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Chemistry 121(01) Winter 2014

Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State) E-mail: upali@latech.edu Office : 311 Carson Taylor Hall ; Phone: 318-257-4941; Office Hours : MTW 9:00 am - 11:00 am; TR 9:00 - 10:00 am & 1:00-2:00 pm.

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Chemistry 121(01) Winter 2014

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  1. Introduction to Organic Chemistry and Biochemistry Instructor Dr. UpaliSiriwardane (Ph.D. Ohio State) E-mail: upali@latech.edu Office: 311 Carson Taylor Hall ; Phone: 318-257-4941; Office Hours: MTW 9:00 am - 11:00 am; TR 9:00 - 10:00 am & 1:00-2:00 pm. Chemistry 121(01) Winter 2014 December 20, Test 1 (Chapters 12-13) January 27Test 2 (Chapters 14-16) February 14Test 3 (Chapters 17-19) February 26, Test 4(Chapters 20-22) February 27, 2014, Make Up Exam: Bring Scantron Sheet 882-E

  2. Chapter 20 and GHW#10 Questions Proteins

  3. Chapter 20: Proteins

  4. Proteins Naturally occurring bioorganic polyamide polymers containing a sequence of various combinations of 20 amino acids. Amino acids contain the elements carbon, hydrogen, oxygen, and nitrogen and few also contain sulfur Amino acids: Polyfunctional bioorganic compounds Zwitterion form R = 20 different alkyl, alcohols, amines , acids and heterocyclic amines

  5. Handedness/Chirality of Amino Acids

  6. Groups of Amino Acids based on R group • Hydrophobic (non-polar, neutral) • Polar, neutral • Polar Acidic • Polar Basic

  7. 1) Hydrophobic (non-polar, neutral) (5 amino acids)

  8. 1) Hydrophobic (non-polar, neutral) continued..( 4 amino acids)

  9. 2) Hydrophilic (polar, neutral) continued..( 6 amino acids).

  10. 3) & 4) Polar amino acids (5 amino acids)

  11. Abbreviations Nonpolar Amino Acids (hydrophobic) (9 amino acids) • glycine Gly G • alanineAla A • valineVal V • leucineLeu L • isoleucineIle I • ProlinePro P • methionine Met M • phenylalanine Phe F • tryptophan TrpW

  12. Abbreviations Polar (hydrophilic) 6 amino acids

  13. AbbreviationsElectrically charged (5 amino acids) Polar (hydrophilic) Electrically Charged (negative) (acidic) • 1. AsparticAspD • 2. Glutamic GluE Electrically Charged (positive) Basic • 3. lysine Lys K • 4. arginine Arg R • 5. histidine His H

  14. 1) Give name, abbreviation and types (neutral, polar, non-polar, basic and acidic).

  15. 1) Give name, abbreviation and types (neutral, polar, non-polar, basic and acidic).

  16. Protein Function • Enzymes - catalyze biological reactions (alcohol dehydrogenase, glucokinase) • Hormones - signals between cells (insulin, growth hormone) • Storage Proteins- store nutrients (ferritin storing iron in the liver) • Transport Proteins- transport nutrients through the body (hemoglobin transport of oxygen) • Structural Proteins- form structure of cells ( keratin, elastin, collagen) • Protective Proteins- have specific protective function (antibodies bind to foreign proteins)

  17. 2) Draw the optical and L isomers for: cys.

  18. 3) Use the following amino acids to answer the questions below: • Which amino acid is most polar? • b. Which amino acid is most non-polar? • c. Which amino acid gives an acidic solution? • d. Which amino acid gives a basic solution?

  19. Primary protein structure Proteins are polymers made up of amino acids. Peptide bond - how the amino acids are linked together to make a protein. + + H2O

  20. 4) Draw the following:a) Dipeptide bond between ala and asp, and identify C- and N-terminal.b) Tripeptide, ile-cys-thr, and identify N- ( left) and C-terminal(right).

  21. 4) Continued….c) How many possible isomers are in the tripeptide formed with ile, cys and thr? Come up with a formula for linear chain with “ n” amino acids.d) Give the IUPAC name of the tripeptide with the sequence, ile-cys-thr.

  22. 5) Use the structure to answer the questions below: Which letter arrow points the end of the peptide that is the "amine“ end-N-terminal? b) Which letter arrow points the end of the peptide that is the "carboxyl" end, C-terminal? c) Which letter arrow points to an amide or peptide bond?

  23. Which amino acids can we synthesize?

  24. Four levels of protein structure 1) Primary structure The sequence of amino acids in a protein. 2) Secondary structure Way that chains of amino acids are coiled or folded - (-helix, -sheet, random coil). 3) Tertiary structure Way -helix, -sheet, random coils fold and coil. 4) Quaternary structure Way that two or more peptide chains pack together.

  25. Three levels of structure: telephone cord

  26. H O | || H2N - C - C | R H O | || - NH - C - C - | R’ H | N - C - COOH | | H R’’ Summary of protein structure primary secondary quaternary tertiary

  27. 6) Explain the differences between primary, secondary, tertiary, and quaternary protein structures by giving brief definitions of each. What types of bonding are used in each?Primary Secondary Tertiary Quaternary

  28. 7) Use the above structures to answer the questions below: a. Which two amino acids may link in a salt bridge in tertiary protein structure? b. Which two amino acids may link in hydrophobic interactions in tertiary protein structure? c. Which two amino acids may link in hydrogen bonding interactions in tertiary protein structure?

  29. Alpha Helix

  30. Alpha Helix

  31. Beta Pleated Sheets

  32. Beta Pleated Sheets

  33. 8) Explain the difference between the alpha helix and the beta pleated sheet protein structures. What are the differences in the hydrogen bonding?

  34. Fibrous Proteins a) a- Keratin b) Collagen etc..

  35. Interconversion of glycogen, fat, and protein

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