7L.6 AminoacidsValPheWArg 35LysAspLysThr 75TyrSerSerThr30Primary StructureLinear chain of amino acids115ThrAmino end80His Val Ala Val Asn lle Ala Pro Ser Gly Arg Val Ala Asp Leu Val Lys70+H₂N-Gly Pro The Gly The Gly Glu Ser Lys Cys4025H4511020Primary structure of transthyretinOAla Ala Asp Asp The Trp Glu Pro Phe Ala Ser Gly Lys Thr Ser Glu Serlle Giu Val Lys Tyr lle Gly Glu Val Pho Giu Glu Glu Thr The Leu Gly120125SooAla Val Val Thr Asn Pro Lys Glu10510509015ProTyr Trp Lys Ala Leu Gly ile Ser Pro Phe His Glu His Ala Glu Val Val10095Ser Tyr Pro Ser Leu Leu Ala Ala Ile The Tyr Arg Arg Pro Gly Ser Asp.......ValLeuMetHisCarboxyl endThe primary structure of a protein is a linked series of aminoacids with a unique sequence. As an example, let's considertransthyretin, a globular blood protein that transports vitaminA 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 thesechains unraveled for a closer look at its primary structure. Eachof the 127 positions along the chain is occupied by one of the20 amino acids, indicated here by its three-letter abbreviation.edly coiled or folded in patterns that contribute to the protein'soverall shape. These coils and folds, collectively referred to as55 Leu secondary structure, are the result of hydrogen bonds betweenthe repeating constituents of the polypeptide backbone (not theamino acid side chains). Within the backbone, the oxygen atomshave a partial negative charge, and the hydrogen atoms attachedto 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 repeatedmany 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 heldtogether by hydrogen bonding between every fourth amino acid,shown above. Although each transthyretin polypeptide has onlyone a helix region (see tertiary structure on the next page), otherglobular proteins have multiple stretches of a helix separated bynonhelical 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.GluPheThrAsnSecondary StructureRegions stabilized by hydrogen bonds betweenatoms of the polypeptide backboneGly Most proteins have segments of their polypeptide chains repeat-a helixThe primary structure is like the order of letters in a very longword. If left to chance, there would be 20¹7 different ways ofmaking a polypeptide chain 127 amino acids long. However, theprecise 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 sidechains (R groups) of the amino acids positioned along the chain.3 pleated sheetHydrogen bond-B strand, shown as a flatarrow pointing towardthe carboxyl end-Hydrogen bondThe other main type of secondary structure is the B pleatedsheet. As shown above, in this structure two or more strands ofthe polypeptide chain lying side by side (called B strands) areconnected by hydrogen bonds between parts of the two parallelpolypeptide backbones. ß pleated sheets make up the core of manyglobular 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 somany hydrogen bonds makes each spider silk fiber stronger thana steel strand of the same weight.Tertiary StructureThree-dimensional shape stabilized byinteractions between side chainsSuperimposed on the patterns of secondary structure is a protein'stertiary structure, shown above in a ribbon model of the trans-thyretin polypeptide. While secondary structure involves interac-tions between backbone constituents, tertiary structure is theoverall shape of a polypeptide resulting from interactions betweenthe side chains (R groups) of the various amino acids. One type ofinteraction that contributes to tertiary structure is somewhat mis-leadingly called a hydrophobic interaction. As a polypeptidefolds into its functional shape, amino acids with hydrophobic(nonpolar) side chains usually end up in clusters at the core of theprotein, out of contact with water. Thus, a "hydrophobic interac-tion" is actually caused by the exclusion of nonpolar substances bywater molecules. Once nonpolar amino acid side chains are closetogether, van der Waals interactions help hold them together.Meanwhile, hydrogen bonds between polar side chains and ionicbonds between positively and negatively charged side chains alsohelp stabilize tertiary structure. These are all weak interactions inthe aqueous cellular environment, but their cumulative effect helpsgive the protein a unique shape.Covalent bonds called disulfide bridges may further reinforcethe shape of a protein. Disulfide bridges form where two cysteinemonomers, which have sulfhydryl groups (-SH) on their sidechains (see Figure 4.9), are brought close together by the foldingof the protein. The sulfur of one cysteine bonds to the sulfur of thesecond, and the disulfide bridge (-S-S-) rivets parts of the pro-tein together (see yellow lines in Figure 5.18a). All of these differentkinds of interactions can contribute to the tertiary structure of atprotein, as shown here in a small part of a hypothetical protein:OHNHO-HydrogenbondDisulfidebridgeH₂TransthyretinpolypeptidePolypeptide-ide/backboneCHCH₂ CH₂CH₂ CH₂-Hydrophobicinteractions andvan der Waalsinteractions.lonic bondQuaternary StructureAssociation of multiple polypeptides,forming a functional proteinCollagenSome proteins consist of two or more polypeptide chains aggregatedinto one functional macromolecule. Quaternary structure is theoverall protein structure that results from the aggregation of thesepolypeptide subunits. For example, shown above is the completeglobular transthyretin protein, made up of its four polypeptides.Another example is collagen, shown below, which is a fibrousprotein that has three identical helical polypeptides intertwinedinto a larger triple helix, giving the long fibers great strength. Thissuits collagen fibers to their function as the girders of connectivetissue 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 cellsshown below, is another example of a globular protein withquaternary structure. It consists of four polypeptide subunits, twoof one kind (a) and two of another kind (B). Both o and ẞ subunitsconsist primarily of a-helical secondary structure. Each subunit hasa nonpolypeptide component, called heme, with an iron atom thatbinds oxygen.a subunitB subunitTransthyretinprotein(four identicalpolypeptides)HemeIronHemoglobinB subunita 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 bondingbetween the backbone constituents of the overall shape of a polypeptidethe polypeptideprimary structurewwwthe aggregation of multiplepolypeptide subunitssecondary structureB pleated sheetresults from interactions between sidechains (R groups) of amino acidsa helixtertiary structureamino acid sequenceResetquaternary structureHelp

There are four classes of biological macromolecules; nucleic acid, proteins, lipids and…

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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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