Structures of -Amino Acids PDF

Structures of Amino Acids  Amino Acids, Peptides and Proteins Introduction Proteins are biopolymers assembled in ribosomes under the control of nucleic acids from a menu of L--amino acids. Proteins play import...

Structures of Amino Acids  Amino Acids, Peptides and Proteins Introduction Proteins are biopolymers assembled in ribosomes under the control of nucleic acids from a menu of L--amino acids. Proteins play important roles in all aspects of cell structure and function: They hold it together, protect and give structure to the body (structural proteins e.g. muscle, skin, hair). As enzymes, hormones and antibodies, they run it (they catalyse, regulate and protect the body chemistry). They are the principal materials of nerves and blood. In the form of haemoglobin and myoglobin, they transport oxygen within an organism. Of all chemical compounds, proteins must almost certainly be ranked first, for they are the substances of life. 3:36 PM 3 Amino Acids and Proteins Proteins are the most abundant and functionally divers molecules in living systems. Every life process depends on this class of molecules. Types and functions of Proteins 1. Enzymes - increase rate of reaction x 1 billion 2. Carriers – hemoglobin, transferrin 3. Receptors – hormones, cytokines 4. Transport – membrane channels 5. Structure – collagen, elastin 6. Protective - immunoglobulins 7. Contractile - muscle, cytoskeleton 8. Regulatory (Hormones)– govern metabolic pathway  Amino Acids, Peptides and Proteins Introduction These building blocks (-amino acids) are linked through amide (peptide) bonds to give macromolecules with polypeptide backbones and side-chains containing a variety of simple functionalities based on the amino acids selected. The -amino acids may be considered to polymerize, atleast conceptually, through the elimination of a water molecule to form an amide bond (peptide bond) We will start by looking at the building blocks of proteins to 3:36 PM gain incite of the entire structure and functions of proteins. 4  Amino Acids Definition The physical, chemical and biochemical properties of a protein or peptide are determined by its constituent -amino acids (building blocks). It is essential, therefore, to look at the individual amino acids and their characteristics to get a clue of how they influence the nature of the peptide or protein which they are incorporated. Amino acids are carboxylic acids that also contain an amino functional group within their structural framework. 3:36 PM 5  Amino Acids Classification Amino acids are classified as  and so on, according to the relative location of the amino group to the carboxylic acid moiety on the parent chain of the amino acid. Since natural proteins are composed of L--amino acids only, the rest of the discussion will focus on -amino acids. 6  a-Amino Acids Definition Although more than 700 different amino acids, of diverse classifications ( and so on), are known to occur naturally; only a group of 20 a-amino acids, called standard amino acids, is found in nearly all natural proteins and commands special attention. The use of these 20-amino acids in the biosynthesis of proteins is governed by the genetic code. 7   -Amino Acids Structure: Things to Note There are some common features of these amino acids that should be noted. All, but one of these a-amino acids, contain a primary amino group and a carboxylic acid group attached to the same carbon and conform to the general structure above. The one exception is proline, which contains a secondary amino group in which the amino nitrogen is incorporated into a five-membered ring. The simplest  -amino acid is glycine (aminoacetic acid). With the exception of glycine, all the other  -amino acids are chiral. The standard amino acids differ from each other only on the structure of the side chains bonded to their a-carbon atoms. 8   -Amino Acids Structures of Standard Amino Acids The 20 amino acids can be grouped based on the nature of the side chain (R). The following categories of side chains can be envisaged: i. The R is hydrogen or an alkyl group ii. The R contains an alcohol function iii. The R contains sulphur iv. The amino group is secondary or part of a ring v. One hydrogen in alanine is replaced by an aromatic or heteroaromatic (indole) ring vi. One amino group and two carbonyl groups vii. One carbonyl group and two amino groups 9  Structures of  -Amino Acids Amino Acids with One Amino Group and One Carbonyl For simplicity, a system of abbreviated codes is used to refer to these amino acids. In this system, each amino acid has a three-letter code, derived from its trivial name. (a) The R is hydrogen or an alkyl group Name Abbreviation Structure Isoelectric point Glycine Gly 6.0 Alanine Ala 6.0 Valine Val 6.0 Leucine Leu 6.0 Isoleucine Ile 6.0 10  Structures of  -Amino Acids Amino Acids with One Amino Group and One Carbonyl (b) The R contains an alcohol function Name Abbreviation Structure Isoelectric point Serine Ser 5.7 Threonine Thr 5.6 (c) The R contains sulphur Cysteine Cys 5.0 Methionine Met 5.7 (d) The amino group is secondary or part of a ring Proline Pro 6.3 11  Structures of  -Amino Acids Amino Acids with One Amino Group and One Carbonyl Name Abbreviation Structure Isoelectric point (d) The amino group is secondary or part of a ring Proline Pro 6.3 (e) One hydrogen in alanine is replaced by an aromatic or heteroaromatic (indole) ring Phenylalanine Phe 5.5 Tyrosine Tyr 5.7 Tryptophan Trp 5.9 12  Structures of  -Amino Acids Amino Acids with One Amino Group and Two Carbonyl Groups Name Abbreviation Structure Isoelectric point (f) One amino group and two carbonyl groups Aspartic acid Asp 2.8 Glutamic acid Glu 3.2 Asparagine Asn 5.4 Glutamine Gln 5.7 13  Structures of  -Amino Acids Amino Acids with Two Amino Groups and One Carbonyl Group (g) One carbonyl group and two amino groups Name Abbreviation Structure Isoelectric point Lysine Lys 9.7 Arginine Arg 10.8 Histidine His 7.6 14  Hydrophilic (polar) R Group Uncharged side chains. These amino acids have zero net charge at neutral pH Uncharged side chains. These amino acids have zero net charge at neutral pH Some side chains act as sites of attachment for the compounds: serine, threonine and tyrosine contain polar hydroxyl group that can serve as site of attachment: phosphorylation. Side chain of serine residue is an important component of the active sites of many enzymes. The –OH of serine and threonine can be linked to oligosaccharide in glycoprotein  Amino Acids as Acids and Bases Ionization of the –NH2 and the –COOH group Zwitterion has both +ve and –ve charge Zwitterion is neutral overall + NH2–CH2–COOH H3N–CH2–COO– glycine Zwitterion of glycine pH and ionization of amino acids H+ OH– + + H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–COO– Positive ion zwitterion Negative ion Low pH neutral pH High pH  Structures of  -Amino Acids Essential Amino Acids While humans posses the capacity to biosynthesize about half of the amino acids needed to make proteins, they must obtain certain of the others from their diet. Those that must be obtained from dietary sources are called essential amino acids. They can be present in the diet in the free form, but most commonly in the combined natural form as proteins. The ten essential amino acids Arginine Histidine Isoleucine Leucine Threonine Lysine Methionine Phenylalanine Tryptophan Valine Mnemonic for the ten essential amino acids 15  Structures of  -Amino Acids Sources of  -Amino Acids Proteins are essential to humans, since they are the only natural source of amino acids that can be used by the body to build its enzymes, hormones and muscle etc. Although the amino acids occur in proteins linked through peptide bonds, they are hydrolysed into their individual amino acids using proteases. These individual amino acids are then combined by the body according to the genetic code to provide the requisite peptides or proteins. Proteins that provide all the essential amino acids in about the right proportions for human nutrition are called complete proteins e.g. meat, fish, milk and eggs. Proteins that are severely deficient in one or more of the essential amino acids are called incomplete proteins. 16  Structures of  -Amino Acids Complete vs Incomplete Proteins Animal proteins are usually complete proteins, while plant proteins are generally incomplete. Plant Protein Source Proteins Deficient in Amino Acid(s) Rice Lysine and Threonine Maize Lysine and Tryptophan Wheat Lysine Beans and other legumes Methionine Beans, peas and other legumes are the nearest to complete proteins among the common plants, but they are deficient in methionine. Combining maize and beans is an economical way of making up for the deficiencies of amino acids inherent in the individual protein sources. 17  Properties of  -Amino Acids Amino acids combine many of the properties and reactions of both amines and carboxylic acids. The proximity of a basic amino group to an acidic carboxyl group in the same molecule also results in some unique properties and reactions. The side chains of some amino acids also have functional groups that lend interesting properties and undergo reactions of their own. 23  Stereospecificity of Amino Acids All the amino acids found in the proteins are L-configuration