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Bio2280 Midterm Notes

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Biochemistry 2280A
Eric Ball

Bio280a Midterm NotesDr Eric Ball Lecture 1 Central DogmaCentral Dogma the way genetic information is stored and retrieved in living cells DNA genotypeRNA phenotypeProteins phenotypeonly protein and some RNAs are the active workers in the cell catalyzing reactions moving things around creating structures etcProteins made from 20 amino acids hereafter aa strung together in long linear polymer chains chains fold and coil in 3D to achieve biological function macromolecules with molecular weight ranging from about 5000 to several million many are biological catalysts enzymes which catalyze a single chemical reaction in the cell but other serve a range of functions most diverse class of macromoleculesLecture 2 Amino Acids properly known as alphaamino acids general structure is NCC backbone amino group on left NH nterminus carboxyl group on right COO cterminus 319 of 20 are amino with same arrangement around alphacarbon praline is imino stereoisomers are possible designated D and Lamino acids Only Lform in proteins net charge is important derived from ionization of weakly acidic or basic groups acidic groupsionization decreases and pH decreases basic groupsionization increases as pH increasesCategories of Amino Acidsnet charge depends on sum of all groups charges Must know the 3letter abbreviation of allAmino Acid Abbreviation Leucine Leu Valine Val Isoleucine Ile Methionine Met Tryptophan Trp Glutamic acid Glu Arginine Arg Histidine His Threonine Thre Tyrosine Tyr Glutamine Gln Asparagine Asn 8 Amino Acids to Memorize Amino Acid Abbreviation PolarNonpolar Side Chains Properties Glycine Gly G Non H smallest Alanine Ala A Non CH3Cysteine Cys C Non CHSH contains sulfur 2Proline Pro P Non CH in a imino acid 2 3ring no hydrogen bonds can form Phenylalanine Phe F Non CHBenzene aromatic2Lysine Lys K Polar basic group basic and CHNH positively2 43charged Aspartic acid Asp D Polar carboxyl acidic and group negatively CHCOO charged 2Serine Ser S Polar hydroxyl uncharged group polar groups CHOH 2only these 20 used to make proteins other aa can be found due to modifications that happen after protein is made allows intro for specialized groups with specific purposes common example phosphorylation of hydroxyl containing aa ser thr and tyr Topic 3 Protein StructurePeptide bondaa connected via kind of amide bond called peptide bond formed between the alpha amino group of one aa and the carboxyl group of another in a condensation reaction individual aa in chain are referred to as amino acid residues water was lost polypeptides elongated at the Cterminus peptide bond is written as a single bond however it is RESONANCE stabilized Six atoms involved are coplanar not free rotation around the CN axis constrains the flexibility of the chain and prevents some folding patternsPrimary sequence of amino acid residues making up the protein involves ONLY covalent bonds peptide bond linking aas together minimum size50 residuesSecondary local folding of the NCC backbone stabilized by ONLY hydrogen bonds between the NH and CO groups two most common structures helix and strandhelix helical arrangement of backbone like a coil spring carbonyl and amino groups are oriented parallel to the axis each carbonyl is hydrogen bonded to an amino group 4 residues further in sequence all groups undergo hydrogen bonding therefore stabilizing cylindrical shape
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