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Lecture

BIOL 201 - Lectures 1 to 6

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Department
Biology (Sci)
Course
BIOL 201
Professor
Greg Brown
Semester
Winter

Description
Lecture 1: Metabolism is the science of energy conversions in living systems. Adult animals, that are not growing, do not consumeenergy; they convert energy from one form to another, Ex: Plants convert Sunlight energy to Chemical bond energy. Animals eat plant and convert chemical bond energy to work. Energy in=energy out. ∗ Organisms store energy during growth. Ex: buildingtissue. ∗ Organisms store energy temporarily during activity.Ex: Convert glucose to ATP which is used to generate heat and work. Metabolism is important: 20% of genome used for metabolism. Fuels are degraded and large molecules are constructed step by step in a series of linkedreactions called metabolic pathways. Catabolism breaks down fuel, releasing cellular energy Anabolism requires energy (ex: synthesis of glucose, fats or DNA) Why do organisms not tend towards disorder?Are we cheating the second law of thermodynamics? ∗ Not all energy is created equal (Joule’s experiment, mass on pulley, potential to thermal energy, not reversible because energy quality consumed). ∗ Animals convert “higher quality” energy to “lower quality” energy, consuming energy quality. Living organisms require a continual input of freeenergy for three major purposes: ∗ The performance of mechanical work in muscle contraction ∗ The active transport of molecules and ions ∗ The synthesis of macromolecules and other biomolecules from simple precursors. Lecture 2: Free Energy, Equilibrium, and Catalysis The total energy of a system, or Enthalpy, is thetotal energy of a system. The Gibbs free energy is a measure of the available energy of a system. The entropy of a system is a measure of disorder. H = Enthalpy G = Free energy G = H - TS S = Entropy ⇨ TS indicates the “unavailable” energy. Universe tends towards disorder, degrading energyquality, releasing Free energy. Hence, change in free energy determines whether a processis spontaneous. Free energy becomes negative because entropy must increase. ∆G = ∆G ▯(▯▯▯▯▯▯▯▯) − ∆G ▯(▯▯▯▯▯▯▯▯▯) ∆G = ∆H − T∆S ∆H = 0▯in▯isolated▯system ∆S > 0,∆▯ < 0▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯▯ - Energy can be released to drive a chemical process. - Standard free energies are additive, and path independent. Equilibrium: State of minimized Free energy, free energy flows are minimized. Equilibrium is a dynamic state. Forward rate is equal to the reverse rate ofa reaction at equilibrium. ∗ Forward reaction generally favored if K > 1 eq Free energies are related to the equilibrium constants! ∆G = −RT▯lnK ▯▯ - Largely negative ∆G result in large changes in K, larger values resultin very small K changes. - Unfavourable reactions are driven by hydrolysis ofATP, which releases free energy. ∗ ∆G does not determine rate of a reaction! Graphite conversion to diamond is an energetically favourable reaction, but does not occur readily. ∗ ∆G determines whether a reaction occurs spontaneously. ΔG < 0 for a spontaneous process ∗ Because catalyst simply lowers the transition stateenergy, it drives both the forward AND the reverse reaction! Free Energy is released during breakdown of glucoseand is used to phosphorylate ADP to ATP. ATP is used to store energy. Lecture 3 ΔG can be calculated from initial conditions and eq ▯ ∆G ▯ = −RT▯lnK ▯▯ ▯▯ ∆G = −1362▯logK ▯(▯▯▯▯▯▯▯▯▯▯▯/▯▯▯) ▯ [▯▯▯▯▯▯▯▯] ∆G = ∆G + RT▯ln [▯▯▯▯▯▯▯▯▯] log (x) = 2.303 ln(x) −1 −1 R = 1.985 cal K  mol How does a process overcome the activation energy? ⇨ The energy of a molecule fluctuates. You can calculate probability that a molecule will make it over a certain energy state, this can be very low (slow reaction, reaction doesn’t occur) Cells capture free energy in ATP and release this energy to drive other by coupling. Thermodynamically unfavorable reactions can be driven by a thermodynamically favorable reaction to which it is coupled. ⇨ Coupling brings reactions into very close proximity, free energy released by one reaction drives the other one. Enzymes catalyze reactions by lowering the free energy oftransition states. TheEnzymes can be regulated by ATP, which can distort the 3D structure of proteins, thereby modifying their function. (ATP can induce strain in protein structure). Km (at ½ V max shows an enzyme’s affinity for its substrate. The strain can distort the bond and induce bond breakage. It can expose an active site or change the shape of an active site. Redox reactions provide a basis for energy transduction --» the oxidation of carbon fuels powers the formation of ATP. ATP has a high phosphoryl-transfer potential, storing a large amount of free energyin its bond with phosphate. Recall: Reduction – Gaining an electron; Oxidation –Losing an electron. In aerobic organisms, the ultimate electron acceptor in the oxidation of carbon is O and 2he oxidation product is CO 2. NAD+ is the principle electron acceptor in metabolic redox reactions. It carries energy and transfers it to other molecules. NAD “harvests” energy, ATP spends it. NAD+ can be used in a wide range of therapies Ex: Tuberculosis NAD in tuberculosis is “stuck”, causes a reductionin bacterial cell wall synthesis Wallerian Degeneration The axon decays all the way back to the cell body (in response to injury). Wallerian-like degeneration is seen in neurodegenerative diseases. A company that manufactures a mouse withwlds genet hat has delayed degeneration. This mutation causes an overproduction of NAD+ FAD is used when the available free energy could not reduce NAD+. More free energy is needed for the reduction of NAD+, FAD is easier to reduce in comparison. GAPDH brings NAD+ into position to be reduced. Lecture 4 Polymers broken down into monomeric subunits: Fats ⇨ Fatty acids and glycerol Polysaccharides ⇨ Glucose and other sugars Proteins ⇨ Amino acids Monomers are taken up through stomach and intestinewalls and delivered to cells. Converted into a 2-Carbon carrier (Acetyl group attached to Coenzyme A) Goes through Citric acid cycle, 2 CO2 released through an oxidation reaction, 8 electrons released. Electrons captured by NAD and transferred to the terminal electron acceptor, oxygen, , which gets converted to water. This whole process synthesizes ATP from ADP through oxidative phosphorilation. ATP drives energy consuming processes through release of a phosphate group. Glycolisis: (Occurs in Cytosol) How glucose is converted to pyruvate, the direct precursor of Acetyl coA. ∗ The part of the glucose breakdown pathway that canoccur in anaerobic conditions is called glycolisis. Sometimes called fermentation under anaerobic conditions. ∗ In muscle, the end product of fermentation is lactic acid. ∗ In yeast, the end product of fermentation is ethanol ∗ Glycolisis is present in nearly all organisms Glucose gets converted to pyruvate, when )2 is absent is in converted to Lactate of Ethanol. If Oxigen is available, Pyruvate enters the citric acid cycle . Process: In vest 2 ATP, recover 4 ATP (2 ATP per pyruvate, 2pyruvate from 1 glucose) Stage 1: Glucose to Fructose-1,6,-biphosphate Kinases transpher γ phorphoryl group of ATP to acceptor (sugars in glycolysis) ATP has a high phosphoryl transfer potential (verynegative free energy change), equilibrium STRONGLY favours formation of ADP and sugar phosphate. Glucose-6-phosphate cannot exit the cell. Phosphorylation of 6th Carbon "traps" the glucose. Phosphorilation of Carbon 1 by phosphofructokinase to Fructose-1,6,-biphosphate, which can be broken down into two 3 C compounds. ***pfk is a pacemaker enzyme. Both phosphorylations consume ATP, a total of 2 ATP consumed per glucose molecule. Stage 2: Fructose-1,6,-biphosphate cleavage triosephosphate salvage Fructose-1,6,-biphosphate is converted into two 3-Carbon molecules using Aldolase (Aldol Condensation reaction) Half of molecules go directly to GAL3P, other molecules converted to Dihydroxyacetone phosphate, which gets converted to GAL3P. Stage 3: NADH, ATP and pyruvate generation GAL3P (GAP) Start off with glyceraldehyde-3- phosphate. GAL3P dehydrogenase forms acyl phosphate. (phosphoryl group on C=O, has high high phosphoryl transfer potential, so transfer of that group to ADP is energetically favorable) Formation of acyl phosphate is unfavourable, but it is driven by energetically favourable oxidation of GAL3P. Phosphoryl group is now on #3 carbon, mutase moves phosphoryl to #2 carbon, enabling it to form an enolate, which is an energetically favourable conformation. Pyruvate kinase transfers phosphate to ADP.
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