Chapter 16 Amino Acids, Proteins, and Enzymes. Functions of Proteins. Examples of Amino Acids. Amino Acids. Nonpolar Amino Acids. Types of Amino Acids
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1 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. 1 2 Amino Acids Examples of Amino Acids Amino acids are the building blocks of proteins. contain a carboxylic acid group and an amino group on the alpha (α) carbon. are ionized in solution. each contain a different side group (R). R side chain R + H 2 N C COOH H 3 N C COO H H Zwitterion (ionized form) H + H 3 N C COO H Glycine + H 3 N C COO H Alanine 3 4 Types of Amino Acids Nonpolar 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 NH 2 side chains. Nonpolar Acidic Polar Basic An amino acid is nonpolar when the R group is H, alkyl, or aromatic. 5 Copyright 2009 by Pearson Education, Inc. 6
2 Polar Amino Acids Acidic and Basic Amino Acids An amino acid is polar when the R group is an alcohol, thiol, or amide. An amino acid is acidic when the R group is a carboxylic acid. basic when the R group is an amine. 7 8 Identify each as (1) polar or (2) nonpolar. + A. H 3 N CH 2 COO Glycine Identify each as (1) polar or (2) nonpolar. + A. H 3 N CH 2 COO Glycine (2) nonpolar CH OH + B. H 3 N CH COO Threonine CH OH + B. H 3 N CH COO Threonine (1) polar 9 10 Fischer Projections of Amino Acids Zwitterions Amino acids are chiral except glycine. have Fischer projections that are stereoisomers. that are L are the only amino acids used in proteins. COOH COOH COOH COOH H 2 N H H NH 2 H 2 N H H NH 2 CH 2 SH CH 2 SH L-Alanine D-Alanine L-Cysteine D-Cysteine A zwitterion has charged NH 3+ and COO groups. 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). O O + NH 2 CH 2 C OH H 3 N CH 2 C O Glycine Zwitterion of glycine 11 12
3 Amino Acids as Acids Amino Acids as Bases In solutions more basic than the pi, the NH 3+ in the amino acid donates a proton. + OH H 3 N CH 2 COO H 2 N CH 2 COO Zwitterion Negative ion at pi ph > pi Charge: 0 Charge: 1- In solution more acidic than the pi, the COO in the amino acid accepts a proton. + H + + H 3 N CH 2 COO H 3 N CH 2 COOH Zwitterion Positive ion at pi ph< pi Charge: 0 Charge: ph and ionization Separation of Amino Acids 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 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. + H 3 N CH COOH H 2 N CH COO (1) (2) Which structure represents A. alanine at a ph above its pi? B. alanine at a ph below its pi? 17 18
4 + H 3 N CH COOH H 2 N 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 The Peptide Bond Formation of a Dipeptide 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 O + + H 3 N CH 2 C O + H 3 N CH C O O H O + H 3 N CH 2 C N CH C O peptide bond Write the dipeptide Ser-Thr. OH CH 2 O HCOH O + + H 3 N CH C O + H 3 N CH C O Ser Thr Write the dipeptide Ser-Thr. OH CH 2 O HCOH O + + H 3 N CH C O + H 3 N CH C O Ser Thr OH CH 2 O H HCOH O + NH 3 CH C N CH C O + H 2 O Ser-Thr 23 24
5 Naming Dipeptides A dipeptide 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. Write the three-letter abbreviations and names of the tripeptides that could form from two glycine and one alanine 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 What are the possible tripeptides formed from one each of leucine, glycine, and alanine? 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 Write the three-letter abbreviation and name for the following tetrapeptide. S CH SH CH 2 O H CH O H CH 2 O H CH 2 O + H 3 N CH C N CH C N CH C N CH C O 29 30
6 Ala-Leu-Cys-Met Alanylleucylcysteinylmethionine S CH SH CH 2 O H CH O H CH 2 O H CH 2 O + H 3 N CH C N CH C N CH C N CH C O Ala Leu Cys Met Chapter 16 Amino Acids, Proteins, and Enzymes 16.5 Levels of Protein Structure Primary Structure of Proteins Primary Structures The primary structure of a protein is the particular sequence of amino acids. the backbone of a peptide chain or protein. O H 3 N CH C CH CH O N CH C N H H SH CH 2 O CH C N H Ala Leu Cys Met S CH 2 CH 2 O CH C O - The nonapeptides oxytocin and vasopressin have similar primary structures. Only the amino acids at positions 3 and 8 differ Primary Structure of Insulin Secondary Structure Alpha Helix 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. 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
7 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 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 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 Tertiary Structure Essential amino acids 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. 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
8 Crosslinks in Tertiary Structures Learning check Crosslinks in tertiary structures involve attractions and repulsions between the side chains of the amino acids in the polypeptide chain. 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 Globular Proteins 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 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 Fibrous Proteins 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 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
9 Summary of Protein Structure Summary of Protein Structure 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 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 Applications of 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. 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
10 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? 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 16.6 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 Classification 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. 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 59 60
11 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 NH 3. 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 NH Active Site Enzyme-Catalyzed Reaction 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. 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. enzyme only binds substrates that exactly fit the active site. enzyme is analogous to a lock. 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
12 Example of an Enzyme-Catalyzed Reaction 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 Diagnostic Enzymes 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 determine the amount of damage in tissues. that are elevated may indicate damage or disease in a particular organ Diagnostic Enzymes Isoenzymes Levels of enzymes CK, LDH, and AST are elevated following a heart attack. are used to determine the severity of the attack. 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
13 Isoenzymes Chapter 16 Amino Acids, Proteins, and Enzymes 16.8 Factors Affecting Enzyme Activity Temperature and Enzyme Action ph 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. 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 Substrate Concentration Enzymes in the body have an optimum ph of about 7.4. certain organs operate at lower and higher optimum ph values. As substrate concentration increases, the rate of reaction increases (at constant enzyme concentration). the enzyme eventually becomes saturated, giving maximum activity
14 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 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 Competitive 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 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. 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
15 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. 85
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