Biomolecules & Polymers Amino Acids

BIOMOLECULES & POLYMERS AMINO ACIDS INTRODUCTION Amino acids are the compounds which contain both an amino group and a carboxy group in their molecules. They constitute a particularly important class of difunctional compounds as they are the building blocks of proteins. While several hundred different amino acids are known to occur naturally, 20 of them deserve special mention as they are present in proteins. These amino acids are listed in Table. As given in this table, for amino acids trivial names are common. The convention to use a three letter code, as an abbreviation, for each amino acid is also given in the table. These abbreviations are particularly useful in designating the sequence of amino acids in peptides and proteins which your will study. Each living cell is made up of thousands of different proteins All proteins contain the elements like carbon, hydrogen, oxygen, nitrogen and sulphur. Some of these also contain phosphorus, iodine and traces of metals such as, Fe, Cu, Zn, & Mn. All proteins are polymers of -amino acids and on partial hydrolysis give peptides of varying molecular masses which upon complete hydrolysis give -amino acids. Proteins Hydrolysis Peptides Hydrolysis -amino acids These organic compounds contain amino as well as carboxylic acid group. On the basis of position of amino group in the chain, these are named as , ,  etc. amino acid. There are around 20 amino acids among which 10 amino acids are synthesis in our body and these are said to be non essential amino acids (eg. Gly, Ala, Glu, Asp, Pro and Cys) and other amino acids which are necessarily be present in our diet are called essential amino acids (eg. Val, Leu, I leu, Lys and Phe). Type of -amino acids : Amino acids with non polar side chain : Amino acids with polar and neutral side chain : R– – R – CH2OH – Serine H– – Glycine CH3– CH – | OH – Threonine CH3– – Alanine HS–CH2– – Cystine (CH3)2CH– – valine (CH3)2CH–CH2 – leucine C6H5CH2 – phenylalanine (3) Amino acids with acidic side chain : (4) Amino acid with basic side chain : R– R– –CH2 – COOH – HOOC–CH2–CH2– – Note : Aspartic acid H2N–(CH2)4– Glutamic acid – – lysine – Arginine All -amino acids except glycine have chiral C-atom and have (L) configuration normally. Amino Acid : Building Blocks of Proteins Amino acids are the building blocks of the molecular structure of the important and very complex class of compounds known as proteins. The proteins on hydrolysis yield mixture of the component amino acids. Amino acids are bifunctional compounds containing both an amino and a carboxylic acid group. They are represented by the general formula : H O | || H2N  C  C  OH or     | Carboxylic Amine R Acid group H2N  CH  COOH | R Where, R = alkyl, aryl, or any other group. Zwitter ion (Dipolar Nature of Amino acids) : .. In a neutral amino acid solution, the –COOH loses a proton and the – NH2 of the same molecule picks up one. The resulting ion is dipolar, charged but overall electrically neutral. This is called Zwitterion (German, “two ions”). Therefore amino acids are amphoteric. BIOMOLECULES & POLYMERS H O H2N  C  C  OH R H H O +  H3N  C  C  O + -H + +H Zwitter ion + H3N  C  C  OH R Low pH(Acid soln.) Cation form (II) H O +  H2N  C  C  O H O + H3N  C  C  O O H + R Zwitterion Neutral form (I) - HO (-H2O) R High pH (Basic soln.) Anionic form (III) Isoelectric point of -amino acids : When an ionised amino acid is placed in an electric field, it will actually migrate towards the opposite electrode. Depending upon the pH of the medium, three things can happen. The positive form (II) will migrate to the cathode, the neutral form (Zwitter ion) will not migrate, while the negative form (III) will migrate to the anode. The pH at which the amino acid shows no tendency to migrate when placed in an electric field is known as its isoelectric point. This is characteristic of a given amino acid. Thus glycine has its isoelectric point at pH 6.1. Isoelectric Point : The pH at which the amino acid shows no tendency to migrate when placed in an electric field is known as its isoelectric point. Because of amphoteric nature in acidic solution it exist as the +ve ion. Hence it migrate towards cathode while in basic solution it exist as –ve ion and migrates towards anode. pH < 7 Cathode pH > 7 Anode At some intermediate pH amino acids exist as a neutral dipolar ion i.e. the concentration of the cation and anions are equal and it does not migrate towards either electrode, this pH is called iso electric point of amino acid which is different for different amino acids. Nature of amino acid O OH R E/N.E Name Abbreviation Glycine Gly Alanine Ala Valine Val Leucine Leu Isoleucine Ile Aspartic Acid Asp Glutamic Acid Glu Lysine Lys N H2 O Neutral amino acid H2N NE OH H O Neutral amino acid Neutral amino acid OH H3 C NE NH2 CH3 H3C E NH2 HO O O Neutral amino acid Neutral amino acid E CH3 HO NH2 CH3 OH O NH2 E CH3 CH3 O Acidic amino acid Acidic amino acid NE OH HO NH2 O NH2 NE HO OH O Basic amino acid E H2N O H2N O OH BIOMOLECULES & POLYMERS Basic amino acid NH NE NH2 NH2 NH O Arginin Arg Histidine His Methionine Met Proline Pro Phenylalanine Phe Tryptophan Trp OH O Basic amino acid N NE OH NH2 HN Neutral amino acid O E S HO CH3 N H2 Neutral amino acid O N NE O OH Neutral amino acid O E H 2N Neutral amino acid OH O OH E NH2 N H O Neutral amino acid OH NE Serine Ser Threonine Thr Cysteine Cys Tyrosine Tyr H2N OH OH Neutral amino acid H 3C NH 2 E HO O Neutral amino acid threonine O OH NE H 2N SH Neutral amino acid HO NE O NH2 OH E = essential amino acid NE = Non essential amino acid AMINO ACID AS DIPOLAR IONS: Amino Acids contain both a basic group (–NH2) and an acidic group (–COOH). In the dry solid state, amino acids exist as dipolar ions, a form in which the carboxyl group is present as a carboxylate ion, –CO2–, and the amino group is present as an ammonium ion, –NH3+ (Dipolar ions are also called zwitterions.) In aqueous solution, an equilibrium exists between the dipolar ion and the anionic and cationic forms of an amino acids. + OH H2 N CHCO2H + – H3 O H3 N CHCO2 + R – H2NCHCO2 R Dipolar ion Cationic form (Predominant in strongly acidic solutions, e.g., At pH 0) – R Anionic form (Predominant in strongly basic solutions, e.g., At pH 14) If alanine is dissolved in a strongly acidic solution (e.g. pH 0), it is present in mainly a net cationic form. In this state the amine group is protonated (bears a formal +1 charge) and the carboxylic acid group is neutral (has no formal charge). As is typical of -amino acids, the pKa for the carboxylic acid hydrogen of alanine is considerably lower (2.3) than the pKa of an ordinary carboxylic acid (e.g., propanoic acid, pKa 4.89): CH3CHCO2H NH3 + Cationic form of alanine pKa = 2.3 CH3CH2CO2H Propanoic acid pKa = 4.89 The reason for this enhanced acidity of the carboxyl group in an -amino acid is the inductive effect of the neighboring aminium cation, which helps to stabilize the carboxylate anion formed when it loses a proton. Loss of proton from the carboxyl group in a cationic -amino acid leaves the molecule electrically neutral (in the form of a dipolar ion). This equilibrium is shown in the red-shaded portion of the equation below. The protonated amine group of an -amino acid is also acidic, but less so that the carboxylic acid group. The pKa of the aminium group in alanine is 9.7. The equilibrium for loss of an aminium proton is shown in the blue-shaded portion of the equation below. The carboxylic acid proton is always lost before a proton from the aminium group in an -amino acid. CH3CHCO2H NH3 + Cationic form pKa = 2.3 OH - H3O + CH3CHCO2 NH3 + Dipolar ion pKa = 9.7 OH - H3O + CH3CHCO2 NH2 + Anionic form The state of an -amino acid at any given pH is governed by a combination of two equilibrium, as shown in the above equation for alanine. The isoelectric point (pI) of an amino acid such as alanine is the average of pK a1 and pKa2; pI = ½ (2.3 + 9.7) = 6.0 (isoelectric point of alanine) BIOMOLECULES & POLYMERS When a base is added to a solution of the net cationic form of alanine (initially at pH 0, for example), the first proton removed is the carboxylic acid proton, as we have said. In the case of alanine, when a pH of 2.3 is reached, the acid proton will have been removed from half of the molecules. This pH represents thepKa of the alanine carboxylic acid proton, as can be demonstrated using the Henderson-Hasselbalch equation. The Henderson - Hasselbalch equation shows that for an acid (HA) and its conjugate base (A–), pKa = pH + log  HA  [A – ] When the acid is half neutralized, b) Co-polymers are another type of polymer. These contains more than one sub-unit (or monomer). Ex. : In the above example styrene and maleic anhydride monomers laternate. Co-polymer can be a block co-polymer. Ex. : Co-polymers can be random as well. — B – A – A – B – A – B – B – A – B – A –B – B – A — A and B are monomers.  There are many polymers in nature. Example: Cellulose, starch, pepsin, insulin, egg albumin, rubber, DNA (Deoxyribonucleic acid) etc. These are called Biopolymers. Man made polymers are, Nylon, Terylene, Polythene, Polystyrene, PVC (Polyvinyl chloride), Bakelite, Perspex, Polysiloxane etc.  The properties of a polymer solution are strikingly different from those of a true solution. For example, when polyvinyl alcohol is added to water, it swells. a) Its shape gets distorted and after a long time it dissolves. b) When more of polymer is added to a given solvent, saturation point is not reached. The mixture of polymer and solvent assumes a soft dough-like consistency.  Addition polymers and condensation polymers are two important types of polymers.  Polymer can be described as linear, branched and network. POLYMERSAND POLYMERIZATION Macromolecules, both natural and man-made, own their great size to the fact they are polymers (Greek: many parts); that is, each one is made up of a great many simpler unit - identical to each other or at least chemically similar - joined together in a regular way. They are formed by a process we touched on earlier: polymerization, the joining together of many small molecules to form very large molecules. The simple compounds from which polymers are made are called monomers. PEPTIDES AND PROTEINS In the last section, you studied the polymers of monosaccharides which act as structural components in plants and serve as energy storage in animals. In this section, you will study another kind of natural polymers called peptides and proteins. Peptides are biologically important polymers in which 2-amino acids are joined by the amide linkages, formed by the reaction of the carboxy group of one amino acid with the amino group of another amino acid. These amide linkages are also called peptide bonds. The general structure of a peptide is shown below: Peptides can be classified as dipeptides, tripeptides and tetrapeptides, depending on whether the number of amino acids, two, three or four, respectively. Peptides containing upto 50 amino acids are called polypeptides. Bradykinin is an important naturally occurring nonapeptide which is present in blood plasma and is involved in the regulation of blood pressure. Arg—Pro — Pro — Gly — Phe — Ser — Pro — Phe — Arg Bradykinin CONFIGURATION OF PROTEINS (a) Biological nature or function of protein was confirmed by its conformation. (b) This conformation is of 4 types Primary Secondary Tertiary Quatemany PRIMARY STRUCTURE :  This type of structure was given by Frederick Sanger in 1953 in Insulin (of one chain)  Primary structure is conformed by a single polypeptide chain in a linear manner.  All amino acid are attached in a straight chain by peptide bond.  No biological importance & soon changed to other forms. SECONDARY STRUCTURE :  In it structure of straight chain from irregular changes to form coils.  H-bond + peptide bond present in secondary. structure.  This H bond is present between hydrogen of Amino group and oxygen atom carboxylic acid group.  This structure is of two types -helix -pleated sheet C N O C C O H N O HO N C H O C N O H N H N C O H H N N 54 pm C N N RCH RCH RCH C C C O H N O O H N H N HCR HCR HCR C C C O O H N H O N H N RCH RCH RCH C C C O O H O H N N H N HCR HCR HCR C C C BIOMOLECULES & POLYMERS (i) -helix  Chain is spiral  3.7 atoms in one coiling  Right handed circular. Ex.  Myosin, Keratin etc. (ii) -pleated sheet  Structure of protein is not arranged in a sequence.  Polypeptide chain are parallel to each other  H - bond form by near chains Ex. Silk fibres. TERTIARY STRUCTURE  In this structure of protein atoms are highly coiled and form a spherical form Ex. Albumin  This structure is formed by 4 regular hydrogen bonds which makes a regularity in it (i) Hydrogen bond : C = O …….. H – N– H Hydrogen bond  They are formed between oxygen of acidic amino acid and H of basic amino acid. (ii) Hydrophobic bond  Non - polar side chains of neutral amino acid tends to be closely associated with one another in proteins.  Present in between the amino Acid.  These are not true bonds. (iii) lonic bond : –COO–.....H3+N– Ionic bond  These are salt bonds formed between oppositely charged groups in side chains of Amino acids Eg. Aspartic acid, Glutamic acid (iv) Disulphide bonds : | ——— S - S —— |  Relatively stable bond and thus is not broken readily under usual conditions of denaturation.  Formed between the -SH group of Amino acid Ex. Cystine and Methionine . QUATERNARYSTRUCTURE  When 2 or more polypeptide chains united by forces other than covalent bonds (i.e. not peptide and disulphide bonds) are called Quaternary structure.  It is most stable structure. Ex. Haemoglobin TYPES OF PROTEINS  Classification of protein is based upon three general properties shape, Solubility and Chemical composition. Proteins Simple Conjugated Derived Simple proteins  It is formed of only Amino Acids Types  Fibrous Globular Fibrous :  It is insoluble  It is of elongated shape.  It is highly resistant to digestion by proteolytic enzymes.  Their main function - Protection. Ex. Collagen, Keratin etc Globular :  These are spherical and oval in shape. Chains are highly coiled  These are soluble. Ex. Albumin Conjugated Proteins  These are complex proteins in which protein molecule is combined with characteristic non-amino acid substance.  Non-amino acid or Non - Protein part is called as prosthetic group Ex. Nucleoproteins (Protein + Nucleic acid), Phosphoproteins (Protein + (PO3)2–) Ex.  Casein of milk., Vitelline of egg - yolk Derived proteins : These are obtained as a result of partial hydrolysis of natural proteins. Eg.  Proteose, Metaproteins, Peptones Denaturation of Proteins When a protein in its native form, is subjected to a physical change like change in temperature, or a chemical change like change in pH, the native conformation of the molecule is disrupted and proteins so formed are called denaturated proteins. The denaturation may be reversible or irreversible. The coagulation of egg on boiling is an example of irreversible protein denaturation. However, it has been shown now that in some cases, the process is actually reversible. The reverse process is called renaturation. BIOMOLECULES & POLYMERS TEST OF PROTEIN : (a) With conc. HNO3 on heating give yellow ppt. Which on more heating give solution On adding NH4OH Red colour appears. It is Xanthoprotic test. (b) (NH4OH) + dil. CuSO4 protein give Blue violet colour. It is a biuret test. (c) Millon reaction. Proteins on adding Millon’s reagent (a solution of mercuric and mercurous nitrates in nitric acid containing a little nitrous acid) followed by heating the solution give red precipitate or colour. (d) Ninhydrin reaction. Proteins, peptides and a-amino acids give a characteristic blue colour on treatment with ninhydrin. Biological Importance of protein : (a) Component of plasma membrane. (b) All enzymes are protein. (c) Many hormones are protein. (d) Antigen and antibody are protein. (e) Actin and myosin protein are important in muscle contraction. (f) Proteins are important in growth, regeneration and repairing. (g) Calorific value 4.0 kcal.