CHAPTER 21: Amino Acids, Proteins, & Enzymes. General, Organic, & Biological Chemistry Janice Gorzynski Smith

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1 CHAPTER 21: Amino Acids, Proteins, & Enzymes General, Organic, & Biological Chemistry Janice Gorzynski Smith

2 CHAPTER 21: Amino Acids, Proteins, Enzymes Learning Objectives: q The 20 common, naturally occurring Amino Acids q stereochemistry q acid/base chemistry q PepFdes q FormaFon q N & C terminals q Proteins q Primary, Secondary, TerFary, Quaternary structure q Hydrolysis and denaturafon q Enzymes q Catalysis q Inhibitors q Zymogens CH 21 Homework: End of Chapter problems: 32, 36, 38, 42, 48, 50, 52, 62, 64, 68, 70, 74, 77, 81, 93, 94 2

3 Amino Acids Definition All amino acids contain two functional groups an amino group (NH 2 ) and a carboxyl group (COOH). Amino acids differ in the R group bonded to the α carbon 3

4 Amino Acids At isoelectric ph The isoelectric point for amino acids is about 6, this is the ph at which the amino acid exists as a neutral molecule The pka of the amine group is usually about 9-11 The pka of the carboxylic acid group is usually about 2-3 4

5 Amino Acids Acid/Base Chemistry 5

6 Amino Acids Stereochemistry Carbohydrates: naturally occurring isomer is the D- isomer (OH group on right in a Fischer projection) Amino Acids: most naturally occurring isomers are the L- isomer (NH3 group on the left in a Fischer projection) 6

7 The 20 common & naturally occurring amino acids in humans. Essential Amino Acids: Isoleucine (Ile) Leucine (Leu) Methionine (Met) Phenylalanine (Phe) Threonine (Thr) Tryptophan (Trp) Valine (Val) Arginine (Arg) Histidine (His) Lysine (Lys) 7

8 Peptides Definition Peptides and proteins are formed when amino acids are joined together by amide bonds. A dipeptide has two amino acids joined together by one amide bond. The amide bond is called a peptide bond. Polypeptides have many amino acids, while proteins have more than 40 amino acids. 8

9 Peptides Amide Bond Formation 9

10 Peptides Amide Bond Formation 10

11 Peptides N & C Terminal Amino Acids The amino acid with the free NH 3 + group is the N-terminal amino acid and is written on the left. The amino acid with the free COO group is the C-terminal amino acid and is written on the right. 11

12 Peptides/ Protein Insulin Gly-Ile-Val-Glu-Gln-Cys-Cys-Thr-Ser-Ile-Cys-Ser-Leu-Tyr-Gln-Leu-Glu-Asn-Tyr-Cys-R Phe-Val-Asn-Gln-His-Leu-Cys-Gly-Ser-His-Leu-Val-Glu-Ala-Leu-Tyr-Leu-Val-Cys-Gly- Glu-Arg-Gly-Phe-Phe-Tyr-Thr-Pro-Lys-Thr-R 12

13 Proteins Primary Structure The primary structure of a protein is the sequence of amino acids joined together by peptide bonds. 13

14 Proteins Secondary Structure The secondary structure is the 3D arrangement of localized regions of a protein. These regions arise due to hydrogen bonding between the N H group of one amide with the C O group of another. 14

15 Proteins Secondary Structure 15

16 Proteins Tertiary Structure The tertiary structure is the 3D shape adopted by the entire peptide chain: Maximize Hydrogen bonding with water (hydrophilic) Stabilize non-polar sidechains by london dispersion forces (hydrophobic) Polar functional groups H-bond with each other Charged sidechains attracted through electrostatic interactions Disulfide bonds form 16

17 Proteins Tertiary Structure 17

18 Proteins Quaternary Structure The quaternary structure of the protein is the shape adopted when two or more folded poly-peptide chains come together into one complex. Ex: Potassium Channel: 18

19 Proteins Quaternary Structure Hemoglobin 19

20 Proteins Quaternary Structure Hemoglobin 20

21 Proteins 1, 2, 3, 4 Structure 21

22 Proteins Peptide Hydrolysis Protein hydrolysis involves breaking the peptide bonds by treatment with aqueous acid, base, or certain enzymes: Pepsin (gastric juices), Trypsin and Chymotrypsin (intestines) 22

23 Proteins Peptide Denaturation Denaturation is the process of altering the shape of a protein without breaking the amide bonds that form the primary structure: heat, acid, base, or agitation 23

24 Enzymes Definition Enzymes are proteins that serve as biological catalysts for reactions in all living organisms. They increase the rate of a reaction (10 6 to times faster), but are unchanged themselves. Enzymes are very specific; each enzyme catalyzes a certain reaction or type of reaction only. The names of most enzymes end with the suffix -ase like peptidase, lipase, and hydrolase A cofactor is a metal ion or an organic molecule needed for an enzyme-catalyzed reaction to occur. 24

25 Enzymes Function hup://leavingbio.net/enzymes.htm 25

26 Enzymes Conformational Changes Upon Binding hup://plantcellbiology.masters.grkraj.org/html/plant_cell_biochemistry_and_metabolism1- Proteins_And_Enzymes.htm 26

27 Enzymes Inhibition hup://o.quizlet.com/i/wrlw8kdwldoy1yzbedkgya_m.jpg 27

28 Enzymes HIV Protease Inhibitor Protease inhibitors are designed to mimic a peptide linkage (-NH-CO-) but replaces the linkage with a CH 2 -CH(OH)- which binds to the active site but the protease cannot cleave a linkage so it stays bound. Saquinavir: hup://en.wikipedia.org/wiki/discovery_and_development_of_hiv- protease_inhibitors 28

29 Enzymes Lipoxygenase Inhibitor Zileuton is an asthma maintenance medication that inhibits 5-lipoxygenase, therefore, inhibiting leukotriene formation. hup://en.wikipedia.org/wiki/zileuton 29

30 Enzymes Differences in Binding Sites Superoxide Dismutase: SOD Hydrophobic Binding Pocket Superoxide Reductase: SOR Hydrophilic Binding Pocket 30

31 Enzymes Mechanistic Differences: SOR vs SOD OH O 2 - O Asp Fe III O 2 - H + O 2 SOD Mechanism O Asp OH Fe III O Asp OH 2 Fe II SOR Mechanism HOOH H + 2H + O Asp OH 2 Fe II O 2 - H 2 O * O 2 - hydrogen bonds to residues in secondary coordination sphere, positioning it near Fe(II), O 2 - His N N S Cys II Fe O 2, H + His His N N HO OH S Cys III Fe O e HOOH His His N N H 2 O S Cys III Fe OH RCO 2 OH Glu 14 CO 2, H + H 2 O His His N N O S Cys III Fe O Glu 14 31

32 Enzymes Zymogens 32

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