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Lecture 3

Biochemistry 2EE3 Lecture 3.docx

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Karen Mc Garry

Biochemistry 2EE3 Lecture 3 • • Number of amino acids is much larger than 20 • Properties of amino acids constrict 3D structure of proteins • • • Amino: NH2group • Acetyl: COOH group • Alpha carbon • Hydrogen • Amino acids different due to different R groups • Physiological pH = 7 • NH2, COOH can be ionized = ionisable groups • Electrostatic forces works at a larger distance than VDW, therefore especially important o Charge is therefore important • At physiological pH, amino acids are zwitterions • • Catalyst required • CO/NH no longer ionized – there are partial charges, but no complete charges • Therefore only the ends are ionized, not groups in the peptide • Number of amino acids in proteins change – varies from 50 to tens of thousands • • Memorize this and structures of amino acids • Try flash cards • Do not know one letter code • Know that each capital letter in word designates amino acid • • Do not need to know this diagram – merely need to understand properties of amino acid from structure • • Non-polar due to no polar groups • Tryptophan does have a polar group (NH) but it is large, therefore non-polar properties win out • Glycine is smallest • Most are chiral, but glycine is not due to two identical groups • Amino acids are tested for importance by substituting them and seeing if properties of protein change • Sulphur in methionine is not polar • Tryptophan is conserved in amino acids – usually does not change in various organisms • Proline encourages kinks in the polypeptide chain • Space-filling diagrams: nitrogen = blue, oxygen = red, hydro
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