Biochemistry-Notes.pdf

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Department
Biochemistry
Course
Biochemistry 2280A
Professor
Verena Brand
Semester
Fall

Description
Topic 1 The Central DogmaTuesday September 10 2013948 AMOther admin notesJudy Penchuck MLB C5 This week 912 and 24Lecture Notes912 25What is biochemistrybiochem2280TAuwocaThe application of chemistry to the bio of our bodyCourse book 20Allows us to understand why a tissue acts the way it does how does the cell perform its function in a Midterm Saturday oct 26 710specific tissueMolecules of lifeProteinsCentral dogmaAmino acidsProtein structureEnzyme catalysisProtein purificationLipidsCarbohydratesNucleic acidsWhat is dogmaDogma is an established belief or doctrine it is authoritative and not to be disputed doubted or diverged fromShould have a very good scientific basisThe central dogmaDNA should be duplicable Modifications to the dogmaEpigeneticsChromatin has a very important role in the expression of DNAMicro RNAsLittle pieces of RNA that will bind to the sense strand and block transcription Post translational modificationMods with phosphate acetyl methyl groups attached to pns to regulate availability of pns for its functionGenotypeThe sum of inheritable potentialPhenotypeThe sum of observable characteristicsTherefore defects in DNA can lead to defects in pnslead to problemsGenotype vs Phenotype Can you have an 8packOnly of you have the right genotype Totally irrelevant Biochemistry Page 1 Topic 2 Amino AcidsTuesday September 24 2013438 PMThey are the building blocks of pnsGeneral structureAmino group carboxyl group hydrogen and R groupSince 4 different groups are attached to a carbon atom stereoisomerismis possibleOnly the Lforms are incorporated into pnsThey have a net chargederived from the ionization of weakly acidic or basic groupsChanges has the H changes because of the association of hydrogen ions with the groupsRecall that for a weak acidThis equilibrium is characterized by a constant Ka for each individual groupCalculating Net ChargeIn low pHAmino and carboxyl groups both protonated 2 Neutral pHCarboxyl group is deprotonated 1 but the amino group is still protonated with a charge of 1 so the net charge would be 0High pHBoth amino group and the carboxylic acid are deprotonated where the amino group would be 0 and the carboxylic acid would be 1 so the net charge is 1At pHpKa 50 of the COOH or NHgroup will be ionized3We will assume that an aa is in soln of pH2pKa this means that 50 of the carboxylic groups are will be protonatedProtonated ca group has charge of 0Deprotonated ca group has charge of 1Total charge of ca groups05005105If the pH of the soln is 2 or more pH units more acidic 100 of the COOH will be protonated 100Recall that if there are 100X more protons at pH 0 than at pH 2 the ratio of COOHCOOwill be 1001In terms ofthis means that there will be 100101 or 99 COOH and 1 COO We assume 100 COOH for simplicityIf the pH of the soln is 2 or more pH units less acidic 100 of the COOH will be deprotonated1111 pH unitmore acidic the pKaThere are 10X more protons at pH 1 than pH 290 COOH10 COO090011011 pH unit less acidic than the pKa10X less protons 90COO10COOH09101009This is the same for the amino groupexact same calculationsCategories of Amino Acids Biochemistry Page 2 The properties of the side chain determine a pns characterHydrophobichydrophilic charged or unchargedPhysical sizeAbility to form hydrogen bondsKnow the followingWhile only these 20 aa are used to make pns other aa are possible as a result of modifications that happen after the pn is made this often changes the properties of that pnPhosphorylation of hydroxylcontaining aa ser and thr and tyr Biochemistry Page 3
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