File Name: classification structure and properties of amino acids .zip
Proteins are large biomolecules or macromolecules that are comprised of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions , DNA replication , responding to stimuli , providing structure to cells and organisms , and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes , and which usually results in protein folding into a specific 3D structure that determines its activity.
NCBI Bookshelf. Molecular Cell Biology. New York: W. Freeman; Proteins are designed to bind every conceivable molecule—from simple ions to large complex molecules like fats, sugars, nucleic acids, and other proteins. They catalyze an extraordinary range of chemical reactions, provide structural rigidity to the cell, control flow of material through membranes, regulate the concentrations of metabolites, act as sensors and switches, cause motion, and control gene function.
The three-dimensional structures of proteins have evolved to carry out these functions efficiently and under precise control. The spatial organization of proteins, their shape in three dimensions, is a key to understanding how they work.
One of the major areas of biological research today is how proteins, constructed from only 20 different amino acids, carry out the incredible array of diverse tasks that they do.
Unlike the intricate branched structure of carbohydrates, proteins are single, unbranched chains of amino acid monomers. The unique shape of proteins arises from noncovalent interactions between regions in the linear sequence of amino acids.
Only when a protein is in its correct three-dimensional structure, or conformation , is it able to function efficiently. A key concept in understanding how proteins work is that function is derived from three-dimensional structure, and three-dimensional structure is specified by amino acid sequence. Amino acids are the monomeric building blocks of proteins.
All 20 different amino acids have this same general structure, but their side-chain groups vary in size, shape, charge, hydrophobicity, and reactivity. Amino acids, the monomeric units that link together to form proteins, have a common structure. The side chain, or R group red , is more Amino acids can be classified into a few distinct categories based primarily on their solubility in water, which is influenced by the polarity of their side chains Figure Amino acids with polar side groups tend to be on the surface of proteins; by interacting with water, they make proteins soluble in aqueous solutions.
In contrast, amino acids with nonpolar side groups avoid water and aggregate to form the waterinsoluble core of proteins.
The polarity of amino acid side chains thus is one of the forces responsible for shaping the final three-dimensional structure of proteins. The structures of the 20 common amino acids grouped into three categories: hydrophilic, hydrophobic, and special amino acids. The side chain determines the characteristic properties of each amino acid.
Shown are the zwitterion forms, which exist at the more Hydrophilic , or water-soluble, amino acids have ionized or polar side chains. At neutral pH , arginine and lysine are positively charged; aspartic acid and glutamic acid are negatively charged and exist as aspartate and glutamate.
These four amino acids are the prime contributors to the overall charge of a protein. A fifth amino acid , histidine, has an imidazole side chain, which has a p K a of 6. As a result, small shifts of cellular pH will change the charge of histidine side chains:. The activities of many proteins are modulated by pH through protonation of histidine side chains. Asparagine and glutamine are uncharged but have polar amide groups with extensive hydrogen-bonding capacities.
Similarly, serine and threonine are uncharged but have polar hydroxyl groups, which also participate in hydrogen bonds with other polar molecules. Because the charged and polar amino acids are hydrophilic , they are usually found at the surface of a water-soluble protein , where they not only contribute to the solubility of the protein in water but also form binding sites for charged molecules. Hydrophobic amino acids have aliphatic side chains, which are insoluble or only slightly soluble in water.
The side chains of alanine, valine, leucine, isoleucine, and methionine consist entirely of hydrocarbons, except for the sulfur atom in methionine, and all are nonpolar. Phenylalanine, tyrosine, and tryptophan have large bulky aromatic side groups.
As explained in Chapter 2, hydrophobic molecules avoid water by coalescing into an oily or waxy droplet. The same forces cause hydrophobic amino acids to pack in the interior of proteins, away from the aqueous environment. Later in this chapter, we will see in detail how hydrophobic residues line the surface of membrane proteins that reside in the hydrophobic environment of the lipid bilayer. Lastly, cysteine, glycine, and proline exhibit special roles in proteins because of the unique properties of their side chains.
The side chain of cysteine contains a reactive sulfhydryl group — SH , which can oxidize to form a disulfide bond — S — S — to a second cysteine:. Regions within a protein chain or in separate chains sometimes are cross-linked covalently through disulfide bonds. Although disulfide bonds are rare in intracellular proteins, they are commonly found in extracellular proteins, where they help maintain the native, folded structure. The smallest amino acid , glycine, has a single hydrogen atom as its R group.
Its small size allows it to fit into tight spaces. Proline is very rigid, and its presence creates a fixed kink in a protein chain. The known and predicted proteins encoded by the yeast genome have an average molecular weight MW of 52, and contain, on average, amino acid residues.
This is a useful number to remember, as we can use it to estimate the number of residues from the molecular weight of a protein or vice versa. Some amino acids are more abundant in proteins than other amino acids. Cysteine, tryptophan, and methionine are rare amino acids; together they constitute approximately 5 percent of the amino acids in a protein.
Four amino acids—leucine, serine, lysine, and glutamic acid—are the most abundant amino acids, totaling 32 percent of all the amino acid residues in a typical protein. However, the amino acid composition of proteins can vary widely from these values. For example, as discussed in later sections, proteins that reside in the lipid bilayer are enriched in hydrophobic amino acids.
Nature has evolved a single chemical linkage , the peptide bond , to connect amino acids into a linear, unbranched chain. The peptide bond is formed by a condensation reaction between the amino group of one amino acid and the carboxyl group of another Figure a. This leaves at opposite ends of the chain a free unlinked amino group the N-terminus and a free carboxyl group the C-terminus. A protein chain is conventionally depicted with its N-terminal amino acid on the left and its C-terminal amino acid on the right Figure b.
The peptide bond. Many terms are used to denote the chains formed by polymerization of amino acids. A short chain of amino acids linked by peptide bonds and having a defined sequence is a peptide ; longer peptides are referred to as polypeptides.
Peptides generally contain fewer than 20—30 amino acid residues, whereas polypeptides contain as many as residues. We reserve the term protein for a polypeptide or a complex of polypeptides that has a threedimensional structure. It is implied that proteins and peptides represent natural products of a cell.
The size of a protein or a polypeptide is reported as its mass in daltons a dalton is 1 atomic mass unit or as its molecular weight a dimensionless number. For example, a 10,MW protein has a mass of 10, daltons Da , or 10 kilodaltons kDa.
In the last section of this chapter, we will discuss different methods for measuring the sizes and other physical characteristics of proteins. The structure of proteins commonly is described in terms of four hierarchical levels of organization. These levels are illustrated in Figure , which depicts the structure of hemagglutinin, a surface protein on the influenza virus. This protein binds to the surface of animal cells, including human cells, and is responsible for the infectivity of the flu virus.
Four levels of structure in hemagglutinin, which is a long multimeric molecule whose three identical subunits are each composed of two chains, HA 1 and HA 2.
The primary structure of a protein is the linear arrangement, or sequence, of amino acid residues that constitute the polypeptide chain. Secondary structure refers to the localized organization of parts of a polypeptide chain, which can assume several different spatial arrangements. A single polypeptide may exhibit all types of secondary structure.
Without any stabilizing interactions, a polypeptide assumes a random-coil structure. Finally, U-shaped four-residue segments stabilized by hydrogen bonds between their arms are called turns. They are located at the surfaces of proteins and redirect the polypeptide chain toward the interior. These structures will be discussed in greater detail later. Tertiary structure , the next-higher level of structure, refers to the overall conformation of a polypeptide chain, that is, the three-dimensional arrangement of all the amino acids residues.
In contrast to secondary structure , which is stabilized by hydrogen bonds, tertiary structure is stabilized by hydrophobic interactions between the nonpolar side chains and, in some proteins, by disulfide bonds. For proteins that consist of a single polypeptide chain, monomeric proteins, tertiary structure is the highest level of organization. Multimeric proteins contain two or more polypeptide chains, or subunits, held together by noncovalent bonds. Quaternary structure describes the number stoichiometry and relative positions of the subunits in a multimeric protein.
Hemagglutinin is a trimer of three identical subunits; other multimeric proteins can be composed of any number of identical or different subunits. In a fashion similar to the hierarchy of structures that make up a protein , proteins themselves are part of a hierarchy of cellular structures. Proteins can associate into larger structures termed macromolecular assemblies. Examples of such macromolecular assemblies include the protein coat of a virus , a bundle of actin filaments, the nuclear pore complex , and other large submicroscopic objects.
Macromolecular assemblies in turn combine with other cell biopolymers like lipids, carbohydrates, and nucleic acids to form complex cell organelles.
Different ways of depicting proteins convey different types of information. The simplest way to represent three-dimensional structure is to trace the course of the backbone atoms with a solid line Figure a ; the most complex model shows the location of every atom Figure b ; see also Figure a. Even though both views are useful, the elements of secondary structure are not easily discerned in them.
Various graphic representations of the structure of Ras, a guanine nucleotide—binding protein. Guanosine diphosphate, the substrate that is bound, is shown as a blue space-filling figure in parts a — d.
This type of representation emphasizes the organization of the secondary structure of a protein , and various combinations of secondary structures are easily seen. However, none of these three ways of representing protein structure conveys much information about the protein surface, which is of interest because this is where other molecules bind to a protein.
Computer analysis in which a water molecule is rolled around the surface of a protein can identify the atoms that are in contact with the watery environment. On this water-accessible surface, regions having a common chemical hydrophobicity or hydrophilicity and electrical basic or acidic character can be mapped. Such models show the texture of the protein surface and the distribution of charge, both of which are important parameters of binding sites Figure d. This view represents a protein as seen by another molecule.
In this section, we explore the forces that favor formation of secondary structures.
Amino acids, as ancient and ubiquitous molecules, have been co-opted by evolution for a variety of purposes in living systems. The importance in reading this section is limited to those who wants to visualize the structures. The common amino acids are known as a-amino acids because they have a primary amino group -NH2 and a carboxylic acid group -COOH as substitutes of the a carbon atoms. Proline is an exception because it has a secondary amino group -NH- , for uniformity it is also treated as alpha-amino acid. Fig 1. General structure of a- amino acid.
Basic Structure of Amino Acids. Introduction Essential amino acids Why learn this? Amino acids play central roles both as building blocks of proteins and as intermediates in metabolism. The 20 amino acids that are found within proteins convey a vast array of chemical versatility. The precise amino acid content, and the sequence of those amino acids, of a specific protein, is determined by the sequence of the bases in the gene that encodes that protein. The chemical properties of the amino acids of proteins determine the biological activity of the protein. Proteins not only catalyze all or most of the reactions in living cells, they control virtually all cellular process.
In the pH range between 4 and 8, amino acids carry both a positive and a negative charge and therefore do not migrate in an electrical field.
Amino acids are a crucial, yet basic unit of protein, and they contain an amino group and a carboxylic group. They play an extensive role in gene expression process, which includes an adjustment of protein functions that facilitate messenger RNA mRNA translation Scot et al. There are over types of amino acids that have been discovered in nature. The amino acids are essential components of peptides and proteins. Twenty important amino acids are crucial for life as they contain peptides and proteins and are known to be the building blocks for all living things on earth. They are used for a protein synthesis.
Your email address will not be published. Required fields are marked *