Peptide Bond

9 Key excerpts on "Peptide Bond"

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  eBook - PDF

  The Molecular Fabric of Cells

  • BIOTOL, B C Currell, R C E Dam-Mieras(Authors)
  • 2013(Publication Date)
  • Butterworth-Heinemann

    (Publisher)

  The reaction is a condensation reaction in which a molecule of water is released. amino acid residues dipeptide, oligopeptide, polypeptide amino acid sequence primary structure The reaction is considerably more complicated, occurs on ribosomes and requires energy. The formation of Peptide Bonds is described in more detail in the BIOTOL text 'Infrastructure and Activities of Cells'. The Peptide Bond formed is an amide bond between the carbonyl carbon of the first amino acid and the amino nitrogen of the second. Notice that the product of this depicted reaction (a dipeptide) still possesses an -amino group and an -carboxyl group, although these are attached to different amino acid residues. Note that after incorporation into proteins, amino acids are referred to as amino acid residues, since part of each amino acid is lost in the formation of the Peptide Bond; what remains is a 'residue'. Since -amino and -carboxyl groups still occur, more Peptide Bonds can be made. Proteins vary in the number of the amino acid residues from a few (an oligopeptide) to many hundreds (a polypeptide). The precise number of amino acid residues, which amino acids they are and their order are determined by the DNA of the gene which codes for them. Each protein has a precise sequence of amino acid residues, giving a macromolecule of a precise size. The sequence of a protein ie the precise order and identity of amino acid residues within it, is called the primary structure of the protein. There is considerable evidence, some of which is presented in Section 3.7, that the primary structure determines the final shape of the protein and, through its shape, its biological properties. Thus the amino acid sequence is vital to produce the correct conformation and biological activity. Proteins 41 The Peptide Bond as it is usually depicted is shown in Figure 3.2a.

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  Available until 8 Dec |Learn more

  Chemical Reagents for Protein Modification

  2nd Edition

  • Roger L. Lundblad(Author)
  • 2020(Publication Date)
  • CRC Press

    (Publisher)

  Chapter 15

  THE CHEMICAL CROSS-LINKING OF PEPTIDE CHAINS

  The formation of either intramolecular or intermolecular covalent cross-links between amino acid residues in proteins is proving to be an extremely valuable tool in biochemistry with particular use in the study of protein-protein interactions. Naturally occurring inter-and intramolecular cross-links are commonly found in proteins, the most common being the disulfide bond. Other examples exist including the transglutaminase-catalyzed formation of a Peptide Bond between the γ-carboxyl groups of glutamic acid and the ϵ-amino groups of lysine.1 , 2 There are also the extremely complex cross-links found in collagen.3 , 4

  In addition to the study of protein-protein interactions, intramolecular cross-linking has been of value in increasing protein stability5-7 as well as stabilizing erythrocyte structure.8 Cross-linking between a biologically active protein and a carrier protein has been advocated for therapeutic purposes9 although this approach will likely be supplanted by the preparation of chimeric proteins. Covalent cross-linking with the reagents described in this chapter have been used to complex peptides to carrier proteins such as hemocyanin or tetanus toxin for the preparation of antipeptide antibodies.10 Care must be exercised in the screening of antibodies resulting from the use of peptide-carrier conjugates not only for cross-reactivity with the carrier protein but also for antibodies directly to coupling groups used in such procedures.11

  Zero-length cross-linking12 is a procedure which joins peptide chains via existing functional groups such that a “spacer” group is not utilized. Examples include the covalent linkage of proteins to nucleic acids, the formation of 3,3’-dityrosine mediated by tetranitromethane (see Chapter 13 ) and isoPeptide Bond formation. IsoPeptide Bond formation (Figure 1 ) mediated by carbodiimide13 , 14 (see Chapter 14 ) has been the most extensively used approach. This technique has been applied to the cross-linking of heavy meromyosin and F-actin15 , 16 and components of the A. vinelandii nitrogenase complex.17 A more recent modification of this technique18 involves a two-step procedure where one protein is first incubated with a water-soluble carbodiimide and N -hydroxysuccinimide resulting in the formation of an N

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  General, Organic, and Biological Chemistry

  An Integrated Approach

  • Kenneth W. Raymond(Author)
  • 2012(Publication Date)
  • Wiley

    (Publisher)

  As we will see in Chapter 13, the process of joining amino acids to one another is a complex process in living things. Because each amino acid has both a carboxyl and an a-amino group, each amino acid can take part in two Peptide Bonds. If, for example, the glycine in this dipeptide 12.2 The Peptide Bond 465 contributes its i CO 2 H to a Peptide Bond with the i NH 2 from a serine, a tripeptide is formed (Figure 12.3b). The addition of successive amino acids leads to the formation of a longer oligopeptide or a polypeptide (Figure 12.3c). It is customary to draw peptides and proteins with the N-terminus (the end of the pep- tide chain with the unreacted amino group) on the left and the C-terminus (the end of the peptide chain with the free carboxyl group) on the right. For the tripeptide in Figure 12.3b, alanine is at the N-terminus and serine is at the C-terminus. Peptides and proteins are named by listing the amino acid residues, in order, from the N- to the C-terminus. The dipeptide in Figure 12.3 is Ala-Gly and the tripeptide is Ala-Gly-Ser. Names of larger oligopeptides, polypeptides, and proteins arrived at using this method can be quite lengthy, so these molecules are sometimes known by common names (Figure 12.4). For the amino acid residues in a peptide or protein, hydrolysis of the Peptide Bond restores their amino and carboxyl groups to their original state (Figure 12.5). This hydrol- ysis, which is identical to amide hydrolysis described in Section 8.13, is a key reaction in the digestion of proteins. Biochemically active peptides and proteins come in all sizes.

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  Bioconjugate Techniques

  • Greg T. Hermanson(Author)
  • 1996(Publication Date)
  • Academic Press

    (Publisher)

  The Peptide Bond possesses no rotational freedom due to the partial double bond character of the carbonyl-amino amide bond. The bonds around the a-carbon atom, however, are true single bonds with considerable freedom of movement. The sequence and properties of the amino acid constituents determine protein structure, reactivity, and function. Each amino acid is composed of an amino group Figure 1 Rigid Peptide Bonds link amino acid residues together to form proteins. Other bonds within the polypeptide structure may exhibit considerable freedom of rotation. 1. Modification of Amino Acids, Peptides, and Proteins o H3N. ^CH ^O Figure 2 Individual amino acids consist of a primary (a) amine, a carboxylic acid group, and a unique side chain structure (R). At physiological pH the amine is protonated and bears a positive charge, while the carboxylate is ionized and possesses a negative charge. and a carboxyl group bound to a central carbon, termed the a-carbon. Also bound to the a-carbon is a hydrogen atom and a side chain unique to each amino acid (Fig. 2). There are 20 common amino acids found throughout nature, each containing an identifying side chain of particular chemical structure, charge, hydrogen bonding capability, hydrophilicity (or hydrophobicity), and reactivity. The side chains do not participate in polypeptide formation and are thus free to interact and react with their environment. Amino acids may be grouped by type depending on the characteristics of their side chains. There are seven amino acids that contain aliphatic side chains that are relatively nonpolar and hydrophobic: glycine, alanine, valine, leucine, isoleucine, methionine, and proline (Fig. 3). Glycine is the simplest amino acid—its side chain consisting of only a hydrogen atom. Alanine is next in line, possessing just a single methyl group for its side chain. Valine, leucine, and isoleucine are slightly more complex w^ith three or four carbon branched-chain constituents.

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  Organic Chemistry

  • David R. Klein(Author)
  • 2016(Publication Date)
  • Wiley

    (Publisher)

  When amino acids join together to form a peptide, the order in which they are connected is important. For example, consider a simple dipeptide made by joining alanine and glycine. The Peptide Bond can be formed between the COOH group of alanine and the NH 2 group of glycine, or from the COOH group of glycine and the NH 2 group of alanine. Ala-Gly Glycine Alanine N OH O H H CH 3 O OH H 2 N N O H OH O CH 3 H 2 N Glycine Alanine Gly-Ala H 2 N OH O CH 3 O OH N H H CH 3 H 2 N O OH N H O These two dipeptides are not the same compound. They are, in fact, constitutional isomers. Peptide chains always have an amino group on one end, called the N terminus, and a COOH group on the other end, called the C terminus (Figure 25.4). By convention, peptides are always drawn with the N terminus on the left side. SKILLBUILDER LEARN the skill 25.3 DRAWING A PEPTIDE Draw a bond-line structure showing the tripeptide Phe-Val-Trp (assume that all three resi- dues are L amino acids). N H C C R O H N H C C R O H N H C C R O H OH C C R O H N H H N H C C R O H N terminus C terminus FIGURE 25.4 The N terminus and C terminus of a peptide chain. The sequence of amino acid residues in a peptide can be abbreviated with one- or three-letter abbreviations, starting with the N terminus. For example, a dipeptide of glycine and alanine can be written as follows: O CH 3 OH N H O H 2 N Glycine residue Alanine residue N terminus C terminus Gly Ala Simple peptide chains will have one N terminus and one C terminus. For example, consider the following decapeptide, for which the alanine residue is the N terminus and the leucine residue is the C terminus: N terminus C terminus Try Glu Gly Phe Met Cys Cys Pyr Leu Ala 1162 CHAPTER 25 Amino Acids, Peptides, and Proteins SOLUTION Begin by drawing a peptide comprised of three residues with the N terminus on the left and the C terminus on the right.

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  Experimental Organic Chemistry

  A Miniscale & Microscale Approach

  • John Gilbert, Stephen Martin(Authors)
  • 2015(Publication Date)
  • Cengage Learning EMEA

    (Publisher)

  891 C H A P T E R a -Amino Acids and Peptides a -Amino acids are organic molecules that contain both an amine and a carboxylic acid functional group on the same carbon atom. a -Amino acids thus undergo some reactions that are typical of both of these functionalities, but they also exhibit special chemical and physical properties that are a consequence of having these two func-tional groups attached to one carbon atom. You have an opportunity to learn about some of the chemistry of amines and carboxylic acids in Chapters 17, 20, and 21. In this chapter, you will study several aspects of the chemistry of a -amino acids and how these compounds can be combined to make peptides, substances that com-prise two or more amino acids joined by an amide bond between the nitrogen atom of one amino acid and the carboxyl carbon atom of another. a -Amino acids are the essential building blocks of proteins, which are high-molar-mass biopolymers comprising many a -amino acids linked by Peptide Bonds. Examples of proteins in living cells include the enzymes that catalyze essential bio-chemical transformations and the receptors in cell membranes that bind smaller molecules such as neurotransmitters, hormones, and pharmaceuticals. Useful ma-terials like wool or silk are also constituted of proteins. In the experiments in this chapter, you will learn how to combine individual a -amino acids to form peptides in exactly the same way such compounds are prepared in research laboratories. 24.1 I N T R O D U C T I O N Amino acids are generally characterized by the presence of an amine functional group , – NH 2 , and a carboxylic acid functional group , – CO 2 H. Although the amino and carboxyl groups may be located anywhere in the molecule, the most important amino acids in biological systems are a -amino acids , as these are the monomeric building blocks for forming proteins in living organisms.

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  Klein's Organic Chemistry

  • David R. Klein(Author)
  • 2020(Publication Date)
  • Wiley

    (Publisher)

  When amino acids join together to form a peptide, the order in which they are connected is important. For example, consider a simple dipeptide made by joining alanine and gly- cine. The Peptide Bond can be formed between the COOH group of alanine and the NH 2 group of glycine, or from the COOH group of glycine and the NH 2 group of alanine. Ala-Gly Glycine Alanine N OH O H H CH 3 O OH H 2 N N O H OH O CH 3 H 2 N Glycine Alanine Gly-Ala H 2 N OH O CH 3 O OH N H H CH 3 H 2 N O OH N H O These two dipeptides are not the same compound. They are, in fact, constitutional isomers. Peptide chains always have an amino group on one end, called the N terminus, and a COOH group on the other end, called the C terminus (Figure 25.4). By convention, peptides are always drawn with the N terminus on the left side. SKILLBUILDER LEARN the skill 25.3 DRAWING A PEPTIDE Draw a bond-line structure showing the tripeptide Phe-Val-Trp (assume that all three residues are L amino acids). N H C C R O H N H C C R O H N H C C R O H OH C C R O H N H H N H C C R O H N terminus C terminus FIGURE 25.4 The N terminus and C terminus of a peptide chain. The sequence of amino acid residues in a peptide can be abbreviated with one- or three-letter abbreviations, starting with the N terminus. For example, a dipeptide of glycine and alanine can be written as follows: O CH 3 OH N H O H 2 N Glycine residue Alanine residue N terminus C terminus Gly Ala Simple peptide chains will have one N terminus and one C terminus. For example, consider the following decapeptide, for which the alanine residue is the N terminus and the leucine residue is the C terminus: N terminus C terminus Try Glu Gly Phe Met Cys Cys Pyr Leu Ala 25.4 Structure of Peptides 1153 SOLUTION Begin by drawing a peptide comprised of three residues with the N terminus on the left and the C terminus on the right. O H N N H O OH O R R R H 2 N N terminus C terminus Next, identify the side chain (R group) associated with each residue.

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  eBook - ePub

  Molecular Biology

  • David P. Clark(Author)
  • 2009(Publication Date)
  • Academic Cell

    (Publisher)

  Fig. 7.05 ). The polypeptide chain must be folded around to bring two peptide groups alongside each other. The hydrogen on the nitrogen of one peptide group is then bound to the oxygen of the other. [Note that hydrogen bonds also contribute to tertiary structure, but here they are not the only or even the major forces involved.]

  Figure 7.05 Hydrogen Bonding between Peptide Groups Two Peptide Bonds of a polypeptide chain may be aligned to form a hydrogen bond by looping the polypeptide chain around.

  Most of the secondary structure found in proteins is due to one of two common secondary structures, known as the α- (alpha) helix and the β- (beta) sheet . Both structures allow formation of the maximum possible number of hydrogen bonds and are therefore highly stable.

  alpha- (α-) helix	A helical secondary structure found in proteins
  β- (beta-) sheet	A flat sheet-like secondary structure found in proteins
  cofactor	Extra chemical group bound (often temporarily) to a protein but which is not part of the polypeptide chain
  primary structure	The linear order in which the subunits of a polymer are arranged
  prosthetic group	Extra chemical group bound (often covalently) to a protein but which is not part of the polypeptide chain
  quaternary structure	Aggregation of more than one polymer chain to form a final structure
  secondary structure	Initial folding up of a polymer into a regular, repeating structure, due to hydrogen bonding
  tertiary structure	Final 3-D folding of a polymer chain

  In the α-helix (Fig. 7.06

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  Therapeutic Peptides and Proteins

  Formulation, Processing, and Delivery Systems, Third Edition

  • Ajay K. Banga(Author)
  • 2015(Publication Date)
  • CRC Press

    (Publisher)

  Of the 20 amino acids, 15 have pI near 6.0. The three basic amino acids have higher pI, while the two acidic ones have lower pI. The amino acid cysteine exhibits some unique properties that play a crucial role in the stability of proteins. The thiol group of Cys is the most reactive of any amino acid side chain and will be readily oxidized to form a dimer, cystine: 2HS CH CH S S CH 2 2 2 -------↔ The resulting S–S bond is called a disulfide bridge and serves to hold the protein in its unique conformation, as will be discussed in Section 2.3. 2.2 STRUCTURE OF PEPTIDES AND PROTEINS Amino acids join with each other by Peptide Bonds to form polymers referred to as peptides or proteins. Thus, the carboxyl and amino groups of each amino acid are participating in the Peptide Bond so that it will have a charge in the peptide only if it has an ionizable side chain. The distinction between peptides and proteins is somewhat arbitrary. Typically, peptides contain fewer than 20 amino acids, while proteins contain 50 or more amino acids. Between these two categories are polypep-tides that contain about 20–50 amino acids. Again, it must be emphasized that the nomenclature is not well defined and different authors use these terms differently. As used in this book, a peptide may be considered to have a molecular weight less than 5000 while a protein lies above this value. By this definition, insulin (Molecular Weight (MW) 5808) is one of the smallest proteins available, while monoclonal anti-bodies are larger structurally more complex proteins (Figure 2.1) (Mellstedt, 2013). Therapeutic proteins are generally referred to as globular proteins as they are of nearly spherical shape in solution. A protein has several levels of structure. These are generally referred to as the primary, secondary, tertiary, and quaternary structures. 2.2.1 P RIMARY S TRUCTURE The sequence of covalently bonded amino acids in the polypeptide chain is known as the primary structure.

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