Chemistry
Primary Structure of Protein
The primary structure of a protein refers to the linear sequence of amino acids that make up the protein. This sequence is determined by the genetic code and is essential for the protein's function. The primary structure dictates the folding and three-dimensional shape of the protein, which in turn influences its biological activity.
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12 Key excerpts on "Primary Structure of Protein"
eBook - PDF- David Ucko(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
Think o f a protein as a long chain, or several chains, o f beads put together from only 20 different kinds of beads. Each protein has a definite, character-istic arrangement of the basic units, the amino acids. T h e primary structure of a protein is the sequence o f its amino acids; it shows you exactly which are present and the order in w h i c h they are connected. You can also think o f a pro-peptide b o n d Ο -N H — C H — C peptide b o n d Ο N H — C H — C ο N H — C H — C -4 -- backbone ί - side chains' u re rt n a e t de an a n a ds t ree are s n ere are n ed e t de n ds n a n a n a t er r t e ns tein as having a b a c k b o n e which consists of nitrogen atoms, alpha carbon atoms, and carbonyl groups, forming a chain that has branches coming from it, the side chains. In this case, the primary structure describes the length of the backbone and its arrangement of side chains. As an example, the primary structure of one chain of hemoglobin is shown in Figure 15-4.
eBook - PDF- Bhupendra Pushkar(Author)
- 2020(Publication Date)
- Delve Publishing(Publisher)
In fact, in cellular DNA, each gene tends to contain the code for any particular protein structure. These proteins are assembled with different amino acid sequences. Along with this, they also are combined together by many different bonds and folded into various three-dimensional structures. The folded shape or conformation relies on the linear amino acid sequence of the protein directly. The shape of a protein is critical to its function. The reason behind this is that it determines whether the proteins can interact with some other molecules. The protein structures are considered to be very complex and therefore, the researchers have gained the ability to easily as well as quickly determine the structure of the complete proteins down to the atomic level. There are techniques that are used in the period of the 1950s but now in today’s era, they were very slow as well as laborious to be used. And this is why the complete protein structures were very slow to be solved. Conceptually, the early structural biochemists divided the protein structures into four levels to make it easier to get a handle on the complexity of the entire structures. It is important to understand these four levels of protein structure named as primary, secondary, tertiary and quaternary in order to determine the way in which the protein gets its final shape or conformation. The primary structure of a protein is the unique sequence of the amino acids in every polypeptide chain which makes up the protein. This is just several amino acids that appear in the order in a polypeptide chain and it is not really a structure. This is referred to as the primary structure of the polypeptide chain because of the fact that the final protein structure ultimately depends on this sequence. An example can be the pancreatic hormone insulin which has two polypeptide chains namely A and B.
- W.C.K. Poon, David Andelman, W.C.K. Poon, David Andelman(Authors)
- 2006(Publication Date)
- CRC Press(Publisher)
The sequence starts at the so-called N terminal and ends at the C terminal; the two ends are not equivalent, i.e., running the sequence backward does not produce the same protein. Typical lengths of protein se-quences are a few hundred amino acids. The extremes are a few tens to a few thousands of amino acids. 202 Ron Elber, Jian Qiu, Leonid Meyerguz and Jon Kleinberg One of the remarkable features of proteins is their ability to fold into a well-defined three-dimensional structure in aqueous solutions, the so-called protein-folding problem. This chapter is concerned with a few indirect aspects of this problem. The working hy-pothesis is that the three-dimensional shape is determined uniquely by the sequence of the amino acids and is the thermodynamically stable state. Anfinsen (1973) put forward this extraordinary hypothesis that protein molecules are stable in isolation with no sup-port from other components of the living system. From a computational and theoretical viewpoint, the Anfinsen hypothesis makes it possible to define and use in predictions an (free) energy function of an isolated protein molecule (in an aqueous solution). This func-tion leads to significant simplification and saving of computational resources compared to studying a complete cellular environment. The free energy has a global minimum that coincides with the three-dimensional structure observed experimentally. Structures of proteins are classified in terms of secondary structure elements, do-mains and individual chains (tertiary structure), and packing of tertiary structural ele-ments (quaternary structure). Secondary structure is determined according to the hy-drogen bond patterns of the backbone atoms that form small structural elements (ten to twenty amino acids). These elements are assembled to form the stable three-dimensional compact structure of the protein.
eBook - PDF- S Bresler(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
The third topic concerns protein tertiary structure, in particular how the exact three-dimensional configuration of a protein molecule can be determined from x-ray struc-ture analysis, the most highly perfected technique applicable. It will be demonstrated that numerous physicochemical properties of proteins—optical, electrical, and hydro-dynamic—directly depend on macromolecular configuration. Finally, we shall take up modern methods for the fractionation, purification, and identification of individual proteins. 2. The Chemical Structure of Proteins Proteins are linear polymers or copolymers composed of amino acids joined together by peptide bonds. That the backbone of all protein molecules consists of a polypeptide chain has been proved without a doubt. Its general formula is 2. The Chemical Structure of Proteins 3 R , R o Ro R 4 I H I 2 H I H I — ' ^ C — N ^ H C — N ^ H C — N ^ H ^ — II II II ο ο ο One can imagine that such a polymer is the product of a series of condensation reac-tions between various amino acids in which the amino (—NH 2 ) and carboxyl (—COOH) groups of successive residues are united to form peptide bonds (—CO—NH—) with the exclusion of a water molecule : H 2 N ^ H ^ C O O H H ^ H ^ C O O H H 2 N ^ H ^ C O O H As a rule, there is a free or acylated amino group at one end of each polypeptide chain (the N-terminus) and a free or amidated carboxyl group at the other end (the C-terminus). All amino acids contain in common both an amino and a carboxyl group attached to the α-carbon atom. They differ in the nature of their side chains, designated by R l9 R 2 , R 3 , . ·., R„ in the above reaction diagram. There are twenty common amino acids which are found in practically all proteins and a few more which occur only rarely. The structural formulas of the twenty universal amino acids are presented in Table 1-1, classified according to the properties of their side chains, R.
eBook - PDF- F. Korte(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
2 Proteins Contributions by K. Hotta, Sagmihara S. Iwanaga, Osaka /. Kato, Tokyo O. Minari, Sappro K. Narita, Osaka K. Onoue, Fukuoka 2.1 Primary Structure of Protein Kozo Narita Institute for Protein Research, Osaka University, Yama-da-kami, Suita, Osaka, 565 Japan 1 Introduction Protein is polypeptide consisted of a number of twenty kinds of L-amino acid residues by peptide bonds on a linear chain. The sequence of amino acid residues on the polypeptide chain of the given protein is called the primary structure 1 . O II The peptide bond, -C-N-, has a partial double H bond character and exists on a plane. However, the bonds between the peptide carbonyl and the α-carbon atom of the amino acid residue and between the peptide imide and the a-carbon atom rotate freely, and thus the backbone of the peptide chain is flexible. Polypeptides, therefore, exist as random coils in solution in the absence of interactions between side chain groups of the amino acid residues on the poly-peptide chain. Most native proteins, however, do not behave as random coils and their mole-cules possess definite ordered spatial structures by folding the peptide chains in a regular man-ner, which controlled by the rotational angles around the α-carbon atoms. The rotational angles are determined by interactions between the side chain groups in the polypeptide chain. Folding of the polypeptide chain which is brought about by linking the carbonyl and imide groups belonging to different amino acid residues on thechain by hydrogen bonds, > C = 0 -H N < , is called the secondary structure of the pro-tein 1 . The helical structures [α-helix (3.6i 3 helix) and 3io helix] and the ^-structure (parallel and antiparallel pleated sheets) are well known secondary structures. The /3-bent 2 which is formed in the regions of sharp U turns of the extended ^-structure may be included in the secondary structure.
eBook - PDF- Lizabeth A. Allison(Author)
- 2021(Publication Date)
- Wiley-Blackwell(Publisher)
The weak acid–base behavior of amino acids provides the basis for many techniques for identification of different amino acids and protein separations that are explored in Chapter 14. The bottom line is that the arrangement of amino acids, with their distinct side chains, gives each protein its characteristic structure and function. How are amino acids joined together? Protein primary structure Amino acids are joined together by peptide bonds , forming the primary structure of a pro-tein (Figure 4.3). The amino group of one molecule reacts with the carboxyl group of the other in a condensation reaction, resulting in the elimination of water and the formation of a dipeptide. A short sequence of amino acids is called a peptide , with the term polypep-tide applied to longer chains of amino acids, usually of known sequence and length. When joined in a series of peptide bonds, amino acids are called residues to distinguish between the free form and the form found in proteins. The peptide bond has a partial double bond 4.2 Primary structure: amino acids and the genetic code 81 character (Figure 4.4). Free rotation occurs only between the α -carbon and the peptide unit. The peptide chain is thus flexible, but more rigid than it would be if there was free rotation about all of the bonds. Protein primary structure is divided into two main components, the polypeptide back-bone that has the same composition in all proteins, and the variable side chain groups (see Figure 4.3).
- Peter Tompa, Alan Fersht(Authors)
- 2009(Publication Date)
- Chapman and Hall/CRC(Publisher)
1 1 Principles of Protein Structure and Function The principles of protein structure surveyed in this chapter have been established mostly by studying globular proteins. The structure of a globular protein can be described by the coordinates of all its atoms, but this information is often too complex to interpret in terms of function. Thus, scientists have devised a hierarchical vocabulary that can describe different levels of structure from the sequence of amino acids to the spatial arrangement of subunits. Further levels of complexity, such as post-translational modifications, the process of acquiring the 3-D structure (folding), and the description of the unfolded state resembling intrinsically disordered proteins (IDPs), also pertain to the comprehensive structural description of proteins. It has long been thought that the description of (ordered) proteins by these concepts provides a universal key to understanding protein function, a notion termed the classical structure-function paradigm. This book is devoted to demon-strating how this knowledge can be extended to understand how IDPs function. 1.1 PHYSICAL FORCES THAT SHAPE PROTEIN STRUCTURE Because structural biology has its roots in studying globular (ordered) proteins, the classical concepts of protein structure are better suited for the description of ordered than disordered proteins. Usually, four hierarchical levels are distinguished, such as primary structure (sequence of amino acids in the polypeptide chain), secondary struc-ture (local, often repetitive structural elements [i.e., α -helix, β -strand, turn and coil]), tertiary structure (the fold in space of the entire polypeptide chain, also meaning the spatial arrangement of its secondary structural elements), and quaternary structure (stoichiometry and spatial arrangement of subunits in a multi-subunit protein).
eBook - PDFElectrophoresis
Theory, Methods, and Applications
- Milan Bier(Author)
- 2013(Publication Date)
- Academic Press(Publisher)
Primary Protein Structures F. Sorm and B. Meloun I. General Conclusions from Present Knowledge of Primary Protein Structure 53 II. Methods for Determining the Primary Structure of Proteins 64 A. Introduction 64 B. Specific Labeling of Active Centers of Enzymes 65 C. Cleavage of Proteins to Peptide Fragments 67 D. Separation of Protein Fragments and Isolation of Pure Peptides 75 E. Determination of Amino Acid Sequence in Peptides 81 III. Separation of Mixtures of Peptides and Amino Acids by High-Voltage Electrophoresis 87 A. Continuous High-Voltage Electrophoresis 88 B. One-Dimensional High-Voltage Electrophoresis 91 C. Electrochromatographic Technique 94 D. Two-Dimensional Electrophoresis 97 E. Combination of High-Voltage Electrophoresis with Thin-Layer Techniques 98 References 98 I. General Conclusions from Present Knowledge of Primary Protein Structure The progress made in the field of protein structure determination can be gauged by the number of full structures now known, including those of naturally occurring (generally biologically active) peptides and of the smaller proteins ranging from insulin, with 51 amino acid residues ar-ranged in two chains, to trypsinogen and chymotrypsinogen (with 229 and 245 amino acids, respectively, in single chains) which are the most complex proteins whose structure is known to date (1). 53 2 54 F. Sorm and B. Meloun An early and important general conclusion from this work which should be stressed at this point follows from the repeatedly confirmed finding that pure proteins (i.e., proteins homogeneous by the criteria of physical properties, composition, and biological activity) are, in fact, microhomo-geneous, that is composed of molecules of identical structure; this had frequently been doubted.
eBook - PDFProteins
Concepts in Biochemistry
- Paulo Almeida(Author)
- 2016(Publication Date)
- Garland Science(Publisher)
Protein Structure 2 You’ll say that reality is under no obligation to be interesting. To which I’d reply that reality may disregard the obligation but that we may not. Jorge Luis Borges 2.1 PROTEINS ARE POLYMERS OF A SPECIAL KIND The history of the discovery of protein structures is a history of a search for beauty. Beauty, as we perceive it, derives in great measure from regularity and symmetry. Max Perutz and John Kendrew sought it in the structures of globins ( Figure 2.1 ). Linus Pauling sought it in the secondary structure of α -keratins, and found it in an unlikely moment. In this chapter, we will explore protein structures, one of the most important aspects of biochemistry. To do that, we must toil for a moment with the details of what proteins are made of. Pauling knew that detail was important: it was crucial for him in discovering the α -helix. Figure 2.1 Three-dimensional structure of myoglobin in a ribbon representation. The heme group is shown in black (PDB 1A6N). Polypeptides are Formed by Amino Acids Connected by Peptide Bonds Proteins are a special kind of polymer in that they have a unique three-dimensional structure. Synthetic organic polymers are not like that. However, like any other polymer, proteins are composed of units, or monomers, connected by covalent bonds. In proteins, the units are 20 different amino acids. The chemical bond that links two amino acids is an amide bond , which biochemists usually call a peptide bond . A peptide bond is formed by linking two amino acids, with release of a water molecule ( Figure 2.2 ). Here a dipeptide is formed. If a third amino acid is added, we form a tripeptide, then a tetrapeptide ( Figure 2.3 ), and so on. In general, H H H N C C O OH R 1 α H H H N C C O OH R 2 α H H H N C C O R 1 α H H N C C O OH R 2 α H 2 0 Figure 2.2 A peptide bond, or amide bond, is a covalent bond formed between two amino acids, with release of a water molecule. Amino acids differ in the groups designated by R 1 and R 2 .
eBook - PDF- William H. Brown, Thomas Poon(Authors)
- 2017(Publication Date)
- Wiley(Publisher)
18.4 What Are Polypeptides and Proteins? • A peptide bond is the special name given to the amide bond formed between α‐amino acids. • A polypeptide is a biological macromolecule containing 20 or more amino acids joined by peptide bonds. • By convention, the sequence of amino acids in a polypep- tide is written from the N‐terminal amino acid toward the C‐terminal amino acid. • A peptide bond is planar; that is, the four atoms of the amide bond and the two α‐carbons bonded to it lie in the same plane. • Bond angles about the amide nitrogen and the carbonyl carbon of a peptide bond are approximately 120°. 18.5 What Is the Primary Structure of a Polypeptide or Protein? • The primary (1°) structure of a polypeptide or protein refers to the sequence of amino acids in its polypeptide chain. • The first step in determination of primary structure is hydrolysis and quantitative analysis of amino acid compo- sition by ion‐exchange chromatography. • Cyanogen bromide is specific for the cleavage of peptide bonds formed by the carboxyl group of methionine. • Trypsin catalyzes the hydrolysis of peptide bonds formed by the carboxyl groups of arginine and lysine. • Chymotrypsin catalyzes the hydrolysis of peptide bonds formed by the carboxyl groups of phenylalanine, tyrosine, and tryptophan. • The Edman degradation selectively cleaves the N‐terminal amino acid without affecting any other peptide bonds in a polypeptide or protein. Quick Quiz 619 18.6 What Are the Three‐Dimensional Shapes of Polypeptides and Proteins? • The four atoms of a peptide bond and the two α‐carbons bonded to it all lie in the same plane; that is, a peptide bond is planar. • Secondary (2°) structure refers to the ordered arrangement (conformations) of amino acids in localized regions of a polypeptide or protein. The two most prevalent types of secondary structure are the α‐helix and the β‐pleated sheet, both of which are stabilized by hydrogen bonding.
eBook - PDF- BIOTOL, B C Currell, R C E Dam-Mieras(Authors)
- 2013(Publication Date)
- Butterworth-Heinemann(Publisher)
The secondary structure(s) are then linked by sections of random coil of irregular structure. extended Other helices can, in principle, occur. Think of either a more extended helix ie greater helices translation along the helix axis per residue, or a more squashed one. Short segments of a more extended helix (the 3.10 helix) are sometimes seen. The fibrous protein of connective tissue, collagen, forms an extended left-handed helix; three of these strands are combined, rope-like, to form a 'super-helix' which is stabilised by inter-chain hydrogen bonds. Proteins 59 Protein a- Keratin Myoglobin Lysozyme Carboxypeptidase Cytochromec % a- helix* 100 77 45 35 15 Table 3.4 Percentage a- helical content of some proteins. *The percentage is the proportion of the total number of amino acids which are found within a- helices. many fibrous proteins have repeated amino acid sequences It is notable that some of the fibrous (ie structural) proteins have primary structures which are 'repeats' of a simple sequence. Thus silk largely consists of a 6-residue repeat: gly-ser-gly-ala-gly-ala, whilst collagen has large amounts of glycine and proline (or hydroxyproline, which is a hydroxylated form of proline). Globular proteins, which constitute the enzymes and proteins which interact with other compounds in cells, have much more varied amino acid sequences. As a consequence, their structures are essentially infinitely varied. myoglobin structure elucidated orientation of polar and hydrophobic sidechains in proteins 3.5 Tertiary structure of proteins The tertiary structure describes the overall shape of the protein. This overall conformation is the consequence of the presence of any secondary structures and how they and the remainder of the chain are positioned. Each protein adopts a unique tertiary structure. This conformation will be the result of the various weak bonds which can arise. It also depends on interaction with the surrounding solvent (usually water).
eBook - PDFBiochemistry
An Integrative Approach
- John T. Tansey(Author)
- 2019(Publication Date)
- Wiley(Publisher)
• Secondary structures are stabilized by hydrogen bonds in the peptide backbone, and can be formed by many different amino acids. • Tertiary structures describe the interaction of different elements of helix and sheet to form a complex structure. • Tertiary structure represents the complete folding of a single polypeptide into a functional protein. • Examples of tertiary motifs include the four-helix bundle and the Greek key motif. • Tertiary structures are stabilized by a combination of many weak forces; these include hydrogen bond- ing, dipole–dipole interactions, salt bridges, disulfide bonds, cation–π interactions, and a phenomenon known as the hydrophobic effect. • Many proteins exhibit quaternary structure interactions between and among different polypeptide chains. WORKED PROBLEM 3.3 Protein structure and disease Sickle cell anemia is a common genetic disorder. The causal mutation in sickle cell anemia is E6V, that is, the substitution of a glutamic acid for valine in the sixth position of the β chain of hemoglobin, a tetrameric protein with the stoichiometry a2β2. In the deoxygenated state, the mutant hemoglobin can polymerize, causing erythrocytes (red blood cells) to form a sickled shape and lyse, leading to the symptoms of this disease. How might this mutation affect all four levels of protein structure? Strategy Examine the information we have been given in the question and think about the four levels of protein structure. How could this alteration in amino acid sequence lead to the observed phenotype and disease? Solution Hemoglobin is a tetrameric protein. The mutation has altered the primary sequence of the β chains of hemoglobin by replacing a negatively charged glutamic acid with a hydrophobic valine residue. It is not apparent from the information provided in the question how this might affect the secondary and tertiary structure of the protein.
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