BCMB 230 1st Edition Lecture 4 Outline of Last Lecture I Cells II Plasma Membrane III Membrane Proteins IV Characteristics of Membranes V Membrane Junctions VI Cytoplasm VII Organelles Outline of Current Lecture I Protein Binding Sites II Transcription and Translation III Posttranslational Modification IV Enzymes and Chemical Reactions Current Lecture Protein Structure and Function and Enzymes Protein structure three dimensional structure provides us with binding site I Protein Binding Sites Protein structure three dimensional structure provides us with binding site Binding 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 done Ligand fits into binding site Binding 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 interaction 4 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 and charge 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 and the shape of the protein II Transcription and Translation DNA 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 hand Transcription take DNA copy code onto RNA can turn proteins on and off to regulate transcription Splicing 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 cell Translation 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 faster III Posttranslational Modification Posttranslational 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 high level 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 needed Other posttranslational modification Splitting break protein into two or several pieces changes primary structure as well as the higher levels which changes functions Methylation 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 label Covalent 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 to it 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 activity IV Enzymes and Chemical Reactions enzyme substrate binds to active site simply speeds up rate of reaction can localize reaction by localizing the protein Things that speed up reaction rates increase enzymes increase temperature increase concentration of reactants increase surface area decrease activation energy C6H12O6 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 cell pre transitional Transcription Splicing Translation posttranslational modification splitting methylation glycoslation covalent modification allosteric