Biomolecules — Study Notes

1. Introduction

All living organisms are made of chemical substances that are responsible for their structure and function. These substances, called biomolecules, are the organic compounds that form the basis of life. When a living tissue is analysed, it is found to contain water, inorganic ions, proteins, carbohydrates, lipids and nucleic acids. The chemical analysis of living tissues reveals that there are an enormous number of organic compounds in any living system, from simple gases to complex polymers. The study of biomolecules helps us understand the chemistry of life, how metabolic reactions occur, and how energy is produced and utilised by the body.

The chapter begins with the chemical analysis of living tissues, then examines the four major classes of biomolecules: carbohydrates, proteins, lipids and nucleic acids. It also introduces enzymes, which are the biological catalysts that accelerate metabolic reactions. The concepts of the living state, metabolism and the relationship between structure and function of biomolecules form the core of biochemistry. Understanding biomolecules is essential for grasping how the thousands of chemical reactions in a living body are organised and controlled.

2. How to Analyse Chemical Composition

Living tissue can be analysed for its chemical composition in a laboratory. If one takes living tissue and grinds it with trichloroacetic acid (TCA), the acid will precipitate all the large molecules such as proteins, nucleic acids, polysaccharides and lipids. The acid-soluble pool contains small molecules like simple sugars, amino acids, nucleotides and salts. This acid-soluble fraction, representing the cytoplasm, is called the acid-soluble pool, while the acid-insoluble fraction represents the macromolecules of the cell.

The elementary analysis of living tissues reveals that carbon, hydrogen, oxygen and nitrogen make up about 98 percent of the total mass of living organisms, along with smaller amounts of other elements. Biomolecules are classified as micromolecules (molecular weight in the range of 18 to 800 Da, e.g., amino acids, sugars, nucleotides, fatty acids) and macromolecules (molecular weight more than 1000 Da, e.g., proteins, polysaccharides, nucleic acids). The sum total of all biomolecules inside a living organism is called the biochemical composition, and the thousands of chemical reactions occurring in the body are collectively called metabolism.

3. Micromolecules and Macromolecules

3.1 Monomeric Units and Polymers

Proteins are polymers of amino acids. Polysaccharides are polymers of monosaccharides. Nucleic acids are polymers of nucleotides. These three classes of biomolecules are called polymers, and their building blocks are called monomers. Lipids, however, are not strictly polymers, because a lipid is made of glycerol and fatty acids, and these components are not in a repeating sequence.

3.2 Analysis of Biomolecules

Amino acids are the building blocks of proteins. A standard amino acid has an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom and a variable R group, all attached to the same carbon atom (the alpha carbon). Amino acids are classified as essential (cannot be synthesised by the body and must be supplied in diet) and non-essential (can be synthesised by the body). Amino acids are linked by peptide bonds to form proteins.

Fatty acids are the building blocks of lipids. They are carboxylic acids with a hydrocarbon chain. They may be saturated (no double bonds, e.g., palmitic acid, stearic acid) or unsaturated (with one or more double bonds, e.g., oleic acid, linoleic acid). Glycerol is a trihydric alcohol, and when three fatty acids esterify with one glycerol molecule, a triglyceride is formed.

Nucleosides and nucleotides: A nucleotide consists of a nitrogenous base, a pentose sugar and a phosphate group. A nucleoside is a base attached to the sugar, without the phosphate. The nitrogenous bases are of two types: purines (adenine and guanine) and pyrimidines (cytosine, uracil and thymine). The sugar may be ribose (in RNA) or deoxyribose (in DNA).

4. Carbohydrates

Carbohydrates are compounds composed of carbon, hydrogen and oxygen, with the general formula Cx(H2O)y. They are primarily a source of energy. The carbohydrates are classified on the basis of the number of sugar units: - Monosaccharides: Simple sugars that cannot be hydrolysed further, e.g., glucose, fructose, galactose. They may be trioses (3C), tetroses, pentoses (5C, e.g., ribose, deoxyribose) or hexoses (6C, e.g., glucose, fructose). - Disaccharides: Formed by the condensation of two monosaccharide units joined by a glycosidic bond, with the release of one water molecule, e.g., sucrose (glucose + fructose), maltose (glucose + glucose), lactose (glucose + galactose). - Polysaccharides: Long chains of monosaccharides joined by glycosidic bonds, e.g., starch (storage form of glucose in plants), cellulose (structural polysaccharide of plant cell walls), glycogen (storage form of glucose in animals, stored in liver and muscles), and chitin (a structural polysaccharide in the exoskeleton of arthropods and fungal cell walls). Polysaccharides are not sweet in taste and are not soluble in water, and they are used for storage and structural functions.

5. Lipids

Lipids are water-insoluble compounds that are soluble in organic solvents like chloroform and benzene. They are important constituents of cell membranes and are a major source of energy, providing about 9 kcal per gram. The important classes of lipids are: - Simple lipids: Fats and oils (triglycerides), formed by glycerol esterified with fatty acids. Fats are solid at room temperature (e.g., butter, ghee), while oils are liquid (e.g., groundnut oil, mustard oil). - Compound lipids: Lipids conjugated with other molecules, e.g., phospholipids (contain phosphate group, present in cell membranes), glycolipids (contain carbohydrates) and lipoproteins (contain proteins). - Derived lipids: Steroids and terpenes. Cholesterol is an important sterol present in cell membranes and is the precursor of steroid hormones and bile acids.

6. Proteins

Proteins are polymers of amino acids joined by peptide bonds. They are the most abundant macromolecules of the cell, constituting about 50 percent of the dry weight of the cell. Proteins perform a vast range of functions: they act as enzymes (catalysts), as structural proteins (keratin in skin, collagen in connective tissue), as transport proteins (haemoglobin carries oxygen), as defence proteins (antibodies), as regulatory proteins (some hormones), and as storage proteins.

6.1 Structure of Proteins

• Primary structure: The linear sequence of amino acids held together by peptide bonds.
• Secondary structure: The folding of the polypeptide chain into a regular pattern, either the alpha-helix or the beta-pleated sheet, stabilised by hydrogen bonds.
• Tertiary structure: The overall three-dimensional shape of the protein, formed by the folding of the secondary structure, stabilised by disulphide bonds, hydrogen bonds and hydrophobic interactions.
• Quaternary structure: The association of two or more polypeptide chains (subunits) to form a functional protein, e.g., haemoglobin has four subunits.

A protein loses its biological activity when it is denatured, which means the unfolding of its three-dimensional structure. Denaturation can be caused by heat, acids or salts, and is often irreversible.

7. Nucleic Acids

Nucleic acids are the hereditary materials of the cell, of two types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). They are polymers of nucleotides.

7.1 DNA

DNA contains the sugar deoxyribose, the bases adenine, guanine, cytosine and thymine, and is double-stranded. It is the genetic material of most organisms. The two strands of DNA are held together by hydrogen bonds between complementary base pairs: adenine pairs with thymine (A-T, two hydrogen bonds) and guanine pairs with cytosine (G-C, three hydrogen bonds). DNA stores genetic information.

7.2 RNA

RNA contains the sugar ribose, the bases adenine, guanine, cytosine and uracil, and is usually single-stranded. The three major types of RNA are: - Messenger RNA (mRNA): Carries genetic information from DNA to the ribosome for protein synthesis. - Transfer RNA (tRNA): Carries amino acids to the ribosome during protein synthesis. - Ribosomal RNA (rRNA): A component of the ribosome, involved in protein synthesis.

8. Enzymes

Enzymes are proteins that act as biological catalysts, accelerating the rate of chemical reactions without being consumed in the reaction. The reactant that an enzyme acts upon is called the substrate. The enzyme binds to the substrate at a specific region called the active site. The mechanism of enzyme action can be explained by the lock and key model, which states that the substrate fits into the active site like a key fits into a lock. The induced fit model is a modified version.

8.1 Properties of Enzymes

• Enzymes are highly specific in their action; each enzyme acts on a specific substrate.
• Enzymes lower the activation energy of a reaction.
• Enzymes are not used up in the reaction and can be reused.
• Enzyme activity is affected by temperature, pH and substrate concentration. Most enzymes work best at an optimum temperature (about 37 degrees Celsius in humans) and an optimum pH (7 for most enzymes).
• Enzymes are denatured by extreme temperature and pH.

8.2 Classification of Enzymes

• Oxidoreductases: Catalyse oxidation-reduction reactions.
• Transferases: Transfer functional groups from one molecule to another.
• Hydrolases: Catalyse hydrolysis reactions, e.g., digestive enzymes.
• Lyases: Catalyse the removal of groups without hydrolysis.
• Isomerases: Catalyse interconversion of isomers.
• Ligases (synthetases): Catalyse the linking of two molecules using energy from ATP.

8.3 Co-factors

Many enzymes require additional non-protein components called co-factors for their activity. These are of three types: prosthetic groups (organic, covalently bound, e.g., haem in peroxidase), co-enzymes (organic, loosely bound, e.g., NAD, NADP, coenzyme A), and metal ions (e.g., Mg2+, Zn2+, Cu2+). Co-enzymes often serve as carriers of chemical groups or electrons.

Quick Revision Tables

Table 1: Classification of Carbohydrates

Table 2: Types of RNA

Table 3: Enzyme Classes

Mind Map

Important Diagrams (SVG)

Common Mistakes

1. Students confuse nucleoside with nucleotide. A nucleoside has no phosphate group; a nucleotide has a base, sugar and phosphate.
2. Lipids are called polymers of fatty acids; they are not true polymers because the fatty acids are not in a repeating sequence.
3. The general formula of carbohydrates (CH2O)n is applied to all sugars, but it does not apply to carbohydrates like deoxyribose and some others.
4. DNA is said to have uracil; DNA contains thymine, while RNA contains uracil.
5. All fats are called bad; saturated fats are solid at room temperature while unsaturated fats are liquid (oils).
6. Enzymes are said to be consumed in reactions; they are catalysts and are not consumed or changed permanently.
7. All enzymes are proteins; this is mostly true, but some RNA molecules (ribozymes) also catalyse reactions, so the statement needs qualification.
8. Students say pH of the stomach is optimum for all enzymes; each enzyme has its own optimum pH, and pepsin works best in acidic medium.

Exam Tips

1. Remember base pairing: A-T (2 H-bonds) and G-C (3 H-bonds) in DNA; A-U in RNA.
2. Learn the monomer-polymer pairs: amino acid-protein, monosaccharide-polysaccharide, nucleotide-nucleic acid.
3. Enzyme classification with the six classes and one example each is a definite scoring area.
4. Co-factors: prosthetic group (covalently bound organic), co-enzyme (loosely bound organic), metal ions.
5. The acid-soluble pool (cytoplasm, small molecules) vs acid-insoluble fraction (macromolecules) is a frequently asked conceptual question.
6. For proteins, remember the four levels of structure and the bonds stabilising each (peptide, hydrogen, disulphide).
7. ATP is the energy currency; note its structure as a nucleotide with three phosphate groups.

Conclusion

Biomolecules form the chemical foundation of life, and their study reveals the elegant simplicity beneath the complexity of living systems. The four major classes of biomolecules, carbohydrates, proteins, lipids and nucleic acids, are built from a surprisingly small number of monomeric units, yet they generate enormous diversity through variations in sequence and structure. Enzymes orchestrate the thousands of metabolic reactions that constitute the living state, and their specificity, efficiency and regulation are central to cellular life. The concept of the living state as a dynamic equilibrium of biomolecules performing continuous chemical reactions ties together the structural knowledge of the previous chapter with the functional biology of the organism. This chemical perspective prepares the learner for understanding cellular energetics and division in the next chapter.