Biol 118 1st Edition Exam 2 Study Guide Enzymes Section 3 4 Chapter 8 3 8 4 Catalysis the speeding up of chemical reactions o Most reactions don t occur fast enough to support life Enzyme A protein that functions as a catalyst o Best catalysts because of variety of reactive functional groups in amino acids Substrate Reactant molecules in a chemical reactions o Lock and Key model enzymes are a lock and the keys are the substrate that fit into the lock then react o Active site location where substrates bind react where catalysis usually occurs Cleft or cavity within the enzyme s shape Catalysts bring substrates together in a precise orientation that makes reactions more likely Reactant must do 2 things before being able to participate in a reaction o Collide in a precise orientation o Have enough kinetic energy to overcome repulsion between electrons that come in contact as bonds form Enzymes are not rigid but actually flexible o Induced fit significant change in enzyme shape so reactant molecules can bind to the active site Transition State Temporary unstable intermediate condition formed by maximum interaction between the substrate the r groups in the active site o Achieved by activation energy certain amount of kinetic energy required to strain chemical bonds in substrates once they achieve this reactions can happen o Stabilized by amino acid R group interactions also lowers the activation energy Reaction rates depend on kinetic energy of reactants activation energy of the reaction 3 steps of enzyme catalysis o Initiation Enzymes orient reactants precisely as they bind to active sites o Transition State Facilitation Inside active site interactions with R groups lower activation energy o Termination Reaction products do not bind to active site enzyme returns to original conformation products released Substrate concentration affects reaction rate the less substrate the slower the reaction o Saturation kinetics some point active sites cannot accept anymore substrate no matter the concentration pH temperature affect enzymes o pH Affects shape reactivity o Temperature Movement of the substrate and enzyme Competitive Inhibition Regulatory molecule is similar to size shape binds to enzyme active site competes with substrate for access to active site Allosteric Regulation Regulatory molecule binds to different location on enzyme changes shape o Can inhibit or activate Chapter 10 Photosynthesis requires sunlight carbon dioxide water glucose water oxygen o Oxygen is made as a by product o Endergonic reaction Chlorophyll Absorb red blue light transmits green light o Most effective at driving photosynthesis Carotenoids Absorb blue green light reflect transmit yellow orange green light o Pass energy not absorbed from light onto chlorophyll Light Dependent Reactions o Produces O2 from H2O o Requires light to function o Produces ATP NADPH o Transfers energy from chlorophyll to chlorophyll until it reaches the reaction center Calvin Cycle Reactions o Does not require light o Produces sugar from carbon dioxide o Uses ATP NADPH turns it back into ADP NADP Reaction Center Light reactions o When chlorophyll is excited in the reaction center excited electron is transferred to an electron acceptor driven by light o Transforms electromagnetic energy into chemical energy o Two types of reaction center Photosystem 2 Make ATP Feeds high energy electrons to an Electron Transport Chain Triggers chemiosmosis ATP synthesis Obtains electrons by oxidizing water when excited electrons leave PS2 becomes highly electronegative Photophosphorylation capture of light energy to produce ATP Chemiosmosis Flow of protons through ATP synthase causes a conformational change drives phosphorylation of ADP Oxygenic photosynthesis splits water replaces lost electrons produces oxygen Photosystem 1 Make NADPH Antenna complex absorbs photons Passes the energy to the reaction center Reduces NADP to NADPH Calvin Cycle Carbon Fixation o Has three phases Fixation Carbon is reduced in redox reaction CO2 reacts with RuBP Produces two 3 phosphoglycerate molecules PGA Reduction 3PGA is phosphorylated by ATP reduced by NADPH Produces glyceraldehyde 3 phosphate G3P Regeneration Remaining G3P is used in reaction that regenerate RuBP o 1 turn of Calvin cycle 1 molecule of CO2 fixed o 3 turns produce one molecule of G3P o Rubisco CO2 fixing enzyme Catalyzes the addition of CO2 to RuBP Chapter 15 DNA Synthesis DNA is polar antiparallel Has directionality o One end has exposed hydroxyl group on 3 end of carbon o Other end has an exposed phosphate group on the 5 carbon Watson Crick secondary structure forms a double helix in antiparallel fashion o Made by complementary base pairing AT GC Watson Crick existing strands of DNA served as template for the production of new strands o Semiconservative Replication Parental DNA strands separate used as a template Daughter molecules each consist of one old one new strand o Conservative replication Parental molecule serves as template for entirely new strand o Dispersive replication Parental molecule cut into sections Daughter molecules contain old DNA interspersed with new DNA Meselson Stahl s Key Experiment o Showed that each parental DNA is copied in its entirety semi conservative replication DNA Polymerase o Can only work in the 5 to 3 direction dNTP o Monomers that act as substrates in DNA polymerization reaction o Make it an exergonic reaction because of its high potential energy 3 closely packed phosphate group Synthesis is bidirectional replication process begins at a single location in bacterial chromosomes origin of replication o Replication bubble forms in a chromosome that is actively being replicated Helicase catalyzes the breaking of hydrogen bonds between DNA strands separates them unzips SSBPs Attach to separated strands to prevent them from reattaching Topoisomerase cuts rejoins the DNA ahead of the replication fork to relieve tension in the helix due to unwinding DNA polymerase requires a free 3 OH group to start but there isn t one requires a primer to start replication o Primer A few nucleotides possessing free 3 hydroxyl group bond to the template strand o Primase type of RNA polymerase that synthesizes a short RNA segment that serves as primer Leading Strand o Synthesized continuously into the replication fork Lagging Strand o Synthesized discontinuously into the replication fork o Creates short fragments of DNA along strand Okazaki fragments DNA polymerase 1 removes the primer
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