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BIOL2170 Week 6 Notes

by: Katie Veselka

BIOL2170 Week 6 Notes BIOL 2170 - 002

Katie Veselka
GPA 3.78

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Contains Lecture 8, and 9 and 10 which were grouped together.
Fundamentals of Life Science: Biomolecules, Cells, and Inheritance
Robert M. Stevens
Class Notes
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This 7 page Class Notes was uploaded by Katie Veselka on Wednesday September 28, 2016. The Class Notes belongs to BIOL 2170 - 002 at University of Toledo taught by Robert M. Stevens in Summer 2016. Since its upload, it has received 18 views. For similar materials see Fundamentals of Life Science: Biomolecules, Cells, and Inheritance in Biology at University of Toledo.


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Date Created: 09/28/16
Lectures 9 and 10: Pathways that Harvest Chemical Energy Lecture 9 A) Metabolism a) Thousands of chemical reactions are occurring in cells simultaneously b) The reactions are organized in metabolic ‘pathways’ I) Each reaction is catalyzed by a specific enzyme II) Regulation of enzymes to control the rates of reactions helps maintain internal homeostasis B) Enzymes a) Every enzyme is most active at a particular pH I) pH Influences the ionization of functional groups. - + (1)Example: at low pH, COO may react with H to form COOH which is no longer charged, this affects folding and thus enzyme function b) Every enzyme has an optimal temperature I) At high temperatures, noncovalent bonds begin to break II) Enzyme can lose its tertiary structure and become denatured C) Isozymes a) Isozymes are enzymes that catalyze the same reactions but have different properties, such as optimal temperature b) Organisms can use isozymes to adjust to temperature changes D) Energy and Fuel a) Fuels: molecules whose stored energy can be released for use I) The most common fuel in organisms is glucose E) Glucose a) Burning or metabolism of glucose: I) C6H12O6 + 6O2 → 6CO2 + 6H2O + free energy b) Glucose metabolism pathway traps the free energy in ATP I) ADP + Pi + free energy → ATP c) The major metabolic pathways involved in harvesting the energy of glucose: I) Glycolysis: glucose in converted to pyruvate, ATP and electron carriers II) Pyruvate Oxidation and Kreb’s Cycle-aerobic: converts pyruvate into H2O, CO2 and ATP III) Fermentation-anaerobic: converts pyruvate into lactic acid or ethanol, CO2 and ATP F) Glycolysis a) Take place in the cytosol b) Converts glucose into pyruvate c) Releases a small amount of energy (2ATP and 2 NADH) d) Generates no CO2 e) Divided into 2 stages I) Energy investing reactions (uses ATP) (1)Glucose split into two 3-carbon molecules II) Energy harvesting reactions (produce ATP and NADH) G) Redox Reactions a) One substance transfers electrons to another substance b) Reductions: Gain of one or more electrons by an atom, ion, or molecule c) Oxidation: loss of one or more electrons d) Also occurs if hydrogen atoms are gained or lost e) Oxidation and reductions always occur together f) The reactant the becomes reduced is the oxidizing agent g) The reactant that becomes oxidized is the reducing agent h) Electron carrier in+the cell: I) Coenzyme NAD is an electron carrier in redox reactions II) Two forms: (1)NAD (oxidized) (2)NADH (reduced) III) Oxygen accepts electrons from NADH: (1)NADH + H + ½ O2 → NAD + H2O + (i) Exergonic—ΔG=-52.4 kcal/mol (ii)Oxidizing agent is molecular oxygen—O 2 H) Transfer of phosphate groups a) Phosphorylation: addition of a phosphate group b) Enzyme catalyzed transfer of a phosphate group from an organic donor molecule to ADP to form ATP is called substrate level phosphorylation c) Oxidative phosphorylation: ATP is synthesized by oxidation of electron carriers in the presence of O2 I) Two components: (1)Electron transport (i) Electrons from NADH and FADH pa2s through the ETC (respiratory chain) of membrane associated carriers (ii)Electron flow results in proton concentration gradient in mitochondria (2)Proton transport and ATP synthesis I) Pyruvate Oxidations a) Links glycolysis and the citric acid cycle b) Take place in the mitochondrial matrix c) Pyruvate is converted to acetyl CoA d) CO2 and NADH are produced J) Citric Acid cycle a) Acetyl CoA is the starting point of the cycle b) Cycle is in a steady state: the concentrations of the intermediates don’t change c) Outputs: CO2, reduced electron carriers, and GTP (converts ADP to ATP) K) Electron transport chain a) Why does the electron transport chain and cellular respiration have so many steps? + + I) Why not just NADH + H + ½ O2 → NAD + H2O ? b) The electron transport chain is located in the inner mitochondrial membrane c) Energy is released as electrons and are passed between carriers I) Examples: protein complexes I,II,III,IV; cytochrome c, CoQ d) During electron transport protons are also actively transported e) Protons accumulate in the intermembrane space and create a concentrations gradient and charge difference, which is a new source of potential energy f) These electrochemical gradients drive protons back across the membrane L) ATP synthesis a) Protons diffuse back into the mitochondria through ATP synthase, a channel protein b) Diffusion is coupled to ATP synthesis Lecture 10 A) What happens when there is no oxygen? a) Cellular respiration if O2 is present b) Fermentation if O2 is not present c) Without O2, ATP can be produced by glycolysis and fermentations d) The electron carriers that are reduced during glycolysis must be reoxidized to take part in glycolysis again B) Fermentation a) Fermentation occurs in the cytosol to regenerate NAD + b) During fermentation pyruvate is reduced by NADH c) Lactic Acid fermentation: I) Occurs in some organisms II) Occurs in starved muscle cells III) Lactic acid (lactate) is the product d) Alcoholic fermentation I) Yeast and some plant cells II) Pyruvate is converted to acetaldehyde, CO2 is released III) Acetaldehyde is reduced by NADH, producing NAD and ethyl alcohol C) Other sources of energy a) Polysaccharides can by hydrolyzed to glucose and enter glycolysis b) Lipids are broken down to glycerol, a glycolysis intermediate I) Fatty acids to acetyl CoA c) Proteins are hydrolyzed to amino acids which feed into glycolysis or the citric acid cycle D) What if we don’t eat? a) Glycogen stores in muscle and liver are used first b) Fats are used next c) Proteins are used last E) Metabolic pathways a) Metabolic homeostasis: concentrations of biochemical molecules remain constant (glucose concentration in blood) b) Allosteric control of enzymes in metabolic pathways c) Activation or inhibition of key enzymes Lecture 8: Energy and Enzymes 09/21/16 A) Origin of eukaryotic cells a) Eukaryotic cells appeared about 1.5 billion years ago b) Endosymbiosis theory explains how eukaryotes could evolve from prokaryotes I) cells engulfed other cells that became mitochondria and chloroplasts. B) Energy a) The capacity to do work, or the capacity for change b) The transformation of energy is hallmark of life c) In cells, energy transformations are linked to chemical transformations and molecular movement. d) Types I) Potential energy (1) Is stored energy-as chemical bonds, concentration gradient, change imbalance, for example. II)Kinetic energy is the energy of movement C) ATP (adenosine triphosphate) a) Captures and transfer energy b) ATP releases a large amount of energy when hydrolyzed c) ATP can donate phosphate groups to other molecules d) Metabolism: the entire set of life-sustaining chemical reactions occurring in the cells of organisms D) Laws of Thermodynamics a) First Law I) When energy is converted from one form to another, the total energy before and after the conversion is the same b) Second Law I) When energy is converted from one form to another, some of the energy becomes unavailable to do work II)No energy transformation is 100 percent efficient E) Entropy a) Entropy is a measure of the disorder of a system b) It takes energy to impose order on a system. Unless energy is applied to a system, it will be randomly arranged or disordered. c) Living organisms must have a constant supply of energy to maintain order d) If a chemical reaction increases entropy, the products will be more disordered I) Example: hydrolysis of a protein into its component amino acids—ΔS is positive II)The products have less energy than the reactants and disorder increased: free energy is released F) Free Energy a) In any system I) Total energy= usable energy + unusable energy II)Enthalpy(H)= free energy (G)+ Entropy (S) IIIH=G+TS (T= absolute temperature) IV) G=H-TS b) Change in free energy (ΔG) in a reaction is the difference in free energy of the products and the reactions I) Change in energy can be measured in calories or joules II) ΔG=ΔH-TS (1) If ΔG is negative, free energy is spontaneous reaction (exergonic) (i) Exergonic reactions: cell respiration, catabolism (2) If ΔG is positive, free energy is not spontaneous (endergonic) (i) Endergonic reactions: active transport, cell movements, anabolism (3) If free energy is not available, the reaction will not occur III)Magnitude of ΔG depends on: (1) ΔH—total energy added (ΔH>0) or released (ΔH<0) (2) ΔS—change in entropy. Increases in entropy make ΔG more negative. G) Enzymes and Catalysts a) Catalysts increase the rate of reaction b) The catalyst is not altered by the reaction c) Most biological catalysts are enzymes (proteins) that act as a framework in which reactions take place d) An enzyme forms a complex with its substrate which turns into the product I) The complex can promote the reaction of two substrates by aligning their reactive groups and limiting their motion II) The enzyme may change when bound to the substrate, but eventually return to its original form. III)Enzymes orient substrate molecules, bringing together the atoms that will bond. IV) Substrate molecules bind to the active site of the enzyme. e) biological catalysts (enzymes and ribozymes) are highly specific I) three dimensional shape of the enzyme determines the specificity II) shape of enzyme active site allows a specific substrate to fit f) Enzymatic reactions I) The rate of a catalyzed reaction depends on substrate concentration II) Concentration of an enzyme is usually much lower than the concentration of a substrate III)At saturation, all enzyme is bound to substrate—reaction at maximum rate H) inhibitors a) inhibitors regulate enzymes: molecules that bind to the enzyme and slow reaction rates b) naturally occurring inhibitors regulate metabolism c) Types I) Irreversible inhibitor: inhibitor covalently bonds to side chains in the active site—permanently inactivates the enzyme (1) Example: DIPF in nerve gas II) Reversible inhibition: inhibitor bonds noncovalently to the enzyme, inhibiting its function (1) Competitive inhibitors bind to the enzyme active site (2) Noncompetitive inhibitors bind to the enzyme at a different site (not the active site) (i) The enzyme changes shape and its activity is reduced (ii) Allostery (allo, ‘different’, stereos, ‘shape’)  Effector binding to a region separate from the avtive site alters enzyme activity 1. Activators bind to stimulate the enzyme 2. Inhibitors bind and inhibit the enzyme function I) Activation energy a) All chemical reactions require input of energy I) The amount of energy required to start a reaction is the activation energy (Ea) II) The larger the (E a the slower the reaction b) Activation energy changes the reactants into unstable forms with higher free energy—transition state intermediates c) Activation energy can come from heating the system—the reactants have more kinetic energy d) Enzymes lower the kinetic barrier by bringing the reactants together


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