1. Proteins—Amides at Work
Chapter 9
Proteins—Amides at Work
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2. Chapter Outline
9.1 Amino Acids—A Second Look 9.2 Protein Formation 9.3 The Three-Dimensional Structure of Proteins 9.4 Denaturation of Proteins 9.5 Examples of Biologically Important Proteins
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3. Introduction
Amino acids are the building blocks of proteins, which have structural and functional properties in our bodies.
Proteins function as follows:
They transport oxygen in the blood.
They are the primary components of skin and muscle.
They work as defense mechanisms against infection.
They serve as biological catalysts called enzymes.
They also control the metabolism of hormones.
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4. Introduction, Continued
Proteins are polymers of amino acids covalently bonded in specific sequences.
There are 20 commonly occurring amino acids that make up proteins, and the order of amino acids in proteins determines its structure and biological function.
When amino acids are covalently linked to one another, this chain can twist and fold to form a unique three-dimensional structure that has a specific function.
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5. 9.1 Amino Acids—A Second Look
Amino Acid Structure
Amino acids contain two functional groups, a protonated amine and carboxylic acid in the form of a carboxylate group.
These functional groups are bonded to a central carbon atom known as the alpha () carbon, and are referred to as alpha amino acids.
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6. 9.1 Amino Acids—A Second Look, Continued
The  carbon is also bonded to a hydrogen atom and a larger side chain. The side chain is unique for each amino acid.
The  carbon on all amino acids, except glycine, is a chiral carbon because it has four different groups bonded to it.
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7. 9.1 Amino Acids—A Second Look, Continued
An amino acid, with a chiral center, has two forms called enantiomers, which are nonsuperimposable mirror images.
When drawing the Fischer projection, the carboxylate group is at the top of the structure and the side chain (R group) is at the bottom.
The protonated amine group can be on the left-hand side (L form) or right-hand side (D form) of the structure.
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8. 9.1 Amino Acids—A Second Look, Continued
The L-amino acids are the building blocks for proteins. Some D-amino acids occur in nature, but not in proteins.
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9. 9.1 Amino Acids—A Second Look, Continued
The R group gives each amino acid its unique identity and characteristics.
Twenty amino acids are found in most proteins.
There are nine different families of organic compounds represented in the structures of different amino acids. They are as follows:
Alkanes
Aromatics
Thioethers
Alcohols
Phenols
Thiols
Amides
Carboxylic acids
Amines
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10. 9.1 Amino Acids—A Second Look, Continued
The functional groups divide the amino acids into the following four categories:
Nonpolar, consisting of nine amino acids
Polar, consisting of six amino acids
Acidic, consisting of two amino acids
Basic, consisting of three amino acids
There are 10 amino acids that are essential amino acids because they cannot be synthesized in the human body and must be obtained in the diet.
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11. 9.1 Amino Acids—A Second Look, Continued
The 10 essential amino acids are: valine, leucine, isoleucine, phenylalanine, methionine, tryptophan, threonine, histidine, lysine, and arginine.
Two of these amino acids, arginine and histidine, are essential in children, but not adults.
Nonessential amino acids can be synthesized in the body from essential amino acids.
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12. 9.1 Amino Acids—A Second Look, Continued
Proteins that contain all the essential amino acids are called complete proteins.
Soybeans and most proteins found in animal products are complete proteins.
Some plant proteins are incomplete proteins because they lack one or more essential amino acid.
Complete proteins can be obtained by combining foods like rice and beans.
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13. 9.1 Amino Acids—A Second Look, Continued
The structure of the amino acids, including side chains, names, functional groups, and abbreviations are shown in the next few slides.
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14. 9.1 Amino Acids—A Second Look, Continued
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15. 9.1 Amino Acids—A Second Look, Continued
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16. 9.1 Amino Acids—A Second Look, Continued
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17. 9.1 Amino Acids—A Second Look, Continued
Classification of Amino Acids
There are two classifications of amino acids based on the side chains:
Nonpolar amino acids
Polar amino acids, which are further divided into:
Neutral amino acids
Acidic amino acids
Basic amino acids
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18. 9.1 Amino Acids—A Second Look, Continued
Amino Acids Classified as Nonpolar
Side chains consists entirely of carbon and hydrogen.
Carbon–hydrogen bond is nonpolar.
Compounds composed of only carbon and hydrogen are nonpolar and hydrophobic.
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19. 9.1 Amino Acids—A Second Look, Continued
Amino Acids Classified as Polar
Contain functional groups, such as hydroxyl (–OH) and amide (–CONH2).
Side chains can form hydrogen bonds with water.
Side chains are hydrophilic.
An exception is cysteine, which does not form hydrogen bonds.
Polar acidic and basic amino acids have charged side chains that can form ion–dipole interactions with water. These amino acids are more polar than those classified as polar neutral.
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20. 9.2 Protein Formation
When two amino acids condense, a dipeptide is formed.
The carboxylate ion (–COO-) of one amino acid reacts with the protonated amine (–NH3+) of a second amino acid.
A water molecule is lost and an amide functional group is formed. An amide bond is formed between the two amino acids.
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21. 9.2 Protein Formation, Continued
When amino acids combine in a condensation reaction, the amide bond that is formed between them is called a peptide bond.
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22. 9.2 Protein Formation, Continued
The product formed during the condensation of alanine and valine is known as a dipeptide, which is represented as Ala—Val or AV.
In this dipeptide, alanine is called the N-terminus because it has an unreacted -amino group.
Valine is called the C-terminus because it has an unreacted -carboxylate group.
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23. 9.2 Protein Formation, Continued
Structures are always written from N-terminus to C-terminus.
Two amino acids can combine in two ways forming two different dipeptides.
The two dipeptides formed from condensation of Ala and Val are Ala—Val and Val—Ala. They are structural isomers, different compounds, and have different properties.
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24. 9.2 Protein Formation, Continued
Peptides formed in the condensation of three amino acids are known as tripeptides; ones with four amino acids are tetrapeptides; ones with five amino acids are pentapeptides; etc.
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25. 9.2 Protein Formation, Continued
A polypeptide is a compound that is formed when the number of amino acids increases.
A biologically active polypeptide consisting of 50 or more amino acids is referred to as a protein.
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26. 9.3 The Three-Dimensional Structure of Proteins
Peptides and proteins have three-dimensional shapes or structures.
Since the simplest dipeptide contains many atoms, it would be impossible to predict its shape by VSEPR as was done with simple organic molecules.
Proteins have four levels of structure:
Primary (1o)
Secondary (2o)
Tertiary (3o)
Quaternary (4o)
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27. 9.3 The Three-Dimensional Structure of Proteins, Continued
Each level of protein structure is a result of interactions between the amino acids of the protein.
Primary Structure
The primary structure is the order in which the amino acids are joined together by peptide bonds that forms the backbone from N-terminus to C-terminus. The amino acid side chains are substituents to this backbone.
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28. 9.3 The Three-Dimensional Structure of Proteins, Continued
The order or sequence of amino acids in a protein chain are important in determining its structure and function.
Arranging amino acids in a different order creates a polypeptide or protein that no longer has the same function as the initial sequence of amino acids.
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29. 9.3 The Three-Dimensional Structure of Proteins, Continued
For example, the eight amino acid peptide angiotensin II, which is involved in normal blood pressure regulation in humans, has the following amino acid sequence:
Asp—Arg—Val—Tyr—Ile—His—Pro—Phe
Any other order of amino acids in this peptide would result in a peptide that would not function as angiotensin II.
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30. 9.3 The Three-Dimensional Structure of Proteins, Continued
Secondary Structure
The secondary structure of a protein describes repeating patterns of structure within the three-dimensional structure of a protein.
The two most common secondary structures are:
Alpha helix (helix)
Beta-pleated sheet (-pleated sheet)
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31. 9.3 The Three-Dimensional Structure of Proteins, Continued
The  helix is a coiled structure, and much like the coil of a telephone cord, it is a right-handed coil.
This coil is stabilized by hydrogen bonds between the carbonyl oxygen of one amino acid and the N—H hydrogen atom of another amino acid located four amino acids from it in the primary structure.
The coil is able to stretch and recoil, and is a strong structure. The side chains project outward from the axis of the helix.
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32. 9.3 The Three-Dimensional Structure of Proteins, Continued
A secondary structure involves hydrogen bonding along the backbone.
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33. 9.3 The Three-Dimensional Structure of Proteins, Continued
The -pleated sheet is an extended structure in which segments of the protein chain align to form a zigzag structure.
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34. 9.3 The Three-Dimensional Structure of Proteins, Continued
Strands called beta strands are held together through hydrogen bonding interactions between the backbone.
The side chains of a -pleated sheet extend above and below the sheet.
The interactions of the side chains within the secondary structure lead to the tertiary structure of proteins.
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35. 9.3 The Three-Dimensional Structure of Proteins, Continued
Tertiary Structure
The tertiary structure is the three-dimensional structure of the protein.
It involves twisting and folding of the polypeptide chain caused by hydrophobic and hydrophilic interactions between the side chains of the amino acids.
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36. 9.3 The Three-Dimensional Structure of Proteins, Continued
The nonpolar amino side chains end up in the interior of the protein away from the aqueous environment.
The polar side chains appear on the surface of the protein since they are attracted to the aqueous surroundings.
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37. 9.3 The Three-Dimensional Structure of Proteins, Continued
Stabilization of the tertiary structure is by:
Attractive forces between the side chains and aqueous environment
Attractive forces between side chains themselves
These attractive forces cause the protein to fold into a specific three-dimensional shape.
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38. 9.3 The Three-Dimensional Structure of Proteins, Continued
Interactions in the tertiary structure involves:
Nonpolar or hydrophobic interactions
Polar or hydrophilic interactions
Salt bridges (ionic interactions)
Disulfide bonds, which are covalent bonds formed between –SH groups of two cysteine molecules.
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39. 9.3 The Three-Dimensional Structure of Proteins, Continued
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40. 9.3 The Three-Dimensional Structure of Proteins, Continued
Proteins are classified into groups based on their
three-dimensional shape.
Globular proteins are compact, spherical structures that are soluble in an aqueous environment. Myoglobin, which stores oxygen in muscle, is an example.
Fibrous proteins are long, threadlike structures that have high helical content. Keratins, found in hair, nails, the scales of reptiles, and collagen, are examples.
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41. 9.3 The Three-Dimensional Structure of Proteins, Continued
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42. 9.3 The Three-Dimensional Structure of Proteins, Continued
Quaternary Structure
The quaternary structure is two or more polypeptide chains interacting to form a biologically active protein.
Hemoglobin, an oxygen transport protein, is an example of a protein with a quaternary structure.
It consists of four polypeptide chains or subunits.
It has two identical alpha subunits and two identical beta subunits.
All four subunits must be present for the protein to function as an oxygen carrier.
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43. 9.3 The Three-Dimensional Structure of Proteins, Continued
Not all proteins have a quaternary structure.
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44. 9.3 The Three-Dimensional Structure of Proteins, Continued
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45. 9.4 Denaturation of Proteins
Denaturation is a process that disrupts secondary, tertiary, and quaternary structures.
The primary structure is not destroyed during denaturation.
Frying an egg is an example of denaturation by heat. Heat disrupts intermolecular forces such as hydrogen bonding, London forces, and other polar interactions.
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46. 9.4 Denaturation of Proteins, Continued
Other denaturing agents:
Changes in pH, which alters the ability of the acidic and basic side chains to form salt bridges
Organic compounds, which will disrupt the disulfide bonds
Heavy metals that disrupt salt bridges and disulfide bonds
Mechanical agitation, which disrupts hydrogen bonds and London forces
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47. 9.4 Denaturation of Proteins, Continued
A protein will lose its biological activity if it loses its three-dimensional shape.
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48. 9.4 Denaturation of Proteins, Continued
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49. 9.4 Denaturation of Proteins, Continued
Curling straight hair or straightening curly hair requires protein denaturation.
Both processes require disruption of disulfide bonds found in the hair protein keratin.
The disruption of disulfide bonds reshapes the hair and forces the reformation of disulfide bonds in new places.
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50. 9.4 Denaturation of Proteins, Continued
Ammonium thioglycolate, which reduces (breaks) disulfide bonds, and hydrogen peroxide (reforms disulfide bonds) are two chemical agents used in hairstyling.
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51. 9.4 Denaturation of Proteins, Continued
The process of denaturation is used as an antidote for lead or mercury poisoning.
Egg whites can be given to an individual who has ingested a heavy metal. Egg whites are denaturated by the heavy metals and a precipitate is formed.
Vomiting is induced to eliminate the metal-protein precipitate.
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52. 9.5 Examples of Biologically Important Proteins
Collagen
Collagen is the most abundant protein in the body. One-third of the bodies protein is collagen.
It is found in connective tissue like cartilage, skin, blood vessels, and tendons.
A special quaternary structure called a triple helix forms the fibrous structure of collagen.
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53. 9.5 Examples of Biologically Important Proteins, Continued
Each polypeptide chain of a triple helix is a left-handed helix.
Collagen primarily contains the amino acids glycine, proline, alanine, and hydroxyproline.
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54. 9.5 Examples of Biologically Important Proteins, Continued
Hydrogen bonds between the polypeptide chains in collagen are formed through the hydroxyl group on hydroxyproline.
Proline is converted to hydroxyproline with the aid of Vitamin C. A deficiency of Vitamin C causes scurvy, which is a collagen malformation disease. Scurvy can be reversed with a vitamin C diet.
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55. 9.5 Examples of Biologically Important Proteins, Continued
Hemoglobin
Hemoglobin transports oxygen in blood.
It is composed of two alpha subunits and two beta subunits held together by hydrogen bonds, London forces, and salt bridges.
Each subunit contains a nonprotein part called a prosthetic group, which is called a heme.
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56. 9.5 Examples of Biologically Important Proteins, Continued
Each heme group binds an Fe2+, which binds O2, so a molecule of hemoglobin can bind up to four molecules of O2.
When O2 binds to the Fe2+ of hemoglobin, the shape of hemoglobin changes, which allows the hemoglobin to hold on to the oxygen until it is delivered to tissues. This change in shape is known as a conformational change.
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57. 9.5 Examples of Biologically Important Proteins, Continued
After the oxygen is delivered to the tissues, the shape of the hemoglobin changes back to its pre-oxygenated form.
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58. 9.5 Examples of Biologically Important Proteins, Continued
Antibodies—Your Body’s Defense System
Antibodies, also known as immunoglobulins, are produced in our bodies when a foreign agent like bacteria enters.
The foreign agent recognized by antibodies is known as an antigen.
Antibodies consists of four polypeptide chains held together by disulfide bonds and intermolecular forces.
Antibodies are “Y” shaped. Antigens bind at the top of each arm of the Y.
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59. 9.5 Examples of Biologically Important Proteins, Continued
Antibodies—Your Body’s Defense System,
Continued
The top of each Y has a unique primary structure for a particular antigen and binds only one antigen, which is then destroyed by the immune system.
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60. 9.5 Examples of Biologically Important Proteins, Continued
Integral Membrane Proteins
Integral membrane proteins span the nonpolar region of a cell membrane and facilitate the movement of polar substances across the membrane.
An important integral membrane protein involved in electrolyte balance is the sodium potassium pump (Na+/K+ ATPase).
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61. 9.5 Examples of Biologically Important Proteins, Continued
The sodium potassium pump protein is composed of four polypeptide chains held together by intermolecular forces.
The side chains embedded in the nonpolar region of the cell membrane are nonpolar, allowing them to interact with the nonpolar region of the membrane.
The central cavity of the protein is lined with polar amino acids, allowing polar molecules to pass.
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62. 9.5 Examples of Biologically Important Proteins, Continued
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63. Chapter Summary 9.1 Amino Acids—A Second Look
Amino acids contain a central carbon called an alpha (α) carbon bonded to four different groups: a protonated amine, carboxylate group, hydrogen atom, and a side chain.
Amino acids are chiral molecules, except for glycine.
L-amino acids are building blocks of proteins.
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64. Chapter Summary, Continued
9.1 Amino Acids—A Second Look, Continued
There are 20 different amino acids identified by their side chains.
Each amino acid has a unique name, and a three-letter abbreviation, as well as a one-letter designation.
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65. Chapter Summary, Continued
9.2 Protein Formation
Amino acids serve as building blocks of proteins.
Two amino acids join by an amide bond through the carboxylate group of one amino acid to the protonated amine group of the second amino acid.
The amide bond is known as a peptide bond.
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66. Chapter Summary, Continued
9.2 Protein Formation, Continued
Each peptide or protein formed has an N-terminus end with a free protonated amine group and a C-terminus end with a free carboxylate group.
Amino acid chains of less than 50 amino acids are referred to as peptides. Chains containing more than 50 amino acids are referred to as proteins.
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67. Chapter Summary, Continued
9.3 The Three-Dimensional Structure of
Proteins
The following are the four levels of protein
structure:
Primary (1o) refers to amino acid sequence.
Secondary (2o) consists of an alpha helix and a beta-pleated sheet.
Tertiary (3o) refers to the folding of the 2o structure.
Quaternary (4o) involves the interaction of two or more polypeptides to form a biologically active protein.
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68. Chapter Summary, Continued
9.3 The Three-Dimensional Structure of Proteins, Continued The 2o, 3o, and 4o structures are stabilized by hydrogen bonding, London forces, and other intermolecular interactions.
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69. Chapter Summary, Continued
9.4 Denaturation of Proteins
Denaturation of a protein disrupts the stabilizing forces in the secondary, tertiary, and quaternary structures.
Denaturing agents consist of heat, pH, heavy metal, organic chemicals, and mechanical agitation.
A denatured protein is not biologically active.
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70. Chapter Summary, Continued
9.5 Examples of Biologically Important Proteins
Collagen, hemoglobin, antibodies, and integral membrane proteins are examples of biologically important proteins.
The biological function of proteins is dictated by their structure.
Changes in the structure of proteins affect their biological function.
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