Chapter 16 Amino Acids, Proteins, and Enzymes 16.1 Functions of Proteins 16.2 Amino Acids 16.3 Amino Acids as Acids and Bases

Functions of Proteins Proteins perform many different functions in the body.

Amino Acids Amino acids are the building blocks of proteins. contain a carboxylic acid group and an amino group on the alpha () carbon. are ionized in solution. each contain a different side group (R). R side chain R │ + │ H2N—C —COOH H3N—C —COO− │ │ H H ionized form

Examples of Amino Acids H + │ H3N—C—COO− │ H glycine CH3 + │ H alanine

Types of Amino Acids Amino acids are classified as nonpolar (hydrophobic) with hydrocarbon side chains. polar (hydrophilic) with polar or ionic side chains. acidic (hydrophilic) with acidic side chains. basic (hydrophilic) with –NH2 side chains. Nonpolar Polar Acidic Basic

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

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

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

Learning Check Identify each as (1) polar or (2) nonpolar. + A. H3N–CH2–COO− (Glycine) CH3 | CH–OH + │ B. H3N–CH–COO − (Threonine)

Solution Identify each as (1) polar or (2) nonpolar. + A. H3N–CH2–COO− (Glycine) (2) nonpolar CH3 | CH–OH + │ B. H3N–CH–COO − (Threonine) (1) polar

Fischer Projections of Amino Acids are chiral except glycine. have Fischer projections that are stereoisomers. that are L are the only amino acids used in proteins. L-Alanine D-Alanine L-Cysteine D-Cysteine C H 2 S N O 3

Zwitterions A zwitterion has charged −NH3+ and COO– groups. forms when both the –NH2 and the –COOH groups in an amino acid ionize in water. has equal + and – charges at the isoelectric point (pI). O O ║ + ║ NH2—CH2—C—OH H3N—CH2—C—O– glycine zwitterion of glycine

Amino Acids as Acids In solutions more basic than the pI, the —NH3+ in the amino acid donates a proton. + OH– H3N—CH2—COO– H2N—CH2—COO– zwitterion Negative ion at pI pH > pI Charge: 0 Charge: 1-

Amino Acids as Bases In solution more acidic than the pI, the COO- in the amino acid accepts a proton. + H+ + H3N—CH2—COO– H3N—CH2—COOH zwitterion Positive ion at pI pH< pI Charge: 0 Charge: 1+

pH and ionization H+ OH– + + H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–COO– + + H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–COO– positive ion zwitterion negative ion low pH pI high pH

Separation of Amino Acids When an electric current is used to separate a mixture of amino acids the positively charged amino acids move towards the negative electrode. the negatively charged amino acids move toward the positive electrode. an amino acid at its pI does not migrate. the amino acids are identified as separate bands on the filter paper or thin layer plate.

Separation of Amino Acids With an electric current, a mixture of lysine, aspartate, and valine are separated.

Learning Check + | | H3N—CH—COOH H2N—CH—COO– (1) (2) CH3 CH3 + | | H3N—CH—COOH H2N—CH—COO– (1) (2) Which structure represents: A. Alanine at a pH above its pI? B. Alanine at a pH below its pI?

Solution + | | H3N—CH—COOH H2N—CH—COO– (1) (2) CH3 CH3 + | | H3N—CH—COOH H2N—CH—COO– (1) (2) Which structure represents: A. Alanine at a pH above its pI? (2) B. Alanine at a pH below its pI? (1)

Chapter 16 Amino Acids, Proteins, and Enzymes 16.4 Formation of Peptides Copyright © 2005 by Pearson Education, Inc. Publishing as Benjamin Cummings

The Peptide Bond A peptide bond is an amide bond. forms between the carboxyl group of one amino acid and the amino group of the next amino acid. O CH3 O + || + | || H3N—CH2—C—O– + H3N—CH—C—O– O H CH3 O + || | | || H3N—CH2—C—N—CH—C—O– peptide bond

Formation of a Dipeptide

Learning Check Write the dipeptide Ser-Thr. OH CH3 | | CH2 O HCOH O | | CH2 O HCOH O + | ║ + | ║ H3N─CH─C─O– + H3N─CH─C─O– Ser Thr

Solution Write the dipeptide Ser-Thr. OH CH3 | | CH2 O HCOH O | | CH2 O HCOH O + | ║ + | ║ H3N─CH─C─O– + H3N─CH─C─O– Ser Thr OH CH3 | | CH2 O H HCOH O + | ║ | | ║ NH3─CH─C─N ─CH─C─O– + H2O Ser-Thr

Naming Dipeptides A dipeptide is named from the free amine (NH3+) using a -yl ending for the name. names the last amino acid with the free carboxyl group (COO-) by its amino acid name.

Learning Check Write the three-letter abbreviations and names of the tripeptides that could form from two glycine and one alanine.

Solution Glycylglycylalanine Gly-Gly-Ala Write the names and three-letter abbreviations of the tripeptides that could form from two glycine and one alanine. Glycylglycylalanine Gly-Gly-Ala Glycylalanylglycine Gly-Ala-Gly Alanylglycylglycine Ala-Gly-Gly

Learning Check What are the possible tripeptides formed from one each of leucine, glycine, and alanine?

Solution Leu-Gly-Ala Leu-Ala-Gly Ala-Leu-Gly Ala-Gly-Leu Gly-Ala-Leu Tripeptides possible from one each of leucine, glycine, and alanine: Leu-Gly-Ala Leu-Ala-Gly Ala-Leu-Gly Ala-Gly-Leu Gly-Ala-Leu Gly-Leu-Ala

Learning Check Write the three-letter abbreviation and name for the following tetrapeptide. CH3 │ CH3 S │ │ CH–CH3 SH CH2 │ │ │ CH3 O H CH O H CH2O H CH2 O + │ ║ │ │ ║ │ │ ║ │ │ ║ H3N–CH–C–N–CH–C–N–CH–C–N–CH–CO–

Solution │ CH3 S │ │ CH–CH3 SH CH2 │ │ │ CH3 O H CH O H CH2O H CH2 O Ala-Leu-Cys-Met Alanylleucylcysteinylmethionine CH3 │ CH3 S │ │ CH–CH3 SH CH2 │ │ │ CH3 O H CH O H CH2O H CH2 O + │ ║ │ │ ║ │ │ ║ │ │ ║ H3N–CH–C–N–CH–C–N–CH–C–N–CH–CO– Ala Leu Cys Met

Chapter 16 Amino Acids, Proteins, and Enzymes 16.5 Levels of Proteins Structure Copyright © 2005 by Pearson Education, Inc. Publishing as Benjamin Cummings

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

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

Primary Structure of 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.

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 © 2005 by Pearson Education, Inc. Publishing as Benjamin Cummings

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.

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.

Learning Check 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

Solution 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

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

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

Crosslinks in Tertiary Structures Crosslinks in tertiary structures involve attractions and repulsions between the side chains of the amino acids in the polypeptide chain. Copyright © 2005 by Pearson Education, Inc. Publishing as Benjamin Cummings

Learning check Select the type of tertiary interaction. 1) disulfide 2) ionic 3) H bonds 4) hydrophobic A. leucine and valine B. two cysteines C. aspartic acid and lysine D. serine and threonine

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

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. Myoglobin

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.

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.

Summary of Protein Structure

Summary of Protein Structure

Learning Check Identify the level of protein structure. 1) Primary 2) 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

Solution Identify the level of protein structure. 1) Primary 2) 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

Denaturation 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.

Applications of Denaturation 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.

Learning check 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?

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

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

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.

Names of Enzymes 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.

Classification of Enzymes Enzymes are classified by the reaction they catalyze. Class Type of Reactions catalyzed Oxidoreductases Oxidation-reduction Transferases Transfer groups of atoms Hydrolases Hydrolysis Lyases Add atoms/remove atoms to or from a double bond Isomerases Rearrange atoms Ligases Use ATP to combine small molecules

Learning Check Match the type of reaction with an enzyme. 1) aminase 2) dehydrogenase 3) isomerase 4) 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 NH3.

Solution Match the type of reaction with an enzyme 1) aminase 2) dehydrogenase 3) isomerase 4) 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 NH3.

Active Site 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.

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

Lock and Key Model In the lock-and-key model the active site has a rigid shape. an enzyme only binds substrates that exactly fit the active site. the enzyme is analogous to a lock. the substrate is the key that fits that lock.

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.

Example of An Enzyme Catalyzed Reaction

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

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

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

Diagnostic Enzymes Levels of enzymes CK, LDH, and AST are elevated following a heart attack. are used to determine the severity of the attack.

Isoenzymes 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.

Isoenzymes

Chapter 16 Amino Acids, Proteins, and Enzymes 16.8 Factors Affecting Enzyme Activity Copyright © 2005 by Pearson Education, Inc. Publishing as Benjamin Cummings

Temperature and Enzyme Action 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.

pH and Enzyme Action 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.

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

Enzyme Concentration As enzyme concentration increases the rate of reaction increases (at constant substrate concentration). more substrate binds with enzyme.

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

Learning Check 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

Solution 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

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

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.

Noncompetitive Inhibition 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.

Malonate and Succinate Dehydrogenase is a competitive inhibitor of succinate dehydrogenase. has a structure that is similar to succinate. inhibition is reversed by adding succinate.

Learning Check Identify each description as an inhibitor that is 1) Competitive 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.

Solution Identify each description as an inhibitor that is: 1) Competitive 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.

Chapter 16 Amino Acids, Proteins, and Enzymes 16.9 Enzyme Cofactors

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

Water-Soluble Vitamins Water-soluble vitamins are soluble in aqueous solutions. cofactors for many enzymes. not stored in the body. Copyright © 2005 by Pearson Education, Inc. Publishing as Benjamin Cummings

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. Copyright © 2005 by Pearson Education, Inc. Publishing as Benjamin Cummings

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

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

Thiamin (Vitamin B1) 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).

Riboflavin (Vitamin B2) 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 H 3 C 2 O D - R i b t o l

Niacin (Vitamin B3) O C H N 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 H

Pantothenic Acid (Vitamin B5) 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. H O C 2 N 3

Cobalamin (Vitamin B12) Cobalamin consists of four pyrrole rings with a Co2+. is a coenzyme for enzymes that transfer methyl groups and produce red blood cells. deficiency can lead to pernicious anemia and nerve damage.

Ascorbic Acid (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 C H 2

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.

Vitamin A 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 C 2 O B e t a - c r o n R i l ( v m A )

Vitamin D Vitamin D (D3) 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.

Vitamin E 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 C H 3

Vitamin K Vitamin K1 in plants has a saturated side chain. Vitamin K2 in animals has a long unsaturated side chain. Vitamin K2 is needed for the synthesis of zymogens for blood clotting. n 3

Learning Check Identify the vitamin associated with each 1) Thiamin (B1) 2) Vitamin A 3) Vitamin K 4) Vitamin D 5) Ascorbic Acid A. Collagen formation B. Beriberi C. Absorption of phosphorus and calcium in bone D. Vision E. Blood clotting

Solution Identify the vitamin associated with each 1) Thiamin (B1) 2) Vitamin A 3) Vitamin K 4) 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