Chemistry 121(001) Winter 2015 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 8:00 - 10:00 am; ThF 9:00 - 10:00 am 1:00 - 2:00 pm. December 19, 2014: Test 1 (Chapters 12-13) January 26 , 2015: Test 2 (Chapters 14-16) February 13, 2015: Test 3 (Chapters 17-19) March 2, 2015: Test 4 (Chapters 20-22 March 3 , 2015: Make Up Exam: Chapters 12-22) Bring Scantron Sheet 882-E CHEM 121 Winter 2015

Chapter 20 and GHW#10 Questions Proteins and Peptides CHEM 121 Winter 2015

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 compunds Zwitterion form R = 20 different alkyl, alcohols, amines , acids and heterocyclic amines CHEM 121 Winter 2015

Handedness/Chirality of Amino Acids CHEM 121 Winter 2015

Groups of Amino Acids based on R group Hydrophobic (non-polar, neutral) Polar, neutral Polar Acidic Polar Basic CHEM 121 Winter 2015

1) Hydrophobic (non-polar, neutral) (5 amino acids) CHEM 121 Winter 2015

1) Hydrophobic (non-polar, neutral) continued.. ( 4 amino acids) G AL VaLI PPerMiT CHEM 121 Winter 2015

2) Hydrophilic (polar, neutral) continued..( 6 amino acids). SeCTAsGulTy CHEM 121 Winter 2015

3) & 4) Polar amino acids (5 amino acids) As Glue Hit Lady Argentina CHEM 121 Winter 2015

Abbreviations glycine Gly G alanine Ala A valine Val V leucine Leu L isoleucine Ile I methionine Met M phenylalanine Phe F tryptophan Trp W Proline Pro P CHEM 121 Winter 2015

Electrically Charged (negative) Electrically Charged (positive) Abbreviations Non Polar             amino acid three letter code single letter code glycine Gly G alanine Ala A valine Val V leucine Leu L isoleucine Ile I methionine Met M phenylalanine Phe F tryptophan Trp W proline Pro P Electrically Charged (negative)       Electrically Charged (positive)             aspartic acid Asp D glutamic acid Glu E lysine Lys K arginine Arg R histidine His H Non Polar Neutral             serine Ser S threonine Thr T cysteine Cys C tyrosine Tyr Y asparagine Asn N glutamine Gln Q CHEM 121 Winter 2015

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

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

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)

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

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?  

Primary protein structure Proteins are polymers made up of amino acids. Peptide bond - how the amino acids are linked together to make a protein. H | H2NCCOOH R H | H2NCCOOH R’ H O | || H2N - C - C - | R H | N - C - COOH | | H R’ + + H2O

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).

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.

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?

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.

Three levels of structure: telephone cord

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

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

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?

Alpha Helix

Alpha Helix

Beta Pleated Sheets

Beta Pleated Sheets

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

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