Biomolecules

HOW TO ANALYSE CHEMICAL COMPOSITION

Living organisms are composed of both organic and inorganic compounds. To understand the chemical composition of living tissues, scientists perform **chemical analysis** through specific laboratory methods.

**Elemental Composition Analysis:**

When elemental analysis is performed on living tissues (plant, animal, or microbial) compared to non-living matter (earth's crust), both contain similar elements. However, the **relative abundance differs significantly**:

Carbon (C): 0.03% in earth's crust vs 18.5% in human body

Hydrogen (H): 0.14% in earth's crust vs 9.5% in human body

Oxygen (O): 46.6% in earth's crust vs 65.0% in human body

Nitrogen (N): Very little in earth's crust vs 3.3% in human body

This higher abundance of carbon and hydrogen is a defining characteristic of living organisms.

**Extraction and Fractionation Method:**

To identify organic compounds in living tissues:

1. Grind living tissue (vegetable, liver, leaf) in **trichloroacetic acid (Cl₃CCOOH)** using mortar and pestle

2. This produces a thick slurry

3. Strain through cheesecloth or cotton to obtain two fractions:

**Acid-soluble pool (Filtrate):** Contains thousands of small organic compounds with molecular weight 18-800 daltons (Da) - called **primary metabolites**

**Acid-insoluble fraction (Retentate):** Contains macromolecules (proteins, nucleic acids, polysaccharides, lipids) with molecular weight >10,000 Da

**Determining Dry Weight and Ash Content:**

**Wet weight:** Fresh tissue (contains water)

**Dry weight:** Tissue after evaporating all water

**Ash:** Remaining mineral content after complete combustion (contains inorganic elements like calcium, magnesium, phosphate, sulphate)

This demonstrates that living tissues contain both **organic compounds** (carbon-based) and **inorganic constituents** (minerals and salts).

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PRIMARY AND SECONDARY METABOLITES

**Primary Metabolites:**

These are compounds directly involved in normal physiological processes with identifiable functions:

Found in all living organisms (plants, animals, fungi, microorganisms)

Examples: amino acids, sugars, fatty acids, nucleotides, vitamins, organic acids

Essential for survival, growth, and reproduction

Constitute the acid-soluble pool in chemical analysis

**Secondary Metabolites:**

These are compounds produced by organisms but whose functions are not always clearly understood in the host organism:

Primarily found in plants, fungi, and microorganisms (rarely in animals)

Do NOT have direct physiological role but have ecological or human welfare importance

**Examples (Table 9.3):**

**Pigments:** Carotenoids, anthocyanins (provide color)

**Alkaloids:** Morphine, codeine (drugs and stimulants)

**Terpenoids:** Monoterpenes, diterpenes (fragrance compounds)

**Essential oils:** Lemongrass oil, jasmine oil (fragrance)

**Toxins:** Abrin, ricin (defensive compounds)

**Lectins:** Concanavalin A (proteins with special properties)

**Drugs:** Vinblastine, curcumin (medicinal compounds)

**Polymeric substances:** Rubber, gums (structural/protective)

**Functional Difference:**

Primary metabolites = Known physiological role (mandatory for life)

Secondary metabolites = Useful to humans but original function unclear (e.g., rubber from plants, drugs for medicines, spices for flavor)

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BIOMACROMOLECULES

**Micromolecules vs Macromolecules:**

**Micromolecules (Biomolecules):**

Molecular weight: 18-800 Da

Found in acid-soluble pool

Include: amino acids, monosaccharides, fatty acids, nucleosides, nucleotides

Simple, small chemical compounds

**Macromolecules (Biomacromolecules):**

Molecular weight: >10,000 Da (except lipids: <800 Da)

Found in acid-insoluble fraction

Include: proteins, nucleic acids, polysaccharides, lipids (membrane structures)

**Polymer nature:** Most are polymeric (except lipids)

**Why Lipids in Acid-Insoluble Fraction?**

Although lipids have small molecular weight (<800 Da), they are found in the macromolecular fraction because:

In living cells, lipids exist as organized membrane structures (cell membrane, organellar membranes)

When tissue is ground, cell membranes break into vesicles (membrane fragments)

These vesicles are **water-insoluble** and sediment with the acid-insoluble fraction

Therefore, lipids are not strictly macromolecules but are grouped with them

**Cellular Composition by Mass (Table 9.4):**

Water: 70-90% (most abundant chemical)

Proteins: 10-15%

Nucleic acids: 5-7%

Carbohydrates: 3%

Lipids: 2%

Ions: 1%

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PROTEINS

**Definition:**

Proteins are **linear polypeptides** composed of amino acids linked together by **peptide bonds** in a specific sequence.

**Building Block - Amino Acids:**

**Structure:** α-amino acids with four substituents on the same carbon (α-carbon):

1. **Hydrogen (H)**

2. **Carboxyl group (-COOH)** - acidic

3. **Amino group (-NH₂)** - basic

4. **R group (variable)** - determines identity of amino acid

**Classification based on R group:**

**Acidic amino acids:** Glutamic acid (excess carboxyl groups)

**Basic amino acids:** Lysine (excess amino groups)

**Neutral amino acids:** Valine, alanine

**Aromatic amino acids:** Tyrosine, phenylalanine, tryptophan

**Zwitterionic form:** In solutions, amino acids exist in an ionizable form where both -NH₂ and -COOH groups can ionize, and the structure changes with pH

**Protein Characteristics:**

**Heteropolymer:** Contains 20 different types of amino acids (unlike homopolymers with one type of monomer)

**Amino acids in proteins:** Only 20 types occur in protein synthesis (specified by genetic code)

**Essential vs Non-essential amino acids:**

**Essential:** Must be obtained from diet (e.g., methionine, leucine, valine, isoleucine, threonine, tryptophan, phenylalanine, histidine, lysine)

**Non-essential:** Can be synthesized by the body

**Peptide Bond:**

Formed between carboxyl group (-COOH) of one amino acid and amino group (-NH₂) of another

**Reaction:** COOH + H₂N → CO-NH + H₂O (condensation)

Result: Covalent bond linking amino acids into a chain

**Functions of Proteins (Table 9.5):**

**Structural:** Collagen (intercellular ground substance, connective tissue)

**Enzymatic:** Trypsin (digestive enzyme), amylase

**Hormonal:** Insulin (blood glucose regulation)

**Immune:** Antibodies (fight infections)

**Transport:** GLUT-4 (glucose transport), hemoglobin (oxygen transport)

**Sensory:** Receptors (smell, taste, hormone binding)

**Most Abundant Proteins:**

**Animal world:** Collagen (in skin, bones, connective tissue)

**Entire biosphere:** RuBisCO (Ribulose-1,5-bisphosphate carboxylase-oxygenase) - enzyme in photosynthesis, makes up ~50% of leaf protein

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POLYSACCHARIDES

**Definition:**

Polysaccharides are **long chains of monosaccharides** linked by glycosidic bonds, serving as structural or energy storage polymers.

**Types of Polysaccharides:**

**1. Homopolysaccharides (Single monomer type):**

**Cellulose:**

Polymer of glucose (homopolymer)

Unbranched linear chain

**Secondary structure:** Does NOT form helical structures

**Property:** Cannot hold I₂ molecules

**Function:** Plant cell wall structure

**Uses:** Paper, cotton fiber

Very stable, resistant to digestion in most animals

**Starch:**

Polymer of glucose (homopolymer)

**Structure:** Forms helical secondary structures

**Property:** Helical portions hold I₂ molecules → **blue-black color** (diagnostic test)

**Function:** Energy storage in plant tissues

**Types:** Amylose (unbranched), amylopectin (branched)

Can be digested by animals

**Glycogen:**

Polymer of glucose (homopolymer)

**Structure:** Highly branched (more branches than starch)

**Function:** Energy storage in animal tissues (liver, muscle)

Provides quick energy for muscle contraction

More soluble than starch due to high branching

**Inulin:**

Polymer of fructose (homopolymer)

Storage carbohydrate in some plants (garlic, onion)

**2. Heteropolysaccharides (Multiple monomer types):**

**Building blocks:** Amino-sugars and chemically modified sugars

**Examples:** Glucosamine, N-acetyl galactosamine

**Chitin:**

Complex polysaccharide from arthropod exoskeletons (insects, crustaceans)

Provides structural support and protection

Mostly homopolymeric despite complexity

**Polysaccharide Chain Terminology:**

**Reducing end:** Right end of the chain (has free aldehyde or ketone group)

**Non-reducing end:** Left end of the chain (no free carbonyl group)

**Branching:** Side chains attached to main chain (seen in glycogen and amylopectin)

**Glycosidic Bond:**

Covalent bond between monosaccharides

Formed by condensation between hydroxyl groups of adjacent sugars

Different types: α-1,4, α-1,6 (in starch and glycogen), β-1,4 (in cellulose)

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NUCLEIC ACIDS

**Definition:**

Nucleic acids are **polynucleotides** - long chains of nucleotides linked by phosphodiester bonds. They function as genetic material and regulate protein synthesis.

**Building Block - Nucleotide Structure (Three Components):**

1. **Nitrogenous Bases:**

**Purines (double-ring):**

Adenine (A)

Guanine (G)

**Pyrimidines (single-ring):**

Cytosine (C)

Thymine (T) - DNA only

Uracil (U) - RNA only

2. **Monosaccharide (5-carbon pentose):**

**Ribose:** In RNA (contains OH on 2' carbon)

**Deoxyribose:** In DNA (lacks oxygen on 2' carbon, hence "deoxy")

3. **Phosphoric Acid/Phosphate Group:**

Attached to 5' carbon of sugar

Links nucleotides together via phosphodiester bonds

**Related Compounds:**

**Nitrogenous base + Sugar = Nucleoside**

Examples: Adenosine, guanosine, thymidine, uridine, cytidine

**Nucleoside + Phosphate = Nucleotide**

Examples: Adenylic acid, thymidylic acid, guanylic acid, uridylic acid, cytidylic acid

**Two Types of Nucleic Acids:**

**DNA (Deoxyribonucleic Acid):**

Contains deoxyribose sugar

Contains thymine (not uracil)

Bases: A, G, C, T

Function: Genetic material, stores hereditary information

**RNA (Ribonucleic Acid):**

Contains ribose sugar

Contains uracil (not thymine)

Bases: A, G, C, U

Functions: Messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA)

**Phosphodiester Bond:**

Links 3' carbon of one nucleotide's sugar to 5' carbon of next nucleotide

Creates backbone of DNA and RNA

Formed by condensation reaction between phosphate and hydroxyl groups

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STRUCTURE OF PROTEINS (FOUR LEVELS)

Protein structure is described at four hierarchical levels, each providing increasing complexity and functional information.

**1. PRIMARY STRUCTURE:**

**Definition:** Linear sequence of amino acids in a polypeptide chain

**Representation:** A to B, left to right

**Directional notation:**

**N-terminus (N-terminal):** First amino acid (has free -NH₂ group)

**C-terminus (C-terminal):** Last amino acid (has free -COOH group)

**Significance:** Determines all higher levels of structure; unique to each protein

**Bonds:** Peptide bonds connect adjacent amino acids

**Example:** A protein with sequence: Met-Gly-Ala-Pro-Lys... (different for each protein)

**2. SECONDARY STRUCTURE:**

**Definition:** Regular, repetitive folding patterns of localized regions of the polypeptide backbone

**Common patterns:**

**α-helix:**

Right-handed spiral structure (like revolving staircase)

Stabilized by hydrogen bonds between C=O of one amino acid and N-H of another

Compact, rod-like appearance

Common in fibrous proteins

**β-pleated sheet:**

Extended, zigzag structure

Polypeptide chains run parallel or antiparallel

Stabilized by hydrogen bonds between adjacent strands

Found in silk fibroin, cellulose-binding proteins

**Random coil/Loop:**

Irregular regions between α-helices and β-sheets

Important for protein flexibility

**Only right-handed helices** occur in proteins (never left-handed)

**Bonds involved:** Hydrogen bonds between backbone atoms (not R groups)

**3. TERTIARY STRUCTURE:**

**Definition:** Overall 3-dimensional folding of the entire polypeptide chain

**Appearance:** Protein folds upon itself like a "hollow woolen ball"

**Driving forces:**

**Hydrogen bonds** (between polar R groups and backbone)

**Ionic bonds** (between charged R groups: lysine-glutamate, etc.)

**Hydrophobic interactions** (nonpolar R groups cluster inside, away from water)

**Disulfide bonds** (covalent bonds between cysteine residues: -S-S-)

**Van der Waals forces**

**Result:** Crevices, pockets, and active sites form

**Significance:** **ABSOLUTELY ESSENTIAL for biological activity**

Determines enzyme activity

Determines protein function (receptor binding, transport, etc.)

Small changes in tertiary structure can destroy function (denaturation)

**Example:** Hemoglobin's tertiary structure allows oxygen binding and release

**4. QUATERNARY STRUCTURE:**

**Definition:** Arrangement of multiple polypeptide subunits in a multi-subunit protein complex

**Applicability:** Only for proteins with MORE than one polypeptide chain

**Arrangement patterns:**

Linear string of spheres

Spheres arranged in cubes

Spheres arranged in plates/sheets

Specific spatial relationships between subunits

**Example - Human Hemoglobin:**

4 subunits total:

2 α (alpha) subunits (identical to each other)

2 β (beta) subunits (identical to each other)

Arrangement: Tetrameric structure (dimer of dimers)

Each subunit can bind one O₂ molecule

Cooperative binding occurs (binding of one O₂ facilitates binding of others)

**Bonds involved:** Hydrogen bonds, ionic bonds, hydrophobic interactions (same as tertiary but between different chains)

**Protein Denaturation:**

Disruption of secondary, tertiary, and quaternary structures

Caused by: Heat (>40°C for most enzymes), pH change, heavy metals, organic solvents

Primary structure remains intact (peptide bonds not broken)

Loss of biological activity

May be reversible (renaturation) in some cases

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ENZYMES

**Definition:**

Enzymes are **biological catalysts** - mostly **proteins** that accelerate chemical reactions by lowering activation energy without being consumed themselves. Some nucleic acids (ribozymes) also act as enzymes.

**Enzyme Structure:**

**Primary structure:** Specific sequence of amino acids (like all proteins)

**Secondary structure:** α-helices and β-sheets present

**Tertiary structure:** Gives enzyme its 3D shape - **CRITICAL for function**

**Active site:** A crevice or pocket formed by tertiary structure folding

**Active Site:**

**Definition:** Specific region on enzyme surface where substrate binds

**Formation:** Created by criss-crossing of polypeptide chains in tertiary structure

**Substrate specificity:** Each enzyme active site fits specific substrate(s) like a "lock and key" or "induced fit"

**Result:** Substrate is held in correct orientation and position for reaction

**Catalytic action:** Active site catalyzes reactions at **HIGH RATES** (millions of times faster than uncatalyzed reactions)

**Differences Between Enzyme and Inorganic Catalysts:**

| Feature | Enzymes | Inorganic Catalysts |

|---------|---------|-------------------|

| Composition | Proteins (or ribozymes) | Metal, metal oxide, salts |

| Optimal Temperature | Low (36-40°C for human) | High (100-200°C+) |

| Stability at High Temp | Denatured >40°C (loses activity) | Remain stable at high temps |

| Specificity | Highly specific for substrate | Non-specific |

| Efficiency | Very efficient at low temps | Require high pressure/temperature |

| Reusability | Not consumed, reusable | Not consumed, reusable |

| Cost | Expensive, complex extraction | Cheap, simple to produce |

| Regulation | Can be regulated in cells | Cannot be regulated easily |

**Thermophilic Enzymes:**

Enzymes from organisms living in extreme environments:

**Hot vents** (geothermal springs, underwater hydrothermal vents)

**Sulphur springs** (high temperature, high sulphur content)

Desert hot springs

**Properties:** Stable and retain catalytic activity at **80-90°C** (not denatured)

**Reason:** Specialized protein structure with extra disulfide bonds, unique amino acid composition

**Applications:** PCR (polymerase chain reaction) uses Taq polymerase from thermophilic bacterium *Thermus aquaticus*

**Enzyme Classification (Brief):**

**EC 1 - Oxidoreductases:** Catalyze oxidation-reduction reactions

**EC 2 - Transferases:** Transfer of functional groups

**EC 3 - Hydrolases:** Hydrolysis (breaking bonds with water) - includes digestive enzymes

**EC 4 - Lyases:** Non-hydrolytic breaking of bonds

**EC 5 - Isomerases:** Rearrangement within molecules

**EC 6 - Ligases:** Formation of new bonds (joins molecules)

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CHEMICAL REACTIONS

**Definition:**

A chemical reaction is a process where reactants (starting materials) are transformed into products through breaking and forming of chemical bonds.

**Two Types of Chemical Changes:**

**1. Physical Change:**

**Definition:** Change in shape or physical state without breaking chemical bonds

**Examples:**

Melting of ice (H₂O solid → liquid)

Folding of paper

Stretching of rubber

Phase changes (solid ↔ liquid ↔ gas)

**Characteristics:**

Reversible

No new substances formed

Molecular bonds remain intact

Energy requirement: Low

**2. Chemical Change:**

**Definition:** Breaking of existing bonds and formation of new bonds, resulting in new substances

**Examples:**

Burning of wood (C + O₂ → CO₂ + energy)

Digestion of food (complex carbohydrates → glucose)

Rusting of iron (Fe + O₂ → Fe₂O₃)

Photosynthesis (CO₂ + H₂O → glucose + O₂)

**Characteristics:**

Often irreversible

New substances with different properties formed

Molecular bonds broken and reformed

Energy released or absorbed

Usually indicates change in color, temperature, or state

**Chemical Reactions in Living Systems:**

**Metabolism:** Sum of all chemical reactions occurring in cells

**Enzyme-catalyzed reactions:** Most biological reactions catalyzed by enzymes

**Energy coupling:** Reactions coupled to release/store energy (ATP)

**Sequential reactions:** Multiple reactions organized in pathways (glycolysis, Krebs cycle, etc.)

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EXAM-IMPORTANT POINTS AND KEY TAKEAWAYS

1. **Water is the most abundant chemical (70-90%)** in living cells by mass

2. **20 types of amino acids** form proteins; must know at least 5 examples

3. **Peptide bonds** link amino acids (COOH + H₂N → CO-NH + H₂O)

4. **Four levels of protein structure:** Primary (sequence), Secondary (helix/sheet), Tertiary (3D folding - CRITICAL), Quaternary (multi-subunit arrangement)

5. **Active site** is the functional region of enzymes where substrate binds

6. **Cellulose** = unbranched, linear, forms cell walls, CANNOT hold I₂

7. **Starch** = can be branched, stores energy in plants, HOLDS I₂ (blue-black color)

8. **Glycogen** = highly branched, stores energy in animals, more soluble than starch

9. **DNA** = deoxyribose + thymine + genetic material

10. **RNA** = ribose + uracil + protein synthesis and regulation

11. **Disulfide bonds (-S-S-)** between cysteine residues stabilize tertiary structure

12. **RuBisCO** = most abundant protein in biosphere (photosynthesis enzyme)

13. **Collagen** = most abundant protein in animal world (structural)

14. **Essential amino acids** must be obtained from diet; non-essential can be synthesized

15. **Zwitterionic form** = amino acid with both ionized -NH₃⁺ and -COO⁻ groups

This comprehensive chapter covers the foundation of biochemistry essential for CBSE Class 11 board exams.