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Chapter 3: Amino Acids, Peptides, Proteins

Chapter 3: Amino Acids, Peptides, Proteins. HLY-JU-JS-CD. Amino Acids (AA) are the building blocks of peptides and proteins. Peptides generally contain 2-10 AA Polypeptides contain 10-100 AA Proteins contain >100 AA General structure of AA: at pH ~7.4:.

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Chapter 3: Amino Acids, Peptides, Proteins

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  1. Chapter 3: Amino Acids, Peptides, Proteins HLY-JU-JS-CD

  2. Amino Acids (AA) are the building blocks of peptides and proteins • Peptides generally contain 2-10 AA • Polypeptides contain 10-100 AA • Proteins contain >100 AA General structure of AA: at pH ~7.4:

  3. L-Amino Acids are the biologically relevant enantiomer

  4. Of the 20 common AA, 10 of them are considered essential • see page 67 of your book

  5. Of the 20 common AA, 10 of them are considered essential • see page 67 of your book • Mnemonics: MILK FTW RHV • “ESSENTIAL” = cannot be produced de novo by the body • Some AA are conditionally essential • Note though that there are now more than 20 AA! (but we will only focus on the 20)

  6. Selenocysteine is a derivative of Cys used to derive protein structures

  7. The 20 AA can be grouped according to functional classes • Aliphatic (GAVLIMP) • Aromatic (WYF) • Polar, uncharged (CHNQST) • Polar, charged – acidic (DE) • Polar, charged – basic (RK) *Histidine is basic but uncharged See structures on page 70 of your book.

  8. There are 7 AA With Aliphatic Side Chains

  9. Pro is an aliphatic AA with the amino and the acid group in one 5-membered ring

  10. There are 3 AA with Aromatic Side Chains

  11. Of the 6 polar uncharged AA, 2 have Hydroxyl Side Chains (except Tyr)

  12. One AA has a Sulfhydryl (-SH) Side Chain

  13. There are 3 AA With Basic Side Chains, 2 of them ccharged (RK)

  14. Two AA have acidic side chains (DE). Their amide counterparts (NQ) are polar, uncharged

  15. Chemical reactivity of AA are dependent on their “R group” • AA structures and reactivity will be important in understanding protein structures and functions • AA electric charges also affects protein structure and function

  16. Isoelectric point (pI) of an AA (or peptide/protein) is equal to the pH when net charge = 0

  17. Isoelectric point (pI) of an AA (or peptide/protein) is equal to the pH when net charge = 0 pK1: -COOH  -COO- + H+ pK2: -NH3+ -NH2 + H+ pKR: -RH  -R- + H+

  18. AA net charge is (-) if pH > pI, and (+) if pH < pI • pI is estimated to be the AVERAGE of the two pK values representing neutral species.

  19. AA net charge is (-) if pH > pI, and (+) if pH < pI • CASE I: ONLY TWO IONIZABLE GROUPS: Ex. Alanine:

  20. AA net charge is (-) if pH > pI, and (+) if pH < pI Case II: MORE THAN TWO IONIZABLE GROUPS. Ex. Aspartic Acid

  21. Activity, open book/notes BUT no talking (20 points) • Determine the pI of Lysine. Show ALL conformations and the net charges at different pH’s. • Draw the titration curve for Lysine. • Determine the inflection points, and draw the structure/s of Lysine at each interval (i.e., before pK1, at pK1, after pK1 but before pK2, etc.)

  22. AA can link together via AMIDE BOND to form peptides • Two ends are form: amino or N terminus and carboxyl or C terminus • Peptide formation is a condensation reaction (loss of H2O)

  23. AA can link together via AMIDE BOND to form peptides • VIDEO!

  24. Peptides are cleaved via hydrolysis • Acids, bases or enzymes can be used to facilitate the hydrolysis • In our stomach or intestine, peptidases or proteases are present • Enzymes specific to some AA are used for protein analysis (more of this later )

  25. Proteins in our body play different important roles • Biological functions of proteins depend on the AA sequence (central dogma!) • Six major classes of protein functions: • Enzyme • Transport and Storage Proteins • Structural Proteins • Muscle Contraction and Mobility Proteins • Regulatory and Receptor Proteins • Immune or Defense Proteins

  26. There are six major classes of functions of proteins • Catalysts (Enzymes) • Transport & Storage • The largest class of proteins, accelerate rates of reactions DNA Polymerase CK2 Kinase Catalase Ovalbumin Ion channels Hemoglobin Serum albumin

  27. There are six major classes of functions of proteins • Structural • Generate Movement Collagen Keratin Silk Fibroin Actin Myosin

  28. There are six major classes of functions of proteins • Regulation of Metabolism and Gene Expression • Protection Lac repressor Insulin Thrombin and Fibrinogen Venom Proteins Immunoglobulin

  29. Proteins have four levels of structure

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