Protein Structure and Function Overview

1. Lecture Presentation Chapter 10Proteins—Workers of the Cell Julie Klare Fortis College Smyrna, GA

2. Outline • 10.1 Amino Acids—A Second Look • 10.2 Protein Formation • 10.3 The Three-Dimensional Structure of Proteins • 10.4 Denaturation of Proteins • 10.5 Protein Functions • 10.6 Enzymes—Life’s Catalysts • 10.7 Factors That Affect Enzyme Activity

3. 10.1 Amino Acids—A Second Look • “Amino” indicates a protonated amine (–NH3+). • “Acid” indicates a carboxylic acid (–COO-). • These groups are bonded to a central alpha () carbon atom. • The  carbon is also bonded to a hydrogen atom and a side chain. Insert colored diagram of amino acid structure from page 382.

4. 10.1 Amino Acids—A Second Look In all but one amino acid (glycine), the  carbonis a chiral center. Insert L- and D- amino acids and Fischer projections from page 383 • The L-amino acids are the building blocks of proteins. Some D-amino acids do occur in nature but rarely in proteins.

5. 10.1 Amino Acids—A Second Look The R group gives each amino acid its unique identity and characteristics. Twenty amino acids are found in most proteins. Nine families of organic compounds are represented: alkanes (hydrocarbon), aromatics, thioethers, alcohols, phenols, thiols, amides, carboxylic acids, and amines. The 10 amino acids designated with an asterisk (*)in the table are called essential amino acids because they must be obtained in the diet. A complete protein meal can be obtained by combining foods like rice and beans or peanut butter on whole-grain bread.

6. 10.1 Amino Acids—A Second Look

7. 10.1 Amino Acids—A Second Look

8. 10.1 Amino Acids—A Second Look

9. 10.1 Amino Acids—A Second Look

10. 10.1 Amino Acids—A Second Look

11. 10.1 Amino Acids—A Second Look Classification of Amino Acids Amino acids are separated into nonpolar and polar. With few exceptions, the side chains of nonpolar amino acids are composed entirely of carbon and hydrogen and are hydrophobic. Polar amino acid side chains contain functional groups that create an uneven distribution of electrons in the side chain. Polar acidic and polar basic amino acids have charged side chains, allowing them to form ion–dipole interactions with water.

12. 10.2 Protein Formation Condensation reactions occur between amino acids, and the product formed is a dipeptide. The carboxylate ion (–COO-) of one amino acid molecule reacts withthe protonated amine (–NH3+) of a second amino acid. A water molecule is removed, and an amide functional group is formed.

13. 10.2 Protein Formation In a dipeptide, the N-terminus (or amino terminus) has an unreacted -amino group. The C-terminus (or carboxy terminus) has an unreacted carboxylate group. By convention, peptides are always written from theN-terminus to the C-terminus.

14. 10.2 Protein Formation Each pair of amino acids can combine to form two different dipeptides. The two dipeptides are structural isomers, different compounds, and have different properties. The order of the amino acids is critical to the structure and function of the compound.

15. 10.2 Protein Formation Dipeptides are the smallest members of thepeptide class. Any compound containing amino acids joined bya peptide bond can be called a peptide. A compound with three amino acids is a tripeptide, one with four amino acids is a tetrapeptide, and so on. As the number of amino acids increases, the compound is referred to as a polypeptide. A biologically active polypeptide containing 50 ormore amino acids is a protein.

16. 10.3 The Three-Dimensional Structure of Proteins Primary Structure The primary (1) structure of a protein is the order in which the amino acids are joined together to form the protein backbone. The side chains of the amino acids are substituents dangling from this backbone.

17. 10.3 The Three-Dimensional Structure of Proteins Secondary (2) Structure The  helix is a coiled structure stabilized by hydrogen bonds formed between the carbonyl (C=O) oxygen atom (-) of one amino acid and the N–H hydrogen atom (+) of the amino acid on the fourth amino acid away from it in the primary structure. The positioning of the hydrogen bonds allows the helix to stretch and recoil. Multiple hydrogen-bonding interactions make the helix a strong structure. In the  helix, the side chains of the amino acids project outward away from the axis of the helix.

18. 10.3 The Three-Dimensional Structure of Proteins Secondary (2) Structure The -pleated sheet is an extended structure in which segments of the protein chain align to form a zigzag structure like a folded paper fan. Beta strands are held together side by side by hydrogen-bonding interactions between their backbones. In the -pleated sheet, the side chains of the amino acids project above and below the sheet.

19. 10.3 The Three-Dimensional Structure of Proteins Tertiary (3) Structure The  helices and -pleated sheets of the polypeptide chain interact with each other and the environment to create the tertiary structure (3). Nonpolar side chains are repelled by an aqueous environment and turn toward the interior of the protein. Polar side chains are attracted to aqueous surroundings and appear on the surface. Tertiary structure is stabilized by attractive forces between side chains and the environment as well as by attractive forces between side chains themselves. To satisfy all the competing interactions, the protein folds into a specific three-dimensional shape.

20. 10.3 The Three-Dimensional Structure of Proteins

21. 10.3 The Three-Dimensional Structure of Proteins Tertiary (3) Structure Interactions Nonpolar interactions. Nonpolar amino acid side chains are repelled by the aqueous environment and aggregate in the interior of the protein. Polar interactions. Polar amino acid side chains interact with water and each other through dipole–dipole, ion–dipole, and hydrogen-bonding interactions. Salt bridges (ionic interactions). Acidic and basic amino acid side chains existin their ionized form in an aqueous environment. The opposite charges attract, thereby forming a stabilizing ionic interaction called a salt bridge. Disulfide bonds Two –SH groups (thiols) can react with each other through an oxidation reaction (losing hydrogens) to form a disulfide bond –S–S–. The disulfide bond is a covalent bond.

22. 10.3 The Three-Dimensional Structure of Proteins Tertiary (3) Structure Globular proteins fold into a compact, spherical shape with polar amino acid side chains on their surface and nonpolar amino acid side chains forming a nonpolar core. Enzymes and many cellular proteins are globular proteins. Fibrous proteins have long, thread-like structures. Aligned helices form strong, durable structures. Fibrous proteins tend to be insoluble in water.

23. 10.3 The Three-Dimensional Structure of Proteins Collagen and Vitamin C Scurvy, a disease caused by a deficiency of vitamin C in the diet, affectscollagen formation. Collagen contains a modified amino acid called hydroxyproline. The additional hydroxyl group on hydroxyproline allows hydrogen bonds between the chains, adding extra strength to the triple helix formed in collagen. Vitamin C is critical to the conversion of proline to hydroxyproline. Without hydroxyproline, collagen is weakened, resulting in spongy and bleeding gums, opening of scars, and nail loss. Scurvy can be reversed by a diet containing adequate vitamin C. In the United States, smokers and people who do not get enough fresh produce or take vitamin supplements are at risk for scurvy.

24. 10.3 The Three-Dimensional Structure of Proteins Quaternary (4) Structure Quaternary (4) structure describes the interactions of two or more polypeptide chains to form a single biologically active protein. The individual polypeptide chains or subunits are held together by the same interactions that stabilize the tertiary structure of a single protein. Not all biologically active proteins have a quaternary (4) structure.

25. 10.3 The Three-Dimensional Structure of Proteins

26. 10.4 Denaturation of Proteins Denaturation is a process that disrupts the stabilizing attractive forces in the secondary, tertiary, or quaternary structure. When a protein is denatured, its primary structureis not changed, but it loses its biological activity.

27. 10.4 Denaturation of Proteins Hair relaxing and perming involve protein denaturation: relaxing and permanent waves both involve denaturing the proteins in hair by disrupting the disulfide bonds found in the keratin, reshaping the keratin, and forcing the disulfide bonds to reform. A person who has ingested lead or mercury is given egg whites to drink. The proteins in the egg whites are denatured by the mercuryor lead and the combination forms a precipitate. An emetic is then administered to induce vomiting.

28. 10.5 Protein Functions Messengers, Receptors, and Transporters A hormone is a chemical, sometimes a peptide or protein, created in one part of the body that affects another part of the body. Receptors are proteins facing the outer surface of a cell that bindto a hormone or other messenger, triggering a signal inside the cell. A transporter is an integral membrane protein spanning a phospholipid bilayer.

29. 10.5 Protein Functions Hemoglobin Four subunits of hemoglobin are attractedto each other through hydrogen bonds, London forces, and salt bridges. Each subunit contains a heme prosthetic group. Each heme group binds Fe2+, which, in turn, binds oxygen (O2). Each Fe2+ can bind one oxygen molecule:one hemoglobin can transport four moleculesof oxygen. The binding of O2 to the hemoglobin inducesa conformational change. At the tissues, the oxygen dissociates from the hemoglobin, and the shape of the hemoglobin changes back to its deoxygenated form.

30. 10.5 Protein Functions Antibodies The substance recognized by an antibody is called an antigen. An antibody consists of four polypeptide subunits, two heavy chains and two light chains. The secondary structure contains -pleated sheets (represented by the flat ribbons) that are stacked tightly together. The quaternary structure is held together through disulfide bridges between the polypeptide chains. The stem of the Y is similar in all antibodies and can bind to receptors on a variety of cells in the body. Antibodies bind antigens at the top of each armof the Y. Insert figure 10.10, page 402

31. 10.6 Enzymes—Life’s Catalysts Enzymes are typically large globular proteins and are present in every cell of the body. Enzymes act as catalysts, compounds that accelerate the reactions of metabolism but are not consumed or changed by those reactions. An enzyme cannot force a reaction to occur that would not normally occur. An enzyme simply makes a reaction occur faster. The tertiary structure of an enzyme plays an important role in its function.

32. 10.6 Enzymes—Life’s Catalysts The enzyme name usually appears above or below the reaction arrow. The reactant is called the substrate. Cofactors are inorganic substances like magnesium ion. Coenzymes are small organic molecules. The active site of hexokinase fitsD-glucose only.

33. 10.6 Enzymes—Life’s Catalysts Rates of Reaction Activation energy loweringis accomplished during the formation of ES through interactions between the enzyme and the substrate. Proximity: When the ES forms, the substrates arein close proximity: they don’t have to find each other as they would in solution. Insert figure 10.15 - page 406

34. 10.6 Enzymes—Life’s Catalysts Rates of Reaction Orientation:In the active site of an enzyme, substrate molecules are held at the appropriate distance and in correct alignment to each other to allow the reaction to occur. The arrangement of amino acid side chains in the active site creates interactions that orient the substrates so they will react. Correct orientation helps lower the activation energy required.

35. 10.6 Enzymes—Life’s Catalysts Rates of Reaction Orientation:when an enzyme interacts with its substrateto form ES, the bonds of the substrate molecule(s) are weakened (strained). The weakening of the bonds means that they will more readily react: weaker bonds break more easily and the activation energy is lowered by this effect.

36. 10.7 Factors That Affect Enzyme Activity Substrate Concentration The first step in an enzyme-catalyzed reaction is the formation of ES. If the amount of enzyme remains unchanged, an increase in the substrate concentration increases the enzyme’s activity up to the point where the enzyme becomes saturated with its substrate.

37. 10.7 Factors That Affect Enzyme Activity Substrate Concentration At maximum activity, the conditions under which the enzyme is operating are considered to be in a steady state. Under steady-state conditions, substrate is being converted to product as efficiently as possible.

38. 10.7 Factors That Affect Enzyme Activity pH Optimum Enzymes are most active at their pH optimum. At this pH, the enzyme maintains its tertiary structure and, therefore, its active site. Changes in the pH may change the nature of an amino acid side chain. If an enzyme requires a carboxylate ion (–COO-), lowering the pH could convert the carboxylate ionto carboxylic acid (–COOH). This change would cause enzyme activity to decrease.

39. 10.7 Factors That Affect Enzyme Activity pH Optimum In the body, an enzyme’s pH optimum is based on the location of the enzyme. For example, enzymes in the stomach function at a much lower pH because of the acidity.

40. 10.7 Factors That Affect Enzyme Activity

41. 10.7 Factors That Affect Enzyme Activity Temperature The temperature optimum for most human enzymes is normal body temperature, 37C. Above their optimum temperature, enzymes lose activity due to the disruption of the attractive forces stabilizing the tertiary structure.At high temperatures, an enzyme denatures. At low temperatures, enzyme activity is reduced due to the lackof energy present for the reaction to take place at all.

42. 10.7 Factors That Affect Enzyme Activity Temperature Because enzymes are major culprits in food spoilage, we store foods in a refrigerator or freezer to slow the spoilage process. The enzymes present in bacteria can also be destroyed by high temperatures, in processes like boiling contaminated drinking water and sterilizing instruments and other equipment in hospitals and laboratories.

43. 10.7 Factors That Affect Enzyme Activity Inhibitors Enzyme inhibitors prevent the active site from interacting with the substrate to form ES. Some inhibitors cause enzymes to lose catalytic activity temporarily, while others cause enzymes to lose activity permanently. In reversible inhibition, the inhibitor causes the enzymeto lose catalytic activity. If the inhibitor is removed, the enzyme becomes functional. Reversible inhibitors can be competitive or noncompetitive.

44. 10.7 Factors That Affect Enzyme Activity Inhibitors A competitive inhibitor has a structure that resembles the substrate. The competitive inhibitor will form an enzyme–inhibitor complex, but no reaction will take place. As long as the inhibitor remains in the active site, the enzyme cannot interact with its substrate and form product. Inhibition caused by a competitive inhibitor can be reversed by adding more substrate.

45. 10.7 Factors That Affect Enzyme Activity Inhibitors Noncompetitive inhibitors bind to another site on the enzyme, changing its shape. In the case of a noncompetitive inhibitor, adding more substrate has no effect. Regardless of the amountof enzyme, a certain portion of the enzyme is inactivated by the inhibitor.

46. 10.7 Factors That Affect Enzyme Activity Inhibitors In irreversible inhibition, the inhibitor forms a covalent bond with an amino acid side chain in the active site. The substrate is excluded or the catalytic reaction blocked. Irreversible inhibitors permanently inactivate enzymes.

47. 10.7 Factors That Affect Enzyme Activity Antibiotics Inhibit Bacterial Enzymes Penicillin is an irreversible inhibitor. Penicillin binds to the active site of an enzyme that bacteria use in the synthesis of their cell walls. When the bacterial enzyme bonds with penicillin, the enzyme loses its catalytic activity, and the growth of the bacterial cell wall slows. Without a proper cell wall for protection, bacteria cannot survive, and the infection stops.

48. Chapter Ten Summary 10.1 Amino Acids—A Second Look • Amino acids contain a central carbon atom, called the  carbon, bonded to four different groups—a protonated amine (amino) group, a carboxylate group, a hydrogen atom, and a side chain. • Amino acids, with the exception of glycine, are chiral compounds. The L-enantiomers of amino acids are the building blocks of proteins. The 20 different amino acids are found in most proteins. • They are characterized by various side chains. The side chains determine whether the amino acids are classified as nonpolar or polar. 10.2 Protein Formation • Amino acids join through a condensation reaction of the protonated amine groupof one and the carboxylate group of the other. • The bond that forms between the two amino acids is called a peptide bond, and the new structure is a dipeptide. The newly formed dipeptide has an N-terminus with a free protonated amine group and a C-terminus with a free carboxylate group. • A compound containing 50 or more amino acids linked by peptide bond is a polypeptide and if it has biological activity is called a protein. Proteins are polymers of amino acids.

49. Chapter Ten Summary 10.3 The Three-Dimensional Structure of Proteins • The primary structure (1) is the sequence of the amino acids that form the protein backbone. The bonding interaction is the peptide bond. • The secondary structure (2) involves the interactions of amino acids near each other in the primary structure and describes patterns of regular or repeating structure. The most common secondary structures are the  helix and the -pleated sheet. The secondary structure is stabilized by hydrogen bonding between atoms in the backbone. • The tertiary structure (3) is formed by folding the secondary structure onto itself and is driven by the hydrophobic interactions of amino acid side chains with their aqueous environment. This level is stabilized by the attractive forces between side chains and disulfide bonds. • Proteins that fold into a roughly spherical shape are globular proteins. Proteins that maintain elongated structures are fibrous proteins. • Some proteins have a quaternary structure (4), which involves the association of two or more peptides to form a biologically active protein.The same forces stabilize the quaternary structure as the tertiary structure.

50. Chapter Ten Summary 10.4 Denaturation of Proteins • Denaturation of a protein disrupts the stabilizing attractive forcesin the secondary, tertiary, or quaternary structure, often unfoldingthe protein. • When a protein is denatured, its primary structure is not changed. Proteins can be denatured by heat, a change in the pH of their environment, reaction with small organic compounds and heavy metals such as lead or mercury, or mechanical agitation. • A denatured protein is no longer biologically active. 10.5 Protein Functions • Proteins act as messengers between cells, receptors on the surfaceof cells, and transporters through the body or across the cell. • Proteins are used to store nutrients, contract muscles, protectthe cell, and support its structure. • Proteins catalyze biochemical reactions as enzymes.