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Amino Acids and the Peptide Bond

Lance Wells Biochemistry & Molecular Biology, CCRC lwells@ccrc.uga.edu All lecture slides and papers for Thursday are available at: http://cell.ccrc.uga.edu/~glycobiology/. Amino Acids and the Peptide Bond. Learning Objectives:. Know your 20 standard AA ’ s

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Amino Acids and the Peptide Bond

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  1. Lance Wells Biochemistry & Molecular Biology, CCRC lwells@ccrc.uga.edu All lecture slides and papers for Thursday are available at: http://cell.ccrc.uga.edu/~glycobiology/ Amino Acids and the Peptide Bond

  2. Learning Objectives: • Know your 20 standard AA’s • Be able to classify based on side chain: ionizable, aliphatic, aromatic, sulfur-containing, polar, non-polar, etc.. • Be able to draw a peptide bond and understand the amide character • Be aware of PTM’s • Appreciate that function of proteins are dictated in large part by side chain properties of AA’s

  3. Central Dogma of Molecular Biology http://www.labgrab.com/users/labgrab/blog/ central-dogma-genetics-incomplete_id%3D904

  4. Four Main Families of Biomolecules in Cells Nucleic Acids (DNA and RNA) Glycans Innate / Genetic Acquired / Metabolic Proteins Lipids Modified from Marth, Nature Cell Biology 10, 1015-16 (2008)

  5. What imparts structure and function to proteins?

  6. Amino Acids:The building blocks of proteins pK2 pK1 a amino acids because of the a carboxylic and a amino groups pK1 and pK2 respectively pKR is for R group pK’s pK1 2.2 while pK2  9.4 In the physiological pH range, both carboxylic and amino groups are completely ionized

  7. Amino acids are Ampholytes They can act as either an acid or a base They are Zwitterions or molecules that have both a positive and a negative charge

  8. Acid - Base properties of amino acids Isoelectric point: the pH where a molecule carries no net electrical charge

  9. Amino acids are the building blocks of proteins • Three major parts: carboxyl group, amino group, and side chain. • Central C atom called alpha carbon. • Amino acids can differ in their side chains (R). • The alpha carbon is a chiral center. (except for one amino acid) • L-form found almost exculsively in proteins (CORN)

  10. + + O R2 O R1 H H3N H3N O- C C OH C C H N H H O R2 O R1 O- C C C N C H H H + H2O Peptide bonds • Proteins are sometimes called polypeptides since they contain many peptide bonds +

  11. + H3N O R2 O R1 O- C C C N C H H H Amide character in the peptide bond • Since the peptide bond is also an amide it also undergoes resonance. • Therefore, peptides are rigid due to resonance around the amide bond, having ≈ 40% double-bond character. • This restricts the rotation due to delocalization of electrons and overlap of the O-C-N  orbitals.

  12. Amino acids can form peptide bonds Amino acid residue peptide units dipeptides tripeptides oligopeptides polypeptides Proteins are molecules that consist of one or more polypeptide chains Peptides are linear polymers that range from ~8 to 4000 amino acid residues How many different naturally occurring amino acids are there in most species encoded by the genome?

  13. Linear arrays of amino acids can make a huge number of molecules Consider a peptide with two amino acids AA1 AA2 20 x 20 = 400 different molecules AA1 AA2 AA3 20 x 20 x 20 = 8000 different molecules For 100 amino acid protein the # of possibilities are: The total number of atoms in the universe is estimated at

  14. Amino Acids If you want to be a protein biochemist you must know (or if you just want to get a good grade on test): Theirnames Theirstructure Theirthree letter code Theirone letter code Their ionization properties Their hydrophobicity and size Their hydrogen bonding properties Their other chemical properties such as ability to be post-translationally modified

  15. Why you need to know your AA’s and their properties?

  16. Which “AA” is not really an “AA” but an imino acid?

  17. Non-polar R-groups tend to be buried in the cores of soluble proteins Myoglobin Blue = non-polar R-group Red = Heme The “Bricks” that make up the hydrophobic core and contribute significantly to folding (hydrophobic interactions)

  18. Polar, non-charged amino acids

  19. Cystine consists of two disulfide-linked cysteine residues Important In Protein Folding And Structure

  20. Beyond 20AA’s for Expanded Functionality -Genetic code (reading stop codons as AA’s—Thursday) Selenocysteine and Pyrrolysine -Post-translational Modifications -Binding of Cofactors (later lectures)

  21. Gene Ultimate Gene Products exon 1 exon 2 exon 3 Functional Diversity Genome Sequencing Genomic DNA RNA-Seq mRNA Traditional Proteomics Protein Functional Proteomics Modified Protein -P -O-GlcNAc -P -Ub -O-GlcNAc -P -O-GlcNAc Transcriptional Regulation Alternative Splicing, Cell Type Specific Expression, etc. Translational Regulation Masking, mRNA Stability etc. Post-translational Regulation Modification by Proteases, O-GlcNAc, Phosphate, Ubiquitin, etc.

  22. Lots, and lots, of PTMs

  23. Post-translational Modification of Amino Acids (just a few examples of impact) Phosphorylation (Typically Ser, Thr, Tyr) gain of charge, binding Glycosylation (Typically Asn, Ser, Thr) solubility, stability, binding Acetylation/Acylation/Methylation (N-term, Lys, Arg) loss of charge, stability Lipidation/prenylation (Typically Cys) membrane anchoring Ubiquitination/Sumoylation (Lys) degradation, signaling

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