Chapter 16 Amino Acids and Proteins 16.1 Functions of Proteins Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

 Structural  Movement  Transport  Storage  Hormone  Protection  Enzymes Collagen Collagen; bones, tendons, cartilage Keratin Keratin; hair, skin, wool, nails, feathers Myosin & Actin Myosin & Actin; muscle contractions Hemoglobin Hemoglobin; transports O 2 Lipoproteins Lipoproteins; transports lipids CaseinAlbumin Casein; in milk. Albumin; in eggs Insulin Insulin; regulates blood glucose Growth hormone Growth hormone; regulates growth Immunoglobulins Immunoglobulins; stimulate immunity Snake venom; plant toxins Snake venom; plant toxins; Sucrase Sucrase; catalyzes sucrose hydrolysis Pepsin Pepsin; catalyzes protein hydrolysis Functions of Proteins

16.2 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 R │ + │ H 2 N—C —COOH H 3 N—C —COO− │ │ H H ionized form

 The building blocks of proteins Amino Acids

Examples of Amino Acids H + │ H 3 N—C—COO− │ Hglycine CH 3 + │ H 3 N—C—COO− │ Halanine

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 –NH 2 side chains. Nonpolar Polar Acidic Basic Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

Nonpolar Amino Acids A nonpolar amino acid has  An R group that is H, an alkyl group, or aromatic. Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

Polar Amino Acids A polar amino acid has  An R group that is an alcohol, thiol, or amide. Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

Acidic and Basic Amino Acids An amino acid is  Acidic with a carboxyl R group (COO − ).  Basic with an amino R group (NH 3 + ). Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings Basic Amino Acids

Learning Check Identify each as (P) polar or (NP) nonpolar. + A. H 3 N–CH 2 –COO − (Glycine) CH 3 | CH–OH + │ B. H 3 N–CH–COO − (Threonine)

Solution Identify each as (P) polar or (NP) nonpolar. + A. H 3 N–CH 2 –COO − (Glycine) (NP) nonpolar CH 3 | CH–OH + │ B. H 3 N–CH–COO − (Threonine) (P) polar

Fischer Projections of Amino Acids Amino acids  Are chiral except for glycine.  Have Fischer projections that are stereoisomers.  That are L are used in proteins. 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 Zwitterions and Isoelectric Points

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 – ZwitterionNegative ion at pI pH > pI Charge: 0Charge: 1− Amino Acids as Acids

In solutions 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: 0Charge: 1+ Amino Acids as Bases

pH and Ionization 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 (at low pH) (at pI) (at high pH)

Electrophoresis: Separation of Amino Acids In electrophoresis, an electric current is used to separate a mixture of amino acids, and  The positively charged amino acids move toward 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 thin­layer plate.

Electrophoresis With an electric current, a mixture of lysine, aspartate, and valine are separated. Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

CH 3 CH 3 + | | 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? Learning Check

CH 3 CH 3 + | | 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) Solution

Formation of Peptides Copyright © 2007 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 CH 3 O + || + | || H 3 N—CH 2 —C—O– + H 3 N—CH—C—O– O H CH 3 O + || | | || H 3 N—CH 2 —C—N—CH—C—O– + H 2 O peptide bond

Formation of A Dipeptide Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Learning Check Write the dipeptide Ser-Thr. OH CH 3 | | CH 2 O HCOH O + | ║ + | ║ H 3 N─CH─C─O – + H 3 N─CH─C─O – Ser Thr

Solution Write the dipeptide Ser-Thr. OH CH 3 | | CH 2 O HCOH O + | ║ + | ║ H 3 N─CH─C─O – + H 3 N─CH─C─O – Ser peptide Thr OH bond CH 3 | | CH 2 OH HCOH O + | ║ | | ║ NH 3 ─CH─C─N ─CH─C─O – + H 2 O Ser-Thr

Naming Dipeptides A dipeptide is named with  A -yl ending for the N-terminal amino acid.  The full amino acid name of the free carboxyl group (COO-) at the C-terminal end. Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

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

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 Solution

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

Solution 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: CH 3 │ CH 3 S │ │ CH – CH 3 SH CH 2 │ │ │ CH 3 O H CH 2 O H CH 2 O H CH 2 O + │ ║ │ │ ║ │ │ ║ │ │ ║ H 3 N – CH–C–N–CH–C–N–CH–C–N–CH–CO –

Solution Ala-Leu-Cys-MetAlanylleucylcysteylmethionine CH 3 │ CH 3 S │ │ CH – CH 3 SH CH 2 │ │ │ CH 3 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–CO – AlaLeuCys Met

Protein Structure: Primary and Secondary Levels Copyright © 2007 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 Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Primary Structures The nonapeptides oxytocin and vasopressin  Have similar primary structures.  Differ only in the amino acids at positions 3 and 8. Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

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. Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Secondary Structure – Alpha Helix The secondary structures of proteins indicate the three-dimensional spatial arrangements of the polypeptide chains. An alpha helix has  A coiled shape held in place by hydrogen bonds between the amide groups and the carbonyl groups of the amino acids along the chain.  Hydrogen bonds between the H of a –N-H group and the O of C=O of the fourth amino acid down the chain.

Secondary Structure – Alpha Helix Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Secondary Structure – Beta Pleated Sheet A beta-pleated sheet is a secondary structure that  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: β-Pleated Sheet Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Secondary Structure: Triple Helix A triple helix  Consists of three alpha helix chains woven together.  Contains large amounts glycine, proline, hydroxy proline, and hydroxylysine that contain –OH groups for hydrogen bonding.  Is found in collagen, connective tissue, skin, tendons, and cartilage. Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Indicate the type of protein structure as 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

Indicate the type of protein structure as: 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

Protein Structure: Tertiary and Quaternary Levels Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Essential amino acids  Must be obtained from the diet.  Are the ten amino acids not synthesized by the body.  Are in meat and diary products.  Are missing (one or more) in grains and vegetables. Essential Amino Acids TABLE 19.3 Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

The tertiary structure of a protein  Gives a specific three dimensional shape to the polypeptide chain.  Involves interactions and cross links between different parts of the peptide chain.  Is stabilized by Hydrophobic and hydrophilic interactions. Salt bridges. Hydrogen bonds. Disulfide bonds. Tertiary Structure

 The interactions of the R groups give a protein its specific three- dimensional tertiary structure. Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Tertiary Structure TABLE 19.5

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 Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

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. Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

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

Select the type of tertiary interaction as: 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

Quaternary Structure The quaternary structure  Is the combination of two or more tertiary units.  Is stabilized by the same interactions found in tertiary structures.  Of hemoglobin consists of two alpha chains and two beta chains. The heme group in each subunit picks up oxygen for transport in the blood to the tissues. Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings hemoglobin

Summary of Protein Structure TABLE 19.6 Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Summary of Protein Structures Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Identify the level of protein structure as: 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

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

Protein Hydrolysis and Denaturation Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

Protein hydrolysis  Splits the peptide bonds to give smaller peptides and amino acids.  Occurs in the digestion of proteins.  Occurs in cells when amino acids are needed to synthesize new proteins and repair tissues. Protein Hydrolysis

Hydrolysis of a Dipeptide  In the lab, the hydrolysis of a peptide requires acid or base, water and heat.  In the body, enzymes catalyze the hydrolysis of proteins.

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

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 © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

What are the products of the complete hydrolysis of the peptide Ala-Ser-Val? Learning Check

The products of the complete hydrolysis of the peptide Ala-Ser-Val are alanine serine valine Solution

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

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

Enzymes = Biological catalysts Large proteins Permit reactions to ‘go’ at body conditions body conditions Process millions of molecules every second Very specific react with only 1 or a few types of molecules substrates (substrates). Model of trios-p-isomerase

Energy Enzyme catalyzed reaction reactants products Effect of enzymes on E act change Enzymes change how how a reaction will proceed. reduces This reduces the activation energy. faster It makes it faster. E act HH reaction For a reaction to go it must get over the activation energy hurdle activation energy hurdle.

Enzyme nomenclature  Name is based on: Examples lactose To react with lactose. lactase carboxylpyruvate To remove carboxyl from pyruvate. pyruvate decarboxylase -ase ending whatwith what with orhow it reacts +

Classification of enzymes  Based on type of reaction Oxireductase  Oxireductase Transferase  Transferase Hydrolase  Hydrolase Lyase  Lyase Isomerases  Isomerases Ligase  Ligase redox catalyze a redox reaction transfer transfer a group hydrolysis catalyze hydrolysis rxns double bonds Make or break double bonds rearrange rearrange atoms join join two molecules

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 a double bond. C. Combines two molecules to make a new compound. D. Adds NH 3. Learning Check

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 a double bond. C. 4 Combines two molecules to make a new compound. D. 1 Adds NH 3. Solution

Catalytic site Wherereaction Where reactionoccurs Binding Siteholdssubstrateinplace Substrate Enzyme The Active Site  Enzymes are typically HUGE proteins, yet only a small part are actually involved in reaction. The active site has two basic components.

Enzyme-substrate complex (All of these steps are in equilibrium)  Step 1: (All of these steps are in equilibrium)  Enzyme and substrate combine to form complex  ESES  E + S ES EnzymeSubstrateComplex  Enzyme Substrate Complex + ESESESES E

Enzyme-product complex  Step 2:  An enzyme-product complex is formed.  ES EP ESESESES EPEPEPEP transition state

Product  The enzyme and product separate  EP E + P The product is made Enzyme is ready for another substrate. EPEPEPEP

Lock and Key Theory  EnzymelockSubstratekey  Enzyme is “lock” and Substrate is “key”. Substrate structure must fit into enzyme’s structure.

Induced Fit Theory  Active site may not fit substrate. Site must change in order to form the complex.

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

Effect of Temp on Enzymatic Rxns Optimum Temp usually 37 o C 37 o C. Optimum Temp usually 37 o C 37 o C. Temperature Reaction Rate Exceeding normal pH and temperature ranges always reduces enzyme reaction rates. Exceeding normal pH and temperature ranges always reduces enzyme reaction rates.

Effect of pH on Enzymatic Rxns pH Most enzymes work best near pH 7.4 Most enzymes work best near pH 7.4 Reaction Rate though not all though not all.

Examples of optimum pH EnzymeLocationSubstratepHPepsin Urease Sucrase Pancreatic Amylase Trypsin Arginase Stomach Liver Small Intestine Pancrease Liver Peptide Bonds 2 Urea 5 Sucrose 6.2 Amylose 7 8 Arginine9.7

Effect of substrate concentration Rate of reaction (velocity) Substrate concentration Rate increases if concentration of the substrate increases Rate increases if concentration of the substrate increases For non-enzyme catalyzed reactions

V max At V max the enzyme is working as fast as it can. V max At V max the enzyme is working as fast as it can. Effect of substrate concentration V max w/ more enzyme Rate of reaction (velocity) Substrate concentration Rate is limited by the concentration of both the substrate and enzyme. Rate is limited by the concentration of both the substrate and enzyme. V max w/ some enzyme For Enzyme catalyzed reactions Rates increase but only to a certain point Saturation point

Factors Affecting Enzyme Activity Enzyme Concentration Enzyme Activity Rates increases when amount of Enzyme increases

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. Increasing the concentration of sucrase C. Changing the pH to 4 D. Running the reaction at 70°C 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. 1 Increasing the concentration of sucrose B. 2 Increasing the concentration of sucrase C. 3 Changing the pH to 4 D. 3 Running the reaction at 70°C Solution

COMPETITIVE INHIBITOR Resembles substrate: Competes with substrate Competes with substrate for the active site. Resembles substrate: Competes with substrate Competes with substrate for the active site. Enzyme mistakes inhibitor for substrate ENZYME INHIBITION Effect reversed by increasing substrate concentration.

Folic Acidobtained Folic Acid : obtained from the diet from the diet or microorganisms in the intestinal tract from microorganisms in the intestinal tract. Microorganisms make folic acid fromPABA Microorganisms make folic acid from PABA. Sulfa Drugs Competitive Inhibitors

antimetabolite.Illnesses caused by invading microorganisms like bacterium can be combated using a competitive inhibitor called an antimetabolite. Folic Acidcoenzyme in many biosynthetic processesFolic Acid is a coenzyme in many biosynthetic processes like synthesis of amino acids and nucleotides. Sulfa Drugs 1930sulfanilamide sulfapyridinesulfathiazolekill bacteria cure several diseasesIn 1930 it was discovered that sulfanilamide, along with sulfapyridine and sulfathiazole, could kill many types of harmful bacteria and help cure several diseases. bacteria are trickedThe bacteria are tricked into using the sulfa drugs instead of PABA. make a molecule not exactly the sameThey make a molecule that also has a folic acid type of structure but is not exactly the same. competitive inhibitorWhen they try to use this fake folic acid as a coenzyme, not only doesn’t it work, it is now a competitive inhibitor. bacteria’s amino acids and nucleotides cannot be madeMany of the bacteria’s amino acids and nucleotides cannot be made, and the bacteria die.

Sulfa Drugs Competitive Inhibitors

ENZYME INHIBITION Binds somewhere other than Binds somewhere other than the active site. Changes Enzyme shape so substrate can’t react NONCOMPETITIVE INHIBITOR Effect can’t be reversed by increasing substrate concentration.

Cofactors Co 2+ + Co 2+ Apoenzyme proteinprotein portion InactiveInactive Cofactor = Non protein Group activate needed to ‘activate’ apoenzyme Cofactor = Non protein Group activate needed to ‘activate’ apoenzyme Co 2+ ESESESES E S

Coenzymes + apoenzyme coenzyme holoenzyme organic moleculetemporarily binds = organic molecule that temporarily binds to apoenzyme in order for it to work. oftenVitaminsoftenVitamins

Vitamin Coenzymes Thiamine (B1) Riboflavin (B2) folic acid biotin Pantothenic Acid Ascorbic Acid (C) Thiamine Pyrophosphate Decarboxlation FAD, FMN Electron Transfer tetrahydrofolic acid amino acid metabolism biocytin CO2 fixation acyl group carrier Vitamin C Collagen synthesis Healing Coenzyme A Vitamin Coenzyme Made Function