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results from hydrogen bonding between the backbone constituents of the overall shape of a polypeptide the polypeptide primary structure the aggregation of multiple polypeptide subunits secondary structure B pleated sheet results from interactions between side chains (R groups) of amino acids a helix tertiary structure amino acid sequence quaternary structure

results from hydrogen bonding between the backbone constituents of the overall shape of a polypeptide the polypeptide primary structure the aggregation of multiple polypeptide subunits secondary structure B pleated sheet results from interactions between side chains (R groups) of amino acids a helix tertiary structure amino acid sequence quaternary structure

Biochemistry
Biochemistry
9th Edition
ISBN:9781319114671
Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Chapter1: Biochemistry: An Evolving Science
Section: Chapter Questions
Problem 1P
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Amino acids Val Phe W Arg 35 Lys Asp Lys Thr 75 Tyr Ser Ser Thr 30 Primary Structure Linear chain of amino acids 115 Thr Amino end 80 His Val Ala Val Asn lle Ala Pro Ser Gly Arg Val Ala Asp Leu Val Lys 70 +H₂N-Gly Pro The Gly The Gly Glu Ser Lys Cys 40 25 H 45 110 20 Primary structure of transthyretin O Ala Ala Asp Asp The Trp Glu Pro Phe Ala Ser Gly Lys Thr Ser Glu Ser lle Giu Val Lys Tyr lle Gly Glu Val Pho Giu Glu Glu Thr The Leu Gly 120 125 Soo Ala Val Val Thr Asn Pro Lys Glu 105 10 50 90 15 Pro Tyr Trp Lys Ala Leu Gly ile Ser Pro Phe His Glu His Ala Glu Val Val 100 95 Ser Tyr Pro Ser Leu Leu Ala Ala Ile The Tyr Arg Arg Pro Gly Ser Asp ....... Val Leu Met His Carboxyl end The primary structure of a protein is a linked series of amino acids with a unique sequence. As an example, let's consider transthyretin, a globular blood protein that transports vitamin A and one of the thyroid hormones throughout the body. Transthyretin is made up of four identical polypeptide chains, each composed of 127 amino acids. Shown here is one of these chains unraveled for a closer look at its primary structure. Each of the 127 positions along the chain is occupied by one of the 20 amino acids, indicated here by its three-letter abbreviation. edly coiled or folded in patterns that contribute to the protein's overall shape. These coils and folds, collectively referred to as 55 Leu secondary structure, are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone (not the amino acid side chains). Within the backbone, the oxygen atoms have a partial negative charge, and the hydrogen atoms attached to the nitrogens have a partial positive charge (see Figure 2.16); therefore, hydrogen bonds can form between these atoms. Individ- ually, these hydrogen bonds are weak, but because they are repeated many times over a relatively long region of the polypeptide chain, they can support a particular shape for that part of the protein. One such secondary structure is the a helix, a delicate coil held together by hydrogen bonding between every fourth amino acid, shown above. Although each transthyretin polypeptide has only one a helix region (see tertiary structure on the next page), other globular proteins have multiple stretches of a helix separated by nonhelical regions (see hemoglobin on the next page). Some fi- brous proteins, such as a-keratin, the structural protein of hair, have the a helix formation over most of their length. Glu Phe Thr Asn Secondary Structure Regions stabilized by hydrogen bonds between atoms of the polypeptide backbone Gly Most proteins have segments of their polypeptide chains repeat- a helix The primary structure is like the order of letters in a very long word. If left to chance, there would be 20¹7 different ways of making a polypeptide chain 127 amino acids long. However, the precise primary structure of a protein is determined not by the ran- dom linking of amino acids, but by inherited genetic information. The primary structure in turn dictates secondary and tertiary struc- ture, due to the chemical nature of the backbone and the side chains (R groups) of the amino acids positioned along the chain. 3 pleated sheet Hydrogen bond -B strand, shown as a flat arrow pointing toward the carboxyl end -Hydrogen bond The other main type of secondary structure is the B pleated sheet. As shown above, in this structure two or more strands of the polypeptide chain lying side by side (called B strands) are connected by hydrogen bonds between parts of the two parallel polypeptide backbones. ß pleated sheets make up the core of many globular proteins, as is the case for transthyretin (see tertiary struc- ture on the next page), and dominate some fibrous proteins, in- cluding the silk protein of a spider's web. The teamwork of so many hydrogen bonds makes each spider silk fiber stronger than a steel strand of the same weight. Tertiary Structure Three-dimensional shape stabilized by interactions between side chains Superimposed on the patterns of secondary structure is a protein's tertiary structure, shown above in a ribbon model of the trans- thyretin polypeptide. While secondary structure involves interac- tions between backbone constituents, tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains (R groups) of the various amino acids. One type of interaction that contributes to tertiary structure is somewhat mis- leadingly called a hydrophobic interaction. As a polypeptide folds into its functional shape, amino acids with hydrophobic (nonpolar) side chains usually end up in clusters at the core of the protein, out of contact with water. Thus, a "hydrophobic interac- tion" is actually caused by the exclusion of nonpolar substances by water molecules. Once nonpolar amino acid side chains are close together, van der Waals interactions help hold them together. Meanwhile, hydrogen bonds between polar side chains and ionic bonds between positively and negatively charged side chains also help stabilize tertiary structure. These are all weak interactions in the aqueous cellular environment, but their cumulative effect helps give the protein a unique shape. Covalent bonds called disulfide bridges may further reinforce the shape of a protein. Disulfide bridges form where two cysteine monomers, which have sulfhydryl groups (-SH) on their side chains (see Figure 4.9), are brought close together by the folding of the protein. The sulfur of one cysteine bonds to the sulfur of the second, and the disulfide bridge (-S-S-) rivets parts of the pro- tein together (see yellow lines in Figure 5.18a). All of these different kinds of interactions can contribute to the tertiary structure of at protein, as shown here in a small part of a hypothetical protein: OH NHO -Hydrogen bond Disulfide bridge H₂ Transthyretin polypeptide Polypeptide- ide/ backbone CH CH₂ CH₂ CH₂ CH₂ -Hydrophobic interactions and van der Waals interactions. lonic bond Quaternary Structure Association of multiple polypeptides, forming a functional protein Collagen Some proteins consist of two or more polypeptide chains aggregated into one functional macromolecule. Quaternary structure is the overall protein structure that results from the aggregation of these polypeptide subunits. For example, shown above is the complete globular transthyretin protein, made up of its four polypeptides. Another example is collagen, shown below, which is a fibrous protein that has three identical helical polypeptides intertwined into a larger triple helix, giving the long fibers great strength. This suits collagen fibers to their function as the girders of connective tissue in skin, bone, tendons, ligaments, and other body parts. (Collagen accounts for 40% of the protein in a human body.) Hemoglobin, the oxygen-binding protein of red blood cells shown below, is another example of a globular protein with quaternary structure. It consists of four polypeptide subunits, two of one kind (a) and two of another kind (B). Both o and ẞ subunits consist primarily of a-helical secondary structure. Each subunit has a nonpolypeptide component, called heme, with an iron atom that binds oxygen. a subunit B subunit Transthyretin protein (four identical polypeptides) Heme Iron Hemoglobin B subunit a subunit
Transcribed Image Text:Amino acids Val Phe W Arg 35 Lys Asp Lys Thr 75 Tyr Ser Ser Thr 30 Primary Structure Linear chain of amino acids 115 Thr Amino end 80 His Val Ala Val Asn lle Ala Pro Ser Gly Arg Val Ala Asp Leu Val Lys 70 +H₂N-Gly Pro The Gly The Gly Glu Ser Lys Cys 40 25 H 45 110 20 Primary structure of transthyretin O Ala Ala Asp Asp The Trp Glu Pro Phe Ala Ser Gly Lys Thr Ser Glu Ser lle Giu Val Lys Tyr lle Gly Glu Val Pho Giu Glu Glu Thr The Leu Gly 120 125 Soo Ala Val Val Thr Asn Pro Lys Glu 105 10 50 90 15 Pro Tyr Trp Lys Ala Leu Gly ile Ser Pro Phe His Glu His Ala Glu Val Val 100 95 Ser Tyr Pro Ser Leu Leu Ala Ala Ile The Tyr Arg Arg Pro Gly Ser Asp ....... Val Leu Met His Carboxyl end The primary structure of a protein is a linked series of amino acids with a unique sequence. As an example, let's consider transthyretin, a globular blood protein that transports vitamin A and one of the thyroid hormones throughout the body. Transthyretin is made up of four identical polypeptide chains, each composed of 127 amino acids. Shown here is one of these chains unraveled for a closer look at its primary structure. Each of the 127 positions along the chain is occupied by one of the 20 amino acids, indicated here by its three-letter abbreviation. edly coiled or folded in patterns that contribute to the protein's overall shape. These coils and folds, collectively referred to as 55 Leu secondary structure, are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone (not the amino acid side chains). Within the backbone, the oxygen atoms have a partial negative charge, and the hydrogen atoms attached to the nitrogens have a partial positive charge (see Figure 2.16); therefore, hydrogen bonds can form between these atoms. Individ- ually, these hydrogen bonds are weak, but because they are repeated many times over a relatively long region of the polypeptide chain, they can support a particular shape for that part of the protein. One such secondary structure is the a helix, a delicate coil held together by hydrogen bonding between every fourth amino acid, shown above. Although each transthyretin polypeptide has only one a helix region (see tertiary structure on the next page), other globular proteins have multiple stretches of a helix separated by nonhelical regions (see hemoglobin on the next page). Some fi- brous proteins, such as a-keratin, the structural protein of hair, have the a helix formation over most of their length. Glu Phe Thr Asn Secondary Structure Regions stabilized by hydrogen bonds between atoms of the polypeptide backbone Gly Most proteins have segments of their polypeptide chains repeat- a helix The primary structure is like the order of letters in a very long word. If left to chance, there would be 20¹7 different ways of making a polypeptide chain 127 amino acids long. However, the precise primary structure of a protein is determined not by the ran- dom linking of amino acids, but by inherited genetic information. The primary structure in turn dictates secondary and tertiary struc- ture, due to the chemical nature of the backbone and the side chains (R groups) of the amino acids positioned along the chain. 3 pleated sheet Hydrogen bond -B strand, shown as a flat arrow pointing toward the carboxyl end -Hydrogen bond The other main type of secondary structure is the B pleated sheet. As shown above, in this structure two or more strands of the polypeptide chain lying side by side (called B strands) are connected by hydrogen bonds between parts of the two parallel polypeptide backbones. ß pleated sheets make up the core of many globular proteins, as is the case for transthyretin (see tertiary struc- ture on the next page), and dominate some fibrous proteins, in- cluding the silk protein of a spider's web. The teamwork of so many hydrogen bonds makes each spider silk fiber stronger than a steel strand of the same weight. Tertiary Structure Three-dimensional shape stabilized by interactions between side chains Superimposed on the patterns of secondary structure is a protein's tertiary structure, shown above in a ribbon model of the trans- thyretin polypeptide. While secondary structure involves interac- tions between backbone constituents, tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains (R groups) of the various amino acids. One type of interaction that contributes to tertiary structure is somewhat mis- leadingly called a hydrophobic interaction. As a polypeptide folds into its functional shape, amino acids with hydrophobic (nonpolar) side chains usually end up in clusters at the core of the protein, out of contact with water. Thus, a "hydrophobic interac- tion" is actually caused by the exclusion of nonpolar substances by water molecules. Once nonpolar amino acid side chains are close together, van der Waals interactions help hold them together. Meanwhile, hydrogen bonds between polar side chains and ionic bonds between positively and negatively charged side chains also help stabilize tertiary structure. These are all weak interactions in the aqueous cellular environment, but their cumulative effect helps give the protein a unique shape. Covalent bonds called disulfide bridges may further reinforce the shape of a protein. Disulfide bridges form where two cysteine monomers, which have sulfhydryl groups (-SH) on their side chains (see Figure 4.9), are brought close together by the folding of the protein. The sulfur of one cysteine bonds to the sulfur of the second, and the disulfide bridge (-S-S-) rivets parts of the pro- tein together (see yellow lines in Figure 5.18a). All of these different kinds of interactions can contribute to the tertiary structure of at protein, as shown here in a small part of a hypothetical protein: OH NHO -Hydrogen bond Disulfide bridge H₂ Transthyretin polypeptide Polypeptide- ide/ backbone CH CH₂ CH₂ CH₂ CH₂ -Hydrophobic interactions and van der Waals interactions. lonic bond Quaternary Structure Association of multiple polypeptides, forming a functional protein Collagen Some proteins consist of two or more polypeptide chains aggregated into one functional macromolecule. Quaternary structure is the overall protein structure that results from the aggregation of these polypeptide subunits. For example, shown above is the complete globular transthyretin protein, made up of its four polypeptides. Another example is collagen, shown below, which is a fibrous protein that has three identical helical polypeptides intertwined into a larger triple helix, giving the long fibers great strength. This suits collagen fibers to their function as the girders of connective tissue in skin, bone, tendons, ligaments, and other body parts. (Collagen accounts for 40% of the protein in a human body.) Hemoglobin, the oxygen-binding protein of red blood cells shown below, is another example of a globular protein with quaternary structure. It consists of four polypeptide subunits, two of one kind (a) and two of another kind (B). Both o and ẞ subunits consist primarily of a-helical secondary structure. Each subunit has a nonpolypeptide component, called heme, with an iron atom that binds oxygen. a subunit B subunit Transthyretin protein (four identical polypeptides) Heme Iron Hemoglobin B subunit a subunit
The four levels of protein structure are primary, secondary, tertiary, and quaternary structure. Review the levels of protein structure by clicking the image below. Drag each label into the appropriate bin depending on whether it applies to primary, secondary, tertiary, or quaternary structure. results from hydrogen bonding between the backbone constituents of the overall shape of a polypeptide the polypeptide primary structure www the aggregation of multiple polypeptide subunits secondary structure B pleated sheet results from interactions between side chains (R groups) of amino acids a helix tertiary structure amino acid sequence Reset quaternary structure Help
Transcribed Image Text:The four levels of protein structure are primary, secondary, tertiary, and quaternary structure. Review the levels of protein structure by clicking the image below. Drag each label into the appropriate bin depending on whether it applies to primary, secondary, tertiary, or quaternary structure. results from hydrogen bonding between the backbone constituents of the overall shape of a polypeptide the polypeptide primary structure www the aggregation of multiple polypeptide subunits secondary structure B pleated sheet results from interactions between side chains (R groups) of amino acids a helix tertiary structure amino acid sequence Reset quaternary structure Help
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