LIFS1901 Midterm Arrangements PDF

LIFS1901 Midterm arrangements Date of exam: Thursday, 17th October Room: LTJ Time: Class time Duration: 1 hour 10 minutes Format: MC questions (70 questions, 1 point per question) Coverage: all of TANG’s lectures Seating plan, line up outside t...

LIFS1901 Midterm arrangements Date of exam: Thursday, 17th October Room: LTJ Time: Class time Duration: 1 hour 10 minutes Format: MC questions (70 questions, 1 point per question) Coverage: all of TANG’s lectures Seating plan, line up outside the specified doors, Student ID card and exam paper will be given at the doors. Row Seat Name L/R set of doors A 1 J. Bloggs L Things to bring: Pencils, eraser, student ID card  Chapter 06 Cellular Respiration make ATP in calls  Lecture outline Cellular Respiration 1. Overview of Cellular Respiration 2. Outside the Mitochondria: Glycolysis 3. Outside the Mitochondria: Fermentation 4. Inside the Mitochondria  Learning Outcomes Explain how the energy in a glucose molecule is released during cellular respiration. Explain how equations for photosynthesis and cellular respiration represent oxidation-reduction reactions. Summarize the relationship between the metabolic reactions of photosynthesis and cellular respiration.  Chemical cycling Photosynthesis and cellular respiration provide energy for life Photosynthesis Cellular respiration In both plants and animals (eukaryotes) sun carbohydrate O2 chloroplast mitochondrion heat heat CO2 + HO2 ATP for cellular reactions heat  Cellular Respiration and Humans Why Do We Need Oxygen? Energy Production: We need oxygen to oxidize glucose, which provides energy in the form of ATP (adenosine triphosphate). O2 CO2 Cellular Respiration is the process that occurs Breathing in our cells to convert nutrients (like glucose) into ATP, using oxygen. Eating Where Do We Get Oxygen From? O2 CO2 Breathing: This is the mechanical action of inhaling (taking in air) and exhaling (breathing out). Respiration: Nutrients Gas Exchange: Respiration is the process of exchanging gases; we take in oxygen (O₂) and Cellular respiration release carbon dioxide (CO₂). Glucose + O2 ➞ CO2 + H2O + ATP break down the bonds -> catabolism Primary source  Oxidation of glucose to produce energy What happens when you burn glucose? Uncontrolled reaction control reaction in our cells gives off heat when glucose is burnt in the presence of oxygen (requires an ignition point) C6H12O6 +O2→H2O + CO2  The release of energy from sugar Small activation energies overcome by High activation energy overcome by flame body heat Each step is controlled by an enzyme stepwise oxidation (left) direct burning of sugar (right) In chemistry, when chemical bonds are broken, it requires energy. Why in biological processes like breakdown of bonds in glucose does it release energy? Net Energy Change = Energy required to break bonds - Energy released from forming new bonds. More stable bonds are produced from converting glucose to CO2, so energy is released  Why do organic compounds have so much energy? C-H bonds are the primary energy bonds found in organic molecules (i.e., glucose, octane etc.). The bonds have high energy as there is a lot of potential energy. This explains why fats (all C-H bonds) have more energy (calories) per gram than proteins or carbohydrates However, the preferred energy source are carbohydrates because they can be broken easily to glucose. Fats need to be broken down to glycerol and fatty acids first.  Potential Energy stored in bonds of glucose Covalent bonds are found in glucose Electrons are shared in covalent bonds Electrons have more potential energy (PE) when they are associated with less electronegative atoms e.g., C or H Because less EN atoms hold electrons less tightly, allowing them to have higher energy levels Electrons with higher PE can participate in chemical reactions more readily, as Electronegativity (EN) is they possess greater energy for forming the pulling power on electrons towards the atomic or breaking bonds. centre. Reactions that move the system from The closer an e- is to the proton the less the PE higher to lower energy states are A higher EN is more stable, as less separation spontaneous and release energy. between +ve and –ve charges.  Energy in glucose and other food molecules The movement of electrons from a high energy to lower energy state causes release of energy C6H12O6 + O2 → H2O + CO2 Carbon dioxide has only Glucose has lots of C-C, and C-H C-O bonds with “low bonds with “high potential potential energy” e-, energy” electrons making the bonds very Electrons in these bonds are less stable tightly held compared to those Carbon is double- bonded bonds with more EN atoms to each of the O atoms= Presence of high-energy bonds very strong and stable makes glucose unstable, driving bonds, as the electrons its reactivity in chemical processes are tightly held by the highly EN O atoms.  Cells must be efficient What would happen if our cells burn glucose (releasing all the electrons) all at once? electrons are not release all as once Glucose + O2 ➞ CO2 + H2O + ATP Electron transport chain (ETC) transfer electrons for ATP synthesis  Oxidation-Reduction and Metabolism How do cells extract the energy from glucose? The answer involves energy released from breaking bonds in glucose and the transfer of electrons from one molecule to the next. As the electrons are passed down electron carriers: NAD+, (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide) co-enzymes, electrons carrier some energy is released to make ATP want to pull electrons down Oxygen being EN, pulls the electrons down the ETC Controlled reaction inside a cell Electron transport chain (ETC)  Cellular respiration involves many redox reactions Transfer of electrons occur in oxidation- reduction reactions Oxygen loves to steal electrons; it is highly electronegative! 6 electrons in outer shell Oxidation-Reduction or Redox A molecule is oxidized when it loses an electron A molecule is reduced when it gains an electron The term oxidation is used even when oxygen is not involved e.g., Na + Cl → Na+Cl- Sodium is oxidized, sodium loses an electron Chlorine is reduced, chlorine gains an electron LEO says GER Loss of Electrons is Oxidation Gain of Electrons is Reduction  Oxidation-Reduction and Metabolism In many cellular oxidations, electrons and protons (H atoms) are removed at the same time. hydrogen atoms can be considered as (H+ + e-) Oxidation is Loss of hydrogen atoms Loss of electrons i.e., loss of H+ + e- Reduction is Gain of hydrogen atoms Gain of electrons i.e., gain of H+ + e- In cellular respiration and photosynthesis, high energy hydrogen atoms provide electrons and hydrogen ions to make ATP gain of hydrogen atoms (H+ + e) (becomes reduced) glucose loss of hydrogen atoms (H+ + e) (becomes oxidized) Oxidation and reduction must occur together and simultaneously, you can’t have one without the other!  NAD+ and FAD NAD+ and FAD are vitamin B coenzymes used cellular respiration NAD+ and FAD act as electron carriers Becomes reduced Adenine NAD+ + 2H+, 2e- → NADH + H+ Ribose Becomes reduced (Nicotinamide Adenine FAD +2H+, 2e- → FADH2 Dinucleotide) (remember 2H = 2H+ + 2e)  Electron carriers Oxidation is the removal of electrons, i.e., in cellular reactions 2H+ + 2e- Here, a 3C molecule is oxidized i.e., 2H+ + 2e- (coenzyme electron carrier) Oxidation and reduction always go together. Reduced molecules have more potential energy because they carry high energy electrons.  NAD+ and FAD electron carriers Electron carriers are required to shuttle electrons. ETC to make ATP ETC to make ATP NADH and FADH2 each carries 2 H atoms i.e., 2 H+ +2e They pick up electrons at specific enzymatic reactions in cytoplasm and mitochondria and carry these electrons to the electron transport chain to make ATP. NAD+ electron carrier is used in the electron transport chain in respiration to make ATP Electrons are collected from NAD+ from the breakdown of bonds in glucose NAD+ NADH 2NADH 2NAD+ + 2H Energy released 2 and available (2H→2H+ + 2e-) for making ATP Enzyme complexes act as electron carriers 2 At the bottom of the hill is oxygen (1/2 O2), 1 − 2 O2 which H2O grabs two electrons, picks up two H+, and 2 H+ becomes reduced to water. electrons lose potential energy when they move towards more electronegative atoms, reactions that move towards the electronegative oxygen atom Animation of how NAD+ works  Nicotinamide mononucleotide (NMN) is a precursor to nicotinamide adenine dinucleotide (NAD+) As we age, the levels of NAD are lowered, leading to less ATP, and cell death It has been shown in animal studies and early human trials, that NMN may support mitochondrial function and promote energy metabolism  Learning Outcomes Stages of Cellular Respiration 1. Summarize the phases of cellular respiration and indicate where they occur in the cell.  Overview of Cellular Respiration Cellular respiration is the release of energy from glucose accompanied by the use of this energy to synthesize ATP molecules. Aerobic – requires O2 Gives off CO2 Note: theoretically, 1 molecule of glucose give around 38 molecules of ATP depending on the cell! High energy Low energy molecule molecules  Overview of the steps required in cellular respiration 3 stages of cellular respiration- Glycolysis, TCA cycle, Electron transport  Where does cellular respiration take place? Process Where does it take place? Glycolysis Cytosol (cytoplasm) of the cell Pyruvate oxidation/Citric acid cycle mitochondrial matrix Electron transport chain/ chemiosmosis cristae in mitochondria Cytosol Cristae studded (outside of the with many mitochondrion) proteins including ATPase Large SA increasing ATP production  Overview of cellular respiration Electrons carried by NADH FADH2 Glycolysis Oxidative Pyruvate Citric Acid Phosphorylation Glucose Pyruvate (Electron transport Oxidation Cycle and chemiosmosis) CYTOSOL MITOCHONDRION ATP Substrate-level Substrate-level Oxidative ATP ATP phosphorylation phosphorylation phosphorylation  Learning Outcomes Outside the Mitochondria-Glycolysis 1. Describe the location and inputs and outputs of glycolysis. 2. Explain why ATP is both an input and output of glycolysis.  Overview of glycolysis 1. Glycolysis (sugar splitting) (simplified) 6 carbons Occurs in the cytosol Glucose Many enzymatic steps are involved in the oxidation of glucose to 2 ADP pyruvate 2 NAD+ +2 P Occurs in both prokaryotes Substrate and eukaryotes and does not level require oxygen (anaerobic) phosphoryl -ation 2 NADH 2 ATP +2 H+ Energy yield of glycolysis 2 NADH 2 ATP two molecules of pyruvate are produced 2 Pyruvate  For each reaction, enzymes are required Glycolysis (all steps) Energy required Energy required ATP can be made by substrate-level phosphorylation ATP is formed in glycolysis by substrate–level phosphorylation An enzyme attaches the phosphate from a substrate molecule to ADP, so that ATP is made Inputs and Outputs of Glycolysis  Learning Outcomes Inside the Mitochondria 1. Recognize the role of mitochondria in cellular respiration. 2. Summarize the inputs and outputs of the preparatory reaction, the citric acid cycle, and the electron transport chain. 3. Identify how each stage of the aerobic pathway contributes to the generation of ATP in the cell. How does glycolysis connect up to the citric acid cycle (Kreb’s cycle)? 2. Preparatory Reaction (pyruvate oxidation) occurs in matrix of mitochondria Pyruvate is oxidized (loss of H+ions and electrons) to form acetyl CoA and carbon dioxide is removed. 2 1 3 Coenzyme A joins with the 2-carbon group to form Acetyl CoA  Preparatory Reaction-conversion of pyruvate to acetyl CoA Preparatory Reaction “Cut and Groom” pyruvate is oxidized and the electron is picked up to form NADH + H+ “Cut”-Carboxyl group (COO-) is removed as carbon dioxide (1 of the 6 carbons to be removed) “Groom”- Acetyl group attaches to CoA (Coenzyme A) to become acetyl CoA Empty NAD+ bus CO2 part acetate part  Phases of Cellular Respiration 3. Citric acid cycle (Krebs cycle), (tricarboxylic acid (TCA) cycle) takes place in matrix of mitochondria is also called the Krebs cycle (after the German-British researcher Hans Krebs, who worked out much of this pathway in the 1930s), completes the oxidation of organic molecules, and generates many NADH and FADH2 molecules (carrying electrons).  Citric Acid Cycle (Kreb’s cycle, tricarboxylic acid (TCA) cycle) GLYCOLYSIS PYRUVATE OXIDATION CITRIC ACID CYCLE OXIDATIVE PHOSPHORYLATION Inputs and Outputs ATP Pyruvate 1 Preparatory reaction CO2 NAD+ 2 Coenzyme A − − NADH 3 inputs outputs + H+ Acetyl CoA CoA 2 pyruvate 2 CO2 2 NAD+ 2 NADH +H+ CoA Per glucose molecule CITRIC 2 CO2 ACID CYCLE − − FADH2 3 NAD+ The 6C atoms from glucose, FAD − − 3 NADH have all been converted to CO2 + 3 H+ so that all C-H bonds have been ATP ADP + P broken and H+ ions and By substrate level phosphorylation electrons are removed  Phases of Cellular Respiration 4. Oxidative phosphorylation= electron transport and chemiosmosis. Most ATP is produced by oxidative phosphorylation e– NADH NADH e– e– e– NADH and e– FADH2 e– e– Glycolysis Electron transport Preparatory reaction Citric acid chain and glucose pyruvate cycle chemiosmosis 2 ATP 2 ADP 4 ADP 4 ATP total 2 ATP net 2 ADP 2 ATP 32 or ADP 32 or ATP 34 34  Phases of Cellular Respiration Electron Transport Chain – FADH2 and NADH unload their electrons to the electron transport chain As the electrons move from a higher energy state to a lower one, energy is released to make ATP. High energy Under aerobic conditions, 32-34 ATP state per glucose molecule can be produced. Note: the final electron acceptor is O2 which is very electronegative Low energy state In electron transport, why is oxygen required in the last step? Oxygen is very electro-negative, it pulls the electrons along. If there were not taken by oxygen, the protein complexes would be stuck with extra electrons, and the chain would be blocked unable to take new electrons.  Oxidative phosphorylation Outer membrane H+ 2 Mobile H+ H+ H+ electron H+ Intermembrane H+ H+ space carriers H+ H+ ATP 4 synthase Cyt c CoQ Complex Complex Complex I III Inner membrane IV Complex II Electron FADH2 FAD 3 flow NADH −12 O2 + 2 H+ NAD+ H+ Mitochondrial matrix 1 H2O ADP + P ATP H+ Electron Transport Chain Chemiosmosis Oxidative Phosphorylation NADH and FADH2 release their electrons to protein complexes (I-IV) All protein complexes bind and release electrons in redox reactions As the electrons are passed along the protein complexes, energy is released to pump the H+ out to the intermembrane space to create a hydrogen gradient.  Generating ATP Electron chain proteins are located in the membranes of the cristae of mitochondria. NADH and FADH2 pass electrons to the first acceptor of the electron transport chain. As electrons pass along a series of electron carriers, the energy released is used to pump H+ into the intermembrane space of mitochondrion. Protons accumulate in the intermembrane space to create a proton gradient.  Oxidative phosphorylation Chemiosmosis-diffusion of hydrogen ions across a membrane via ATP synthase to generate ATP from ADP Can H+ ions just diffuse across the membrane? Where does the energy required come from? OUTER MITOCHONDRIAL MEMBRANE Protein complex of H+ Mobile H+ H+ H+ High electron electron carriers H+ carriers H+ H+ concentration Intermem- brane Proton pumps H+ ATP H+ synthase of H+ ions space Cyt c III IV I Q diffusion Inner mito- chondrial II membrane Electron FADH2 FAD flow NADH 1 − O2 + 2 H+ NAD+ 2 Mito- H+ chondrial matrix H2O ADP + P H+ ATP Low concentration Electron Transport Chain Chemiosmosis of H+ ions Oxidative Phosphorylation  ATP synthase— a membrane protein that acts as a molecular rotary motor INTERMEMBRANE SPACE H+ Rotor Function: as H+ turns the rotor of the ATP synthase, a phosphate group is Internal rod added to ADP to make ATP Catalytic knob ADP + P ATP MITOCHONDRIAL MATRIX mader2d_proton_pump Fermentation- Anaerobic Harvesting of Energy  Learning Outcomes Outside the Mitochondria: Fermentation 1. Explain how ATP can continue to be produced in the absence of oxygen. 2. Describe the advantages and disadvantages of fermentation.  What if there is no oxygen available for cellular respiration? Pyruvate serves as crucial link between different pathways in cellular respiration Anaerobic Aerobic If O2 is limited, cells may utilize anaerobic pathways, such as fermentation. Fermentation results in a net gain of two ATP/glucose molecule.  What if there is no oxygen available for cellular respiration? Anaerobic Respiration Fermentation – Lactic acid fermentation During exercising muscles Glucose→ ATP + lactic acid Bacteria make yoghurt – Alcohol fermentation Yeast, and other types of fungi and some bacteria Glucose → ATP + CO2 + alcohol What process makes What process makes bread rise? alcohol? required yeast all from one mother cell Saccharomyces cerevisiae, a yeast (single celled fungi)  Lactate fermentation Glucose In lactate fermentation, animal cells and certain bacteria, glucose is 2 ADP 2 NAD+ Glycolysis oxidized to pyruvate 2 P reduced 2 ATP Pyruvate accepts two hydrogen ions 2 NADH and two electrons and is reduced to lactate. 2 Pyruvate The NAD+ is recycled in glycolysis 2 NADH which is essential for glycolysis to continue. 2 NAD+ 2 Lactate  Lactate fermentation Why do muscles ache when sprinting hard? use so much oxygen builfd up of the lactic acid  Alcoholic fermentation Glucose In yeast and other fungi, the fermentation product is ethanol 2 NAD+ Glycolysis 2 ADP 2 P 2 ATP are generated 2 ATP 2 NADH from glycolysis NAD+ can be recycled for use by glycolysis 2 Pyruvate 2 NADH 2 CO2 Why do you get bubbles in 2 NAD+ beer and champagne? carbon dioxide 2 Ethanol  Energy Yield of Fermentation Fermentation yields only two ATP by substrate-level ATP synthesis. These two ATP represent a small fraction of potential energy stored in glucose. In cellular respiration, 36 to 38 ATP molecules are produced. Therefore, most of the potential energy stored in glucose has not been released. Connections Between Metabolic Pathways Although glucose is the primary source of ATP, fats and proteins can be used too. Food Fats (triglycerides) broken down to glycerol and fatty many carbohydrates acids by lipase Carbohydrates Fats Proteins Fatty acids undergo beta 1 st choice 2 nd last oxidation where they are many complex processes broken down into acetyl-CoA. Sugars Glycerol Fatty acids Amino acids Before amino acids enter Amino Citric Acid cycle, amino groups groups are removed (deamination) electron transport chain Citric Glucose G3P Pyruvate Acetyl Acid Oxidative Glycolysis CoA Cycle Phosphorylation G3P=glyceraldehyde 3-phosphate ATP