Biol 118 1st EditionExam # 2 Study Guide EnzymesSection 3.4 & Chapter 8.3/8.4- Catalysis: the speeding up of chemical reactionso Most reactions don’t occur fast enough to support life- Enzyme: A protein that functions as a catalysto Best catalysts because of variety of reactive functional groups in amino acids- Substrate: Reactant molecules in a chemical reactionso Lock and Key model: enzymes are a lock and the keys are the substrate that fit into the lock & then reacto 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 flexibleo 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 happeno 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 siteso Transition State Facilitation Inside active site; interactions with R-groups lower activation energyo 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 reactiono Saturation kinetics: some point active sites cannot accept anymore substrate no matter the concentration- pH & temperature affect enzymeso pH: Affects shape & reactivityo 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 shapeo Can inhibit or activateChapter 10- Photosynthesis requires sunlight, carbon dioxide & water glucose, water & oxygeno Oxygen is made as a by-producto Endergonic reaction- Chlorophyll: Absorb red & blue light, transmits green lighto Most effective at driving photosynthesis- Carotenoids: Absorb blue & green light, reflect/transmit yellow, orange & green lighto Pass energy not absorbed from light onto chlorophyll- Light Dependent Reactionso Produces O2 from H2Oo Requires light to functiono Produces ATP & NADPHo Transfers energy from chlorophyll to chlorophyll until it reaches the reaction center- Calvin Cycle Reactions o Does not require lighto Produces sugar from carbon dioxideo 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 lighto Transforms electromagnetic energy into chemical energyo 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 Fixationo 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 RuBPo 1 turn of Calvin cycle= 1 molecule of CO2 fixedo 3 turns= produce one molecule of G3Po Rubisco CO2 fixing enzyme Catalyzes the addition of CO2 to RuBPChapter 15DNA Synthesis- DNA is polar & antiparallel- Has directionalityo One end has exposed hydroxyl group on 3’ end of carbono Other end has an exposed phosphate group on the 5’ carbon- Watson & Crick: secondary structure forms a double helix in antiparallel fashiono Made by complementary base pairing AT & GC- Watson & Crick: existing strands of DNA served as template for the production of new strandso Semiconservative Replication Parental DNA strands separate & used as a template Daughter molecules each consist of one old & one new strando Conservative replication Parental molecule serves as template for entirely new strando Dispersive replication Parental molecule cut into sections Daughter molecules contain old DNA interspersed with new DNA- Meselson & Stahl’s Key Experimento Showed that each parental DNA is copied in its entirety; semi-conservative replication- DNA Polymeraseo Can only work in the 5’ to 3’ direction- dNTPo Monomers that act as substrates in DNA polymerization reactiono 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 inthe helix due to unwinding- DNA polymerase requires a free 3’ OH group to start but there isn’t one requires a primer to start replicationo 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
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