Energy is converted to a usable form in cell respiration. AHL Topic 8.2 IB Biology Miss Werba

TOPIC 8 – HL MOLECULAR BIOLOGY 8.1 METABOLISM 8.2 CELL RESPIRATION 8.3 PHOTOSYNTHESIS J WERBA – IB BIOLOGY 2

THINGS TO COVER U.1 U.2 U.3 U.4 U.5 U.6 U.7 U.8 Statement Guidance Cell respiration involves the oxidation and reduction of electron carriers. U.2 Phosphorylation of molecules makes them less stable. U.3 In glycolysis, glucose is converted to pyruvate in the cytoplasm. - the names of the intermediate compounds are not required. U.4 Glycolysis gives a small net gain of ATP without the use of oxygen. U.5 In aerobic cell respiration pyruvate is decarboxylated and oxidized, and converted into acetyl compound and attached to coenzyme A to form acetyl coenzyme A in the link reaction. U.6 In the Krebs cycle, the oxidation of acetyl groups is coupled to the reduction of hydrogen carriers, liberating carbon dioxide. – the names of the intermediate compounds are not required. U.7 Energy released by oxidation reactions is carried to the cristae of the mitochondria by reduced NAD and FAD. U.8 Transfer of electrons between carriers in the electron transport chain in the membrane of the cristae is coupled to proton pumping. J WERBA – IB BIOLOGY 3

THINGS TO COVER U.9 U.10 U.11 A.1 S.1 S.2 Statement Guidance NOS 2.3 In chemiosmosis protons diffuse through ATP synthase to generate ATP. U.10 Oxygen is needed to bind with the free protons to maintain the hydrogen gradient, resulting in the formation of water. U.11 The structure of the mitochondrion is adapted to the function it performs. A.1 Electron tomography used to produce images of active mitochondria. S.1 Analysis of diagrams of the pathways of aerobic respiration to deduce where decarboxylation and oxidation reactions occur. S.2 Annotation of a diagram of a mitochondrion to indicate the adaptations to its function. NOS 2.3 Paradigm shift—the chemiosmotic theory led to a paradigm shift in the field of bioenergetics. J WERBA – IB BIOLOGY 4

CELL RESPIRATION The controlled release of energy from organic compounds in cells to form ATP Involves enzymes Involves metabolic pathways (chains and cycles) Involves end-product inhibition Involves glucose Phosphorylates to ADP to make ATP J WERBA – IB BIOLOGY 5

CELL RESPIRATION C6H12O6 + 6O2 – RESPIRATION –> 6CO2 + 6H2O Respiration includes: glycolysis link reaction Kreb’s cycle Electron Transport Chain (ETC) chemiosmosis There’s lots to learn – so stay sharp! = OXIDATIVE PHOSPHORYLATION J WERBA – IB BIOLOGY 6

MITOCHONDRIA U.11 S.1 If oxygen is present, the reactions move to the mitochondria. The structure of the mitochondrion is adapted to the function it performs. You need to be able to annotate a diagram of a mitochondrion to show the way its structure is adapted to its function. J WERBA – IB BIOLOGY 7

MITOCHONDRIA U.11 S.1 J WERBA – IB BIOLOGY 8

MITOCHONDRIA Outer mitochondrial membrane 70S ribosomes & naked DNA Matrix Intermembrane space Cristae Inner mitochondrial membrane Ref: Biology for the IB Diploma, Allott J WERBA – IB BIOLOGY 9

MITOCHONDRIA Cristae: Intermembrane space: Matrix: U.11 S.1 Cristae: form a large surface area have enzymes needed for the electron transport chain embedded in their membrane Intermembrane space: small to allow ions to accumulate and create a concentration gradient Matrix: fluid containing enzymes needed for the Krebs cycle. J WERBA – IB BIOLOGY 10

MITOCHONDRIA A.1 Electron tomography: technique for getting 3D structures of sub-cellular structures using electron micrographs Technique has been used to produce images of active mitochondria http://www.sci.sdsu.edu/TFrey/MitoMovie.htm J WERBA – IB BIOLOGY 11

http://www.sci.sdsu.edu/TFrey/MitoMovie.htm 12

http://www.sci.sdsu.edu/TFrey/MitoMovie.htm 13

OXIDATION & REDUCTION Oxidation Is Loss (of electrons) Cell respiration involves different reactions that are known as redox reactions (ie. oxidation or reduction reactions) Oxidation & reduction occur together - as one reactant is oxidised, the other is reduced. Remember: OIL RIG Oxidation Is Loss (of electrons) Reduction Is Gain (of electrons) J WERBA – IB BIOLOGY 14

OXIDATION & REDUCTION Reduction reactions may include: Gain of electrons Removal of oxygen Gain of hydrogen Oxidation reactions may include: Loss of electrons Addition of oxygen Loss of hydrogen J WERBA – IB BIOLOGY 15

OXIDATION & REDUCTION NAD+ + 2H+ + 2e- ⇌ NADH + H+ Cell respiration involves the oxidation and reduction of electron carriers. What are the electron carriers in cell respiration? NAD – Nicotinamide Adenine Dinucleotide NAD+ + 2H+ + 2e- ⇌ NADH + H+ FAD – Flavin Adenine Dinucleotide FAD+ + 2H+ + 2e- ⇌ FADH2 J WERBA – IB BIOLOGY 16

CELL RESPIRATION THROUGH ART

Glycolysis Krebs cycle Electron Transport Chain Glucose C6H12O6

Glycolysis Glucose C6H12O6 anaerobic 2 pyruvate (3C) Electron Krebs cycle Electron Transport Chain Glucose C6H12O6 anaerobic aerobic 2 pyruvate (3C)

Glycolysis Krebs cycle Electron Transport Chain Glucose C6H12O6 anaerobic aerobic 2 pyruvate (3C)  2 ATP  4 ATP 2 NADH  2 ATP (net gain)

Glycolysis Krebs cycle Electron Transport Chain Glucose C6H12O6 anaerobic aerobic 2 pyruvate (3C)  2 ATP  4 ATP 2 NADH  2 lactic acid 2 ethanol + 2 CO2 Alcohol fermentation 2 ATP (net gain) Lactate fermentation (plants/yeast) (animals)

Glycolysis 2 acetyl CoA 2 CO2 Krebs cycle Electron Transport Chain Glucose C6H12O6 anaerobic aerobic 2 pyruvate (3C)  2 ATP  4 ATP 2 NADH  2 lactic acid 2 ethanol + 2 CO2 2 ATP (net gain)  2 NADH Alcohol fermentation Lactate fermentation (plants/yeast) (animals)

Glycolysis Krebs cycle Electron Transport Chain Glucose C6H12O6 anaerobic aerobic 2 pyruvate (3C)  2 ATP  4 ATP 2x NADH  2 lactic acid 2 ethanol + 2 CO2 2 acetyl CoA 2CO2  4C 6 NADH  2 ATP  4 CO2   2 FADH2 2 ATP (net gain)  2 NADH Alcohol fermentation Lactate fermentation (plants/yeast) (animals)

(2 x 3) + (2 x 1) + ( 2 x 3) + (6 x 3) + (2 x 1) + (2 x 2) THE ETC CASINO Let’s add up what we have and see how many chips we can get for the ETC casino Don’t forget the link reaction! NADH 3 FADH2 2 ATP 1 (2 x 3) + (2 x 1) + ( 2 x 3) + (6 x 3) + (2 x 1) + (2 x 2) = 38 chips or 38 ATP

Glycolysis Krebs cycle Electron Transport Chain Glucose C6H12O6 anaerobic aerobic 2 pyruvate (3C)  2 ATP  4 ATP worth 6 ATP  2 NADH  2 lactic acid 2 ethanol + 2 CO2 2 acetyl CoA 2 CO2  4C worth 18 ATP  6 NADH  worth 2 ATP  2 ATP  4 CO2   2 FADH2  worth 4 ATP 2 ATP  worth 2 ATP (net gain)  2 NADH  worth 6 ATP Alcohol fermentation Lactate fermentation (plants/yeast) (animals)

AEROBIC RESPIRATION Aerobic cellular respiration involves four major reaction pathways: Glycolysis  conversion of glucose to pyruvate The Link Reaction  conversion of pyruvate to acetyl CoA The Krebs Cycle  mitochondrion The Electron Transport chain  chemiosmosis J WERBA – IB BIOLOGY 27

GLYCOLYSIS Glycolysis occurs without the use of oxygen Occurs in the cytoplasm One glucose molecule is converted into two pyruvate molecules. 2 ATP molecules are used but 4 ATP are produced, so there is a net yield of 2 ATP. 2 NAD+ are converted into 2 NADH + H+ You don’t need to remember the names of the intermediate compounds in glycolysis. J WERBA – IB BIOLOGY 28

http://www. mheducation http://www.mheducation.ca/school/applets/abbio/quiz/ch05/how_glycolysis_works.swf 29

http://www. science. smith. edu/departments/Biology/Bio231/glycolysis http://www.science.smith.edu/departments/Biology/Bio231/glycolysis.html 30

GLYCOLYSIS There are 4 main stages to Glycolysis: 1) Phosphorylation U.3 U.4 There are 4 main stages to Glycolysis: 1) Phosphorylation 2) Lysis 3) Oxidation 4) ATP formation J WERBA – IB BIOLOGY 31

GLYCOLYSIS 1) Phosphorylation 2 phosphates are added to glucose 2 ATP molecules are needed to provide the phosphates Phosphorylation of molecules makes them less stable. 2) Lysis The 6C molecule (glucose bisphophate) is then split into two 3C molecules (triose phosphate). J WERBA – IB BIOLOGY 32

GLYCOLYSIS 3) Oxidation U.3 U.4 3) Oxidation 2 hydrogen atoms are removed from each 3C molecule  NAD+ accepts them 2 phosphate groups are added to each molecule using the energy released. 4) ATP formation 2 phosphate groups are removed from each molecule  passed to ADP This forms two molecules of pyruvate and ATP. This is called substrate level phosphorylation. J WERBA – IB BIOLOGY 33

GLYCOLYSIS U.3 U.4 J WERBA – IB BIOLOGY 34

Glycolysis Krebs cycle Electron Transport Chain Glucose C6H12O6 G6P anaerobic aerobic 2x pyruvate (3C)  2x ATP  4x ATP worth 6 ATP  2x NADH  lactic acid ethanol & CO2 fermentation acetyl CoA 2CO2  4C worth 18 ATP  6x NADH  worth 2 ATP  2x ATP  4x CO2   2x FADH2  worth 4 ATP 2x ATP  worth 2 ATP (net gain)  2x NADH  worth 6 ATP

THE LINK REACTION U.5 After glycolysis, pyruvate moves to the mitochondrion. Enzymes in the mitochondrial matrix are used to: oxidise the pyruvate remove hydrogen  NAD+ accepts it decarboxylate the pyruvate remove carbon  CO2 is released J WERBA – IB BIOLOGY 36

THE LINK REACTION This conversion is called oxidative decarboxylation. U.5 This conversion is called oxidative decarboxylation. The product of this is an acetyl compound, which attaches to coenzyme A (CoA) to form acetyl CoA. J WERBA – IB BIOLOGY 37

Glycolysis Krebs cycle Electron Transport Chain Glucose C6H12O6 anaerobic aerobic 2 pyruvate (3C)  2 ATP  4 ATP worth 6 ATP  2 NADH  2 lactic acid 2 ethanol + 2 CO2 2 acetyl CoA CO2  4C worth 18 ATP  6 NADH  worth 2 ATP  2 ATP  4 CO2   2 FADH2  worth 4 ATP 2 ATP  worth 2 ATP (net gain)  2 NADH  worth 6 ATP Alcohol fermentation Lactate fermentation (plants/yeast) (animals)

THE KREBS CYCLE Also known as the Citric Acid Cycle U.6 Also known as the Citric Acid Cycle Happens in the mitochondrial matrix Yields 2 ATP No O2 used but process is O2-dependent C and O from C6H12O6 are released as CO2 H is left over J WERBA – IB BIOLOGY 39

THE KREBS CYCLE The Krebs Cycle occurs in a number of stages: 1) C2 + C4 = C6 Acetyl CoA (C2) from the link reaction joins to oxoaloacetate (C4), forming citrate (C6) CoA is released and recycled J WERBA – IB BIOLOGY 40

THE KREBS CYCLE 2) C6  C5 + CO2 U.6 2) C6  C5 + CO2 Decarboxylation – CO2 is released from citrate (C6), leaving a 5-carbon (C5) compound Reduction – NAD+ accepts 2 H atoms  forms NADH 3) C5  C4 + CO2 Decarboxylation – CO2 is released from the C5 compound  forms a C4 compound J WERBA – IB BIOLOGY 41

THE KREBS CYCLE 4) ATP synthesis (substrate level phosphorylation) ATP is synthesised from ADP two reduction reactions: NAD+ + 2H  NADH + H+ FAD + 2H  FADH2 Manga guide to Biochemistry  http://www.slideshare.net/dekar001/nostarchmangaguide J WERBA – IB BIOLOGY 42

THE KREBS CYCLE One turn of the Krebs Cycle yields: 2 CO2 3 NADH + 3H+ 1 FADH2 1 ATP (by substrate level phosphorylation) Remember that there are 2 turns of the Krebs cycle for each glucose molecule!!! J WERBA – IB BIOLOGY 43

THE KREBS CYCLE U.6 J WERBA – IB BIOLOGY Ref: Biology for the IB Diploma, Allott 44

https://youtu.be/WWZ0_cHwhX8 45

Glycolysis Krebs cycle Electron Transport Chain Glucose C6H12O6 anaerobic aerobic 2 pyruvate (3C)  2 ATP  4 ATP worth 6 ATP  2 NADH  2 lactic acid 2 ethanol + 2 CO2 2 acetyl CoA CO2  4C worth 18 ATP  6 NADH  worth 2 ATP  2 ATP  4 CO2   2 FADH2  worth 4 ATP 2 ATP  worth 2 ATP (net gain)  2 NADH  worth 6 ATP Alcohol fermentation Lactate fermentation (plants/yeast) (animals)

THE ELECTRON TRANSPORT CHAIN (ETC) U.7 The reduced forms of NAD (NADH) and FAD (FADH2) carry H+ ions and electrons to the ETC. The ETC is in the cristae – the folds of the inner mitochondrial membrane (IMM). J WERBA – IB BIOLOGY 47

THE ELECTRON TRANSPORT CHAIN (ETC) U.7 The Electron Transport Chain (ETC) is composed of electron carriers embedded in the IMM. Electrons are removed from NADH or FADH2 and passed from one carrier to another by a series of redox reactions. J WERBA – IB BIOLOGY 48

THE ELECTRON TRANSPORT CHAIN (ETC) U.7 U.8 The transfer of electrons is coupled to proton pumping. Hydrogens are pumped across the membrane to the inter-membrane space by the energy released from the electrons. Results in a high concentration of H+ ions in the space between the membranes J WERBA – IB BIOLOGY 49

CHEMIOSMOSIS U.9 U.10 In chemiosmosis, protons diffuse through ATP synthase to generate ATP. Oxygen is needed to bind with the free protons to maintain the hydrogen gradient, resulting in the formation of water. This occurs in the matrix of the mitochondrion. J WERBA – IB BIOLOGY 50

CHEMIOSMOSIS Paradigm shift NOS.2.3 Paradigm shift The chemiosmotic theory led to a paradigm shift in the field of bioenergetics. J WERBA – IB BIOLOGY 51

CHEMIOSMOSIS NOS 2.3 In 1961, Peter Mitchell, a British biochemist, proposed the chemiosmotic theory of ATP production. He received a Nobel prize for this work in 1978. His ideas explained how ATP synthesis is coupled to electron transport and the movement of protons. His ideas were different to previous explanations, but after many years, the theory was accepted. J WERBA – IB BIOLOGY 52

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http://highered. mheducation http://highered.mheducation.com/sites/dl/free/0073525707/291136/electron_transport.swf 54

CELLULAR RESPIRATION Thus the net production of energy from aerobic respiration from ONE glucose: Stage ATP Glycolysis 2 ATP used at the start 2 NADH + H+ Substrate level phosphorylation -2 ATP 6 ATP 4 ATP Link Reaction Krebs cycle 6 NADH + H+ 2FADH2 2 ATP 18 ATP Net Yield of ATP 38 ATP J WERBA – IB BIOLOGY 55

Glycolysis Krebs cycle Electron Transport Chain Glucose C6H12O6 anaerobic aerobic 2 pyruvate (3C)  2 ATP  4 ATP worth 6 ATP  2 NADH  2 lactic acid 2 ethanol + 2 CO2 2 acetyl CoA CO2  4C worth 18 ATP  6 NADH  worth 2 ATP  2 ATP  4 CO2   2 FADH2  worth 4 ATP 2 ATP  worth 2 ATP (net gain)  2 NADH  worth 6 ATP Alcohol fermentation Lactate fermentation (plants/yeast) (animals)

CELL RESPIRATION Q1. During glycolysis, a hexose sugar is broken down to two pyruvate molecules. What is the correct sequence of stages? A. phosphorylation → oxidation → lysis B. oxidation → phosphorylation → lysis C. phosphorylation → lysis → oxidation D. lysis → oxidation → phosphorylation J WERBA – IB BIOLOGY 57

CELL RESPIRATION Q2. What is the role of NADH + H+ in aerobic cell respiration? A. To transfer hydrogen to the electron transport chain B. To reduce intermediates in the Krebs cycle C. To accept electrons from the electron transport chain D. To combine with oxygen to produce water J WERBA – IB BIOLOGY 58

CELL RESPIRATION Q3. a) Indicate two places where decarboxylation occurs. (1) b) Explain why the given places were selected. (1) Q4. Explain the link reaction that occurs between glycolysis and the Krebs cycle. [4] J WERBA – IB BIOLOGY 59

CELL RESPIRATION Q5. The enzyme ATP synthase has an essential role in aerobic cell respiration. Describe its location. [1] Describe its function. [1] J WERBA – IB BIOLOGY 60