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Week 6 Notes

by: Cara Schildmeyer

Week 6 Notes BIOS 1700

Cara Schildmeyer
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These notes cover Chapter 6 and Chapter 7 from the textbook.
Biological Sciences I: Molecules and Cells
Dr. Tanda
Class Notes
Cellular, Respiration, Photosynthesis




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This 9 page Class Notes was uploaded by Cara Schildmeyer on Friday September 30, 2016. The Class Notes belongs to BIOS 1700 at Ohio University taught by Dr. Tanda in Fall 2016. Since its upload, it has received 101 views. For similar materials see Biological Sciences I: Molecules and Cells in Biological Sciences at Ohio University.

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Date Created: 09/30/16
Week 6 Notes Color Coding Key Pink = Vocab Yellow = General Important Info Green = Examples Orange = Important Concepts/Lists and Steps Blue = Things Mentioned/Emphasized in Lecture Chapter 7: An Overview of Cellular Respiration  Cellular respiration: breaking down inorganic molecules to make organic molecules, releasing energy to do the work of the cell o Process of extracting energy from glucose  ATP: cellular respiration is a series of chem rxns that convert chem energy in fuel molecules into this kind of chem energy to be readily used  Plants use energy of sun to make carbs, break down carbs to make ATP in respiration 7.1: An Overview of Cellular Respiration  Cellular respiration is catabolic Cellular respiration uses chemical energy in carbs and lipids to produce ATP  Cellular respiration in presence of oxygen is aerobic, in absence of oxygen is anaerobic o C6H12O6 (Glucose) + 6O2 (Oxygen)-->6CO2 (Carbon Dioxide) + 6H2O (Water) + energy  Cellular respiration releases lots of energy b/c PE in bonds of reactants > than in products  Energy released in series of steps to let some energy be used in the form of ATP o 32 molecules ATP produced from aerobic respiration of 1 glucose molecule o 34% energy released by aerobic respiration harnessed in ATP form  NADH pumps 5 H+, FADH2 pumps 3 H+ into intermembrane space  2 H+ produces 1 ATP ATP is generated by substrate-level phosphorylation  Substrate-level phosphorylation: Making ATP when phosphate group is transferred to ADP (from an enzyme substrate-organic molecule) o Produces only 12% ATP from respiration  Electron carriers: chem energy of organic molecules is transferred to these, and they carry e- and energy from one set of rxns to another  E- transport chain: transfer e- along a series of membrane-associated proteins to a final e-acceptor and in the process harness energy released to make ATP o Generating ATP this way is called oxidative phosphorylation Redox rxns play a central role in cellular respiration  Oxidation-reduction rxns: chem rxns in which e- are transferred from one atom or molecule to another o Oxidation is e- loss, reduction is e- gain  E- carriers are nicotinamide adenine dinucleotide and flavin adenine dinucleotide  Reduction rxn: NAD+ + 2e- + H+ --> NADH and FAD + 2e- + 2H+ --> FADH2 o E- from chem rxns or from glucose  Oxidation rxn: NADH --> NAD + + 2e- + H+ and FADH2 --> FAD + 2e- + 2H+ o E- from chem rxns or from glucose  Losing H+ means losing energy (reduction)  In CO2, O- more e-neg, so carbon is oxidized (releases energy)  In H2O, O- more e-neg, so it gains e- to be reduced Cellular respiration occurs in 4 stages 1 Glyocolysis: glucose broken down to make pyruvate, energy transferred to ATP and reduced e- carriers o Occurs in cytoplasm 2 Pyruvate is oxidized to acetyl-CoA, producing reduced e- carriers, releasing CO2 o Occurs in matrix of mitochondria 3 Citric acid cycle (Krebs cycle): acetyl group oxidized to CO2, energy transferred to ATP and reduced e- carriers o Amount of energy transferred to ATP 2x that of stage 1 + stage 2 o Occurs in matrix of mitochondria 4 Oxidative phosphorylation: reduced e- carriers donate e- to ETC, making lots of ATP o Occurs in intermembrane space, inner membrane, and matrix o Majority of ATP produced this way  Glycolysis in cytoplasm, other 3 stages in mitochondria in eukaryotes  In bacteria, rxns in cytoplasm, ETC in plasma membrane  2 ways of making ATP are substrate-level phosphorylation and oxidative phosphorylation (mostly use oxidative for ATP) 7.2: Glycolysis: The Splitting of Sugar  In glycolysis, 6-carbon glucose split into 2 to get 2 3-carbon molecules o Anaerobic, evolved when O2 wasn't in Earth's atmosphere Glycolysis is partial breakdown of glucose 1 2 phosphate groups added to glucose (requires 2 ATP) o Glucose is trapped in cell, and 2 neg-charged phosphate groups destabilize the molecule so it can be broken apart 2 Cleavage phase: 6-carbon molecules split into 2 3-carbon molecules 3 Payoff phase: ATP and e- carrier NADH produced, 2 molecules pyruvate produced o Net gain of 2 ATP molecules, 2 NADH molecules, 2 pyruvate 7.3: Pyruvate Oxidation W/O2, pyruvate can be further oxidized to release more energy   Intermembrane space: b/t inner and outer membranes of mitochondria  Mitochondrial matrix: space enclosed by inner membrane of mitochondria  Pyruvate transported to matrix and converted to acetyl-CoA 1. Pyruvate is oxidized, splits off to form CO2 2. Lost e- are donated to NAD+, becoming NADH 3. Acetyl group is transferred to coenzyme A (CoA)  Net gain: 2 CO2, 2 NADH, 2 acetyl-CoA 7.4: Citric Acid Cycle  Starts w/oxaloacetate and ends w/oxaloacetate  Fuel molecules are completely oxidized in the matrix  In 1st rxn, 2-carbon acetyl group of acetyl-CoA is transferred to 4-carbon oxaloacetate to make 6-carbon citric or tricarboxylic acid  Citric acid is oxidized, generating oxaloacetate  Carbons released as CO2  Energy released in oxidation rxns is transferred to NADH  3 NADH and 1 FADH2, 1 ATP made, and CO2(waste) per pyruvate molecule by using all energy from acetyl group  Substrate-level phosphorylation rxn generates GTP, which transfers a phosphate to ADP to make ATP  Net: 2 acetyl-CoA, 2 ATP, 6 NADH, 2 FADH What were the earliest energy-harnessing rxns?  Reverse citric acid cycle requires sun energy  Running cycle in reverse allows building organic molecules o Pyruvate is the start for sugars and alanine, acetate is the start for lipids, oxaloacetate forms amino acids and pyrimidine bases, alpha ketoglutarate makes other amino acids  Forward cycle maked energy-storing molecules and intermediates, reverse generates intermediates and incorporates carbon into organic molecules 7.5: The ETC and Oxidative Phosphorylation ETC transfers e- and pumps protons  Energy source is e-, not ATP  Membrane proteins are embedded in mitochondrial inner membrane  E- donated by NADH enter through complex I, those donated by FADH2 enter through complex II  W/chain complex movement, e- passed from donors to acceptors (making redox couples) o O- accepts e- at end of ETC, reduced to make H2O using PE: O2 + 4e- --> 2H2O  Coenzyme Q (CoQ): accepts e- from complex I and II  Cytochrome c: in complex II, e- transferred from CoQH2 to this, protons released into intermembrane space  Transfer of e- through complexes I, III, and IV coupled w/proton pumping, accumulating protons in intermembrane space Proton gradient is source of PE  Protons have high conc in intermembrane, low conc in matrix o Protons tend to diffuse back into matrix, but are blocked by membrane ATP synthetase converts energy of proton gradient into energy of ATP  Mitchell's hypothesis (chemiosmotic hypothesis): 1 Must be opening in membranes for protons to flow through (protons move down gradient through transmembrane protein) 2 Movement of protons must be coupled w/ATP synthesis  ATP synthase: enzyme w/2 subunits (Fo forms channel for protons, F1 is catalytic unit for ATP) o Flow of protons through Fo cause rotation, and proton gradient converted to mechanical rotational energy, causing F1 to rotate and make ATP from ADP and phosphate group  Experiment: measure pH by turning on light, and the pH goes down o Turn off light, and pH goes up 2.5 molecules ATP produced for each NADH, 1.5 for each FADH2  7.6: Anaerobic Metabolism and Evolution of Cellular Respiration Fermentation extracts energy from glucose in the absence of oxygen  Fermentation: does not rely on O2 or e- acceptors o Important for anaerobic organisms, and yeast (favors fermentation over oxidative phosphorylation), used when O2 can't be delivered fast enough  Lactic acid fermentation: occurs in animals and bacteria, e- from NADH transferred to pyruvate to make lactic acid and NAD+ o Glucose + 2ADP + 2Pi --> 2 lactic acid + 2ATP + 2H2O  Ethanol fermentation: occurs in plants and fungi, pyruvate releases CO2 to make acetaldehyde, and e- fro NADH transferred to acetaldehyde to make ethanol and NAD+ o Glucose + 2ADP + 2Pi --> 2 ethanol + 2CO2 + 2ATP + 2H2O o No net production or loss of NADH/NAD+ in fermentation  Lactic acid and ethanol not fully oxidized and have lots of chem energy in bonds How did early cells meet energy requirements?  Fermentation occurs in cytoplasm, doesn't require proteins embedded in specialized membranes  Cellular respiration can occur w/o O2, but sulfate and nitrate need to be final e- acceptor  ETC in bacteria is in plasma membrane (not internal membrane)  Prokaryotes evolved pumps to drive protons out of cell b/c acidic environment  Proton pumps generated electrochem gradient so protons could pass back through pump in reverse to make ATP o Shows evolution works in steps, building on what is already present 7.7: Metabolic Integration Excess glucose stored as glycogen in animals and starch in plants  Glucose stored as glycogen in animals, starch in plants  Glucose molecules not consumed by glycolysis link to form glycogen in liver and muscle o Liver is central glycogen storehouse, released glucose into bloodstream  Glucose molecules at end of chains cleaved one at a time, glucose 1- phosphate is released and converted to glucose 6-phosphate Sugars other than glucose contribute to glycolysis  Monosaccharides are converted to intermediates of glucose that come late in pathway o Ex.: Fructose produced by hydrolysis of sucrose receives phosphate group to make fructose 6-or 1-phosphate Fatty acids and proteins are useful sources of energy  Fatty acids have C-C and C-H bonds (lots of chem PE), produce lots of ATP  Triacylglycerols converted to glycerol and fatty acids  Beta-oxidation: fatty acids shortened by rxns that remove 2 carbon units from end, releasing NADH and FADH2 that provide e- for making ATP by oxidative phosphorylation o End product is acetyl-CoA, which produces more e- carriers Intracellular level of ATP is key regulator of cellular respiration  When low ATP levels, cell activates pathways for ATP synthesis (high NAD+ and ADP levels stimulate respiration, high NADH and ATP levels inhibit) o Example of Allosteric Regulation  Enzymes that control pathway steps are regulated o Ex.: Fructose 6-phosphate converted to fructose 1, 6-biphosphate, consuming 1 ATP o This is irreversible, and rxn is catalyzed by PFK-1 (change enzyme shape to increase rate of glycolysis) o When there's lots of ATP, it binds to same site and inhibits catalysis Exercise requires several types of fuel molecules and coordination of metabolic pathways  Muscle cells have mitochondria that produce ATP by aerobic respiration (greater energy yield, slower process)  For longer exercise, liver releases glucose to blood that is taken up by muscle cells and oxidized to produce ATP o Fatty acids released from adipose tissue, broken down by beta- oxidation Chapter 8: Photosynthesis 8.1: photosynthesis: An Overview  Photosynthesis: biochem. process for building carbs using energy from sunlight and CO2 taken from air Photosynthesis is widely distributed  60% carried out by terrestrial organisms, 40% in ocean  Photic zone: in ocean, photosynthesis occurs in this surface layer 100m deep  Tropical rain forests, grasslands, and forests have high photosynthetic productivity Photosynthesis is redox rxn  Reduction: rxns in which molecules acquires e-, releases energy o E- come from PETC  Oxidation: rxns in which molecule loses e-, releases energy  CO2 molecules reduced to form higher-energy carbs, requiring transfer of e- from electron-donor 6CO2 + 6H20 --> C6H12O6 + O2 o Carbon in CO2 is reduced o H2O is the electron-donor  Photosynthetic transport chain: series of redox rxns in which e- are passed from one compound to another o Begins w/absorption of sunlight that gives energy to drive e- through photosynthetic ETC o Movement of e- produces ATP and NADPH, which are used to synthesize carbs w/CO2 in Calvin cycle o ATP, NADPH, O2 synthesized from sunlight and H2O o Energy source: light; end products: NADPH by NADP reductase and ATP by ATP synthase; mediators: e- for NADPH production and H+ gradient for ATP production; proton pump: cytochrome b6f complex and Pq  CO2 has low energy bonds vs. carbs, which have high energy C-C and C-H bonds Photosynthetic ETC takes place on specialized membranes  In photosynthetic bacteria, photosynthetic ETC (PETC) is in membrane w/in cytoplasm, but is in chloroplasts in eukaryotes  Thylakoid membrane: highly folded chloroplast center o Where ETC is/where sunlight is captured and transformed to chem energy  Grana: stacks of thylakoid membranes grouped into structures  Stroma: region surrounding thylakoid membrane o Where carb synthesis is  Photosynthetic organisms need ATP, and ATP from chloroplasts isn't exported (only carbs are exported), so they need mitochondria and cellular respiration 8.2: The Calvin Cycle  Carboxylation: CO2 added to 5-carbon molecule  Reduction: Energy and e- transferred to compounds formed in carboxylation  Regeneration: 5-carbon molecule needed for carboxylation is regenerated Incorporation of CO2 is catalyzed by rubisco  CO2 added to 5-carbon sugar RuBP (catalyzed by enzyme rubisco)  Once CO2 and RuBP diffuse into active site, 3-PGA (3-carbon molecules) are 1st stable products of Calvin cycle NADPH is reducing agent of Calvin cycle  NADPH: reducing agent of Calvin cycle, transfers e- that allow carbs to be synthesized from CO2 o Energy and e- only transferred under catalysts of specific enzyme  Reduction of 3-PGA: 1 ATP donates phosphate group to 3-PGA 2 NADPH transfers 2 e- and one H+ to phosphorylated compound 3 This releases a phosphate group (Pi)  These steps form 3-carbon molecules called triose phosphates o Principal form in which carbs are exported from chloroplast  If every triose phosphate were exported, RuBP couldn't be regenerated o For every 6 triose phosphates, only 1 can be withdrawn Regeneration of RuBP requires ATP  2 molecules NADPH and 3 molecules ATP required for each CO2 molecule incorporated by rubisco  Calvin cycle doesn't use sunlight directly--needs energy input provided by cofactors (supplied by PETC), and Calvin cycle enzymes are regulated by cofactors that must be activated by PETC Steps of Calvin cycle were determined by using radioactive CO2 1 Radioactive CO2 supplied to alga Chlorella, then cells put in boiling alcohol, stopping enzyme rxns 2 Carbon compounds were radioactively labeled 3 To determine how 3-PGA is formed, CO2 supply was cut off, increasing amount of RuBP  Conclusion: 1st step in Calvin cycle was adding CO2 to RuBP Carbs are stored as starch  Excess carbs stored as starch (not soluble), providing storage that doesn't lead to osmosis o Otherwise, excess glucose would increase glucose conc. In cytoplasm, causing influx of water  Starch is the source of carbs for plants at nighttime 8.3: Capturing Sunlight into Chem Forms Chlorophyll is major entry point for light energy in photosynthesis  Visible light: portion of electromagnetic spectrum apparent to our eyes (includes range of wavelengths used in photosynthesis)  Chlorophyll: major photosynthetic pigment; appears green b/c poor at absorbing green wavelengths o Has light-absorbing head w/Mg atom at center and hydrocarbon tail  Alternating single and double bonds in head explain efficiency at absorbing visible light  Photosystems: protein-pigment complexes that absorb light energy to rive e- transport o Rich in chlorophyll pigments  Accessory pigments: pigments other than chlorophyll, absorb light from regions of visible spectrum that are poorly absorbed by chlorophyll Photosystems use light energy to drive PETC  When visible light is absorbed, e- elevated to higher energy state o Most energy converted to heat, small amount to light in extracted chloroplasts o Energy transferred to adjacent chlorophyll molecules, raising energy level of adjacent e-  Rxn center: energy is transferred b/t chlorophyll molecule antennas until it is transferred to this specially configured pair of chlorophyll molecules o H2O is the e- donor that creates a protons gradient (potential energy) o There is an e- acceptor and e- carrier, and the potential energy is converted to chemical energy  Rxn center becomes oxidized, adjacent e- acceptor reduced, converting light energy to chem form --> leads to formation of NADPH  For PETC to continue, another e- must be delivered to take place of the one that entered transport chain PETC connects 2 photosystems  Water is abundant, serves as e- donor (but it takes a lot of energy to pull e- from water)  Energy supplied by 1st photosystem allows e- to be pulled from H2O, energy from 2nd photosystem allows e- to be transferred to NADP+ o This is exergonic  Z scheme: overall energy trajectory has up and down configuration resembling "z," so this is what PETC is called  Photosystem II: supplies e- to beginning of ETC, when it loses e-, pulls e- from H2O  Photosystem I: energizes e- w/input of light energy to reduce NADP+  Cytochrome-b6f complex: e- pass b/t Photosystem II and I to cyt by diffusing through membrane  Pc is water soluble, carries e- from cyt to Photosystem I by diffusing through thylakoid lumen  Enzyme ferredoxin-NADP+ reductase catalyzes formation of NADPH by transferring 2 e- from 2 molecules of reduced ferredoxin to NADP+ as well as an H+ o NADP+ + 2e- + H+ --> NADPH Accumulation of protons in lumen drives synthesis of ATP  2 ways H+ accumulates in lumen: 1 In chloroplasts, ATP synthesis is a result of H+ movement from lumen to stroma 2 Oxidation of H2O releases H+ and O2 into lumen  Cyt and pq fnt as proton pump  Proton pump: 1 Transports 2 e- and 2 H+ by diffusion of pq from stroma side of photosystem II to lumen side of cyt 2 Transfers e- w/in cyt to different molecule of pq, causing more H+ to be picked up from stroma and released in lumen  H+ on one side of thylakoid membrane used to power ATP synthesis by oxidase phosphorylation Cyclic e- transport increases ATP production  Cyclic e- transport from photosystem I redirected from ferredoxin back into ETC so e- reenter PETC by pq  Additional H+ are transported from stroma to lumen, so more H+ in lumen to drive ATP synthesis 8.4: Challenges to Photosynthetic Efficiency Excess light can cause damage  Reactive oxygen species: highly reactive forms of O formed by transfer of absorbed light energy from antenna chlorophyll directly to O2, or by transfer of e-, forming O2  Any factor that causes rate of NADPH use to fall behind rate of light-driven e- transport can lead to damage o Ex.: In middle of day when light intensity is highest  Rate at which Calvin cycle makes NADPH influenced by cold temps (slower fnt)  2 ways photosynthetic organisms defend against not keeping up w/light: 1 Antioxidants neutralize reactive O2 2 Xanthophylls: Yellow-orange pigments that slow formation of reactive O2 by reducing excess light energy (converted to heat) Photorespiration leads to net loss of energy and carbon  Enzyme that adds O2 to another molecule is oxygenase (ex. Rubisco)  When rubisco adds O2, not CO2, to RuBP, one 3-PGA and 2 phosphoglycolates form (2-carbon molecule can't be used by Calvin cycle and is partially converted to 3-PGA, partially released as O2)  Photorespiration: consumption of O2 and release of O2 in presence of light o Consumes ATP and results in oxidation and loss of carbon atoms, draining energy  2 x 2-phosphoglycolate + ATP --> 3-PGA + CO2 + ADP + Pi  Cycle 2x --> 3-PGA  Cycle 4x --> 6x 3-PGA = 3x Calvin --> 1 triose phosphate  Additional loss of 2 ATP  Turn Calvin cycle 6x --> 2 triose phosphate to make one glucose  Better rubisco is at discriminating O2 and CO2, slower it catalyzes  Rubiscos of land plants are very selective, must make lots of rubisco  1/4 reduced carbon lost through photorespiration Photosynthesis captures just a small percentage of incoming solar energy  1-2% of sun's energy that lands on leaf ends up in carbs o 60% not visible light and not absorbed, 8% reflected/passes through, 8% given off as heat, 20% incorporated into CO2 in carbs (loss of energy), so max energy conversion efficiency is 4% 8.5: Evolution of Photosynthesis How did early cells use sun to meet energy requirements?  Earliest interactions w/sun were evolution of UV-absorbing compounds that could shield from damaging rays o One may have used sun to meet energy needs  Light-driven e- transport coupled to net movement of H+ across membrane, allowing for ATP synthesis  Now-intermediate compounds were once the end product used as pigment Ability to use H2O as e- donor in photosynthesis evolved in cyanobacteria  Photosynthetic organisms w/one photosystem use more easily oxidized compounds (H2S used as e- donor)  Cyanobacteria had one photosystem to pull e- from H2O, one to increase level of e- so they can reduce CO2  Theories for development of 2 photosystems: 1 Genetic material associated w/one photosystem transferred to bacteria w/other photosystem 2 Genetic material for one photosystem duplicated, diverging in sequence  Photosynthesis could occur anywhere w/sun and water since H2O can be e- donor  All O2 in Earth's atmosphere from photosynthesis by organisms w/2 photosystems Eukaryotic organisms gained photosynthesis by endosymbiosis (one cell takes up residence in another)  Complimentary metabolic processes: o Cellular respiration breaks down carbs in presence of O2 to give energy, making CO2 and H2O o Photosynthesis uses CO2 and H2O w/sun to build carbs, release O2


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