Biochemistry Exam 2: Thermodynamics, Enzymes, and Glycolysis, Exams of Biochemistry

Download Biochemistry Exam 2: Thermodynamics, Enzymes, and Glycolysis and more Exams Biochemistry in PDF only on Docsity! Exam 2 Biochem (weeks 5 and 6) first law of thermodynamics - ANS The principle of conservation of energy. Energy can be transferred and transformed, but it cannot be created or destroyed. examples to review: cellular respiration and. photosynthesis second law of thermodynamics - ANS Every energy transfer or transformation increases the entropy of the universe. Entropy - ANS a measure of the disorder of a system Bioenergetics - ANS the study of how energy flows through living organisms (energy involved in making and breaking of chemical bonds) Property of all living organisms - ANS the ability to harness energy from a variety of metabolic pathways Thermodynamics - ANS the study of energy transformations isolated system - ANS A system that can exchange neither energy nor matter with its surroundings. ex: liquid in a thermos open system - ANS a system in which exchanges of matter or energy occur between the system and its surroundings Organisms are open systems Spontaneous processes occur - ANS without energy input; they can happen quickly or slowly free energy change (delta G) - ANS a measure of the change in free energy as a chemical reaction or physical change occurs negative delta G - ANS spontaneous, exergonic, favorable, exothermic, entropy increases Most catabolic reactions are - ANS exergonic exergonic reaction - ANS A spontaneous chemical reaction in which there is a net release of free energy. endergonic reaction - ANS A non-spontaneous chemical reaction in which free energy is absorbed from the surroundings. Most anabolic reactions are - ANS endergonic (require ATP) positive delta G - ANS non-spontaneous, endergonic, unfavorable, endothermic, entropy decreases energy coupling - ANS The use of an exergonic process to drive an endergonic one. cell does three main kinds of work - ANS 1. Chemical 2. Transport 3. Mechanical energy coupling in cells is mediated by - ANS ATP ATP in coupled reactions - ANS Energy released by an exergonic reaction (or reactions) is captured in ATP. ATP is then used to drive an endergonic reaction. Enzymes are - ANS proteins that function as catalysts enzyme function - ANS speed up chemical reactions by lowering activation energy delta G at equilibrium - ANS delta G = 0 enzyme catalysis - ANS the increase in the rate of a chemical reaction by the active site of a protein Enzymes - ANS increase reaction rates without being used up Some RNA also catalyze reactions, they are - ANS Ribozymes and Ribosomal RNA The oldest field of biochemistry (dating back to 1700s) is - ANS the study of enzymatic processes In catalyzed reactions - ANS -activation energy decreases -delta G (free energy ) does not change - reaction rate increases -enzymes do not affect equilibrium - enzymes bind best to transition state In catalyzed reactions - ANS -enzyme uses binding energy of substrates to organize reactants to a fairly rigid ES complex -entropy cost is paid during binding -rigid reactant complex --> transition state conversion is entropically neutral proximity model - ANS Enzymes organize reactants into close proximity and proper orientation (work by Thomas C Bruices group) Cofactors - ANS -nonprotein enzyme helpers -usually metal ions connected temporarily or transiently to enzyme -stabilizes negative charges Enzyme active sites are - ANS complimentary to the transition state of the reaction Fischer Mechanism - ANS Active site fixed in shape Kochland's Induced Fit theory - ANS -active site adapts to substrate -active site of induced fit enzymes becomes complementary only after the substrate is bound Coenzymes are - ANS organic molecules connected temporarily or transiently to enzyme -they are often vitamins or derivatives of vitamins prosthetic group - ANS A cofactor or coenzyme that is covalently bonded to a protein to permit its function - connected permanently to enzymes -Examples: FAD or Heme Ribozymes - ANS -catalytic RNA molecules that function as enzymes and can splice RNA -splicing in the tRNA molecules is carried by tRNA itself, and doesn't require a spliceosome -rRNA in the ribosomes carries the peptide bond formation of the ribosomes Rate of enzymatic reaction is affected by: - ANS -temperature -enzyme -substrate concentration -effectors (activators/inhibitors) enzyme inhibitors - ANS -substrate imposters that plug up the active site -compounds that decrease an enzymes activity removes Na+ brings in K+ active transport example - ANS Na/K pump Sodium/potassium pump 3 Na+ out 2 K+ in sodium-potassium pump steps - ANS 1. 3 Na+ ions inside the cell bind to the pump. A phosphate group from ATP also binds to the pump. 2. Pump changes shape transporting 3 Na+ ions across the cell membrane. Na+ ions are released outside the cell. 3. 2 K+ ions, outside the cell bind to the pump. The K+ ions are transported across the cell membrane. 4. The phosphate group is released, and the 2 K+ ions are released into the cell. 4 ways glucose is used by living organisms - ANS 1. energy production 2. Storage 3. production of NADPH and pentoses 4. Structural carbohydrate production energy production by glucose - ANS generates energy via oxidation of glucose- short- term energy needs storage - ANS - can be stored in the polymeric form (starch, glycogen)- used for later energy needs Production of NADPH and pentoses - ANS -generates NADPH for use in relieving oxidative stress and synthesizing fatty acids -generates pentose phosphates for use in DNA/RNA biosynthesis structural carbohydrate production - ANS used for generation of alternate carbohydrates used in cell walls of bacteria, fungi, and plants Many organisms can use glucose to generate:• - ANS all the amino acids• membrane lipids• nucleotides in DNA and RNA• cofactors needed for the metabolism Glycolysis - ANS Primary Energy Source of Cells• Central Metabolic Pathway• All Reactions Occur in Cytoplasm• Two Phases• Produces 2 Pyruvates, 2 ATP, 2 NADH What is phase 1 in glycolysis - ANS energy (ATP) investment phase Name all the steps in phase 1 (substrates/enzyme/prods) - ANS Review Isoforms for hexokinase - ANS hexokinase I, II, III, and IV (glucokinase)) Hexokinase - ANS glucose to glucose-6-phosphate example for induced fit model difference between hexokinase and glucokinase - ANS glucokinase is in the liver. Glucose will encounter glucokinase before it encounters hexokinase. Glucokinase has a HIGH VMAX and a HIGH KM, hexokinase is in all other tissues, deals with lower amounts of glucose, so has a LOWER KM (and LOWER VMAX Kinase - ANS An enzyme that transfers phosphate ions from one molecule to another (responsible for phosphoryl group transfer reactions aldose---ketose - ANS phosphoglucoisomerase ketose --- aldose - ANS triose phosphate isomerase PFK - ANS rate limiting enzyme in glycolysis phosphofructokinase what happens to PFK in the presence of low and high ATP - ANS low ATP- enzyme becomes active high ATP-enzyme becomes inactive The end products of glycolysis are - ANS 2 pyruvate, 2 ATP, 2 NADH Where glycolysis takes place - ANS cytoplasm of the cell, no oxygen required Which steps require ATP? - ANS 1 and 3