1 Announcements & Agenda (04/23/07) Pick Up Grade Sheets Exam 3 back later this week Class in VWF 102 on Wed! Today Amino acids ( ) Amino acids ( ) Peptides (16.4) Peptides (16.4) Protein Structure (16.5) Protein Structure (16.5)

2 I Thought Exam 3 was… 1.Piece of Cake 2.Easier than I Expected 3.Mostly What I Expected 4.Much Harder than I Expected 5.Uh Oh…

3 Ch 16: Amino Acids, Proteins, & Enzymes! Baaaaaa…….

4 Functions of Proteins Proteins perform many different functions in the body. Proteins perform many different functions in the body. Function of proteins determined by amino acids used and how they are put together in 2-D and 3-D

5 Proteins are made of Amino Acids 20 Amino acids are the building blocks of proteins.are the building blocks of proteins. contain a carboxylic acid group and an amino group on the alpha (  ) carbon.contain a carboxylic acid group and an amino group on the alpha (  ) carbon. are ionized in solution.are ionized in solution. each contain a different side group (R).each contain a different side group (R). R side chain R R side chain R │ + │ │ + │ H 2 N—C —COOH H 3 N—C —COO − │ │ │ │ H H ionized form H H ionized form

6 must be obtained from the diet.must be obtained from the diet. not synthesized by the body.not synthesized by the body. are in meat and diary products.are in meat and diary products. are missing (one or more) in grains and vegetables.are missing (one or more) in grains and vegetables. “Essential” Amino Acids

7 Types of Amino Acids 4 main kinds: nonpolar (hydrophobic) with hydrocarbon side chains.nonpolar (hydrophobic) with hydrocarbon side chains. polar (hydrophilic) with polar or ionic side chains.polar (hydrophilic) with polar or ionic side chains. acidic (hydrophilic) with acidic side chains.acidic (hydrophilic) with acidic side chains. basic (hydrophilic) with –NH 2 side chains.basic (hydrophilic) with –NH 2 side chains. Nonpolar Polar Acidic Basic Be able to recognize these 4 kinds, no need to memorize all 20 for the Final Exam!!!!!!!!!!!!!!!!!

8 Nonpolar Amino Acids An amino acid is nonpolar when the R group is H, alkyl, or aromatic.

9 Polar Amino Acids An amino acid is polar when the R group is an alcohol, thiol, or amide.

10 Acidic & Basic Amino Acids An amino acid is acidic when the R group is a carboxylic acid.acidic when the R group is a carboxylic acid. basic when the R group is an amine.basic when the R group is an amine.

11 Fischer Projections of Amino Acids are chiral except glycineare chiral except glycine have Fischer projections that are stereoisomers.have Fischer projections that are stereoisomers. ONLY “L” amino acids used in proteins.ONLY “L” amino acids used in proteins. L-Alanine D-Alanine L-Cysteine D-Cysteine L-Alanine D-Alanine L-Cysteine D-Cysteine CH 2 SH H 2 NH COOH CH 2 SH HNH 2 COOH CH 3 HNH 2 COOH CH 3 H 2 NH COOH

12 A zwitterion has charged −NH 3 + and COO – groups.has charged −NH 3 + and COO – groups. forms when both the –NH 2 and the –COOH groups in an amino acid ionize in water.forms when both the –NH 2 and the –COOH groups in an amino acid ionize in water. has equal + and – charges at the isoelectric point (pI).has equal + and – charges at the isoelectric point (pI). O O O O ║ + ║ ║ + ║ NH 2 —CH 2 —C—OH H 3 N—CH 2 —C—O – glycine zwitterion of glycine glycine zwitterion of glycine Zwitterions

13 pH and ionization H + OH – H + OH – + + H 3 N–CH 2 –COOH H 3 N–CH 2 –COO – H 2 N–CH 2 –COO – positive ion zwitterion negative ion low pH pI high pH

Formation of Peptides Formation of Peptides

15 The Peptide Bond is an amide bond.is an amide bond. forms between the carboxyl group of one amino acid and the amino group of the next amino acid.forms between the carboxyl group of one amino acid and the amino group of the next amino acid. O CH 3 O O CH 3 O + || + | || + || + | || H 3 N—CH 2 —C—O – + H 3 N—CH—C—O – O H CH 3 O O H CH 3 O + || | | || + || | | || H 3 N—CH 2 —C—N—CH—C—O – peptide bond peptide bond

16 Formation of a Dipeptide

17 Naming Dipeptides (Tri… etc.) (NO NEED TO MEMORIZE NAMING RULES) A dipeptide is named from the free amine (NH 3 + ) using a - yl ending for the name.is named from the free amine (NH 3 + ) using a - yl ending for the name. names the last amino acid with the free carboxyl group (COO - ) by its amino acid name.names the last amino acid with the free carboxyl group (COO - ) by its amino acid name.

18 Tour of Protein Structure…

19 Primary Structure of Proteins sequence of amino acidssequence of amino acids different proteins have different sequencesdifferent proteins have different sequences the backbone of a peptide chain or protein.the backbone of a peptide chain or protein. Ala─Leu ─ Cys ─ Met

20 Oxytocin (pitocin) V. du Vigneaud Nobel prize in chemistry 1955 Uterine contracting and milk letdown hormone

21 Primary Structures The nonapeptides oxytocin and vasopressin have similar primary structures.The nonapeptides oxytocin and vasopressin have similar primary structures. Only the amino acids at positions 3 and 8 differ.Only the amino acids at positions 3 and 8 differ.

22 Primary Structure of Insulin Insulin was the first protein to have its primary structure determined.was the first protein to have its primary structure determined. has a primary structure of two polypeptide chains linked by disulfide bonds.has a primary structure of two polypeptide chains linked by disulfide bonds. has a chain A with 21 amino acids and a chain B with 30 amino acids.has a chain A with 21 amino acids and a chain B with 30 amino acids.

23 Modification of insulin

24 Newer drugs for diabetics m m m m view/ /38/ view/ /38/ Glitazone htm htm htm

25 Insulin can be administered by… 1.Inhalation 2.Injection 3.oral

26 Secondary Structure Elements a 3-D arrangement of amino acids in a polypeptide chain.a 3-D arrangement of amino acids in a polypeptide chain. result from intermolecular forces such as hydrogen bondingresult from intermolecular forces such as hydrogen bonding Several types of secondary structureSeveral types of secondary structure Alpha helices Alpha helices Beta sheets Beta sheets Triple helices Triple helices

27 Beta Pleated Sheet polypeptide chains side by side.polypeptide chains side by side. hydrogen bonds between chains.hydrogen bonds between chains. has R groups above and below the sheet.has R groups above and below the sheet. is typical of fibrous proteins such as silk.is typical of fibrous proteins such as silk.

28 Secondary Structure – Triple Helix The secondary structure of a triple helix is The secondary structure of a triple helix is three polypeptide chains woven together.three polypeptide chains woven together. typical of collagen, connective tissue, skin, tendons, and cartilage.typical of collagen, connective tissue, skin, tendons, and cartilage.

29 Tertiary Structure overall 3-D shape.overall 3-D shape. determined by attractions & repulsions between side chains of amino acidsdetermined by attractions & repulsions between side chains of amino acids

30 Crosslinks in Tertiary Structures involve attractions and repulsions between the side chains of the amino acids in the polypeptide chain.

31 Quaternary Structure combination of 2 or more protein units.combination of 2 or more protein units. Example: hemoglobin consists of 4 subunits.Example: hemoglobin consists of 4 subunits. stabilized by the same interactions found in tertiary structures.stabilized by the same interactions found in tertiary structures.

32 Summary of Protein Structure

33 the disruption of bonds in the secondary, tertiary and quaternary protein structures.the disruption of bonds in the secondary, tertiary and quaternary protein structures. heat and organic compounds: break apart H bonds and disrupt hydrophobic interactions.heat and organic compounds: break apart H bonds and disrupt hydrophobic interactions. acids and bases: break H bonds between polar R groups and disrupt ionic bonds.acids and bases: break H bonds between polar R groups and disrupt ionic bonds. heavy metal ions: react with S-S bonds to form solids (among many other things)heavy metal ions: react with S-S bonds to form solids (among many other things) agitation such as whipping that stretches peptide chains until bonds break.agitation such as whipping that stretches peptide chains until bonds break. Denaturation

34 cooking.cooking. the skin is wiped with alcohol.the skin is wiped with alcohol. heat is used to cauterize blood vessels.heat is used to cauterize blood vessels. instruments are sterilized in autoclaves.instruments are sterilized in autoclaves. Applications of Denaturation