{"id":116,"date":"2021-12-07T06:35:37","date_gmt":"2021-12-07T06:35:37","guid":{"rendered":"https:\/\/pressbooks.publishdot.com\/anatomyphysiology\/?post_type=chapter&p=116"},"modified":"2021-12-07T06:41:56","modified_gmt":"2021-12-07T06:41:56","slug":"2-4-protein","status":"publish","type":"chapter","link":"https:\/\/pressbooks.publishdot.com\/anatomyphysiology\/chapter\/2-4-protein\/","title":{"raw":"2.4 Protein","rendered":"2.4 Protein"},"content":{"raw":"
\r\n

Learning Objectives<\/strong><\/p>\r\n\r\n<\/header>\r\n

\r\n\r\nBy the end of this section, you will be able to:\r\n
    \r\n \t
  • Describe the functions proteins perform in the cell and in tissues<\/li>\r\n \t
  • Discuss the relationship between amino acids and proteins<\/li>\r\n \t
  • Explain the four levels of protein organisation<\/li>\r\n \t
  • Describe the ways in which protein shape and function are linked<\/li>\r\n<\/ul>\r\n<\/div>\r\n<\/div>\r\nProteins\u00a0<\/strong>are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however,\u00a0amino acid<\/strong>\u00a0polymers arranged in a linear sequence.\r\n

    Types and Functions of Proteins<\/h2>\r\nEnzymes, which living cells produce, are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. The enzyme may help in breakdown, rearrangement, or synthesis reactions. We call enzymes that break down their substrates catabolic enzymes. Those that build more complex molecules from their substrates are anabolic enzymes, and enzymes that affect the rate of reaction are catalytic enzymes. Note that all enzymes increase the reaction rate and, therefore, are organic catalysts. An example of an enzyme is salivary amylase, which hydrolyses its substrate amylose, a component of starch.\r\n\r\nHormones\u00a0are chemical-signalling molecules, usually small proteins or steroids, secreted by endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps regulate the blood glucose level.\u00a0Table 2.4.1\u00a0lists the primary types and functions of proteins.\r\n

    Protein Types and Functions<\/h2>\r\nTable 2.4.1. Types of proteins and their functions.<\/strong>\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n
    Type<\/td>\r\nExamples<\/td>\r\nFunctions<\/td>\r\n<\/tr>\r\n
    Digestive Enzymes<\/td>\r\nAmylase, lipase, pepsin, trypsin<\/td>\r\nHelp in food by catabolising nutrients into monomeric units<\/td>\r\n<\/tr>\r\n
    Transport<\/td>\r\nHaemoglobin, albumin<\/td>\r\nCarry substances in the blood or lymph throughout the body<\/td>\r\n<\/tr>\r\n
    Structural<\/td>\r\nActin, tubulin, keratin<\/td>\r\nConstruct different structures, like the cytoskeleton<\/td>\r\n<\/tr>\r\n
    Hormones<\/td>\r\nInsulin, thyroxine<\/td>\r\nCoordinate different body systems\u2019 activity<\/td>\r\n<\/tr>\r\n
    Defences<\/td>\r\nImmunoglobulins<\/td>\r\nProtect the body from foreign pathogens<\/td>\r\n<\/tr>\r\n
    Contractile<\/td>\r\nActin, myosin<\/td>\r\nEffect muscle contraction<\/td>\r\n<\/tr>\r\n
    Storage<\/td>\r\nLegume storage proteins, egg white (albumin)<\/td>\r\nProvide nourishment in early embryo development and the seeding<\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\nProteins have different shapes and molecular weights. Some proteins are globular in shape; whereas, others are fibrous in nature, for example, haemoglobin is a globular protein, but collagen, located in our skin, is a fibrous protein. Protein shape is critical to its function, and many different types of chemical bonds maintain this shape. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the protein\u2019s shape, leading to loss of function, or\u00a0denaturation. Different arrangements of the same 20 types of amino acids comprise all proteins. Two rare new amino acids were discovered recently (selenocystein and pirrolysine), and additional new discoveries may be added to the list.\r\n

    Amino Acids<\/h2>\r\nAmino acids\u00a0are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (\u03b1<\/em>) carbon, bonded to an amino group (-NH2), a carboxyl group (-COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group (Figure 2.4.1).\r\n
    \"Amino
    Figure\u00a02.4.1.<\/strong>\u00a0Amino acids.<\/strong>\u00a0Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached.<\/figcaption><\/figure>\r\nScientists use the name \u201camino acid\u201d because these acids contain both amino group and carboxyl-acid-group in their basic structure. As we mentioned, there are 20 common amino acids present in proteins. Nine of these are essential amino acids in humans because the human body cannot produce them and we obtain them from our diet. For each amino acid, the R group (or side chain) is different (Figure 2.4.2).\r\n\r\n \r\n
    \"Diagram
    Figure\u00a02.4.2. Common amino acids.<\/strong>\u00a0There are 20 common amino acids commonly found in proteins, each with a different R group (variant group) that determines its chemical nature.<\/figcaption><\/figure>\r\nWhich categories of amino acid would you expect to find on a soluble protein\u2019s surface, and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?\r\n\r\nThe chemical nature of the side chain determines the amino acid\u2019s nature (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and therefore these amino acids are also basic amino acids. Proline has an R group that is linked to the amino group, forming a ring-like structure. Proline is an exception to the amino acid\u2019s standard structure since its amino group is not separate from the side chain (Figure 2.4.2).\r\n\r\nA single upper-case letter or a three-letter abbreviation represents amino acids, for example, the letter \u2018V\u2019 or the three-letter symbol \u2018val\u2019 represent the amino acid, valine. Just as some fatty acids are essential to a diet, some amino acids also are necessary. These essential amino acids in humans include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary to build proteins in the body, but not those that the body produces. Which amino acids are essential varies from organism to organism.\r\n\r\nThe sequence and the number of amino acids ultimately determine the protein\u2019s shape, size, and function. A covalent bond, or\u00a0peptide bond, attaches to each amino acid, which a dehydration reaction forms. One amino acid\u2019s carboxyl group and the incoming amino acid\u2019s amino group combine, releasing a water molecule. The resulting bond is the peptide bond (Figure 2.4.3).\r\n
    \"Peptide
    Figure\u00a02.4.3.<\/strong>\u00a0Peptide bond.<\/strong>\u00a0Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid is linked to the incoming amino acid\u2019s amino group. In the process, it releases a water molecule.<\/figcaption><\/figure>\r\nThe products that such linkages form are peptides. As more amino acids join to this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end the N terminal, or the amino terminal, and the other end has a free carboxyl group, also the C or carboxyl terminal. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function. After protein synthesis (translation), most proteins are modified. These are known as post-translational modifications. They may undergo cleavage, phosphorylation, or may require adding other chemical groups. Only after these modifications is the protein completely functional.\r\n

    Evolution Connection<\/h2>\r\nThe Evolutionary Significance of Cytochrome c<\/strong>\r\n\r\nCytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally located in the cellular organelle, the mitochondrion. This protein has a haem prosthetic group, and the haem\u2019s central ion alternately reduces and oxidises during electron transfer. Because this essential protein\u2019s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of cytochrome c amino acid sequence homology among different species. In other words, we can assess evolutionary kinship by measuring the similarities or differences among various species\u2019 DNA or protein sequences.\r\n\r\nScientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule from different organisms that scientists have sequenced to date, 37 of these amino acids appear in the same position in all cytochrome c samples. This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, scientists did not find a sequence difference. When researchers compared human and rhesus monkey sequences, the single difference was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position.\r\n

    Protein Structure<\/h2>\r\nAs was discussed earlier, a protein\u2019s shape is critical to its function, for example, an enzyme can bind to a specific substrate at an active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.\r\n

    Primary Structure<\/h2>\r\nAmino acids\u2019 unique sequence in a polypeptide chain is its\u00a0primary structure<\/strong>. For example, the pancreatic hormone insulin has two polypeptide chains, A and B, and they are linked together by disulphide bonds. The N terminal amino acid of the A chain is glycine; whereas, the C terminal amino acid is asparagine (Figure 2.4.4). The amino acid sequences in the A and B chains are unique to insulin.\r\n
    \"Bovine
    Figure\u00a02.4.4.<\/strong>\u00a0Bovine serum insulin amino acid sequence<\/strong>.\u00a0Bovine serum insulin is a protein hormone comprised of two peptide chains, A (21 amino acids long) and B (30 amino acids long). In each chain, three-letter abbreviations that represent the amino acids\u2019 names in the order they are present indicate primary structure. The amino acid cysteine (cys) has a sulfhydryl (SH) group as a side chain. Two sulfhydryl groups can react in the presence of oxygen to form a disulphide (S-S) bond. Two disulphide bonds connect the A and B chains together, and a third helps the A chain fold into the correct shape. Note that all disulphide bonds are the same length, but we have drawn them different sizes for clarity.<\/figcaption><\/figure>\r\nThe gene encoding the protein ultimately determines the unique sequence for every protein. A change in nucleotide sequence of the gene\u2019s coding region may lead to adding a different amino acid to the growing polypeptide chain, causing a change in protein structure and function. In sickle cell anaemia, the haemoglobin\u00a0\u03b2<\/em>\u00a0chain (a small portion of which we show in\u00a0Figure 2.4.5) has a single amino acid substitution, causing a change in protein structure and function. Specifically, valine in the\u00a0\u03b2<\/em>\u00a0chain substitutes the amino acid glutamic. What is most remarkable to consider is that a haemoglobin molecule is comprised of two alpha and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal haemoglobin molecule and a sickle cell molecule\u2014which dramatically decreases life expectancy\u2014is a single amino acid of the 600. What is even more remarkable is that three nucleotides each encode those 600 amino acids, and a single base change (point mutation), 1 in 1800 bases causes the mutation.\r\n
    \"Haemoglobin
    Figure\u00a02.4.5.<\/strong>\u00a0Haemoglobin amino acid composition.<\/strong>\u00a0The beta chain of haemoglobin is 147 residues in length, yet a single amino acid substitution leads to sickle cell anaemia. In normal haemoglobin, the amino acid at position seven is glutamate. In sickle cell haemoglobin, a valine replaces glutamate.<\/figcaption><\/figure>\r\nBecause of this change of one amino acid in the chain, haemoglobin molecules form long fibres that distort the biconcave, or disc-shaped, red blood cells and causes them to assume a crescent or \u201csickle\u201d shape, which clogs blood vessels (Figure 2.4.6). This can lead to myriad serious health problems such as breathlessness, dizziness, headaches and abdominal pain for those affected by this disease.\r\n
    \"Blood
    Figure\u00a02.4.6.<\/strong>\u00a0Blood smear.<\/strong>\u00a0In this blood smear, visualised at 535x magnification using bright field microscopy, sickle cells are crescent shaped, while normal cells are disc-shaped. (Credit: modification of work by Ed Uthman; scale-bar data from Matt Russell).<\/figcaption><\/figure>\r\n

    Secondary Structure<\/h2>\r\nThe local folding of the polypeptide in some regions gives rise to the\u00a0secondary structure<\/strong>\u00a0of the protein. The most common are the\u00a0\u03b1<\/em>-helix\u00a0and\u00a0\u03b2<\/em>-pleated<\/strong>\u00a0sheet\u00a0structures (Figure 2.4.7). Both structures are held in shape by hydrogen bonds. The hydrogen bonds form between the oxygen atom in the carbonyl group in one amino acid and another amino acid that is four amino acids farther along the chain.\r\n
    \"Secondary
    Figure\u00a02.4.7. Secondary protein structure.<\/strong>\u00a0The\u00a0\u03b1<\/em>-helix and\u00a0\u03b2<\/em>-pleated sheet are secondary structures of proteins that form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone. Certain amino acids have a propensity to form an\u00a0\u03b1<\/em>-helix, while others have a propensity to form a\u00a0\u03b2<\/em>-pleated sheet.<\/figcaption><\/figure>\r\nEvery helical turn in an\u00a0alpha helix<\/strong>\u00a0has 3.6 amino acid residues. The polypeptide\u2019s R groups (the variant groups) protrude out from the\u00a0\u03b1<\/em>-helix chain. In the\u00a0\u03b2<\/em>-pleated sheet, hydrogen bonding between atoms on the polypeptide chain\u2019s backbone form the \u201cpleats\u201d. The R groups are attached to the carbons and extend above and below the pleat\u2019s folds. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive hydrogen atom in the amino group and the partially negative oxygen atom in the peptide backbone\u2019s carbonyl group. The\u00a0\u03b1<\/em>-helix and\u00a0\u03b2<\/em>-pleated sheet structures are in most globular and fibrous proteins and they play an important structural role.\r\n

    Tertiary Structure<\/h2>\r\nThe polypeptide\u2019s unique three-dimensional structure is its\u00a0tertiary structure<\/strong>\u00a0(Figure 2.4.8). This structure is in part due to chemical interactions at work on the polypeptide chain. Primarily, the interactions among R groups create the protein\u2019s complex three-dimensional tertiary structure. The nature of the R groups in the amino acids involved can counteract forming the hydrogen bonds we described for standard secondary structures. For example, R groups with like charges repel each other and those with unlike charges are attracted to each other (ionic bonds). When protein folding takes place, the nonpolar amino acids\u2019 hydrophobic R groups lie in the protein\u2019s interior; whereas, the hydrophilic R groups lie on the outside. Scientists also call the former interaction types hydrophobic interactions. Interaction between cysteine side chains forms disulphide linkages in the presence of oxygen, the only covalent bond that forms during protein folding.\r\n
    \"Protein
    Figure\u00a02.4.8.<\/strong>\u00a0Protein tertiary structure.<\/strong>\u00a0A variety of chemical interactions determine the proteins\u2019 tertiary structure. These include hydrophobic interactions, ionic bonding, hydrogen bonding, and disulphide linkages.<\/figcaption><\/figure>\r\nAll these interactions, weak and strong, determine the protein\u2019s final three-dimensional shape. When a protein loses its three-dimensional shape, it may no longer be functional.\r\n

    Quaternary Structure<\/h2>\r\nIn nature, some proteins form from several polypeptides, or subunits, and the interaction of these subunits forms the\u00a0quaternary structure<\/strong>. Weak interactions between the subunits help to stabilise the overall structure. For example, insulin (a globular protein) has a combination of hydrogen and disulphide bonds that cause it to mostly clump into a ball shape. Insulin starts out as a single polypeptide and loses some internal sequences in the presence of post-translational modification after forming the disulphide linkages that hold the remaining chains together. Silk (a fibrous protein), however, has a\u00a0\u03b2<\/em>-pleated sheet structure that is the result of hydrogen bonding between different chains.\r\n\r\nFigure 2.4.9\u00a0illustrates the four levels of protein structure (primary, secondary, tertiary, and quaternary).\r\n
    \"Protein
    Figure\u00a02.4.9. Protein structure levels.<\/strong>\u00a0Observe the four levels of protein structure in these illustrations. (Credit: modification of work by National Human Genome Research Institute).<\/figcaption><\/figure>\r\n

    Denaturation and Protein Folding<\/h2>\r\nEach protein has its own unique sequence and shape that chemical interactions hold together. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape without losing its primary sequence in what scientists call\u00a0denaturation<\/strong>. Denaturation is often reversible because the polypeptide\u2019s primary structure is conserved in the process if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to loss of function. One example of irreversible protein denaturation is frying an egg. The albumin protein in the liquid egg white denatures when placed in a hot pan. Not all proteins denature at high temperatures. For instance, bacteria that survive in hot springs have proteins that function at temperatures close to boiling. The stomach is also very acidic, has a low pH and denatures proteins as part of the digestion process; however, the stomach\u2019s digestive enzymes retain their activity under these conditions.\r\n\r\nProtein folding is critical to its function. Scientists originally thought that the proteins themselves were responsible for the folding process. Only recently researchers discovered that often they receive assistance in the folding process from protein helpers, or\u00a0chaperones<\/strong>\u00a0(or chaperonins) that associate with the target protein during the folding process. They act by preventing polypeptide aggregation that comprise the complete protein structure, and they disassociate from the protein once the target protein is folded.\r\n
    \r\n

    Section Review<\/strong><\/p>\r\n\r\n<\/header>\r\n

    \r\n\r\nProteins are a class of macromolecules that perform a diverse range of functions for the cell. They help in metabolism by acting as enzymes, carriers, or hormones, and provide structural support. The building blocks of proteins (monomers) are amino acids. Each amino acid has a central carbon that bonds to an amino group, a carboxyl group, a hydrogen atom, and an R group or side chain. There are 20 commonly occurring amino acids, each of which differs in the R group. A peptide bond links each amino acid to its neighbours. A long amino acid chain is a polypeptide.\r\n\r\nProteins are organised at four levels: primary, secondary, tertiary, and (optional) quaternary. The primary structure is the amino acids\u2019 unique sequence. The polypeptide\u2019s local folding to form structures such as the\u00a0\u03b1<\/em>-helix and\u00a0\u03b2<\/em>-pleated sheet constitutes the secondary structure. The overall three-dimensional structure is the tertiary structure. When two or more polypeptides combine to form the complete protein structure, the configuration is the protein\u2019s quaternary structure. Protein shape and function are intricately linked. Any change in shape caused by changes in temperature or pH may lead to protein denaturation and a loss in function.\r\n\r\n<\/div>\r\n<\/div>\r\n
    \r\n

    Review Questions<\/strong><\/p>\r\n\r\n<\/header>\r\n

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    [h5p id=\"40\"]<\/div>\r\n<\/div>\r\n<\/div>\r\n<\/div>\r\n
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    Critical Thinking Questions<\/strong><\/p>\r\n\r\n<\/header>\r\n

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    [h5p id=\"41\"]<\/div>\r\n<\/div>\r\n
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    [h5p id=\"43\"]<\/div>\r\n<\/div>\r\n<\/div>\r\n<\/div>\r\nClick the drop down below to review the terms learned from this chapter.\r\n
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    [h5p id=\"44\"]<\/div>\r\n<\/div>","rendered":"
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    Learning Objectives<\/strong><\/p>\n<\/header>\n

    \n

    By the end of this section, you will be able to:<\/p>\n

      \n
    • Describe the functions proteins perform in the cell and in tissues<\/li>\n
    • Discuss the relationship between amino acids and proteins<\/li>\n
    • Explain the four levels of protein organisation<\/li>\n
    • Describe the ways in which protein shape and function are linked<\/li>\n<\/ul>\n<\/div>\n<\/div>\n

      Proteins\u00a0<\/strong>are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however,\u00a0amino acid<\/strong>\u00a0polymers arranged in a linear sequence.<\/p>\n

      Types and Functions of Proteins<\/h2>\n

      Enzymes, which living cells produce, are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. The enzyme may help in breakdown, rearrangement, or synthesis reactions. We call enzymes that break down their substrates catabolic enzymes. Those that build more complex molecules from their substrates are anabolic enzymes, and enzymes that affect the rate of reaction are catalytic enzymes. Note that all enzymes increase the reaction rate and, therefore, are organic catalysts. An example of an enzyme is salivary amylase, which hydrolyses its substrate amylose, a component of starch.<\/p>\n

      Hormones\u00a0are chemical-signalling molecules, usually small proteins or steroids, secreted by endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps regulate the blood glucose level.\u00a0Table 2.4.1\u00a0lists the primary types and functions of proteins.<\/p>\n

      Protein Types and Functions<\/h2>\n

      Table 2.4.1. Types of proteins and their functions.<\/strong><\/p>\n\n\n\n\n\n\n\n\n\n\n
      Type<\/td>\nExamples<\/td>\nFunctions<\/td>\n<\/tr>\n
      Digestive Enzymes<\/td>\nAmylase, lipase, pepsin, trypsin<\/td>\nHelp in food by catabolising nutrients into monomeric units<\/td>\n<\/tr>\n
      Transport<\/td>\nHaemoglobin, albumin<\/td>\nCarry substances in the blood or lymph throughout the body<\/td>\n<\/tr>\n
      Structural<\/td>\nActin, tubulin, keratin<\/td>\nConstruct different structures, like the cytoskeleton<\/td>\n<\/tr>\n
      Hormones<\/td>\nInsulin, thyroxine<\/td>\nCoordinate different body systems\u2019 activity<\/td>\n<\/tr>\n
      Defences<\/td>\nImmunoglobulins<\/td>\nProtect the body from foreign pathogens<\/td>\n<\/tr>\n
      Contractile<\/td>\nActin, myosin<\/td>\nEffect muscle contraction<\/td>\n<\/tr>\n
      Storage<\/td>\nLegume storage proteins, egg white (albumin)<\/td>\nProvide nourishment in early embryo development and the seeding<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

      Proteins have different shapes and molecular weights. Some proteins are globular in shape; whereas, others are fibrous in nature, for example, haemoglobin is a globular protein, but collagen, located in our skin, is a fibrous protein. Protein shape is critical to its function, and many different types of chemical bonds maintain this shape. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the protein\u2019s shape, leading to loss of function, or\u00a0denaturation. Different arrangements of the same 20 types of amino acids comprise all proteins. Two rare new amino acids were discovered recently (selenocystein and pirrolysine), and additional new discoveries may be added to the list.<\/p>\n

      Amino Acids<\/h2>\n

      Amino acids\u00a0are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (\u03b1<\/em>) carbon, bonded to an amino group (-NH2), a carboxyl group (-COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group (Figure 2.4.1).<\/p>\n

      \"Amino
      Figure\u00a02.4.1.<\/strong>\u00a0Amino acids.<\/strong>\u00a0Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached.<\/figcaption><\/figure>\n

      Scientists use the name \u201camino acid\u201d because these acids contain both amino group and carboxyl-acid-group in their basic structure. As we mentioned, there are 20 common amino acids present in proteins. Nine of these are essential amino acids in humans because the human body cannot produce them and we obtain them from our diet. For each amino acid, the R group (or side chain) is different (Figure 2.4.2).<\/p>\n

       <\/p>\n

      \"Diagram
      Figure\u00a02.4.2. Common amino acids.<\/strong>\u00a0There are 20 common amino acids commonly found in proteins, each with a different R group (variant group) that determines its chemical nature.<\/figcaption><\/figure>\n

      Which categories of amino acid would you expect to find on a soluble protein\u2019s surface, and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?<\/p>\n

      The chemical nature of the side chain determines the amino acid\u2019s nature (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and therefore these amino acids are also basic amino acids. Proline has an R group that is linked to the amino group, forming a ring-like structure. Proline is an exception to the amino acid\u2019s standard structure since its amino group is not separate from the side chain (Figure 2.4.2).<\/p>\n

      A single upper-case letter or a three-letter abbreviation represents amino acids, for example, the letter \u2018V\u2019 or the three-letter symbol \u2018val\u2019 represent the amino acid, valine. Just as some fatty acids are essential to a diet, some amino acids also are necessary. These essential amino acids in humans include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary to build proteins in the body, but not those that the body produces. Which amino acids are essential varies from organism to organism.<\/p>\n

      The sequence and the number of amino acids ultimately determine the protein\u2019s shape, size, and function. A covalent bond, or\u00a0peptide bond, attaches to each amino acid, which a dehydration reaction forms. One amino acid\u2019s carboxyl group and the incoming amino acid\u2019s amino group combine, releasing a water molecule. The resulting bond is the peptide bond (Figure 2.4.3).<\/p>\n

      \"Peptide
      Figure\u00a02.4.3.<\/strong>\u00a0Peptide bond.<\/strong>\u00a0Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid is linked to the incoming amino acid\u2019s amino group. In the process, it releases a water molecule.<\/figcaption><\/figure>\n

      The products that such linkages form are peptides. As more amino acids join to this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end the N terminal, or the amino terminal, and the other end has a free carboxyl group, also the C or carboxyl terminal. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function. After protein synthesis (translation), most proteins are modified. These are known as post-translational modifications. They may undergo cleavage, phosphorylation, or may require adding other chemical groups. Only after these modifications is the protein completely functional.<\/p>\n

      Evolution Connection<\/h2>\n

      The Evolutionary Significance of Cytochrome c<\/strong><\/p>\n

      Cytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally located in the cellular organelle, the mitochondrion. This protein has a haem prosthetic group, and the haem\u2019s central ion alternately reduces and oxidises during electron transfer. Because this essential protein\u2019s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of cytochrome c amino acid sequence homology among different species. In other words, we can assess evolutionary kinship by measuring the similarities or differences among various species\u2019 DNA or protein sequences.<\/p>\n

      Scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule from different organisms that scientists have sequenced to date, 37 of these amino acids appear in the same position in all cytochrome c samples. This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, scientists did not find a sequence difference. When researchers compared human and rhesus monkey sequences, the single difference was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position.<\/p>\n

      Protein Structure<\/h2>\n

      As was discussed earlier, a protein\u2019s shape is critical to its function, for example, an enzyme can bind to a specific substrate at an active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.<\/p>\n

      Primary Structure<\/h2>\n

      Amino acids\u2019 unique sequence in a polypeptide chain is its\u00a0primary structure<\/strong>. For example, the pancreatic hormone insulin has two polypeptide chains, A and B, and they are linked together by disulphide bonds. The N terminal amino acid of the A chain is glycine; whereas, the C terminal amino acid is asparagine (Figure 2.4.4). The amino acid sequences in the A and B chains are unique to insulin.<\/p>\n

      \"Bovine
      Figure\u00a02.4.4.<\/strong>\u00a0Bovine serum insulin amino acid sequence<\/strong>.\u00a0Bovine serum insulin is a protein hormone comprised of two peptide chains, A (21 amino acids long) and B (30 amino acids long). In each chain, three-letter abbreviations that represent the amino acids\u2019 names in the order they are present indicate primary structure. The amino acid cysteine (cys) has a sulfhydryl (SH) group as a side chain. Two sulfhydryl groups can react in the presence of oxygen to form a disulphide (S-S) bond. Two disulphide bonds connect the A and B chains together, and a third helps the A chain fold into the correct shape. Note that all disulphide bonds are the same length, but we have drawn them different sizes for clarity.<\/figcaption><\/figure>\n

      The gene encoding the protein ultimately determines the unique sequence for every protein. A change in nucleotide sequence of the gene\u2019s coding region may lead to adding a different amino acid to the growing polypeptide chain, causing a change in protein structure and function. In sickle cell anaemia, the haemoglobin\u00a0\u03b2<\/em>\u00a0chain (a small portion of which we show in\u00a0Figure 2.4.5) has a single amino acid substitution, causing a change in protein structure and function. Specifically, valine in the\u00a0\u03b2<\/em>\u00a0chain substitutes the amino acid glutamic. What is most remarkable to consider is that a haemoglobin molecule is comprised of two alpha and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal haemoglobin molecule and a sickle cell molecule\u2014which dramatically decreases life expectancy\u2014is a single amino acid of the 600. What is even more remarkable is that three nucleotides each encode those 600 amino acids, and a single base change (point mutation), 1 in 1800 bases causes the mutation.<\/p>\n

      \"Haemoglobin
      Figure\u00a02.4.5.<\/strong>\u00a0Haemoglobin amino acid composition.<\/strong>\u00a0The beta chain of haemoglobin is 147 residues in length, yet a single amino acid substitution leads to sickle cell anaemia. In normal haemoglobin, the amino acid at position seven is glutamate. In sickle cell haemoglobin, a valine replaces glutamate.<\/figcaption><\/figure>\n

      Because of this change of one amino acid in the chain, haemoglobin molecules form long fibres that distort the biconcave, or disc-shaped, red blood cells and causes them to assume a crescent or \u201csickle\u201d shape, which clogs blood vessels (Figure 2.4.6). This can lead to myriad serious health problems such as breathlessness, dizziness, headaches and abdominal pain for those affected by this disease.<\/p>\n

      \"Blood
      Figure\u00a02.4.6.<\/strong>\u00a0Blood smear.<\/strong>\u00a0In this blood smear, visualised at 535x magnification using bright field microscopy, sickle cells are crescent shaped, while normal cells are disc-shaped. (Credit: modification of work by Ed Uthman; scale-bar data from Matt Russell).<\/figcaption><\/figure>\n

      Secondary Structure<\/h2>\n

      The local folding of the polypeptide in some regions gives rise to the\u00a0secondary structure<\/strong>\u00a0of the protein. The most common are the\u00a0\u03b1<\/em>-helix\u00a0and\u00a0\u03b2<\/em>-pleated<\/strong>\u00a0sheet\u00a0structures (Figure 2.4.7). Both structures are held in shape by hydrogen bonds. The hydrogen bonds form between the oxygen atom in the carbonyl group in one amino acid and another amino acid that is four amino acids farther along the chain.<\/p>\n

      \"Secondary
      Figure\u00a02.4.7. Secondary protein structure.<\/strong>\u00a0The\u00a0\u03b1<\/em>-helix and\u00a0\u03b2<\/em>-pleated sheet are secondary structures of proteins that form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone. Certain amino acids have a propensity to form an\u00a0\u03b1<\/em>-helix, while others have a propensity to form a\u00a0\u03b2<\/em>-pleated sheet.<\/figcaption><\/figure>\n

      Every helical turn in an\u00a0alpha helix<\/strong>\u00a0has 3.6 amino acid residues. The polypeptide\u2019s R groups (the variant groups) protrude out from the\u00a0\u03b1<\/em>-helix chain. In the\u00a0\u03b2<\/em>-pleated sheet, hydrogen bonding between atoms on the polypeptide chain\u2019s backbone form the \u201cpleats\u201d. The R groups are attached to the carbons and extend above and below the pleat\u2019s folds. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive hydrogen atom in the amino group and the partially negative oxygen atom in the peptide backbone\u2019s carbonyl group. The\u00a0\u03b1<\/em>-helix and\u00a0\u03b2<\/em>-pleated sheet structures are in most globular and fibrous proteins and they play an important structural role.<\/p>\n

      Tertiary Structure<\/h2>\n

      The polypeptide\u2019s unique three-dimensional structure is its\u00a0tertiary structure<\/strong>\u00a0(Figure 2.4.8). This structure is in part due to chemical interactions at work on the polypeptide chain. Primarily, the interactions among R groups create the protein\u2019s complex three-dimensional tertiary structure. The nature of the R groups in the amino acids involved can counteract forming the hydrogen bonds we described for standard secondary structures. For example, R groups with like charges repel each other and those with unlike charges are attracted to each other (ionic bonds). When protein folding takes place, the nonpolar amino acids\u2019 hydrophobic R groups lie in the protein\u2019s interior; whereas, the hydrophilic R groups lie on the outside. Scientists also call the former interaction types hydrophobic interactions. Interaction between cysteine side chains forms disulphide linkages in the presence of oxygen, the only covalent bond that forms during protein folding.<\/p>\n

      \"Protein
      Figure\u00a02.4.8.<\/strong>\u00a0Protein tertiary structure.<\/strong>\u00a0A variety of chemical interactions determine the proteins\u2019 tertiary structure. These include hydrophobic interactions, ionic bonding, hydrogen bonding, and disulphide linkages.<\/figcaption><\/figure>\n

      All these interactions, weak and strong, determine the protein\u2019s final three-dimensional shape. When a protein loses its three-dimensional shape, it may no longer be functional.<\/p>\n

      Quaternary Structure<\/h2>\n

      In nature, some proteins form from several polypeptides, or subunits, and the interaction of these subunits forms the\u00a0quaternary structure<\/strong>. Weak interactions between the subunits help to stabilise the overall structure. For example, insulin (a globular protein) has a combination of hydrogen and disulphide bonds that cause it to mostly clump into a ball shape. Insulin starts out as a single polypeptide and loses some internal sequences in the presence of post-translational modification after forming the disulphide linkages that hold the remaining chains together. Silk (a fibrous protein), however, has a\u00a0\u03b2<\/em>-pleated sheet structure that is the result of hydrogen bonding between different chains.<\/p>\n

      Figure 2.4.9\u00a0illustrates the four levels of protein structure (primary, secondary, tertiary, and quaternary).<\/p>\n

      \"Protein
      Figure\u00a02.4.9. Protein structure levels.<\/strong>\u00a0Observe the four levels of protein structure in these illustrations. (Credit: modification of work by National Human Genome Research Institute).<\/figcaption><\/figure>\n

      Denaturation and Protein Folding<\/h2>\n

      Each protein has its own unique sequence and shape that chemical interactions hold together. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape without losing its primary sequence in what scientists call\u00a0denaturation<\/strong>. Denaturation is often reversible because the polypeptide\u2019s primary structure is conserved in the process if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to loss of function. One example of irreversible protein denaturation is frying an egg. The albumin protein in the liquid egg white denatures when placed in a hot pan. Not all proteins denature at high temperatures. For instance, bacteria that survive in hot springs have proteins that function at temperatures close to boiling. The stomach is also very acidic, has a low pH and denatures proteins as part of the digestion process; however, the stomach\u2019s digestive enzymes retain their activity under these conditions.<\/p>\n

      Protein folding is critical to its function. Scientists originally thought that the proteins themselves were responsible for the folding process. Only recently researchers discovered that often they receive assistance in the folding process from protein helpers, or\u00a0chaperones<\/strong>\u00a0(or chaperonins) that associate with the target protein during the folding process. They act by preventing polypeptide aggregation that comprise the complete protein structure, and they disassociate from the protein once the target protein is folded.<\/p>\n

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      Section Review<\/strong><\/p>\n<\/header>\n

      \n

      Proteins are a class of macromolecules that perform a diverse range of functions for the cell. They help in metabolism by acting as enzymes, carriers, or hormones, and provide structural support. The building blocks of proteins (monomers) are amino acids. Each amino acid has a central carbon that bonds to an amino group, a carboxyl group, a hydrogen atom, and an R group or side chain. There are 20 commonly occurring amino acids, each of which differs in the R group. A peptide bond links each amino acid to its neighbours. A long amino acid chain is a polypeptide.<\/p>\n

      Proteins are organised at four levels: primary, secondary, tertiary, and (optional) quaternary. The primary structure is the amino acids\u2019 unique sequence. The polypeptide\u2019s local folding to form structures such as the\u00a0\u03b1<\/em>-helix and\u00a0\u03b2<\/em>-pleated sheet constitutes the secondary structure. The overall three-dimensional structure is the tertiary structure. When two or more polypeptides combine to form the complete protein structure, the configuration is the protein\u2019s quaternary structure. Protein shape and function are intricately linked. Any change in shape caused by changes in temperature or pH may lead to protein denaturation and a loss in function.<\/p>\n<\/div>\n<\/div>\n

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      Review Questions<\/strong><\/p>\n<\/header>\n

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