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BIOL 130 Study Notes Unit IV Energy

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University of Waterloo
BIOL 130
Richard Ennis

BIOL 130 Unit IV Study Notes Part A: Cellular Respiration Activated Carrier Molecules: • Carrier molecules store energy obtained from oxidizing food molecules o Contains one or more high energy content bonds • When the energy is required for biosynthetic reactions, carriers will transport the energy (relocation) to the area that requires the energy to be used o Endergonic reactions break the high energy bonds of carrier molecules in order to release their energy to be used • Common activated carrier molecules covered in this unit: o ATP – uses phosphate as its high-energy linkage o NADH, NADPH, FAH - u2es electrons and hydrogen as its H.E linkage o Acetyl CoA – uses acetyl group as its H.E linkage Formation of Macromolecules & ATP: • The synthesis of complex molecules require endergonic reactions, therefore ATP is required to fuel that reaction to occur • The polymerization (i.e. condensation) reactions that create proteins, nucleic acids, and polysaccharides, all require the input of energy (usually by ATP) o Thus, energy needs to be harvested in some way to continually produce ATP to be used by these reactions • Example: Nucleic Acids o In order to link nucleosides together to form chains of nucleic acids, ATP is required o 2 ATP molecules are hydrolyzed in order for the reaction to occur, whereby 2 phosphate groups are attached to the single phosphate on a nucleotide  This creates a high-energy intermediate that can cause it to link to another nucleotide • When ATP is used, it becomes ADP and releases energy; this energy is used for cellular work • However, when ATP is depleted and is in its ADP form, it must be replenished • Energy from sunlight or food is used to synthesize more ATP, by adding on inorganic phosphate to ADP to reform ATP: The Electron Carriers: • Are modified nucleotides that act as coenzymes to carry electrons from one reaction to another o Readily accept hydrides (H-, 2 electrons and a proton) and donate them • Important in harvesting energy during the oxidation of glucose • Key examples of electron carriers: o NAD+ = nicotinamide adenine dinucleotide (Vitamin B3) o FAD = Flavin adenine dinucleotide (Vitamin B2) o NADP+ = nicotinamide adenine dinucleotide phosphate • Example using NAD(P)H: o In the schematic on the next page, nicotinamide adenine dinucleotide phosphate changes between its oxidized and reduced forms, depending on whether it is accepting a hydride and transporting it or donating the hydride to a chemical reaction o NADP+ is the oxidized form  Remember “OIL” – OXIDATION is the LOSS of electrons, so therefore because NADP+ has a positive charge, it means that it has donated a hydride to a chemical reaction  NADP+ is readily able to accept a hydride (electron) any time to undergo the transport process again o NADPH is the reduced form  Remember “RIG” – REDUCTION is the GAIN of electrons, so therefore because NADPH has a neutral charge, it means that it must have picked up a hydride/electron and is transporting it toward a chemical reaction  NADPH is readily able to donate the electron to a chemical reaction if need be Obtaining Energy from Food: Catabolism & Anabolism • Catabolism: o The breakdown of complex molecules into simpler ones by the use of enzymes • Anabolism: o The reverse process, where simpler molecules/energy is used to form complex molecules • Schematic: • Based on the schematic previously, the enzymatic breakdown of food molecules, which is a catabolic pathway, release useful forms of energy and breaks the complex molecules down into simpler building block components • The energy and building blocks can then be used in anabolic pathways for the biosynthesis of complex molecules that are useful to the cell (e.g. macromolecules) Why is Catabolism Useful to a Cell? • Chemically, there is little difference between burning sugar and catabolizing sugar o The reactants are the same; the products produced are the same; the energy released is identical o So why doesn’t a cell just use combustion to burn the sugar and release the energy right away? • The difference between combustion and catabolism are: o Burning glucose releases a lot of heat all at once, and therefore all of the energy is released/lost at once in the form of heat o It also takes smaller activation energies to catabolize something in smaller intervals than it does to combust it • Cells cannot use heat, and therefore catabolism is important to the cell because it allows the cell to harvest in tiny, discrete amounts in controlled steps to capture and store released energy in the form of ATP Three Methods of Making ATP: • Substrate level phosphorylation: o This method generates a few ATP during glycolysis o ATP is formed by the addition of an inorganic phosphate to ADP by an enzyme o Despite that it is an endergonic reaction, the required input of energy is achieved because the phosphate that is to be added is bonded to another high-energy state molecule • Oxidative Phosphorylation (AEROBIC RESPIRATION): o Electrons are harvested from organic molecules using redox reactions o This is used to pump protons across a membrane (proton pump) o Protons are then allowed back across by diffusion down their gradient to produce energy to allow ATP synthase to produce ATP • Photophosphorylation: o Only able to be employed if the organism is able to use photosynthesis o Two types: cyclic and non-cyclic A General Overview of How Energy is Extracted from Food by Cellular Respiration: • Occurs in three stages: 1. Digestion  Breaking down of large macromolecules into simple subunits  Occurs outside of cell in intestines or in lysosomes 2. Glycolysis  Encompasses the breakdown of glucose in glycolysis and the processing of pyruvate  Takes place in cytosol or cell 3. TCA (Kreb) Cycle and Oxidative Phosphorylation:  Occurs in mitochondria  Encompasses both the Kreb Cycle (stage a) and the Electron Transport Chain (stage b) to ultimately synthesize ATP • Overall, energy is harvested by removing H atoms from glucose and the transferring of electrons from molecule to molecule  Electron transport from protein to protein causes some energy to be lost, but some of it is also captured to make ATP, or they are used to make reduced energy carriers  Depleted electrons are eventually transferred to a final electron acceptor to regenerate oxidized carriers (NAD+ or FAD) allowing the cycle to repeat • Oxygen = aerobic respiration • Other organic molecule = fermentation Note about Redox Reactions: • Electrons are the most important source of chemical potential energy in cells • They are mobile because carrier molecules in cellular respiration have the potential to readily donate and accept them • OIL RIG o OIL = Oxidation is Loss (of electrons) o RIG = Reduction is Gain (of electrons) • Redox reactions are always coupled o Whenever something donates an electron (oxidized) something must accept them (reduced) in a given coupled reaction o Reducing power:  Refers to the ability of an organism to store energy in molecules by transferring electrons to them Note about Redox Reactions on Electron Carriers (Specifically NAD+) • Prominent electron carriers are: o NAD+ = Nicotinamide adenine dinucleotide (Vitamin B3) o FAD = Flavin adenine dinucleotide (Vitamin B2) o NADP+ = Nicotinamide adenine dinucleotide phosphate • Redox of NAD+: o A high energy molecule binds to an enzyme and gives up a hydride (H-), therefore becoming oxidized o NAD+ will accept the hydride, which is a proton and 2 electrons, therefore becoming reduced  It also contains more energy now o Reduced energy carriers carry electrons to electron transport chain and donate them In-depth Look at Each Part of the Cellular Respiration Cycle: STEP 1: Digestion • Occurs outside of the cell in lysosome or intestines • Digestive enzymes break down macromolecules into their monomer subunits o Proteins  Amino acids o Polysaccharides  Simple sugars (monosaccharides/disaccharides) o Fats  Fatty acids + glycerol • The smaller organic monomer molecules then make their way to the cytosol of cells o Oxidation process begins to generate ATP STEP 2: Glycolysis (“Sweet Splitting”) – Anaerobic Part of Cellular Respiration • Occurs in the cytosol of cells to produce a small yield of ATP • It is the anaerobic part of cellular respiration, meaning that it does not require oxygen to take place. • Essentially it is the breakdown of glucose and the processing of pyruvate to produce a small yield of ATP • The process: PLOA o Phosphorylation: 2 molecules of ATP are invested/used to provide 2 phosphate groups that are added to glucose to form fructose 1,6-biphosphate  This step is important b/c the input of energy and phosphate by the investment of ATP is required for successive stages of glycolysis to occur o Lysis: the fructose 1,6 biphosphate (a 6 carbon sugar) is cleaved into two glyceraldehyde 3-triphosphates (3 carbon sugars) o Oxidation: Each of the 2 glyceraldehyde 3-triphosphates are oxidized by removing 2 hydrogen atoms from each  Energy released by oxidation is used to link on another phosphate group to each of the triose phosphates  The 2 hydrogen are collected by NAD+ causing it to become NADH + H . +  2 NADH are created and go to the electron transport chain o ATP Synthesis: 2 phosphate groups are removed from each triose phosphate to form 2 pyruvates  These 2 phosphate groups are given back to ADP to form ATP  4 ATP is generated, but because 2 ATP was used in the beginning, the net gain is 2 ATP. • Glycolysis isn’t very effective b/c of its small yield • The cell can further process pyruvate to extract energy, however… o The further oxidation of pyruvate requires OXYGEN o If oxygen is present, then the oxidation of pyruvates may occur, which progress along into the aerobic respiration part of cellular respiration which takes place in the mitochondria • Glycolysis can be regulated where high levels of ATP inhibits the enzyme phosphofructokinase, which is the enzyme that makes the fructose 1, 6 biphosphate o This is because phosphofructokinase has 2 sites for ATP to bind on, a normal active site and an allosteric site  When ATP is too abundant, ATP (which is an end-product) will go through the process of end-product inhibition and bind onto the allosteric site of phosphofructokinase to inhibit it by changing its shape NET OUTCOME OF GLYCOLYSIS: • 4 ATP (but since 2 were used, it’s really just a net of +2ATP), 2 NADH STEP 3: The TCA/Kreb Cycle (Part A) & the Electron Transport Chain (Part B) – Aerobic Respiration • Occurs in the mitochondria as the aerobic respiration part of cellular respiration, where oxygen is needed to oxidize pyruvate obtained from glycolysis in step 2 • Note about the mitochondria structure: o Matrix:  A space containing a concentrated mixture of enzymes that can oxidize pyruvate and fatty acids in the Kreb Cycle  Including ATP synthase that actually is directly involved in making ATP o Inner Membrane:  This membrane, unlike the outer membrane, is not nearly as permeable, and is the location of the electron transport chain  Folded into many cristae containing proteins that carry out the oxidation reactions of the electron-transport chain as well as the ATP synthase that makes ATP in the matrix o Outer Membrane:  Contains a large channel-forming protein called porin that allows it to be mostly permeable to molecules of 5000 Daltons or less o Intermembrane space:  The space between the outer and inner membranes contains enzymes that use the ATP passing out of the matrix to phosphorylate other nucleotides Part A: The Prep-Step & the TCA/Kreb Cycle • Pyruvate cannot simply dif
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