthesis | Some bacteria use substance, like H₂S, S, or H₂, instead of water for electron donors because they live in anaerobic conditions. |
| Chemosynthesis | Some bacteria oxidize reduced inorganic compounds to obtain energy to fix CO₂ into carbohydrates. |
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