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Bio Exam 2
Biology 2010; Ch. 6, 7, 8, 14
| Question | Answer |
|---|---|
| Thermodynamics | Branch of chemistry concerned with energy changes |
| What are cells governed by? | laws of physics and chemistry |
| Energy | Capacity to do work |
| What are the 2 states of energy? | kinetic and potential |
| Kinetic energy | Energy of Motion |
| Potential Energy | Stored Energy |
| What are some forms of energy? | Mechanical, heat, sound, electrical current, light, radiatioactivity |
| What is the most convenient way of measuring energy? | Heat |
| What is 1 calorie? | Heat required to raise 1 gram of water 1 degree C |
| What is a calorie on a food label? | Kilocalorie with a capital C |
| Where does energy from the sun flow into? | Biological world |
| What captures energy from the sun? | Photosynthetic organisms |
| When photosynthetic organisms capture energy from the sun, what is it stored as? | Potential energy in chemical bonds |
| What does breaking bonds between atoms require? | Energy |
| Energy stored in chemical bonds may be used to make ______. | New bonds |
| Oxidation | Atom/Molecules LOSES an electron |
| Reduction | Atom/Molecule GAINS an electron |
| What has a higher level of energy? Reduction or Oxidation? | Reduction |
| Oxidation-Reduction reactions (__(1)__) are always ___(2)___. | 1. Redox 2. Paired |
| According to the First Law of Thermodynamics, energy cannot be created or destroyed, but it can do what? | Change from 1 form to another |
| According to the First Law of Dynamics, does the total amount of energy change? | No. The total amount of energy in the whole universe remains constant |
| According to the 1st Law of Thermodynamics, during each conversion, how is energy lost? | As heat |
| Second Law of Thermodynamics | Entropy (disorder) is continuously increasing. Energy transformations proceed spontaneously to convert matter from a more ordered/less stable form to a less ordered/more stable form |
| What does G stand for? | Energy available to do work |
| What is the formula for the Change in Free Energy? | ΔG = ΔH - TS |
| What is the formula for the Energy available to do Work? | G = H - TS |
| What does the H stand for in the formula? | Enthalphy, energy in a molecule's chemical bonds |
| What does the T stand for in the formula? | Absolute temperature |
| What does the S stand for in the formula? | Entropy, unavailable energy |
| What is ΔG? | Change in Free Energy |
| What does positive (+) ΔG stand for? | Products have more free energy than reactants H is higher or S is lower Endergonic Not spontaenous --> requires input of energy |
| What does a negative (-) Δ G stand for? | Products have less free energy than reactants H is lower or S is higher or both Exergonic Spontaneous (may not be instantaneous) |
| What is required to destabilize existing bonds and initiate a chemical reaction? | Extra energy |
| What does an exergonic reaction's rate depend on? | The activation energy required |
| Does a larger activation energy proceed faster or slower? | slower |
| Activation energy rate can proceed faster in 2 ways. Name them. | 1. Increasing energy of reacting molecules (heating) 2. Lowering activation energy |
| Catalysts | Susbtances that influence chemical bonds in a way that lowers activation energy |
| Catalysts Cannot do the following: | - violate laws of thermodynamics - make an endergonic reaction spontaneous - alter proportion of reactant turned into product |
| Adenosine Triphosphate | ATP |
| What is the chief "currency" that all cells use? | ATP |
| What is the structure of ATP? | - Ribose - 5 carbon sugar - Adenine - Chain of 3 phosphates |
| The chain of 3 phosphates in ATP bonds are _____. | Unstable |
| In the structure of ATP, where does the key to energy storage lie? | The chain of 3 phosphates |
| What drives energonic reactions? | ATP hydrolysis - Coupled reaction results in net negative (-) ΔG (exergonic and spontaneous) |
| ATP is not suitable for what? | Long-term energy storage |
| What are better sources of long-term energy storage? | Fats and carbohydrates |
| How long does a cell store ATP? | Few seconds worth of ATP |
| What are enzymes? | - Biological catalysts - Most are protein, some are RNA |
| What does the shape of an enzyme do? | It stabilizes a temporary association between substrates |
| What are some things that enzymes CANNOT do? | not change or be consumed in reaction |
| Carbonic Anyhydrase | 200 molecules of carbonic acid per hour make WITHOUT enzyme 600,000 molecules formed per second WITH an enzyme |
| What is an Active Site? | - Pockets or clefts for substrate binding - Precise fit of substrate |
| What forms the enzyme-substrate complex? | Active site |
| Why does an active site apply stress to distort a particular bond? | to lower activation energy |
| Where can enzymes be found? | May be suspended in cytoplasm or attached to cell membranes and organelles |
| What are multienzyme complexes? | Subunits that work together to form a molecular machine |
| What happens in multienzyme complexes? | - Product can be delivered easily to next enzyme - Unwanted side reactions prevented - All reactions can be controlled as a unit |
| What are Ribozymes? | Nonprotein enzymes (I think they are RNA molecules also) |
| Can RNA molecules catalyze certain reactions? | Yes. - 1981 discovery that certain reactions catalyzed in cells by RNA molecule itself |
| What are 2 kinds of Ribozymes/RNA molecules that catalyze certain reactions? | 1. Intramolecular catalysis 1. Intermolecular catalysis |
| Intramolecular catalysis | Catalyze reaction on RNA molecule itself |
| Intermolecular catalysis | RNA acts on another molecule |
| What does the rate of enzyme-catalyzed reaction depends on? | concentration of substrates and enzyme |
| What affects the enzyme's 3-D shape? | - All chemical or physical conditions - Optimum temperature and/or pH |
| If you change an enzyme's 3-D shape, what else do you change? | The rate |
| Inhibitor | substance that binds to enzyme and decreases its activity |
| Competitive Inhibitor | Competes with substances for active site |
| Noncompetitive Inhibitor | Binds to enzyme at a site other than active site |
| Which inhibitor causes the shape of an enzyme to change and therefore unable to bind to a substrate? | Noncompetitive Inhibitor |
| Allosteric Enzymes | enzyme that exists in active and inactive forms |
| What do most noncompetitive inhibitors bind to? | Allosteric site - chemical on/off switch) |
| Allosteric inhibitor | Binds to allosteric site and REDUCES enzyme activity |
| Allosteric activator | binds to allosteric site and INCREASES enzyme activity |
| Metabolism | Total of all chemical reactions carried out by an organism |
| Anabolic Reaction / ANABOLISM | Expend energy to build up molecules |
| Catabolic Reaction / CATABOLISM | Harvest Energy by breaking down molecules |
| In a biological pathway, where reactions occur in a sequence, what happens? | Many steps take place in a specific organelle. The product of 1 reaction may be the substrate for the next |
| Feedback Inhibition | - End product of pathway binds to an allosteric site on enzyme that catalyzes 1st reaction in pathway - Shuts down pathway so raw materials and energy are not wasted |
| Autotrophs | Able to prodce their own organic molecules through photosynthesis |
| Heterotrophs | Live on organic compounds produced by other organisms |
| What do ALL organisms use to extract energy from organic molecules? | Cellular Respiration |
| Oxidized | Loss of electrons |
| Reduced | Gain of electrons |
| Dehydrogenation | Lost electrons are accompanied by protons Ex: A hydrogen atom is lost ( 1 electron, 1 proton) |
| What happens during Redox reactions? | Electrons carry energy from 1 molecule to another |
| Wat is Nicotinamide Adenosine Dinucleotide (NAD+)? | an electron carrier |
| How does an NAD+ become NADH? | It needs to accept 2 electrons and 1 proton |
| Is the reaction from NAD+ --> NADH reversible? | Yes |
| In overall cellular energy harvest? | - Dozens of redox reactions take place - # of electron acceptors including NAD+ |
| Redox Reactions: In the end, what happens? | High-energy electrons from initial chemical bonds have lost much of their energy Transferred to a final electron acceptor |
| Aerobic respiration | Final electron receptor is Oxygen (O2) |
| Anaerobic respiration | Final electron acceptor is an inorganic molecules (not O2) |
| Fermentation | Final electron acceptor is an organic molecule |
| What kind of Respiration is this: C6H12O6 +6O2 --> 6CO2 + 6H2O | Aerobic respiration |
| Free-energy # | -686 kcal/mol of glucose (can be even higher than this in a cell). |
| What must happen if the free-energy has a large amount of energy? | It need to be released in small steps rather than all at once |
| All electron carriers can be _____. | reversibly oxidized and reduced |
| What do electron carriers carry? | Some carry just electrons, some carry both electrons and protons |
| What does NAD + require to become NADH? | 2 electrons and a proton |
| What kind of reactions are driven when cells use ATP? | Endergonic reactions |
| What is the number and unit for Δ G (free energy) of hydrolyzing phosphate? | -7.3 kcal/mol |
| Substrate-Level phosphorylation Mechanism | - Transfer phosphate group directly to ADP - During glycolysis |
| Oxidative Phosphorylation Mechanism | ATP synthase uses energy from a proton gradient |
| Name the stages in the Complete Oxidation of Glucose | 1. Glycolysis 2. Pyruvate Oxidation 3. Krebs Cycle 4. Electron Transport Chain and chemiosmosis |
| What happens in Glycolysis | Conversion of 1 glucose (6 carbons) into 2 pyruvate (3 carbon) |
| Where does Glycolysis occur? | In the cytoplasm |
| What is the Net production of Glycolysis? | 2 ATP molecules by subtrate-level phosphorylation |
| 2 NADH produced by the reduction of NAD+ happens in what stage of glucose oxidation? | Glycolysis |
| NADH must be ____ for glycolysis to continue | recycled to NAD+ |
| Name 2 ways that can recycle NADH | 1. Aerobic Respiration 2. Fermentation |
| Aerobic Respiration | - Oxygen is available as final electon acceptor - Produces significant amount of ATP |
| Fermentation | - Occurs when oxygen is not available - Organic molecule is the final electron acceptor |
| Fate of pyruvate depends on what? | oxygen availability |
| What is the fate of pyruvate in Aerobic Respiration? | When oxygen is present, pyruvate is oxidized to acetyl-CoA which enters the Krebs Cycle |
| What is the Fate of the Pyruvate in Fermentation? | Without oxygen, pyruvate is reduced in order to oxidize NADH back to NAD+ |
| In the presence of oxygen, what happens to a pyruvate? | It becomes oxidized |
| Pyruvate Oxidation occurs where in EUKARYOTES? | In mitochondria |
| Pyruvate Oxidation occurs where in Prokaryotes? | At plasma membrane |
| Pyruvate dehydrogenase | A multienzyme complex that catalyzes the reaction of pyruvate oxidation in the mitochondria of eukaryotes |
| For each 3-carbon pyruvate molecule, what is its product? | - 1 CO2, decarboxylation by pyruvate dehydrogenase - 1 NADH - 1 acetyl-CoA which consists of 2 carbons from pyruvate attached to a coenzyme A; Acetyl-CoA proceeds to Krebs Cycle |
| In which phase does the oxidation of acetyl group from pyruvate occur? | Krebs Cycle |
| Where does the Krebs Cycle occur in? | Matrix of mitochondria |
| Name the 3 segments in the Krebs Cycle | 1. Acetyl-CoA + oxaloacetate --> citrate 2. Citrate rearrangement and decarboxylation 3. Regeneration of oxalocetate |
| Krebs Cycle Yield For each, Acetyl-CoA entering, what happens? | - Release 2 molecules of CO2 - Reduce 3 NAD + to 3 NADH - Reduce 1 FAD (electron carrier) to FADH2 - Produce 1 ATP - Regenerate Oxaloacetate |
| Glucose Yield After Krebs Cycle: Glucose has been oxidized to | - 6 CO2 - 4 ATP - 10 NADH - 2 FADH2 - the 2 lectron carriers proceed to electron transport chain |
| Electron transfer has released _____ of energy by gradual energy extraction. | 53 kcal/mol |
| Glucose Yield After Krebs Cycle: Energy will be put to use to do what? | Manufacture ATP |
| Electron Transport Chain | Series of membrane-bound electron carriers embedded in the inner mitochondrial membrane |
| Where are the electrons from NADH and FADH2 transferred to? | The complexes of the ETC |
| Each complex in the ETC operates as a what? | Proton pump, driving protons to the intermembrane space |
| In the ETC, what do the electrons do? | Move from protein complex to protein complex |
| Accumulation of protons in the intermmebrane space drives protons into the matrix via diffusion, but this occurs slowly since ______. | The membrane is relatively impermeable to ions. |
| Most protons can only reenter the matrix of mitochondria through what? | ATP synthase - Uses energy of gradient to make ATP from ADP + Pi - Process called chemiosmosis |
| How is ATP synthase carried out? | By a tiny rotary motor driven by proton gradient |
| F0 Membrane | bound complex |
| F1 complex | stalk and knob has enzymatic activity |
| In ATP Synthase, protons travel through __(1)__, which causes __(2)__ to rotate | 1. F0 channel 2. F0 |
| Mechanical changes in ATP synthase changes confirmation of ______ | catalytic domain in F1 |
| Theoretical Energy Yield of Respiration | - 32 ATP per glucose for bacteria - 30 ATP per glucose for eukaryotes |
| P/O Ratio (Phosphate-to-oxygen ratio) | Amount of ATP synthesized per O2 molecule |
| When does this happen: Phosphofructokinase is allosterically inhibited by ATP and/or citrate | In glycolysis |
| When does this happen: -Pyruvate dehydrogenase inhibited by high levels of NADH - Citrate synthetase inhibited by high levels of ATP | In pyruvate oxidation / Krebs cycle |
| Anaerobic Respiration | - use of inorganic molecules (other than O2) as final electron acceptor - Many prokaryotes use sulfur, nitrate, carbon dioxide, or inorganic metals |
| Fermentation | Use of organic molecules as final electron acceptor |
| In Methanogens under Anaerobic Respiration: CO2 is reduced to what? And where is it found? | CH4 (methane) and in diverse organisms including cows |
| In Sulfur Bacteria in Anaerobic Respiration: What is Inorganic sulfate (SO4) reduced to and what does it set the stage for? | To hydrogen sulfide (H2S) and for evolution of photosynthesis. |
| Fermentation reduces organic molecules in order to do what? | Regenerate NAD+ |
| Ethanol Fermentation | Produces CO2, ethanol, and NAD +, and it occurs in yeast |
| Lactic Acid Fermentations | When electrons are transferred from NADH to pyruvate to produce lactic acid Occurs in animals cells (esp. muscles) |
| In order to remove the amino group, what do amino acids under during the catabolism of a protein? | deamination |
| The remainder of amino acid that underwent the catabolism of a protein is converted to what? | A molecule that enters glycolysis or Krebs Cycle |
| In a catabolism of protein, what does Alanine convert to? | Pyruvate |
| In a catabolism of protein, what does aspartate convert to? | Oxaloacetate |
| In the catabolism of fat, fats are broken down into what? | Fatty acids and glycerol |
| In the catabolism of fat, fatty acids are converted to what? | Acetyl groups by β-oxidation |
| The catabolism of fat is what kind of process? | Oxygen-dependent process |
| What does the respiration of a 6-carbon fatty acid yield? | 20% more energy than 6-carbon glucose |
| Hypothetical Timeline of the Evolution of Metabolism | 1. Ability to store chemical energy in ATP 2. Evolution of Glycolysis 3. An oxygenic photosynthesis (using H2S) 4. Use of H2O in photosynthesis (not H2S) 5. Evolution of nitrogen fixation 6. Aerobic respiration evolved most recently |
| Photosynthesis formula | 6CO2 + 12H2O --> C6H12O0 + 6H2O + 6O2 |
| Where does the energy for all life on earth ultimately come from? | Photosynthesis |
| Oxygenic photosynthesis is carried out by Cyanobacteria | - Cyanobacteria - 7 groups of algae - All land plants - chloroplasts |
| Light-Dependent Reactions | - Require Light 1. Capture Energy from sunlight 2. Make ATP and reduce NADP+ to NADPH |
| Carbon Fixation Reactions / Light - Independent Reactions | - Does not Require light 3. Use ATP and NADPH to synthesize organic molecules from CO2 |
| Thylakoid membrane | Internal membrane of chloroplast that contains chlorophyll II and other photosynthetic pigments clustered into photosystems |
| Grana | stacks of flattened sacs of thylakoid membrane in the chloroplast |
| Stroma Lamella | Connects the grana of the chloroplast |
| Stroma | Semi-Liquid surrounding the thylakoid membranes |
| Jan Baptista van Helmont (1580-1644) | Demnostrated that the substance of the plant was not produced only from soil |
| Joseph Priestly (1733 - 1804) | Living vegetations adds something to the air |
| Jan Ingenhousz (1730-1799) | Proposed plants carry out a process that uses sunlight to split carbon dioxide into carbon and oxygen (O2 gas) |
| F.F. Blackman (1866-1946) | - Came to conclusion that photosynthesis is a multistage process, only one portion of which uses light directly - Light vs. Dark reactions - Enzymes involved |
| C.B. van Niel (1897-1985) | - Found purple sulfur bacteria do not release O2 but accumulate sulfur - Proposed general formation: CO2 + 2H2A +light energy --> CH20 + H2O + 2A - Later researches found O2 produced comes from water |
| Robin Hill (1899-1991) | Demonstrated Niel was right that light energy could be harvested and used in a reduction reaction |
| Pigment | Molecules that abosrb light energy in the visible range |
| Light is a form of what? | Energy |
| Photon | A particle of light that acts as a discrete bundle of energy |
| Energy content of a photon is inversely proportional to what? | The wavelength of light |
| Photoelectric effect | Removal of an electron from a molecule by light |
| When a photon strikes a molecule, its energy it either : ____ | 1. Lost as heat 2. Absorbed by electron of molecule --> Boosts electrons into higher energy level |
| Absorption Spectrum | Range and efficiency of photon molecule is capable of absorbing |
| What are the 2 general types of pigments used in green plant photosynthesis? | Chlorophylls and Carotenoids |
| What is the only pigment that can act directly to convert light energy to chemical energy? | Chlorophyll α |
| What is chlorophyll α? | The main pigment in plants and cyanobacteria that absorbs violet-blue and red light |
| Chlorophyll β | The accessory pigment of secondary pigment absorbing light-wave lengths that chlorophyll α does not absorb |
| What is the structure of Chlorophyll? | A porphyrin Ring that has a magnesium ion at the center |
| Porphyrin ring | Complex ring structure with alternating double and single bonds |
| What excites the electrons in the porphyrin ring? | Photons |
| What do electrons do when in the presence of a porphyrin ring? | They shutte away |
| Relative effectiveness of different wavelengths of light in promoting photosynthesis corresponds to what? | The absorption spectrum for chlorophylls |
| Carotenoids | Carbon rings linked to chains with alternating single and double bonds |
| What Pigment can absorb photons with a wide range of energies, as well as scavenge free radicals-antioxidant as a protective role? | Carotenoids |
| What pigment is important in low-light ocean areas | Phycobiloproteins |
| Light is captured by photosystems, each of which consists of 2 components which are the ____ | Antenna Complex and the Reaction Center |
| Antenna Complex | A component of photosystems that has hundreds of accessory pigment molecules. It gathers photons and feed the captured light energy to the reaction center. |
| Reaction center | A component of photosystems that has 1 or more chlorophyll α molecules and passes excited electrons out of the photosystem |
| What is the Antenna Complex also called? | Light-harvesting complex |
| What does the Antenna Complex do? | It captures photons from sunlight and channels them to the reaction center chlorophylls |
| In chloroplasts, light-harvesting complexes consist of what? | A web of chlorophyll molecules linked together and held tightly in the thylakoid membrane by a matrix of proteins |
| What kind of complex is the reaction center component of a photosystem? | Transmembrane protein-pigment complex |
| What happens in the reaction center component of a photosystem? | When a chlorophyll in the reaction center absorbs a photon of light, an electron is excited to a higher level. Light-energized electron can be transferred to primary electron acceptor, reducing it. |
| What happens at the end of the reaction center? | Oxidizing chlorophyll then fills its electron "hold" by oxidizing a donor molecule |
| Name the 4 steps in Light - Dependent Reactions. | 1. Primary Photoevent 2. Charge Separation 3. Electron Transport 4. Chemiosmosis |
| What happens in the first step in Light- Dependent Reactions (Primary Photoevent)? | Photon of light is captured by a pigment molecule |
| What happens in the second step in Light- Dependent Reactions? (Charge Separation) | Energy is transferred to the reaction center; an excited electron is transferred to an acceptor molecule |
| What happens in the third step in Light- Dependent Reactions? (Electron Transport) | Electrons move through carriers to reduce NADP + |
| What happens in the fourth and last step in Light- Dependent Reactions (Chemiosmosis)? | Produces ATP |
| What are the 2 connected photosystems of Chloroplast? | Photosystem I and Photosystem II |
| When the 2 Photosystems work together, what happens? | They carry out a noncyclic transfer of electrons that is used to generate both ATP and NADPH |
| What does Photosystem I do? | It transfers electrons ultimately to NADP+, producing NADPH |
| What happens to electrons that are lost from Photosystem I? | They are replaced by electrons from photosystem II |
| What does Photosystem II do? | It oxidizes water to replace the electrons transferred to photosystem I |
| What are the 2 photosystems connected by? | cytochrome/ b6 -f factor |
| Why do plants use Photosystems II and I? | To produce both ATP and NADPH |
| How are photosystems replenished? | With electrons obtained by splitting water |
| What does Photosystem II resemble? | The reaction center of purple bacteria |
| What is Photosystem II 's core? | 10 Transmembrane protein subunits with electron transfer components and 2 P680 (Photosystem II) chlorophyll molecules |
| What is essential for the oxidation of what in Photosystem II? | 4 Magnesium atoms |
| b6-f Complex | proton pump embedded in the thylakoid membrane in Photosystem II |
| What does the reaction center consist of in Photosystem I? | a core transmembrane complex consisting of 12-14 protein subunits with 2 bound P700 (Photosystem I) chlorophyll molecules |
| What does Photosystem I accept? | An electron from plastocyanine into the "hold" created by the exit of a light energized electron |
| Where does Photosystem I pass its electrons? | to NADP+ to form NADPH |
| What can be used to synthesize ATP? | Electrochemical gradient |
| What does Chloroplast have that allows protons back into the stroma? | ATP synthase enzymes in thylakoid membrane |
| What does the stroma contain? | Enzymes that catalyze the reactions of carbon fixation - the Calvin Cycle reactions |
| What does noncyclic photphosphorylation generate? | NADPH and ATP |
| Building organic molecules take more energy than what? | the energy produced by noncyclic photophosphorylation |
| Why is Cyclic photophosphorylation used? | to produce a larger additional ATP |
| What is used to make a larger proton gradient to make more ATP? | Short-circuit photosystem |
| What do cells use to build carbohydrates? | Energy and Reduction Potential |
| Carbon-Fixation - Calvin Cycle Energy used to build carbohydrates | - ATP from light-dependent reactions -Cyclic and noncyclic-dependent reactions - Drives endergonic reaction |
| Carbon-Fixation - Calvin Cycle Reduction Potential used to build carbohydrates | - NADPH from photosystem I - Source of protons and energetic electrons |
| What is another name for the Calvin Cycle? | C3 Photosynthesis |
| What is the key step the Calvin Cycle? | Attachment of CO 2 to RuBP to form PGA |
| What does the Calvin Cycle use? | Enzyme ribulose biphosphate carboxylase / oxygenase or rubisco |
| What are the 3 phases of the Calvin Cycle? | 1. Carbon fixation 2. Reduction 3. Regeneration of RuBP |
| What happens in the 1st phase of the Calvin Cycle (Carbon Fixation)? | RuBP + CO 2 --> PGA |
| What happens in the 2nd phase of the Calvin Cycle (Reduction)? | PGA is reduced to G3P |
| What happens in the last phase of the Calvin Cycle (Regeneration of RuBP)? | PGA is used to regenerate RuBP |
| What happens when the Calvin Cycles makes 3 turns? | incorporate enough carbon to produce a new G3P |
| What happens when the Calvin cycle makes 6 turns? | Incorporate enough carbon for 1 glucose |
| What is not a direct product of the Calvin Cycle? | Glucose |
| What is G3P? | 3 carbon sugar used to form either sucrose or starch |
| Sucrose | A disaccharide made of fructose and glucose |
| What is a major transport sugar in plants? | sucrose |
| What is an insoluble glucose polymer that is used for storage? | Starch |
| What does Photosynthesis use? | The produces of respiration as starting substrates |
| What does Respiration use? | The products of photosynthesis as starting substrates |
| Production of glucose from ______ even uses part of the ancient glycolytic pathway, run in reverse. | G3P |
| Principal proteins involved in electron transport and ATP production in plants are evolutionary related to _______> | Those in mitochondria |
| What are the 2 enzymatic activities of Rubisco? | Carboxylation and Photorespiration |
| What happens in Rubisco's enzymatic activity of Carboxylation? | Addition of CO2 to RuBP (favored under normal conditions) |
| What happens in Rubisco's enzymatic activity of Photorespiration? | Oxidation of RuBP by addition of O2; creates ow-CO2 and high O2 (favored when stroma are closed in hot conditions) |
| What do CO2 and O2 compete for? | Active site on RuBP |
| Name the types of photosynthesis. | C3; C4 and CAM |
| What happens in C3? | Plants that fix carbon using only C3 photosynthesis (Calvin Cycle) |
| What happens in C4 and CAM? | - Add CO2 to PEP to form 4 carbon molecules - Use PEP carboxylase - C4 = spatial solution - CAM - temporal solution - Greater affinity for CO2, no oxidase activity |
| Name some C4 plants. | Corn, sugar cane, sorghum, and a number of other grasses |
| How do C4 plants initially fix carbon? | Using PEP carboxylase in mesophyll cells |
| What does C4 produce? | Oxaloacetate, converted to malate, transported to bundle-sheath cells where within it, malate is decarboxylase to produce pyruvate and CO2. Carbon fixation then by rubisco and Calvin Cycle |
| C4 Plants Within bundle-sheath cells, what happens? | Malate is decarboxylated to produce pyruvate and CO2? Carbon fixation then by rubisco and Calvin Cycle |
| Although C4 Pathway overcomes the problems of photorespiration, it does have a cost. To produce a single glucose, it requires what? | 12 additional ATP compared with the Calvin Cycle alone |
| Where/when is C4 photosynthesis is advantageous? | In hot dry climates where more than 1/2 of carbon fixed by usual C3 pathway alone |
| What are some CAM plants? | Many succulent (water-storing) plants, such as cacti, pineapples, and some members of about 2 dozen other plant groups |
| In CAM plants what happens to the stroma? | The stroma opens during the night and close during the day (in most plants, its reversed) |
| How do CAM plants fix CO2? | By using PEP carboxylation during the night and stored in vaculoe |
| What happens when the stromata is closed during the day, such those found in CAM plants? | Its organic acts are decarboxylated to yield high levels of CO2 |
| CAM plants: High levels of CO2 drive ______ and minimizes _______. | The Calvin Cycle ; Photorespiration |
| What are some similarities between C4 and CAM? | - Use C3 AND C4 pathways |
| What are two pathways that occur in different cells? | C4 |
| What is a C4 pathway at night and C3 pathway during the day? | CAM |
| Frederick Griffith (1928) | Studied Streptococcus Pneumoniae |
| What are the 2 strains of Streptococcus Pneumoniae? | S strain and R strain |
| Which strain in Streptococcus is virulent? | The S strain |
| Which strain in Streptococcus is nonvirulent? | The R strain |
| How did Griffith do his experiment? | Infected mice with strains of streptococcus to understand the difference between the strains |
| What is the modern interpretation of Griffith's results? | Genetic material was actually transferred between cells |
| Who repeated Griffith's experiment using purified cell extracts? | Avery, MacLeod, and McCarthy (1944) |
| How did Avery, MacLeod, and McCarthy (1944) do the experiment? | Removal of all protein from the transforming material did not destroy its ability to transform R cells. |
| What is the findings of Avery, MacLeod, and McCarthy (1944)? | - DNA -digesting enzymes destroyed all transforming ability -Supported DNA as genetic material |
| What are bacteriophages? | Viruses that infect bacteria composed of only DNA and protein |
| Who investigated bacteriophages? | Hershey and Chase - 1952 |
| Hershey and Chase (1952) | Wanted to determine which of the molecules in bacteriophages is the genetic material that is injected into the bacteria. |
| What is Hershey and Chases' findings? | Only the bacteriophage DNA (32P) entered the bacteria and was used to produce more bacteriophage |
| What is Hershey and Chases' Conclusion? | DNA is the genetic material |
| What is essentially DNA? | A nucleic acid |
| What is DNA structure composed of? | Composed of nucleotides - 5-carbon sugar called deoxyribose - Phosphate group (PO4) attached to 5' Carbon of sugar - Nitrogenous Base (A, T, G, C) - Free Hydroxyl group (-OH) attached at 3' carbon of sugar |
| Phosphodiester bond | Bonds between adjacent nucleotides formed between the phosphate group of 1 nucleotide and the 3' -OH of the next nucleotides |
| What orientation does the chain of nucleotides have? | 5' - to - 3' orientation |
| What nitrogenous bases are the purines? | A and G |
| What nitrogenous bases are the pyrimidines? | C and T |
| What did Chargaff determine? | There is always an equal proportion of purines and pyrimidines - Amount of A = Amount of T - Amount of G = Amount of C |
| Who performed X-ray diffraction studies to identify the 3-D structure of DNA? | Rosalind Franklin |
| What did Rosalind Franklin discover? | That DNA is helical |
| Who deduced the structure of DNA without performing a single experiment, but rather used evidence from Chargaff, Franklin and others | James Watson and Francis Crick - 1953 |
| What did James Watson and Francis Crick propose? | A double helix structure |
| Phosphodiester Backbone | Repeating sugar and phosphate units joined by phosphodiester bonds. Extends in a 5' to 3- direction |
| Double Helix | 2 strands of polymer nucleotides wrapped around an axis. Anti-parallel strands |
| How many hydrogen bonds does A form with T? | 2 Hydrogen Bonds |
| How many hydrogen bonds does G form with C? | 3 hydrogen bonds |
| What does the amount of hydrogen bonds between complementary bases (nucleotides) do? | Give a consistent diameter |
| What are the 3 models of DNA replication? | 1. Conservative model 2. Semiconservative model 3. Dispersive model |
| Conservative Model of DNA Replication | Both strands of parental duplex remain intact; new DNA copies consist of all new molecules |
| Semiconservative Model of DNA Replication | Daughter strands each consist of one parental strand and one new strand |
| Dispersive Model of DNA Replication | New DNA is dispersed throughout each strand of both daughter molecules after replication |
| What are Meselon and Stahl's Results? | 1. Conservative model was rejected 2. Sermiconservative model was supported 3. Dispersive model was rejected |
| Why was the conservative model of DNA replication rejected? | The 2 densities were not observed after round 1 |
| Why was the Sermiconservative model supported? | It was consistent with all observation : 1 band after 1 round, 2 bands after round 2 |
| Why was the dispersive model rejected? | While the 1st round was consistend, the 2nd round did not observe 1 band |
| What are the 3 things that DNA Replication requires? | 1. Something to copy - Parental DNA 2. Something to do the copying - Enzymes 3. Building blocks to make copy - Nucleotide triphosphates |
| What are the stages of DNA Replication? | 1. Initiation - replication begins 2. Elongation - New strands of DNA are synthesized by DNA polymerase 3. Termination - replication is terminated |
| What does DNA polymerase do? | Matches existing DNA bases with complementary nucleotides and links them |
| What are the several common features of DNA polymerase? | - Adds new bases to 3' end of existing strands - Synthesize in 5'-to=3' direction - Require a primer of RNA |
| Prokaryotic Replcation | - Single circular model of DNA beginning at origin of replcaiton - Proceeds in both directions around chromosome - Replicon - DNA controlled by an origin |
| E. Coli has 3 what? | DNA Polymerases 1. DNA polymerase I (pol I) 2. DNA polymerase II (pol II) 3. DNA polymerase III (pol III) |
| What does DNA polymerase I (pol I) do? | Acts on lagging strand to remove primers and replace them with DNA |
| What is DNA polymerase II (pol II) do? | Involved in DNA repair process |
| What is DNA polyermase III (pol III)? | Main replication enzyme |
| What do all DNA polymerases have? | Have 3'-to-5' exonuclease activity - proofreading |
| What does DNA pol I have that apparently the others do not? | Have 5'-to-3' exonuclease activity - removing RNA primers |
| What causes torsional strain? | unwinding helix |
| What uses energy from ATP to unwind DNA? | Helicases |
| What protein coat strands to keep them apart? | Single-strand-binding proteins (SSBs) |
| Topoisomerases | Enzymes that prevent supercoiling |
| DNA gyrase | The topoisomerase involved in DNA replication |
| Okazaki Fragments | DNA fragments on lagging strand |
| In how many directions can DNA polymerase synthesize? | DNA polymerase can synthesize in only 1 direction |
| Leading strand synthesized ______ from an initial primer | Continuously |
| Lagging strand synthesized _____ with multiple priming events | Discontinuously (Leads to Okazaki Fragments) |
| Replication Fork | Partial opening of helix |
| DNA primase - RNA polymerase that makes _____ | RNA primer |
| Leading Strant synthesis | Read it on notes or slides |
| Enzymes involved in DNA replciation form a ______ | macromolecular assembly |
| What are 2 main components in Replisome??? | Primosome and Complex of 2 DNA pol III |
| List 3 primosome. | Primase, Helicase, Accessory proteins |
| Why does replisome need 2 DNA pol III? | For each strand |
| What does Eukaryotic Replication require? | New Enzymatic activity for dealing with ends only |
| Multiple Replicons | Multiple origins of replications for each chromosome; not sequence specific and can be adusted |
| Initiation phase of Eukaryotic replication requires more factors to assemble both _______ onto template, then load polymerase with its sliding clamp unit. | helicase and primase complexes |
| What does Primase include? | DNA and RNA polymerase |
| Main repliccation polymerase is a ______ | Complex of DNA polymerase epsilon (pol E) and DNA polymerase delta (pol 8) |
| Telomeres | Specialized structures found on ends of eukaryotic chromosomes that protect the ends of chromosomes from nucleases and maintain the integrity of linear chromosomes |
| Why is there gradual shortening of chromosomes with each round of cell division? | Unable to replicate the last section of lagging strand |
| What is a telomere composed of? | Short repeated sequences of DNA |
| Telomerase | enzyme makes telomere section of lagging strand using internal RNA template (not the DNA itself) and leading strand can be replicated to the end |
| How id Telomerase developmentally regulated? | Relationship between senescence and telomere length. |
| What slows the activation of telomerase? | Cancer cells |
| What molecule/protein/whatever it is has proofreading ability? | DNA polymerase |
| Mutagens | Any agent that increases the number of mutations above background level such as radiation and chemicals |
| How is the importance of DNA repair indicated by? | The multiplicity of repair systems that have been discovered |
| Name the 2 categories in which repair systems fall under | Specific and Nonspecific Repair |
| Which repair system targets a single kind of lesion in DNA and repairs only that damage? | Specific Repair |
| Which category uses a single mechanism to repair multiple kinds of lesions in DNA? | Nonspecific Repair |
| What kind of repair system does Photorepair use? | Specific repair mechanism for one particular form of damage caused by UV light |
| Thymine dimers | Covalent link of adjacent thymind bases in DNA |
| Photolyase | Absorbs light in visible range and uses this energy to cleave thymine dimer |
| Excision repair is what kind of repair? | Nonspecific repair |
| What happens in an Excision Repair? | Damaged region is removed and replaced by DNA synthesis |
| Name the 3 steps in Excision Repair. | 1. Recognition of damaged region 2. Removal of damaged region. 3. Resynthesis using information on undamaged strand as template |
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