BCMB 230 1st Edition Lecture 4 Outline of Last Lecture I.CellsII.Plasma MembraneIII.Membrane ProteinsIV.Characteristics of MembranesV.Membrane JunctionsVI.CytoplasmVII.OrganellesOutline of Current Lecture I.Protein Binding SitesII.Transcription and TranslationIII.Posttranslational ModificationIV.Enzymes and Chemical ReactionsCurrent LectureProtein Structure and Function and EnzymesProtein structure- three dimensional; structure provides us with binding siteI. Protein Binding SitesProtein structure-three dimensional; structure provides us with binding siteBinding site- specifically interacts with a ligand-portion of the protein with two main characterisitics: particular shape and distribution of charge gives it a unique characteristic-something can fit into binding site (called ligands); protein can be a wide variety of things depending on what needs to be doneLigand-fits into binding siteBinding site/ligand interaction -In enzymes, an active site is similar to a binding site, a substrate is similar to a ligand-most of a protein’s actions are due to binding site-ligand interaction4 important qualities of binding site-ligand interaction (lots of things in physiology can be explained by these things):These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.(1)Specificity- ligand has to have the right key for the lock; limited amount of ligands to react with the binding site (can be more than one, but has to be specific) due to the shape andcharge distribution; not just anything can bond(2)Affinity- if it’s going to bond, how easy is it to get that bonding and how long does the bond last (only has a temporary bonding); has to have the right charge distribution. the right shape, and the level of concentration—right charge, right fit, and high concentration gives high affinity(3)Saturation- occurs when all possible binding sites are full—protein is being used to its maximum and can’t work any faster; as ligand concentration goes up below 100% saturation, the saturation is going to go up; leads to a maximal physiological characteristic but can act on it by making proteins; only way to increase the function after saturation is to make more proteins(4)Competition- occurs when there are different ligands (ligands with different shapes); if there is more than one ligand that will fit then there will be more competition; the one with more affinity will be more likely to bond; can be manipulated by changing the concentration or number/shape of protein-Ex. hemoglobin protein with oxygen bonding site; if there is monoxide in the air, it has more affinity so it will bind to the bonding site; adding more oxygen will increase the competition as well as decreasing monoxide; can also change the number of protein andthe shape of the proteinII. Transcription and TranslationDNA is found in the nucleus-gene-section of DNA codes for protein; leads to transcription of DNA to RNA-Exons-sections of DNA that are needed-Introns- sections of DNA not needed for the particular task at handTranscription-take DNA, copy code onto RNA-can turn proteins on and off to regulate transcriptionSplicing-get rid of part of RNA that is not needed (put all the exons together); occurs in the nucleus-can control splicing—can regulate which proteins are in the cellTranslation-take mRNA out of nucleus into the cytoplasm, bind to a ribosome and use code to make protein (polypeptide chain)-if want more a protein, then make translation fasterIII. Posttranslational ModificationPosttranslational modification (of a protein)- changes to a protein once it has been translated from mRNA- put them in the right places, make them wait for a signal to start-splitting- acts on the protein, can occur in the cytoplasm or even outside the cell—can cut off a piece of the protein off to change the primary structure which changes the highlevel of structure (three dimensional shape) which will change how the protein reacts with other things -can turn on/off transcription, splicing, and translation—can stop process at several points if protein is not neededOther posttranslational modification:Splitting-break protein into two or several pieces—changes primary structure as well as the higher levels, which changes functionsMethylation- stick methyl groups at some particular sites; can turn a protein on (make it active); can help that protein get to the right place within the cell (can act like an address label, make sure protein goes where it is supposed to in the cell)Glycosalation- add sugar groups to the protein (make it into a glycoprotein); sugar groups in right places can also make protein active to act as an address labelCovalent modification- manipulation of the shape of the binding site-can only have a single binding site-phosphorylation-have a particular amino acid that can easily have a phosphate attach toit-when molecule is phospholated, it has changes at that site; makes the protein functional; phosphate group comes from ATP-kinase- puts phosphate on (enzyme for phosphorylation)-dephosphorylation-causes shape of binding site to change back, turns protein off-phophatases-takes phosphate off (enzyme for dephosphorylation)Allosteric modifitation- manipulation of binding site-need two different binding sites: functional binding site and regulatory binding site (controls functional binding site shape)-modulator molecule binds to regulatory site, which causes functional binding site to change shape—“turns on”-once modulator molecule leaves, functional binding site goes back to original shape—“turns off”-increase activity of protein by turning protein on-great mechanism for negative feedback-common mechanism for controlling activityIV. Enzymes and Chemical Reactions-enzyme: substrate binds to active site; simply speeds up rate of reaction; can localize reaction by localizing the proteinThings that speed up reaction rates:- increase enzymes-increase temperature-increase concentration of reactants- increase surface area -decrease activation energyC6H12O6+6O26CO2+6H2O +energy (exothermic reaction, release energy) (irreversible-can’t get energy back in)CO2+H2O-><-H2CO3-><-H++HCO3- (reversible reaction) Can use enzymes for both reactions-Carbonic anhydrase- enzyme that catalyzes reaction of carbonic acid (both ways)Review: Mechanisms available to control number and activity of proteins in a