Levels of Protein Structure Chapter 16 Amino Acids, Proteins, and Enzymes Copyright © 2009 by Pearson Education, Inc.

2 Primary Structure of Proteins The primary structure of a protein is the particular sequence of amino acids. the backbone of a peptide chain or protein. Ala─Leu ─ Cys ─ Met

3 Primary Structures The nonapeptides oxytocin and vasopressin have similar primary structures. Only the amino acids at positions 3 and 8 differ. Copyright © 2009 by Pearson Education, Inc.

4 Primary Structure of Insulin Insulin was the first protein to have its primary structure determined. 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.

5 Secondary Structure–Alpha Helix The secondary structure of an alpha helix is a three-dimensional spatial arrangement of amino acids in a polypeptide chain. held by H bonds between the H of –N-H group and the O of C=O of the fourth amino acid down the chain. a corkscrew shape that looks like a coiled “telephone cord.” Copyright © 2009 by Pearson Education, Inc.

6 Secondary Structure–Beta-Pleated Sheet The secondary structure of a beta-pleated sheet consists of polypeptide chains arranged side by side. has hydrogen bonds between chains. has R groups above and below the sheet. is typical of fibrous proteins, such as silk.

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

8 Indicate the type of protein structure. 1) primary 2) alpha helix 3) beta-pleated sheet 4) triple helix A. polypeptide chains held side by side by H bonds B. sequence of amino acids in a polypeptide chain C. corkscrew shape with H bonds between amino acids D. three peptide chains woven like a rope Learning Check

9 Indicate the type of protein structure. 1) primary 2) alpha helix 3) beta-pleated sheet 4) triple helix A. 3 polypeptide chains held side by side by H bonds B. 1 sequence of amino acids in a polypeptide chain C. 2 corkscrew shape with H bonds between amino acids D. 4 three peptide chains woven like a rope Solution

10 must be obtained from the diet. are 10 amino acids not synthesized by the body. are in meat and dairy products. are missing (one or more) in grains and vegetables. Essential Amino Acids Essential amino acids

11 Tertiary Structure The tertiary structure of a protein is an overall 3- dimensional shape. is determined by attractions and repulsions between the side chains of the amino acids in a peptide chain.

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

13 Select the type of tertiary interaction. 1) disulfide2) ionic 3) H bonds4) hydrophobic A. leucine and valine B. two cysteines C. aspartic acid and lysine D. serine and threonine Learning check

14 Select the type of tertiary interaction. 1) disulfide2) ionic 3) H bonds4) hydrophobic A. 4 leucine and valine B. 1 two cysteines C. 2 aspartic acid and lysine D. 3 serine and threonine Solution

15 Globular Proteins Globular proteins have compact, spherical shapes. carry out synthesis, transport, and metabolism in the cells. such as myoglobin store and transport oxygen in muscle. Copyright © 2009 by Pearson Education, Inc. Myoglobin

16 Quaternary Structure The quaternary structure is the combination of two or more protein units. of hemoglobin consists of four polypeptide chains as subunits. is stabilized by the same interactions found in tertiary structures. Copyright © 2009 by Pearson Education, Inc.

17 Fibrous Proteins Fibrous proteins consist of long, fiber-like shapes. such as alpha keratins make up hair, wool, skin, and nails. such as feathers contain beta keratins with large amounts of beta-pleated sheet structures.

18 Summary of Protein Structure

19 Summary of Protein Structure

20 Identify the level of protein structure. 1) primary2) secondary 3) tertiary 4) quaternary A. beta-pleated sheet B. order of amino acids in a protein C. a protein with two or more peptide chains D. the shape of a globular protein E. disulfide bonds between R groups Learning Check

21 Identify the level of protein structure. 1) primary2) secondary 3) tertiary 4) quaternary A. 2 beta-pleated sheet B. 1 order of amino acids in a protein C. 4 a protein with two or more peptide chains D. 3 the shape of a globular protein E. 3 disulfide bonds between R groups Solution

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

23 Denaturation of protein occurs when an egg is cooked. the skin is wiped with alcohol. heat is used to cauterize blood vessels. instruments are sterilized in autoclaves. Applications of Denaturation Copyright © 2009 by Pearson Education, Inc.

24 Tannic acid is used to form a scab on a burn. An egg is hard boiled by placing it in boiling water. What is similar about these two events? Learning Check

25 Acid and heat cause the denaturation of protein. They both break bonds in the secondary and tertiary structures of proteins. Solution

26 Chapter 16 Amino Acids, Proteins, and Enzymes 16.6 Enzymes 16.7 Enzyme Action

27 Enzymes are Biological Catalysts Enzymes are proteins that Catalyze nearly all the chemical reactions taking place in the cells of the body. Increase the rate of reaction by lowering the energy of activation.

28 The name of an enzyme usually ends in –ase. identifies the reacting substance. For example, sucrase catalyzes the reaction of sucrose. describes the function of the enzyme. For example, oxidases catalyze oxidation. could be a common name, particularly for the digestion enzymes, such as pepsin and trypsin. Names of Enzymes

29 Enzymes are classified by the reaction they catalyze. ClassType of Reactions Catalyzed OxidoreductasesOxidation-reduction TransferasesTransfer groups of atoms Hydrolases Hydrolysis LyasesAdd atoms/remove atoms to or from a double bond IsomerasesRearrange atoms LigasesUse ATP to combine small molecules Classification of Enzymes

30 Match the type of reaction with an enzyme. 1) aminase2) dehydrogenase 3) isomerase4) synthetase A. Converts a cis-fatty acid to a trans-fatty acid. B. Removes 2 H atoms to form double bond. C. Combines two molecules to make a new compound. D.Adds NH 3. Learning Check

31 Match the type of reaction with an enzyme 1) aminase2) dehydrogenase 3) isomerase4) synthetase A. 3 Converts a cis-fatty acid to a trans-fatty acid. B. 2 Removes 2 H atoms to form double bond. C. 4 Combines two molecules to make a new compound. D. 1 Adds NH 3. Solution

32 The active site is a region within an enzyme that fits the shape of the reacting molecule called a substrate. contains amino acid R groups that bind the substrate. releases products when the reaction is complete. Active Site

33 Enzyme-Catalyzed Reaction In an enzyme-catalyzed reaction a substrate attaches to the active site. an enzyme-substrate (ES) complex forms. reaction occurs and products are released. an enzyme is used over and over. E + S ES E + P

34 Lock-and-Key Model In the lock-and-key model, the active site has a rigid shape. enzyme only binds substrates that exactly fit the active site. enzyme is analogous to a lock. substrate is the key that fits that lock. Copyright © 2009 by Pearson Education, Inc.

35 Induced-Fit Model In the induced-fit model enzyme structure is flexible, not rigid. enzyme and substrate adjust the shape of the active site to bind substrate. the range of substrate specificity increases. shape changes improve catalysis during reaction. Copyright © 2009 by Pearson Education, Inc.

36 Example of an Enzyme-Catalyzed Reaction

37 Learning Check A. The active site is (1) the enzyme (2) a section of the enzyme (3) the substrate B. In the induced-fit model, the shape of the enzyme when substrate binds (1) stays the same (2) adapts to the shape of the substrate

38 Solution A.The active site is (2) a section of the enzyme B. In the induced-fit model, the shape of the enzyme when substrate binds (2) adapts to the shape of the substrate

39 Diagnostic Enzymes Diagnostic enzymes determine the amount of damage in tissues. that are elevated may indicate damage or disease in a particular organ.

40 Diagnostic Enzymes Levels of enzymes CK, LDH, and AST are elevated following a heart attack. are used to determine the severity of the attack. Copyright © 2009 by Pearson Education, Inc.

41 Isoenzymes catalyze the same reaction in different tissues in the body. can be used to identify the organ or tissue involved in damage or disease. such as lactate dehydrogenase (LDH), which converts lactate to pyruvate, consists of five isoenzymes. such as LDH have one form more prevalent in heart muscle and another form in skeletal muscle and liver.

42 Isoenzymes Copyright © 2009 by Pearson Education, Inc.

43 Chapter 16 Amino Acids, Proteins, and Enzymes 16.8 Factors Affecting Enzyme Activity

44 Enzymes are most active at an optimum temperature (usually 37 °C in humans). show little activity at low temperatures. lose activity at high temperatures as denaturation occurs. Temperature and Enzyme Action

45 Enzymes are most active at optimum pH. contain R groups of amino acids with proper charges at optimum pH. lose activity in low or high pH as tertiary structure is disrupted. pH and Enzyme Action

46 Optimum pH Values Enzymes in the body have an optimum pH of about 7.4. certain organs operate at lower and higher optimum pH values.

47 Substrate Concentration As substrate concentration increases, the rate of reaction increases (at constant enzyme concentration). the enzyme eventually becomes saturated, giving maximum activity.

48 Sucrase has an optimum temperature of 37 °C and an optimum pH of 6.2. Determine the effect of the following on its rate of reaction. 1) no change 2) increase 3) decrease A. Increasing the concentration of sucrose B. Changing the pH to 4 C. Running the reaction at 70 °C Learning Check

49 Sucrase has an optimum temperature of 37 °C and an optimum pH of 6.2. Determine the effect of the following on its rate of reaction. 1) no change 2) increase 3) decrease A. 2 Increasing the concentration of sucrase B. 3 Changing the pH to 4 C. 3 Running the reaction at 70 °C Solution

50 Inhibitors are molecules that cause a loss of catalytic activity. prevent substrates from fitting into the active sites. E + SESE + P E + I EI no P Enzyme Inhibition

51 Competitive Inhibition A competitive inhibitor has a structure that is similar to that of the substrate. competes with the substrate for the active site. has its effect reversed by increasing substrate concentration.

52 A noncompetitive inhibitor has a structure that is much different than the substrate. distorts the shape of the enzyme, which alters the shape of the active site. prevents the binding of the substrate. cannot have its effect reversed by adding more substrate. Noncompetitive Inhibition Copyright © 2009 by Pearson Education, Inc.

53 Identify each description as an inhibitor that is 1) competitive or 2) noncompetitive. A. Increasing substrate reverses inhibition. B. Binds to enzyme surface, but not to the active site. C. Structure is similar to substrate. D. Inhibition is not reversed by adding more substrate. Learning Check

54 Identify each description as an inhibitor that is 1) competitive or 2) noncompetitive. A. 1 Increasing substrate reverses inhibition. B. 2 Binds to enzyme surface, but not to the active site. C. 1 Structure is similar to substrate. D. 2 Inhibition is not reversed by adding more substrate. Solution

Enzyme Cofactors Chapter 16 Amino Acids, Proteins, and Enzymes

56 Function of Coenzymes A coenzyme prepares the active site for catalytic activity.

57 Water-Soluble Vitamins Water-soluble vitamins are soluble in aqueous solutions. cofactors for many enzymes. not stored in the body. Copyright © 2009 by Pearson Education, Inc.

58 Fat-Soluble Vitamins Fat-soluble vitamins are A, D, E, and K. are soluble in lipids, but not in aqueous solutions. are important in vision, bone formation, antioxidants, and blood clotting. are stored in the body.

59 Learning Check Identify each compound as a 1) water-soluble vitamin or 2) fat-soluble vitamin. A. Folic acid B. Retinol (vitamin A) C. Vitamin C D. Vitamin E E. Niacin

60 Solution Identify each compound as a 1) water-soluble vitamin or 2) fat-soluble vitamin. A. 1 Folic acid B. 2 Retinol (vitamin A) C. 1 Vitamin C D. 2 Vitamin E E. 1 Niacin

61 Thiamin (Vitamin B 1 ) Thiamin was the first B vitamin identified. is part of the coenzyme thiamin pyrophosphate (TPP), required in the decarboxylation of  -keto carboxylic acids. deficiency results in beriberi (fatigue, weight loss, and nerve degeneration). Copyright © 2009 by Pearson Education, Inc.

62 Riboflavin (Vitamin B 2 ) Riboflavin is made of the sugar alcohol ribitol and flavin. part of the coenzymes flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN). needed for good vision and healthy skin. N NN N HH 3 C H 3 C CH 2 CHCHCHCH 2 OH OHOHOH O O D-Ribitol

63 Niacin (Vitamin B 3 ) Niacin is part of the coenzyme nicotinamide adenine dinucleotide (NAD + ) involved in oxidation- reduction reactions. deficiency can result in dermatitis, muscle fatigue, and loss of appetite. is found in meats, rice, and whole grains. N C O OH Copyright © 2009 by Pearson Education, Inc.

64 Pantothenic Acid (Vitamin B 5 ) Pantothenic acid is part of coenzyme A needed for energy production, as well as glucose and cholesterol synthesis. deficiency can result in fatigue, retarded growth, cramps, and anemia. is found in salmon, meat, eggs, whole grains, and vegetables. HOCH 2 CCHCNCH 2 CH 2 COH O H OHOCH 3 CH 3

65 Cobalamin (Vitamin B 12 ) Cobalamin consists of four pyrrole rings with a Co 2+. is a coenzyme for enzymes that transfer methyl groups and produce red blood cells. deficiency can lead to pernicious anemia and nerve damage. Copyright © 2009 by Pearson Education, Inc.

66 Ascorbic Acid (Vitamin C) Vitamin C is required in collagen synthesis. deficiency can lead to weakened connective tissue, slow-healing wounds, and anemia. is found in blueberries, citrus fruits, tomatoes, broccoli, red and green vegetables. O CHOH CH 2 OH OHHO O Copyright © 2009 by Pearson Education, Inc.

67 Folic Acid (Folate) Folic acid (folate) consists of pyrimidine, p-aminobenzoic acid, and glutamate. forms the coenzyme THF used in the transfer of carbon groups and the synthesis of nucleic acids. deficiency can lead to abnormal red blood cells, anemia, and poor growth. Copyright © 2009 by Pearson Education, Inc.

68 Vitamin A is obtained from meats and beta-carotenes in plants. has beta-carotenes that are converted by liver enzymes to vitamin A (retinol). H 3 CCH 3 CH 3 CH 3 CH 3 CH 3 CH 3 H 3 CCH 3 H 3 C CH 3 CH 3 CH 2 OH H 3 CCH 3 CH 3 Beta-carotene Retinol (vitamin A) Copyright © 2009 by Pearson Education, Inc.

69 Vitamin D Vitamin D (D 3 ) is synthesized in skin exposed to sunlight. regulates the absorption of phosphorus and calcium during bone growth. deficiency can result in weakened bones. sources include cod liver oil, egg yolk, and enriched milk. Copyright © 2009 by Pearson Education, Inc.

70 Vitamin E is an antioxidant in cells. may prevent the oxidation of unsaturated fatty acids. is found in vegetable oils, whole grains, and vegetables. O CH 3 HO H 3 C CH 3 CH 3 CH 3 CH 3 CH 3 CH 3

71 Vitamin K Vitamin K 1 in plants has a saturated side chain. Vitamin K 2 in animals has a long unsaturated side chain. Vitamin K 2 is needed for the synthesis of zymogens for blood clotting. 3 n

72 Learning Check Identify the vitamin associated with each: 1) Thiamin (B 1 )2) Vitamin A 3) Vitamin K4) Vitamin D 5) Ascorbic acid A. Collagen formation B. Beriberi C. Absorption of phosphorus and calcium in bone D. Vision E. Blood clotting

73 Solution Identify the vitamin associated with each: 1) Thiamin (B 1 )2) Vitamin A 3) Vitamin K4) Vitamin D 5) Ascorbic acid A. 5 Collagen formation B. 1 Beriberi C. 4 Absorption of phosphorus and calcium in bone D. 2 Vision E. 3 Blood clotting