Chemistry 121 Winter 17
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1 Chemistry 121 Winter 17 Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State) Office: 311 Carson Taylor Hall ; Phone: ; Contact me trough if you have questions Online Tests on Following days December 16, 2016: Test 1 (Chapters 12-13) January 23, 2017 : Test 2 (Chapters 14-16) February 10, 2017 : Test 3 (Chapters 17-19) February 22, 2017 : Test 4 (Chapters 20-22) February 23, 2017: Make Up Exam: Chapters 12-22) 1
2 Chapter 20 and GHW#10 Questions Proteins and Peptides CHEM 121 Winter
3 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
4 Handedness/Chirality of Amino Acids CHEM 121 Winter
5 Groups of Amino Acids (20) based on R group Non-polar, hydrophobic (neutral)(9) Polar, neutral (6) Polar, Acidic (2) Polar, Basic (3) CHEM 121 Winter
6 1) Hydrophobic (non-polar, neutral) (5 amino acids of 9) GA VaLI CHEM 121 Winter
7 1) Hydrophobic (non-polar, neutral) continued.. ( 4 amino acids) ProsPher MinisTry CHEM 121 Winter
8 2) Hydrophilic (polar, neutral) continued..( 6 amino acids). CHEM 121 Winter 2015 See CysT As GluilTy 8
9 3) Polar acidic &Basic (5 amino acids) As Glue Hit Lady Argentina CHEM 121 Winter
10 Abbreviations (non-poar) glycine Gly G alanine Ala A valine Val V leucine Leu L isoleucine Ile I Proline Pro P phenylalanine Phe F methionine Met M tryptophan Trp W CHEM 121 Winter
11 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 proline Pro P phenylalanine Phe F methionine Met M tryptophan Trp W Polar Neutral Abbreviations Polar acidic Electrically Charged (negative) aspartic acid Asp D glutamic acid Glu E Polar acidic &Basic Electrically Charged (positive) histidine His H lysine Lys K arginine Arg R serine Ser S cysteine Cys C threonine Thr T asparagine Asn N glutamine Gln Q tyrosine Tyr Y CHEM 121 Winter
12 1) Give name, abbreviation and types (neutral, polar, nonpolar, basic and acidic). 12
13 1) Give name, abbreviation and types (neutral, polar, nonpolar, basic and acidic). 13
14 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) 14
15 2) Draw the optical and L isomers for: cys. 15
16 3) Use the following amino acids to answer the questions below: a. Which amino acid is polar neutral? b. Which amino acid is the non-polar neutral? c. Which amino acid gives an acidic solution? d. Which amino acid gives a basic solution? 16
17 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 H 2 NCCOOH R + H H 2 NCCOOH R H O H H 2 N - C - C - N - C - COOH R H R + H 2 O 17
18 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). 18
19 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-cysthr. 19
20 5) Use the structure to answer the questions below: Use the structure to answer the questions below ) Which letter arrow points the end of the peptide that is the "amine end-n-terminal? ) Which letter arrow points the end of the peptide that is the "carboxyl" end, C-terminal? ) Which letter arrow points to an amide or peptide bond? 20
21 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. 21
22 Three levels of structure: telephone cord 22
23 Summary of protein structure primary H O H 2 N - C - C R tertiary H O - NH - C - C - R H N - C - COOH H R secondary quaternary 23
24 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 24
25 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? 25
26 Alpha Helix 26
27 Beta Pleated Sheets 27
28 8) Explain the difference between the alpha helix and the beta pleated sheet protein structures. What are the differences in the hydrogen bonding? 28
29 Alpha Helix 29
30 Fibrous Proteins a) - Keratin b) Collagen etc.. 30
31 Beta Pleated Sheets 31
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Amino acids You are required to know and identify the 20 amino acids : their names, 3 letter abbreviations and their structures. If you wanna make any classification in the world, you have to find what