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McGill University
PHYS 183
Tracy Webb

Dr.Thomas Lectures: Catabolic pathway: breaks down molecules into subunits used as building blocks for biosynthesis reactions. Anabolic pathways: are syntheses of biomolecules which assemble building blocks and utilizes the form of energy to make the molecule. First law of thermodynamics: Energy cannot be created nor destroyed but changes from one form to another. Second law of thermodynamics: entropy is the measure of disorder, the total entropy of the universe is always increasing. Gibbs free energy will determine whether a process or mechanism will occur or not. - It can be entropy favoured; entropy is going up - It can be enthalpy favoured; exothermic reaction - If the value of Gibbs energy is negative, process is favoured Determinants of Gibbs Free energy: - The concentration of the reactants will influence deltaG; the more reactant available the more likely to be pushed toward the product side (Le Chatelier’s Principle) - K is the equilibrium constant, meaning at that point there are as much product being made as to reactants being made (from reaction between products) o Thus deltaG = 0; not favouring forward or reverse reaction - All reaction will reach at one point or another equilibrium - K can be measure to [X]/[Y]; where X is the product You can have two types of Gibbs free energy - You can have standard Gibbs (Go) o which all components will have the same concentration of 1mol/L and this will occur at body temperature 37C or 310K o this allows one to measure intrinsic properties of the REACTING MOLECULES  Intrinsic properties: An intrinsic property is a property of a substance that is independent of the amount of the substance present. • ie: boiling point, density, and melting point. Enzymes: - Lowers the activation energy of a reaction - Does not change the concentration of the product being made at equilibrium - ONLY accelerates the procedure Coupling of Reactions: - Many mechanism in the body uses this - By activating one reaction it may favour the next. o Example would be energy is required for the catabolism of food molecules into subunits. This creates molecules with high energy bond that can be used to drive reaction that are unflavoured such as the anabolism of molecules. These high energy bond molecules are referred to as activated carriers. Activated Carriers: - Example ATP; o Adenine – ribose – 3 phosphate bounded to each other by Phosphoanhydride bonds. o The release of 1 phosphate by hydrolysis releases 11-13kCal/mol of energy which can be utilized to drive a reaction. o From ATP – AMP ; about 26kCal/mol o Condensation reaction (water is formed) – are unflavoured; less disorder  A-H + B-OH  A-B + H2O ; unfavourable BUT  B-OH + ATP  B-O-PO3 + ADP AND  B-O-PO3 + A-H A-B + Pi; FAVOURABLE thus net equation can be  B-OH + A-H + ATP  A-B + H2O + ADP + Pi - Example NADPH: o Acts as a mediator between an oxidation-reduction reaction o It takes 2 electrons from 1 molecule (oxidation) and gives it to another molecule (reduction) o Used in the last step of cholesterol synthesis - Acetyl CoA: o adds 2 carbons to a biomolecule o used in biogenesis of a lipid o The acetyl CoA is a molecule attached to CH3CH=O via a thioester bond. o Thioester bonds are high-energy bonds - Activated carriers are used for the sysnthesis (or anabolism) of polysaccharides, proteins, nucleic acids which are all condensation reaction. Glycolysis: Glycolysis is the breaking down of sugar to release energy from the high energy bonds. Kinase: are enzymes which adds a phosphate to a molecule from the gamma phosphate (last phosphate) of ATP Phosphatase: do the reverse of Kinases, as they remove phosphate from a molecule Glucose molecule: - Comes from startch if digested - Glycogen stored mainly in the liver - Glucogenesis, transformation of certain amino acids Notice: at carbon 1 and 2 both hydroxyl groups are syn to each other There are 3 phases to glycolysis, for a total of 10 steps 1. Energy investment to be recouped later I. Starting with a glucose molecule Hexokinase phosphorylates carbon 6 using ATP; GLUCOSE- 6-PHOSPHATE IS MADE i. This traps glucose-6-phosphate within the cell because it gives the glucose a negative charge and as we know charged molecules do not pass through the bilayer easily. 2. Cleavage of six carbons sugar to two three-carbon sugars II. Glucose – 6 – phosphate is in equilibrium with its open chain. In the open chain conformation Phosphoglucose isomerase can form a 5 member ring named FRUCTOSE – 6 – PHOSPHATE. III. New formed hydroxyl group is phosphorylated by Phosphofructokinase (PFK)using ATP i. PFK is allosterically regulated by ADP molecule. ii. PFK has a binding domain for the phosphorylation of fructose-6-P with ATP, as well as an ADP/AMP regulator domain (located b/w subtunits). This domain when bounded to ADP the conformation of PFK is placed in a way to be very active. This is because when high dose of ADP in the cell, PFK can be activated and make more ATP but if ATP is high in the cell it will bind ATP and it will be down regulated, by changing to another less favoured conformation. IV. Aldolase enzyme will convert fructose – 6 – phosphate into 2 three member chains. i. The first chain will be glyceraldehyde 3 phosphate which will be able to be used directly through glycolysis. ii. The second chain is dihydoxyacetone phosphate and it CANNOT be used directly for glycolysis V. Dihydroxyacetone phosphate is isomerized into the proper usable form glyceraldehyde 3 phosphate via triose phosphate isomerase. This enzyme is driven by HEAT 2. Energy generation!! VI. 2 molecules of glyceraldehyde 3 – phosphate are oxidized from NAD+ by enzyme Glyceraldehyde 3-phosphate dehydrogenase. This will add a high energy anhydride bond linked to a phosphate. Doing so will generate NADH + H . + a. Procedure: i. The cysteine side chain of the enzyme (SH) will COVALENTLY bind to the glyceraldehyde 3-P and NONCOVALENTLY TO NAD+ ii. Oxidation of glyceraldehyde 3-P is done as 2 electrons and 1 hydride ion are transferred from glyceraldehyde 3-P to NAD+ forming NADH. iii. The energy released from glyceraldehyde is stored within NADH and to make a high energy thioester bond between the cysteine side chain of the enzyme and glyceraldehyde 3-P iv. Thioester bond is replaced by Pi (iorganic phosphate) which keeps the high energy bond property. v. Final product is 1,3-bisphosphoglycerate VII. ADP is utilized by Phophoglycerate kinase to make ATP from ripping off a phosphate that was just added in the previous step. The energy released from the bond is then stored within ATP i. This will make 3 phosphoglycerate (1 anhydride phosphate bond left, low energy bond) VIII. Phosphoglycerate mutase will invert the anhydride phosphate bond with the hydroxyl. IX. Enolase will remove water from the molecule and make a double bond (this cause the low energy bond to become a+high energy bond) X. Pyruvate kinase uses ADP and H to make ATP and Pyruvate. ** Net cost, after investing 2 ATP molecule at Step 1 and 3, from this 2 glyceraldehyde 3- phosphates are made each generating 1 NADH, 2 ATP molecules and 1 pyruvate. Thus net gain is 2 ATP, 2NADH, 2 pyruvate molecules from 1 glucose molecule. ** Side note: bumblebees use glycolysis in order to warm up their wings during cold summer morning. This allows them compete for the pollen, as they can function earlier than the rest of the insects. Short summary of Glycolysis: 1. Phosphorylation of glucose at position 6 by hexokinase 2. Isomerization fo glucose-6-phosphate to fructose-6-phosphate by phosphoexose isomerase 3. Phosphorylation of fructose-6-phsophate by phosphofructokinase 4. Cleavage of fructose-1,6-bisphosphate by aldolase yielding two different products a. Dihydroxyacetone phosphate b. Glyceraldehyde 3-Phosphate 5. Isomerization of dihrydoxyacetone phosphate to another molecule of glyceraldehyde phosphate by triose phosphate isomerase 6. Dehydrogenation and phosphorylation of glyceraldehyde-3-p to 1,3 bisphosphoglycerate by glyceraldehyde-3-P dehydrolase 7. Transfer of 1-phosphate group from 1,3 bisphosphoglycerate to ADP to yield ATP by phosphoglycerate to 2-phosphoglycerate by phosphoglycerate mutase 8. Isomarization of 3-phosphoglycerate to 2-phosphoglyycerate by phosphoglycerate 9. Dehydration of 2-phosphoglycerate to phosphoenolpyruvate by enolase 10. Transfer of the phosphate group from phofphoenolpyruvate to ADP by pyruvate kinase to yield another ATP. **DO NOT NEED TO KNOW THE NAMES OF THE ENZYMES..MAYBE ONLY FOR STEP 6 AND 7. From glycolysis: - Can occur with or without oxygen - Generates 2 ATP and 2NADH - 2 NADH is used to export lactic acid or fermentation for yeast Different types of phosphate bond can release different amount of energy upon breakage. The energy release will favour the reaction; as more energy is released more is favoured. Creatine phosphate is an activated carrier found in the muscles, it is a rapid energy source and thus the first source of energy when muscles are working. It is used to make ATP by creatine kinase before glycolysis starts. This process occurs in the cytoplasm of the cell when the concentration of ADP is to high. This process occurs in anaerobic conditions. Creatine phosphate, 1,3 bisphosphoglycerate and phosphoenolpyruvate all have lower Gibbs free energy value (
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