Course Teacher: Dr. A.H. Rashadul Hossain Professor Depart of Chemistry Chittagong University of Engineering & Technology (CUET). Chittagong 4349, Bangladesh.
Structure and Bonding: Atomic orbitals, hybridization, molecular shape, sigma and pi bonding, electronegativity and polarity, resonance, isomerism. 6 Organic reactions and their mechanism: Carbocation, carboanion, nucleophile , electrophile, nucleophilic and electrophilic substitution reaction and their mechanism, steric hindrance and stereoCHEMistry, role of solvent in SN1 and SN2 reaction, E1 and E2 reaction. 8 Aromatic Compounds: Nomenclature of aromatic compounds, benzene and aromaticity, unusual stability of benzene, modern theories of of the structure of benzene, aromatic compounds (phenol, aniline, pyrrole). 7 Polymers: Macromolecules and polymers, degree of polymerization, classification of polymers, copolymerization, types and mechanism of polymerization: addition (free radical, cationic and anionic/living), condensation and coordination polymerization, structure and properties of polymer. 7 Biomolecules: Structure and reaction of cellulose, structure of amino acids, peptide linkage, structure of proteins. 5 Spectroscopic Techniques: UV-Visible spectroscopy: Introduction, principle, instrumentation, electronic transition and application. IR Spectroscopy: Introduction, principle, instrumentation, sample handling, chemical shift, coupling constant and application. 6 Referred textbooks: 1. Organic Chemistry by I.L. Finar 2. Organic Chemistry by McMurry 3. A Guide book to Mechanism in Organic Chemistry by Peter Sykes 4. Advanced Organic Chemistry by Arun Bahl and B.S Bahl 2 Proteins Proteins are probably the most complex materials produced in nature. The name protein is derived from the Greek word ‘protelos’, meaning ‘of prime importance’. Without proteins life would not be possible. Proteins are present in muscle, skin, hair and other tissue that make up the bulk of the body's nonbony structure. As enzymes they catalyze biochemical reactions; as hormones they regulate metabolic processes; and as antibodies they resist and nullify the effects of toxic substances. Elements in proteins Proteins have very high moleculur weights. Their molecular weights may range from 10,000 to over 50 million. All proteins yield amino acids upon complete hydrolysis. Thus proteins may be defined as the high-molecular- weight organic materials which, upon complete hydrolysis, yield amino acids. 3 Amino acids Amino acids are organic acids having an amino (—NH2) group attached to a chain containing an acid group. Although the amino group can be anywhere on the chain, amino acids derived from proteins have the amino group on the alpha (α) carbon, that is, the carbon atom next to the carboxyl group. These α-amino acids may be represented by the following general formula.
where R may be a hydrogen, a
straight or branched-chain aliphatic group, an aromatic ring or a heterocylic ring.
1. About 20 amino acids are commonly found in portions, but hundreds
occurs naturally. 2. All amino acids found in proteins are α-amino acids. 3. All amino acids found in proteins (except glycine) are optically active. 4 Classification of amino acids Amino acids are classified as neutral, acidic, or basic according to the relative number of amino and carboxyl groups in the molecule. Neutral amino acids contain one amino group and one carboxyl group. Acidic amino acids contain one amino group and two carboxyl groups. Basic amino acids contain two amino groups and one carboxyl group.
5 Nomenclature of amino acids About 30 amino acids have been obtained from hydrolysis of proteins, and 20 of these are- relatively common. The names, structures, and 3-letter abbreviations of the common amino acids are given in Table in next. Notice that all the amino acids have trivial names, even those for which the systematic names whould not be cumbersome. Thus the compound H2N—CH2—COOH is called glycine rather than α-amino acetic acid or 2-aminoethanoic acid. The compound CH3—CH(NH2)—COOH is called alanine rather than α- aminopropionic acid or 2-aminopropanoic acid. These trivial names usually reflect the origin or a property of the compound. For example, glycine, is so named because it has a sweet taste (or glykos, sweet), and tyrosine was first obtained from cheese (Gr., tyros, cheese).
6 Neutral Amino acids
7 Neutral Amino acids
8 Neutral Amino acids
9 Acidic Amino acids
Basic Amino acids
10 Essential & Non essential amino acids
Essential Amino acids: Those amino acids that cannot be
synthesized by the body and must be supplied in the diet are called Essential Amino acids. Minimum daily requirements of all essential amino acids for human beings have not been established requirements vary from 0-25 g to 1-5 g a day. Examples- Valine, Phenylalanine, Tryptophen etc. 9 are essential amino acid.
Non-essential Amino acids: The amino acids that can be
synthesized from other compounds by the tissues of the body are called non essential amino acids. Examples- Glycine, Alanine, Serine etc. 11 are non essential, 7 of them are conditionally essential amino acids.
11 Essential & Non essential amino acids
12 Essential amino acids
13 Zwitter Ion Amino acid has both a basic amine group and an acidic carboxylic acid group. In neutral solution (pH 7.0), the amino acid contains a negative charge and a positive charge. It is called a zwitterion.
14 Isoelectric point
15 16 Optical Activity of Amino acids Glycine does not have an asymmetric carbon atom and, therefore, does not have optical isomers. Alanin and all other amino acids have an asymmetric carbon at position 2, the α-carbon atom. For this reason they are all optically active and exist in D and L forms, which are nonsuperimposable mirror image isomers. If the carboxyl group is written at the top, the D-form refers to the isomer with the —NH2 group on the right; the L-form is the isomer with the —NH2 group on the left. The reference compound for this assignment is glyceraldehyde.
17 Optical Activity of Amino acids Recall that the letters D and L refer only to the relative configuration around the asymmetric carbon atom and not to the direction of optical rotation.
The direction of optical rotation is indicated by a (+) sign for a
dextrorotatory amino acid and a (—) sign for a laevorotatory one.
Most of the naturally occurring amino acids have the L-configuration.
The products of laboratory synthesis are generally optically inactive. This is due to the formation of racemates containing equal amounts of D- and L-forms.
The optical rotation of amino acids depends upon the pH of the
solution.
In neutral solution, most of the amino acids are dextrorotatory.
18 Synthesis of amino acids (1) By Amination of α-Halo Acids. α-Chloro or α-bromo carboxylic acids react with excess of liquid ammonia to form the ammonium salt of an amino acid. The free amino acid can be obtained by hydrolysis of the ammonium salt. (1)
19 Synthesis of amino acids
20 Chemical reactions of amino acids
21 Chemical reactions of amino acids
22 Chemical reactions of amino acids
23 Peptide Bond
24 Proteins
25 Classification of proteins
26 Classification of proteins There are two methods for classifying proteins. I) On the Basis of Composition A) Simple proteins, B) Conjugate proteins A) Simple proteins : Simple proteins are those which yield only α-amino acids upon hydrolysis. They are further subdivided according to their solubility in various solvents and also whether they are coagulated by heat. (1) Albumins: Albumins are water-soluble proteins, which are coagulated by heat. Examples are egg-albumin and serum-Albumin. (2) Globulins: Globulins are insoluble in water but soluble in dilute salt solutions, which are coagulated by heat. Examples are serum globulin and vegetable-globulin. (3) Scleroproteins, (Albuminoids): Scleroproteins are insoluble in water and most other solvents. Example is keratin in hair and fingernails. (4) Glutenins: Glutenins are insoluble in water but soluble in dilute acids and alkalis, which are coagulated by heat. Example is glutenin from wheat. (5) Histones: Histories' are soluble in water but insoluble in dilute ammonium hydroxide, which are not coagulated by heat. They are found in animals. Example is globin in hemoglobin. 27 Classification of proteins (6) Prolamines: Prolamines are insoluble in water but soluble in 70 per cent ethanol, which are not coagulated by heat. Examples are zein from corn and gliadin from wheat. (7) Protamines: Protamines are soluble in water and dilute ammonium hydroxide, which are not coagulated by heat. Examples are salmine from salmon and sturine from sturgeon.
According to solubility the Simple proteins also divided into two groups: a) Fibrous protein: They are elongated or fiber like protein and insoluble in water. b) Globular protein: They are spherical or globular in shape with higher degree of complexity in structure and soluble in water.
28 Classification of proteins B) Conjugated proteins: Conjugated proteins are those which yield α-amino acids plus a nonprotein material upon hydrolysis. The nonprotein material is called the prosthetic group. The conjugated proteins are also subdivided into several classes according to the nature of the prosthetic group. (1) Glycoproteins: Glycoproteins contain a carbohydrate derivative as their prosthetic group. Mucin, a constituent of saliva, is a glycoprotein. (2) Phospoproteins: Phosphoproteins are proteins which contain α-amino acids linked to phosphoric acid. Example- Casein, which is found in milk. (3) Chromoproteins: Chromoproteins consist of a pigmented prosthetic group combined with a simple protein. Haemoglobin and cytochromes are examples of chromoproteins. (4) Nucleoprotiens: Nucleoproteins are complex substances that occur abundantly in the nuclei of plant and animal cells. The prosthetic groups are nucleic acids. Examples of nucleoproteins are the nuclein and nucleohis:ons of glandular tissues, yeast, chromosomes, and other materials rich in ccii nuclei. (5) Lipoproteins: Lipoproteins consist of cholestrol esters and phospholipids attached to protein molecules. They are found in brain and nerve tissue and are an integral part of cell membranes. 29 Classification of proteins II) On the Basis of Physiological Functions. The functional classification of proteins includes the following groups: (1) Structural proteins: These are fibrous proteins, such as collogen which comprises half of man's total protein in the form of skin, cartilage and bone. (2) Contractile Proteins: Contractile proteins are found in muscles. Examples are myosin, actin. (3) Hormones: Many proteins function as hormones, that is, as communication links between different parts of organism. Insulin is a common example of a protein harmone, (4) Enzymes: Proteins of this group serve as catalyst for the chemical reactions in living organisms, rendering specificity and control to these reactions. Pepsin and Irypsin are examples of the class, (5) Antibodies: When the body is invaded by infectious species that release foreign proteins or antigens, antibodies are produced to remove the invading species from the system. Gamma globulins present in the blood are examples of antibodies. (6) Blood Proteins: The three major protein constituents of the blood are albumins, hemoglobin and fibrinogen. Their presence contributes to the maintenance of osmotic pressure, oxygen transport and blood coagulation 30 respectively. 31 Isolation of Proteins
32 Structure of proteins The simplest level of protein structure, primary structure, is simply the sequence of amino acids in a polypeptide chain. For instance, the sequence of the A chain starts with glycine at the N-terminus and ends with asparagine at the C-terminus, and is different from the sequence of the B chain. Image of insulin. Insulin consists of an A chain and a B chain. They are connected to one another by disulfide bonds (sulfur-sulfur bonds between cysteines). The A chain also contains an internal disulfide bond. The amino acids that make up each chain of insulin are represented as connected circles, each with the three-letter abbreviation of the amino acid's name.
33 Structure of proteins The next level of protein structure, secondary structure, refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone. The most common types of secondary structures are the α helix and the β pleated sheet. Both structures are held in shape by hydrogen bonds, which form between the carbonyl ‘O’ of one amino acid and the amino ‘H’ of another.
34 Structure of proteins In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon, with each turn of the helix containing 3.6 amino acids. The R groups of the amino acids stick outward from the α helix, where they are free to interact cubed. In a β pleated sheet, two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet cubed. The strands of a β pleated sheet may be parallel, pointing in the same direction (meaning that their N- and C-termini match up), or antiparallel, pointing in opposite directions (meaning that the N- terminus of one strand is positioned next to the C-terminus of the other).
35 Structure of proteins The overall three-dimensional structure of a polypeptide is called its tertiary structure. The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein. R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces – basically, the whole gamut of non-covalent bonds. For example, R groups with like charges repel one another, while those with opposite charges can form an ionic bond. Similarly, polar R groups can form hydrogen bonds and other dipole-dipole interactions. Also important to tertiary structure are hydrophobic interactions, in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules.
36 Structure of proteins
Some proteins are made up of multiple polypeptide chains, also
known as subunits. When these subunits come together, they give the protein its quaternary structure. We’ve already encountered one example of a protein with quaternary structure: hemoglobin. As mentioned earlier, hemoglobin carries oxygen in the blood and is made up of four subunits, two each of the α and β types.
37 38 General Properties of Proteins The important general properties of proteins are given below: 1) Most proteins are colourless amorphous solids. They have no definite melting points. 2) Proteins, like amino acids exist as Zwitterions. 3) Most proteins are optically active. 4) Proteins, like amino acids, have isoelectric points. 5) Proteins form colloidal dispersions in water. They can pass through a filter paper but not through a membrane. 6) Precipitation: Proteins are easily precipitated (or coagulated) by (a) by heat, (b) by ethyl alcohol, (c) by con. inorganic acid, (d) by silver nitrate, (e) by picric acid or tannic acid, (f) by ultraviolet ray or X-ray. 7) Hydrolysis: Simple proteins can be hydrolysis with acids (HCl), alkalis (NaOH), or enzymes to give component amino acids. Conjugated proteins also yield the prosthetic groups along with the amino acids. 8) Oxidation: Proteins are oxidized on burning and putrefaction. The products include nitrogen, carbon dioxide and water.
39 Denaturation of Proteins
40 Color test of proteins
41 Color test of proteins
42 Determination of Proteins It is often desirable to know the protein content of various foods and biological material. The analysis of the protein content of such a material is based on its nitrogen content.
Since the average nitrogen content of proteins is 16 per cent, the
protein content of a substance may be obtained by multiplying-its nitrogen value by the factor 100/16 = 6.25. For example, if a certain food contains 2 per cent nitrogen, on analysis its protein content would equal 2*6.25, or 12.5 per cent.
The total nitrogen content of proteins and peptides may be
determined by the Dumas method or the Kjeldahl method.
The aromatic amino acids in proteins absorb ultraviolet light at a
wavelength of 2800 Å. The measurement of light absorption at 2800Å is a convenient method for determining the amount of protein in solution. 43 Dr. A.H. Rashadul Hossain Professor, Department of Chemistry CUET. 44
