Organic Chemistry - Bio-Molecules

SECTION 1 - Carbohydrates:

Q1. What are carbohydrates? How are they defined chemically?

Carbohydrates are optically active polyhydroxy aldehydes or ketones, or compounds that on hydrolysis give such units. They are also called saccharides. Chemically, most carbohydrates have the empirical formula Cₙ(H₂O)ₙ, which is why they were once thought to be hydrates of carbon. They are the most abundant biomolecules on earth and serve as the primary source of energy for living organisms.

Q2. How are carbohydrates classified? Give examples of each.

Carbohydrates are classified into three groups. Monosaccharides are the simplest carbohydrates that cannot be hydrolysed further - examples are glucose, fructose, galactose, and ribose. Disaccharides are formed by the joining of two monosaccharides with loss of water - examples are sucrose, maltose, and lactose. Polysaccharides are formed by the joining of many monosaccharide units - examples are starch, cellulose, and glycogen.

Q3. What are reducing and non-reducing sugars ?

Reducing sugars are carbohydrates that can reduce Fehling's solution or Tollens' reagent because they have a free aldehyde or ketone group. All monosaccharides and some disaccharides like maltose and lactose are reducing sugars. Non-reducing sugars do not reduce Fehling's solution because they have no free aldehyde or ketone group - the anomeric carbons of both units are involved in the glycosidic bond. Sucrose is the most important non-reducing sugar.

Q4. What is glucose? What are its important chemical properties ?

Glucose is the most important monosaccharide and the primary source of energy for mammals. It is an aldohexose - it has 6 carbons and an aldehyde group. Its molecular formula is C₆H₁₂O₆. It has five hydroxyl groups. Key chemical properties are - it gives a silver mirror with Tollens' reagent (confirming aldehyde group), it reduces Fehling's solution, it reacts with acetic anhydride to form glucose pentaacetate (confirming five OH groups), and it does not give 2,4-DNP test in its cyclic form (the aldehyde is masked).

Q5. Why does glucose not give certain reactions expected of an aldehyde ?

Glucose exists predominantly in a cyclic (ring) form called the pyranose form, where the aldehyde group has reacted internally with the C-5 hydroxyl group to form a hemiacetal ring. In this cyclic form, the free aldehyde group is not available, so glucose does not give the 2,4-DNP test, Schiff's test, or react with sodium bisulphite - reactions typically given by free aldehydes. However, a small fraction exists in the open chain form in solution, which is why it still gives the silver mirror test and reduces Fehling's solution.

Q6. What are alpha and beta glucose? What is mutarotation ?

When glucose forms its cyclic (ring) structure, a new asymmetric carbon (C-1) is created. If the OH at C-1 is on the same side as the CH₂OH group, it is called beta glucose. If it is on the opposite side, it is called alpha glucose. When either pure alpha or pure beta glucose is dissolved in water, the optical rotation gradually changes and reaches an equilibrium value - this is called mutarotation. It happens because the two forms interconvert through the open chain form in solution.

Q7. What is fructose? How is it different from glucose ?

Fructose is a ketohexose — it has 6 carbons and a ketone group at C-2. Its molecular formula is also C₆H₁₂O₆, making it an isomer of glucose. Unlike glucose, it forms a 5-membered ring (furanose form). Despite being a ketone, fructose is still a reducing sugar because ketones adjacent to a hydroxyl group can tautomerise to an aldehyde in alkaline conditions. Fructose is the sweetest naturally occurring sugar.

Q8. What are the important polysaccharides? Compare starch, cellulose, and glycogen.

Starch is the storage form of carbohydrates in plants. It has two components - amylose (linear, α-1,4 glycosidic linkages, forms a helical coil) and amylopectin (branched, α-1,4 linkages in chain and α-1,6 linkages at branch points). Cellulose is the structural polysaccharide of plant cell walls. It has β-1,4 glycosidic linkages forming long straight chains that pack together via hydrogen bonds, giving it great mechanical strength. Humans cannot digest cellulose because we lack the enzyme to break β-1,4 bonds. Glycogen is the storage form of carbohydrates in animals, stored in liver and muscles. Its structure is similar to amylopectin but more highly branched.

Q9. Why are glucose and sucrose soluble in water while cyclohexane is not ?

Glucose has five and sucrose has eight hydroxyl (OH) groups. These OH groups form extensive hydrogen bonds with water molecules, making them very soluble. Cyclohexane and benzene have no OH groups and are non-polar molecules, so they cannot form hydrogen bonds with water and are insoluble. This follows the principle "like dissolves like."

Q10. What is the glycosidic linkage? How is sucrose formed ?

A glycosidic linkage is a covalent bond formed between two monosaccharide units with the loss of a water molecule. Sucrose is formed by the joining of glucose (through its C-1) and fructose (through its C-2) with the elimination of water. Since both anomeric carbons (C-1 of glucose and C-2 of fructose) are involved in the bond, sucrose has no free aldehyde or ketone group, making it a non-reducing sugar.

Q11. What are the products of hydrolysis of lactose and maltose ?

Lactose (milk sugar) on hydrolysis gives one molecule of glucose and one molecule of galactose. Both are joined by a β-1,4 glycosidic bond. Maltose (malt sugar) on hydrolysis gives two molecules of glucose. Both units are joined by an α-1,4 glycosidic bond. Both lactose and maltose are reducing sugars because one glucose unit in each has a free anomeric carbon.

SECTION 2 - Proteins

Q12. What are proteins? What are amino acids ?

Proteins are high molecular mass biomolecules made up of large numbers of amino acid units joined by peptide bonds. They perform a vast variety of functions in the body - structural, catalytic, hormonal, transport, defence, and regulatory. Amino acids are the building blocks of proteins. They are organic compounds containing both an amino group (−NH₂) and a carboxyl group (−COOH) attached to the same carbon atom (the alpha carbon). About 20 different amino acids are found in proteins.

Q13. What are essential and non-essential amino acids ?

Essential amino acids are those that the human body cannot synthesise on its own and must be obtained from the diet. Examples are valine, leucine, isoleucine, lysine, threonine, methionine, phenylalanine, and tryptophan. Non-essential amino acids are those that the body can synthesise by itself from other compounds. Examples are glycine, alanine, serine, aspartic acid, and glutamic acid.

Q14. What is a zwitterion? How do amino acids show amphoteric behaviour ?

In aqueous solution, the carboxyl group of an amino acid loses a proton (acts as acid) while the amino group accepts a proton (acts as base). This produces a dipolar ion called a zwitterion, which carries both a positive and negative charge but has no net charge. Because of this, amino acids can act as both acids and bases - this is called amphoteric behaviour. The pH at which the amino acid exists mainly as the zwitterion with no net charge is called the isoelectric point.

Q15. What is a peptide bond? How is it formed ?

A peptide bond is the amide bond formed between the carboxyl group of one amino acid and the amino group of another, with the elimination of a water molecule. It is a covalent bond represented as −CO−NH−. When two amino acids join, a dipeptide is formed. When many amino acids are linked by peptide bonds, the result is a polypeptide or protein. The sequence of amino acids in the chain is called the primary structure of the protein.

Q16. What are the four levels of protein structure ?

Primary structure is the linear sequence of amino acids in the polypeptide chain, held by peptide bonds. Secondary structure is the three-dimensional arrangement of the polypeptide chain due to hydrogen bonds between −NH and −C=O groups of the backbone. The two common secondary structures are the alpha helix (a right-handed coil stabilised by hydrogen bonds within the same chain) and the beta pleated sheet (extended chains held side by side by hydrogen bonds). Tertiary structure is the overall three-dimensional folding of the polypeptide chain into a compact shape, stabilised by disulphide bonds, hydrogen bonds, hydrophobic interactions, and ionic interactions. Quaternary structure exists in proteins with two or more polypeptide chains (subunits) -it describes how these subunits are arranged together. Haemoglobin is a classic example with four subunits.

Q17. What is the difference between fibrous and globular proteins ?

Fibrous proteins have polypeptide chains arranged parallel to each other along one axis, forming long fibre-like structures. They are insoluble in water and are tough and strong -used mainly for structural purposes. Examples are keratin (hair, nails, wool), collagen (tendons), and myosin (muscles). Globular proteins have polypeptide chains folded into a spherical or globe-like compact shape. They are usually soluble in water and are biologically active. Examples are enzymes, haemoglobin, insulin, and antibodies.

Q18. What is denaturation of proteins ? What causes it ?

Denaturation is the process by which a protein loses its natural three-dimensional structure (secondary, tertiary, and quaternary) without breaking the primary structure (peptide bonds). The biological activity of the protein is lost on denaturation. It is caused by heat, strong acids or bases, heavy metal ions, organic solvents, and detergents. A familiar example is the coagulation of egg white (albumin) on boiling - the protein unfolds and cannot refold. Curdling of milk by adding acid is another example.

SECTION 3 - Enzymes

Q19. What are enzymes? What are their characteristics ?

Enzymes are biological catalysts that speed up chemical reactions in living organisms. They are almost always proteins. Key characteristics are - they are highly specific (each enzyme catalyses only one type of reaction or acts on one type of substrate), they are required in very small amounts, they function under mild conditions of temperature and pH, they are not consumed in the reaction, and their activity can be regulated.

Q20. What is the lock and key mechanism of enzyme action ?

In the lock and key model, the enzyme has a specific region called the active site whose shape fits the substrate exactly like a key fits a lock. The substrate binds to the active site to form an enzyme-substrate complex. The reaction then takes place, the products are released, and the enzyme is regenerated unchanged. The high specificity of enzymes is explained by this model - only the substrate with the correct shape and chemical groups can fit into the active site.

Q21. What factors affect enzyme activity ?

Temperature - enzyme activity increases with temperature up to an optimum (usually 37°C in humans), beyond which the enzyme denatures and activity drops sharply. pH - each enzyme has an optimum pH at which it is most active (e.g., pepsin works best at pH 2, trypsin at pH 8). Substrate concentration - increasing substrate concentration increases activity up to a maximum point where all active sites are saturated. Inhibitors - competitive inhibitors block the active site while non-competitive inhibitors bind elsewhere and change the shape of the active site.

SECTION 4 - Vitamins:

Q22. What are vitamins? How are they classified ?

Vitamins are organic compounds required in very small amounts in the diet for normal growth, development, and body functions. They are not synthesised in adequate amounts by the body, so they must be obtained from food. Vitamins are classified into two groups - fat-soluble vitamins (A, D, E, K) that are stored in body fat and liver, and water-soluble vitamins (B complex and C) that are not stored and must be taken regularly in the diet.

Q23. What are the important vitamins, their sources, and deficiency diseases ?

Vitamin A (retinol) - sources are fish liver oil, carrots, butter; deficiency causes night blindness and xerophthalmia. Vitamin B₁ (thiamine) -sources are yeast, whole grains; deficiency causes beriberi. Vitamin B₂ (riboflavin) -sources are milk, eggs; deficiency causes cheilosis and photophobia. Vitamin B₁₂ (cyanocobalamin) - sources are meat, milk; deficiency causes pernicious anaemia. Vitamin C (ascorbic acid) - sources are citrus fruits, amla; deficiency causes scurvy. Vitamin D (calciferol) - synthesised in skin on sunlight exposure; deficiency causes rickets in children and osteomalacia in adults. Vitamin E (tocopherol) - sources are vegetable oils; deficiency causes sterility. Vitamin K -sources are green leafy vegetables; deficiency causes poor blood clotting (haemorrhage).

Q24. What is the difference between fat-soluble and water-soluble vitamins ?

Fat-soluble vitamins (A, D, E, K) dissolve in fats and oils, are stored in the body's fatty tissues and liver, and do not need to be taken every day. Excess intake can cause toxicity because they accumulate in the body. Water-soluble vitamins (B complex and C) dissolve in water, are not stored in the body, and excess amounts are excreted in the urine. They must be supplied regularly through diet and overdose toxicity is rare.

SECTION 5 - Nucleic Acids

Q25. What are nucleic acids? What are their two types ?

Nucleic acids are biomolecules found in the nucleus of all living cells as constituents of chromosomes. They are also called polynucleotides because they are long-chain polymers of nucleotides. There are two types - deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is found mainly in the nucleus and is the genetic material. RNA is found in the nucleus and cytoplasm and is involved in protein synthesis.

Q26. What is a nucleotide? How is it different from a nucleoside?

A nucleoside is formed by the attachment of a nitrogenous base to C-1 of a sugar (deoxyribose in DNA or ribose in RNA) through a N-glycosidic bond. A nucleotide is formed by the attachment of a phosphate group to the 5' carbon of the sugar in a nucleoside. So nucleotide = nitrogenous base + sugar + phosphate group, while nucleoside = nitrogenous base + sugar only. Nucleotides are the monomers of nucleic acids, joined by phosphodiester bonds.

Q27. What are the nitrogenous bases present in DNA and RNA?

Both DNA and RNA contain adenine (A), guanine (G), and cytosine (C). The fourth base differs - DNA contains thymine (T) while RNA contains uracil (U) instead of thymine. Adenine and guanine are purines (double-ring structures). Cytosine, thymine, and uracil are pyrimidines (single-ring structures).

Q28. What is the structure of DNA? Explain Watson-Crick model.

DNA is a double-stranded helix made of two polynucleotide strands wound around each other in a right-handed manner. The sugar-phosphate backbone runs on the outside while the nitrogenous bases point inward. The two strands are held together by specific hydrogen bonds between complementary bases- adenine pairs with thymine through two hydrogen bonds, and guanine pairs with cytosine through three hydrogen bonds. This is called Chargaff's rule. The two strands run antiparallel to each other (one runs 5' to 3' and the other 3' to 5'). The distance between two base pairs is 0.34 nm and the pitch of the helix is 3.4 nm.

Q29. What is the difference between DNA and RNA ?

DNA has deoxyribose sugar while RNA has ribose sugar. DNA contains thymine while RNA contains uracil. DNA is double-stranded while RNA is usually single-stranded. DNA is found mainly in the nucleus and is the permanent genetic material. RNA is found in both nucleus and cytoplasm and is involved in protein synthesis. DNA is more stable than RNA because the absence of the 2' hydroxyl group in deoxyribose makes it less prone to hydrolysis.

Q30. What are the three types of RNA and their functions ?

Messenger RNA (mRNA) carries the genetic information from DNA in the nucleus to the ribosomes in the cytoplasm, where it serves as the template for protein synthesis. Ribosomal RNA (rRNA) is a structural and functional component of ribosomes, where protein synthesis actually occurs. Transfer RNA (tRNA) carries specific amino acids to the ribosome during protein synthesis - it reads the codons on mRNA through its anticodon loop and brings the correct amino acid to be added to the growing protein chain.

Q31. What are the two important functions of nucleic acids ?

The first function is replication -DNA can make exact copies of itself during cell division, so each daughter cell receives an identical copy of the genetic information. This is the basis of heredity. The second function is protein synthesis - the sequence of bases in DNA codes for the sequence of amino acids in proteins. This information is transcribed from DNA to mRNA and then translated into protein at the ribosomes, with the help of tRNA and rRNA. Through protein synthesis, nucleic acids control all metabolic activities of the cell.