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Biochemistry 301 Week 9 Notes

by: Emily

Biochemistry 301 Week 9 Notes BBMB 301

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One week of lecture notes.
Survey of Biochemistry
Robert Thornburg
Class Notes
biochemistry, BBMB
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This 10 page Class Notes was uploaded by Emily on Thursday March 3, 2016. The Class Notes belongs to BBMB 301 at Iowa State University taught by Robert Thornburg in Spring 2016. Since its upload, it has received 23 views. For similar materials see Survey of Biochemistry in General Science at Iowa State University.


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Date Created: 03/03/16
Biochemistry 301 – Survey of Biochemistry Professor Robert Thornburg LECTURE 22 – CHAPTER 22 – PHOTOSYNTHESIS: LIGHT HARVESTING By: Emily Settle  Electron transport coupled to oxidative phosphorylation o High energy electron sources  Respiration: reduced carbon  Photosynthesis: water plus photon energy, producing oxygen o Terminal electron acceptor  Respiration: oxygen, producing water  Photosynthesis: NADP, producing NADPH o Both respiration and photosynthesis operate proton pumps during electron transport  Same ATP synthase mechanism  Two phases of Photosynthesis o Light-dependent reactions  Electrons from oxygen in H2O transferred to NADP+  Large +ΔG  Photons from sunlight provide energy input  Electron transport  Products are NADPH and ATP o Carbon-fixation reactions  ATP and NADPH used to reduce carbon  CO2 converted to glucose  Chloroplast Structure o Photosynthesis occurs in chloroplasts of green plants o Similar to mitochondria  Outer membrane, intermembrane space, inner membrane, internal soluble compartment (stroma) o In addition:  Third membrane – thylakoid membrane  Folded from the inner membrane into sacs – thylakoids  Thylakoids stacked together – grana  Soluble interior of sacs – thylakoid lumen o Electron transfer reactions occur in the thylakoid membranes  Protons pumped from the stroma to the thylakoid lumen  Chloroplasts (and mitochondria) have their own genomes  These genomes encode their own genes and proteins  These organelles are thought to have arisen via cellular invasion and cellular endosymbiosis o Pumping protons from chloroplast stroma into the thylakoid lumen  Visible Light Wavelengths o Wavelength (λ) determines energy of a photon  Quantum o Specific electrons can absorb specific quanta  Molecular structure determines quanta that can be absorbed  Electron moves to higher-level orbital o Visible light λs  Quanta match light harvesting pigment π bond electrons  Minor alterations in structure of the absorbing compound provide different absorption spectrum  Photon absorbing molecules o Chlorophyll  Abundant in thylakoid membranes  Synthesized from glutamic acid, from α-ketoglutarate  From citric acid cycle  Phytol (R) is an isoprenoid lipid  Synthesized from acetyl-CoA  A and b forms differ by formyl group vs. methyl group o Accessory pigments: carotenoids  Also abundant in thylakoid membranes  Tetraterpenes (40 carbons)  Synthesized from acetyl-CoA  Conjugated double bonds  Allow electrons to move to excited state orbital after photon absorption  This applies also to chlorophyll o Resonance energy transfer  Fates of Energy After Electron Excitation o Fluorescence  Photon emitted as electron returns to ground state orbital o Heat  Emitted when electron returns to ground state o Resonance energy transfer  Between excited energy states  If absorption spectra overlap, an excited state of one molecule can activate another neighboring molecule  This is due to electron orbital overlap of activated o Redox reaction  Electron transfer from original excited molecule to acceptor  Acceptor reduced, original oxidized  Referred to as photoinduced charge separation o Electron transport  Electrons are transferred from one molecule to another and energy is captured along the way  Similar to electron transport chain  Light harvesting complexes o Chlorophylls and accessory pigments located in large protein complexes that are abundant in the thylakoid membrane  Large surface area for photon absorption  Energy is passed from one molecule to another and winds up at the reaction center o Resonance energy transfer to reaction center  Photoinduced charge separation occurs and the reaction center  In plants these are called photosystem I and photosystem II  Reaction center chlorophylls function differently than light- harvesting chlorophylls  Photosystem I o Transfers electron from “special pair” chlorophyll a molecules (P700)  First to the primary acceptor A 0another chlorophyll molecule)  Then to plastoquinone  Then to Fe-S proteins  Then to ferredoxin  An iron-sulfur protein  Then to NADP+ to form NADPH o At the end of this process P700 is positively charged  Has given away an electron  P700+ must be reduced back to P700 o Plastocyanin: source of electron to reduce P700+ back to P700  Ferridoxin-NADP+ Reductase o NADPH formed  One of the end products of the light-dependent reactions of photosynthesis  Two electrons transferred in two cycles  Proton absorbed from stroma onto NADPH as it is reduced  Increases stroma pH  Connection Between Photosystem I and Photosystem II o Photosystem II moves an electron from P680 eventually to pastocyanin  Plastocyanin reduces P700+ back to P700  P680 converted to P680+  During electron transport a pump moves protons from stroma to thylakoid lumen o Another part of photosystem II moves electron from H2O to P680+  P680 regenerated  O2 formed  Photosystem II o Associated with light harvesting complex II  Three proteins that hold many chlorophylls and carotenoids  Absorbs photons , passes energy to PSII  First to chlorophyll CP43 and CP47  From there to P680 o Electron transfer components 2+  Pheophytin a (Chl aith no Mg ion) is the electron acceptor from P680  Then successively through bound Q to mobile Q, forming reduced QH c2me from the stroma  Cytochrome b f 6omplex o Electron transfer from photosystem II to plastocyanin  Accepts electrons from QH 2  Donates to Cu atom in plastocyanin  Plastocyanin is mobile in membrane o Cyt b 6 complex works the same way as complex III of mitochondria  Q cycle shuttles protons from the stroma to the thylakoid lumen  See Lecture 20 for description of Q cycle shuttle system o pH gradient generated  higher [H+] in lumen, lower pH  lower [H+] in stroma, higher pH  Water oxidation o Electron from Tyr 161side chain of PSII protein reduces P680+  P680 reset to begin another cycle of electron transfer  Tyrosine radical formed: R-O• o Tyr161reduced by Mn atom in manganese center protein of PSII  Mn 2+ Mn 3+ + e- - o Four cycles (4e )  Mn2+, Mn3+ oxidized to Mn5+ (3e-), Mn4+ (1e-)  Four electrons have been transferred to P680 that has donated an electron four separate times o 2H2O now oxidized  4e- returned to Mn atoms in MSP, back to starting point  4H+ released to lumen (pH increase)  O2 produced  Energy Conversion o After all this, 4e- from H2O to Q  2OH2 + 2Q  O2 + QH2 o More chemical energy in QH2 than OH2  Less positive standard reduction potential  Energy difference explained by photons o Electromagnetic energy converted to chemical energy  This is the ultimate source of all new reduced carbon on earth  Food  Oil, coal  Photophosphorylation o Same mechanism as mitochondrial ATP synthase o Light required to energize proton pump  In contrast, fuel energy (oxidation of reduced carbon) is used in mitochondria o Direction of proton flow  Chloroplast – protons pumped in  Mitochondria – protons pumped out  Cyclic Electron Transfer (Q cycle) o Modified form of photosynthesis occurs when [NADP+] is low  ATP synthesis continues without formation of NADPH o Only Photosystem I is used  Electron transfer to ferredoxin as usual  Instead of ferredoxin-NADP+ reductase, electron is given to plastoquinone  Cytochrome b f complex continues Q cycle 6  Protons moved from stroma to thylakoid lumen  Electron transfer to plastocyanin  Plastocyanin reduces P700+, cycle continues  Summary o Photosynthesis  Initial electron donor: H2O  O2 generated  Ultimate electron acceptor: NADP+ o Respiration  Initial electron donor: NADH  Ultimate electron acceptor: O2  H2O generated Biochemistry 301 – Survey of Biochemistry Professor Robert Thornburg LECTURE 23 – CHAPTER 23 – PHOTOSYNTHESIS: CARBOHYDRATE SYNTHESIS By: Emily Settle  Gluconeogenesis (review) o Photosynthesis provides 3-phosphoglycerate (3-PGA)  Also generates sugar (ribose) from CO2 (calvin cycle) o Gluconeogenesis in chloroplasts  ATP and NADPH from light reactions  NADPH used in place of NADH  Calvin Cycle Overview o Stage 1 – CO2 fixation  1 CO2 (1 C) molecule attached to 1 molecule of ribulose-1,5- bisphosphate (RuBP) (5 C)  Intermediate (6 C) split by insertion of water giving two molecules (3 C each)  Glycerate-3-phosphate (3-PGA)  Repeat 6 times (for each glucose produced)  Forms 12 3-PGA, consumes 6 RuBP o Stage 2 – Reduction  3-PGA converted to glyceraldehyde-3-phosphate (Gly-3-P)  Reduction of carboxylic acid to carbonyl  Chemical energy and e- required  NADPH is oxidized to NADP+  ATP expended, ADP is formed  Repeat 12 times  12 3-PGA to 12 Gly-3-P o Stage 3 – Regeneration  10 Gly-3-P (3 C each) converted to 6 RuBP (5 C each)  2 Gly-3-P (3 C each) converted to glucose (6 C) by gluconeogenesis o Summary  6 RuBP, 6 CO2 enter the cycle  6 RuBP out, 1 glucose out  ATP and NADPH consumed  Overall reaction  6CO2 + 12NADPH + 18ATP  Glucose + 12NADP+ + 18ADP + 18Pi  CO2 Fixation – Stage 1 o Attachment of inorganic CO2 to organic RuBP  Catalyzed by ribulose-1,5-bisphosphate carboxylase  RUBISCO  L8S8quaternary structure  Chloroplast stroma  6 carbon intermediate  Immediately split by insertion of H2O  Forms 2 molecules of 3-PGA  CO2 Fixation Reaction o Β-ketoacids are notoriously unstable and readily breakdown between the α and β carbons  Reduction of Carbon – Stage 2 o Leads to production of sugars via gluconeogenesis o 3-PGA reduced to Glyc-3-P  Enzymes are:  Glyceraldehyde-3-phsophate dehydrogenase  Phosphoglycerate kinase  Stromal forms of glycolysis enzymes  ATP and NADPH required  Regeneration of RuBP – Stage 3 o Complex pathways: 16% of Gly-3-P goes through gluconeogenesis to make carbohydrates for starch and sucrose but 84% is required to regenerate ribulose-5-phosphate  Aldolase, Dephosphorylation, and Transketolase reactions o These enzymes convert 3-carbon compounds back into 5-carbon compounds exchange 2 carbons from one compound to another  3 + 3  6 aldolase dephosphorylation  6 + 3  4 +5 transketolase  4 + 3  7 aldolase dephosphorylation  7 + 3  5 + 5 transketolase o 10 Gly-3-P from CO2 fixation used to regenerate six RuBP  Fate of Glucose made in photosynthesis o Sucrose biosynthesis occurs in leaves at site of photosynthesis  Glc-6-P  Glc-1-P (phosphoglucomutase)  Glc-6-P from gluconeogenesis  Glc-1-P + UTP  UDP-glucose + PPi (UDP-glucose pyrophosphorylase)  Fructose-6-P + UDP-glucose  sucrose-6-P + UDP  Fructose-6-P from gluconeogenesis  Sucrose-6-P + H2O  sucrose + Pi  Sucrose transported from leaves to other places in the plant  Converted back to hexoses and used as fuel for glycolysis or other pathways o Starch biosynthesis occurs in leaves and seeds  Glc-6-P  Glc-1-P (phosphoglucomutase)  Glc-6-P from gluconeogenesis in leaves  Glc-1-P + ATP  ADP-glucose + PPi (ADP-glucose pyrophosphorylase)  Glc-1-P from imported sucrose in seeds  ADP-glucose + starch n residuesDP + starch n+1 residues  Coordination of Photosynthetic Pathways o RUBISCO activity elevated when light-dependent reactions are active  Enzyme activity requires  Carboxylation of Lys 205 o Light reactions pump H+ out of stroma into thylakoid lumen, reduces [H+] in environment of RUBISCO favors the carboxylation reaction  Mg2+ binding to that carboxylate group  Light reactions cause Mg2+ to leave lumen and enter stroma o Calvin cycle enzymes and a wide variety of other enzymes are activated when light reactions are active  Reduced ferredoxin transfers e- to enzymes, indirectly  Thioredoxin is intermediate e- carrier  Disulfide bonds in enzymes reduced  Covalent modification changes enzyme structure  Causes activation  C4 Metabolism o Alternative CO2 fixation  PEP carboxylase instead of RUBISCO o CO2 then delivered to inner part of leaf  RUBISCO takes over as normal o Function  Protects RUBISCO from O2  O2 competes with CO2 for binding to RUBISCO  PEP carboxylase not sensitive to O2 o Grasses use this pathway  Maize, wheat, rice are grasses  The most successful plants  CAM Metabolism o Variation of C4 pathway for desert plants necessary in hot dry environments  Only one cell type  PEP carboxylase active only at night  Leaves open to atmosphere only at night  Malate stored overnight  Pathway continues during day  Light available to generate ATP, NADPH  CO2 provided to RUBISCO  Leaves closed to atmosphere  Necessary in hot, dry environment Biochemistry 301 – Survey of Biochemistry Professor Robert Thornburg LECTURE 24 – CHAPTER 24 – GLYCOGEN METABOLISM I By: Emily Settle  Phosphorylase Activity o Phosphorolysis is like hydrolysis  Except inorganic phosphate is inserted into the glycoside bond rather than H2O  Phosphorylase reaction cleaves α(14) bonds o Hydrolysis  Hydrolase reaction (GDE) cleaves α(16) bonds  Conversion of Glycogen to Glucose-1-P o Phosphorylase releases Glc-1-P from the non-reducing ends, stops four residues from a branch point o Glycogen debranching enzyme (GDE) has two activities  Transfers three glucose units from the branch chain to the end of the main chain  Hydrolyzes the remaining glucose unit on the branch o Phosphorylase then continues degrading the linear chain  Phosphoglucomutase o Product of phosphorolysis is Glc-1-P o Phosphoglucomutase converts Glc-1-P to Glc-6-P  In muscle Glc-6-P enters glycolysis  In liver, Glc-6-P converted to Glc by glucose-6-phosphate (a hydrolase)  Glc released to bloodstream, supplied to other tissues o An enzyme-bound phosphate group is used to generate G-1,6- bisphosphate  Regulation of glycogen breakdown o Glycogen breakdown to release glucose is highly regulated  Maintains constant blood glucose level o Glycogen phosphorylase activity is regulated by phosphorylation  Be careful about terminology  Phosphorylation is transfer of a phosphate group from ATP to the enzyme  Phosphorylase catalyzes a completely different reaction o Insertion of a phosphate group into a glycoside bond o Phosphorylase kinase adds phosphate group to glycogen phosphorylase  Phosphorylase a vs. phosphorylase b o Phosphorylase a  Phosphorylated form  With phosphate group added to a serine R group  R (relaxed) state favored over T (tense) state in equilibrium between R and T  R is the active state, so phosphorylase a is usually active o Phosphorylase b  Not phosphorylated  T state favored over R state, so usually inactive  Phosphorylase b Regulation in Muscle o Regulation of T to R state transition for phosphorylase b  AMP/ATP ratio governs phosphorylase b activity  AMP is allosteric activator, ATP is allosteric inhibitor  AMP binds to regulatory site  Allosteric change in structure favors R state  Thus, when [AMP] is high: o Phosphorylase b active, glycogen degraded, Glc-1-P is released o Low energy in muscle cell (high AMP) signals need to release fuel from storage  ATP blocks access of AMP to regulatory site  This keeps phosphorylase b in T state, inactive o High energy in muscle cell (high [ATP]) signals that fuel should be kept in storage o High [Glc-6-P] also allosterically keeps phosphorylase b in T state, inactive, fuel not needed  Phosphorylase a vs. phosphorylase b in liver  Phosphorylase in liver and muscle are encoded by different genes o 90% amino acid identity o Highly similar but not identical structures cause different regulatory properties  Liver phosphorylase not regulated by AMP/ATP ratio o Thus, liver phosphorylase b usually in inactive T state  Liver phosphorylase activated by conversion to phosphorylase a o Response to hormone signals that indicate blood glucose level is low o Glucagon  Liver phosphorylase a is inhibited by glucose o Feedback inhibition from end product of pathway o Shifts equilibrium to inactive T state  Thus, liver functions to regulate the level of free glucose  Regulation of Phosphorylase Kinase o Phosphorylase kinase converts phosphorylase b to phosphorylase a  Thus, it controls rate of glucose release from glycogen o Phosphorylase kinase activity is regulated by phosphorylation  Protein Kinase A (PKA) transfers phosphate group from ATP to phosphorylase kinase, and activates it  Thus, PKA activity controls rate of glucose release from glycogen o Ca2+ ions also regulate PKA activity  Ca2+ released during muscle contraction  Thus, muscle contraction stimulates PKA activity  This, in turn, stimulates phosphorylase kinase activity  This then stimulates phosphorylase by converting it from phosphorylase b to phosphorylase a and thus shifting the equilibrium to the active R state  Finally, this releases more Glc-1-P from glycogen  Overall, muscle activity stimulates fuel release from storage  Regulation of Phosphorylase Kinase o Phosphorylase is “tuned” in response to multiple signals  Is the muscle contracting (Ca2+)?  Is a nerve signal telling the muscle to contract (ca2+)?  Fight or flight imminent (epinephrine signal)? o Intermediate levels of activation possible, to integrate information


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