UMass Amherst BIOLOGY 285 - Bio 285 SI Before Exam 2 (5 pages)

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Bio 285 SI Before Exam 2



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Bio 285 SI Before Exam 2

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Pages:
5
School:
University of Massachusetts Amherst
Course:
Biology 285 - Cellular & Molecular Biology
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Bio 285 SI Before Exam 2 March 6 Mechanism of Enzyme Function Q What do enzymes do to a reaction energy of the graph o They lower the activation energy and the transition state o Peak of graph is transition state lowers o Speeds up rate of reaction Enzymes are catalysts Do we change free energy of reactants and products NO If energy of the reactants is higher than products exergonic o Released energy so molecule is STABLE If energy of products is higher than reactants endergonic o Considered UNSTABLE Enzymes take a substrate form a complex then switch substrate into product then release product o 3 ways to do this Enzyme binds to 2 substrate molecules and orients them precisely to encourage a reaction to occur between them Binding of substrate to enzyme rearranges electrons in the substrate creating partial negative and positive charges that favor a reaction Enzyme strains the bound substrate molecule forcing it toward a transition state to favor a reaction o Enzyme with substrate has higher binding affinity b c wants to let product go needs to hold onto substrate to be able to turn it into product Q pull down assay effective way to look for substrates o Reaction takes a long time so by that time substrate would be product so not useful Enzymes lower the activation energy of a chemical reaction Allostery Regulation of Enzyme Protein Function Allostery when something other than the substrate binds to somewhere other than the active site causes conformational change o Activate enzyme or inhibit enzyme When allosteric enzyme binds changes shape function o Can be positive or negative Ex Hemoglobin o When one molecule of O2 binds to a hem group changes conformation of the other 3 hem groups which then have a higher affinity to O2 Post translational modifications you modifying the protein after protein has been created o Phosphorylation ubiquitination methylation acetylation Post translational modify RTK through phosphorylation Nucleotide binding hydrolysis can lead to different conformational and active states Hydrolyze GTP to GDP use GAP inactive Kick out GDP to put GTP in use GEF active General Principles of Cell Signaling Signal Transduction Cell is always receiving signals survive grow divide differentiate If cell doesn t receive a signal dies programmed cell death apoptosis Cannot grow human cells in labs b c need to be able to tell it to SURVIVE all the time Two general outcomes for cell signaling when dealing with proteins o Changing level of proteins slower o Changing the existing function of an existing protein faster b c don t need to go through transcription translation etc more time to synthesize more proteins Activating Receptor Tyrosine Kinases RTKs draw pathway out over and over until known by heart RTKs involved in both growth pathways survival pathways How activate RTKs Two subunits of RTK separated Signal molecules that forms a dimer dimerization two subunits come together and form a functional unit o Intrinsic kinase activity activated kinase activity stimulated b c dimerized o Add phosphates through cross phosphorylation o no keys can t start car car can t move no gas car can start car can t move difference is car CAN start in second scenario If can t phosphorylate the sites dimerization can happen because phosphorylation happens after dimerization If can t dimerize can t phosphorylate because dimerize happens before phosphorylation o Adding phosphates to tyrosine on receptors causes receptors to be active o Then other molecules proteins bind to those phosphorylated tyrosines for pathway to happen These proteins have SH2 domain SH2 domain binds only to phosphotyrosine residues will NOT bind to any other amino acid o Then go onto the Ras pathway Mechanism of Ras Signaling Continues from above Adaptor protein Grb2 binds to a phosphorylated tyrosine Ras activating protein SOS binds to Grb2 Grb2 activates Ras activating protein Ras activating protein looks for an inactive Ras protein Kicks out GDP in inactive Ras allows for GTP to bind in Ras to become active acts as a GEF Ras now active goes to find a MapKKK kinase Activates MapKKK MapKKK goes and activates MapKK by exchanging an ATP for an ADP needs 2 phosphates get one phosphate from ATP and already had a phosphate MapKK goes and activates MapK by exchanging an ATP for and ADP needs 2 phosphates get one phosphate from ATP and already had a phosphate o MapKKK is different than MapKK is different than MapK NOT the same kinase at all o Activating each other Map kinase cascade MapK goes and activates protein X and protein Y OR transcription regulated A and transcription regulator B by giving them phosphates o Proteins X and Y cause a change protein activity o Transcription factors A and B cause a change gene expression Survival Signal Pathway that go through RTK End game is to prevent cell death apoptosis Get a signal that causes dimerization that causes cross phosphorylation for receptor Tyrosines phosphorylated PI3 kinase binds to phosphotyrosines has an SH2 domain PI3 kinase activates inositol phospholipid by adding another phosphate to it goes from 2 phosphates to 3 phosphates active Phosphorylated inositol phospholipid now has 3 phosphates creates a binding site for AKT and protein kinase 1 Protein kinase 1 attached to inositol phospholipid and AKT attached to another active 3 phosphates inositol phospholipid o Need 2 binding sites 1 for AKT and 1 for protein kinase 1 Protein kinase 1 and protein kinase 2 another protein kinase add a phosphate to AKT to make it active need 5 phosphates to be active shares 3 phosphates with inositol phospholipid when binds to it gets 2 more phosphates from protein kinase 1 1 and protein kinase 2 1 Once add two phosphates to AKT AKT disassociates from inositol phospholipid and goes to target Bad o Bad inhibits Bcl2 cell death causes Bcl2 to not do its function cell going to die Bad active when bound to Bcl2 Bcl2 inactive when bound to Bad o Bcl2 inhibits cell death no cell death o o AKT phosphorylates adds 1 Bad changes conformation of it and that causes Bad to release Bcl2 causes Bad to become inactive causes Bcl2 to become active Inactivated Bad goes off Bcl2 now active so goes to cause cell death Q can t add a phosphate to AKT can t activate what happens o CELL DEATH Q overactive Bcl2 what happens o Too much cell survival not good for cell b c cancer Always going to be Bad Bcl2 complex in cells lot of them try to phosphorylate as many Bads as you can until you reach a threshold


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