Cellular Organisation, Biomolecules, and Cell Division

Biology is the study of living organisms. The cell theory highlights the unity in the diversity of life forms, emphasising the cellular organisation of all life. A physico-chemical approach, called Reductionist Biology, uses concepts and techniques from physics and chemistry to understand living phenomena in molecular terms.

Cell: The Unit of Life (Chapter 8)

What is a Cell?

The cell is the basic unit of life, making an organism living. All organisms are composed of cells; they can be unicellular (single-celled) or multicellular (many cells). Unicellular organisms are capable of independent existence and performing essential life functions. Anything less than a complete cell structure cannot ensure independent living, thus the cell is the fundamental structural and functional unit of all living organisms.

Discoveries in Cell Biology

• Antonie Von Leeuwenhoek first saw and described a live cell.
• Robert Brown later discovered the nucleus.
• The invention and improvement of the microscope, including the electron microscope, revealed detailed cell structures.

Cell Theory

• Matthias Schleiden (1838), a German botanist, observed that all plants are composed of different kinds of cells forming plant tissues.
• Theodore Schwann (1839), a German zoologist, studied animal cells and reported a thin outer layer, now known as the plasma membrane. Based on plant studies, he concluded the cell wall is unique to plant cells. Schwann hypothesised that animal and plant bodies are composed of cells and their products.
• Schleiden and Schwann together formulated the initial cell theory, but it did not explain how new cells were formed.
• Rudolf Virchow (1855) first explained that cells divide, and new cells arise from pre-existing cells (Omnis cellula-e cellula). He modified Schleiden and Schwann’s hypothesis to give the cell theory its final shape.

Cell Theory as understood today:

1. All living organisms are composed of cells and products of cells.
2. All cells arise from pre-existing cells.

An Overview of Cell

Cells exhibit a dense membrane-bound structure called the nucleus. The nucleus contains chromosomes, which in turn contain the genetic material, DNA.

• Eukaryotic cells possess membrane-bound nuclei.
• Prokaryotic cells lack a membrane-bound nucleus.

In both prokaryotic and eukaryotic cells, a semi-fluid matrix called cytoplasm occupies the cell volume and is the main arena of cellular activities where various chemical reactions occur to keep the cell living.

Eukaryotic cells possess other membrane-bound distinct structures called organelles, such as the endoplasmic reticulum (ER), golgi complex, lysosomes, mitochondria, microbodies, and vacuoles. Prokaryotic cells lack these membrane-bound organelles, except for ribosomes.

Ribosomes are non-membrane bound organelles found in all cells (eukaryotic and prokaryotic). In eukaryotes, they are found in the cytoplasm, chloroplasts (in plants), mitochondria, and on rough ER. Animal cells also contain another non-membrane bound organelle called a centrosome, which aids in cell division.

Cell Size and Shape

Cells vary greatly in size, shape, and activities.

• Smallest cells: Mycoplasmas (0.3 µm in length).
• Bacteria: 3 to 5 µm.
• Largest isolated single cell: Egg of an ostrich.
• Human red blood cells: ~7.0 µm in diameter.
• Nerve cells: Some of the longest cells.
• Shapes can be disc-like, polygonal, columnar, cuboid, thread-like, or irregular, varying with their function.

Prokaryotic Cells

Prokaryotic cells are represented by bacteria, blue-green algae, mycoplasma, and PPLO (Pleuro Pneumonia Like Organisms). They are generally smaller and multiply more rapidly than eukaryotic cells.

Basic shapes of bacteria:

• Bacillus: rod-like
• Coccus: spherical
• Vibrio: comma-shaped
• Spirillum: spiral

Organisation of Prokaryotic Cell:

• Cell Wall: All prokaryotes have a cell wall surrounding the cell membrane, except for mycoplasma.
• Cytoplasm: The semi-fluid matrix filling the cell.
• Nucleus: No well-defined nucleus. The genetic material is basically naked, not enveloped by a nuclear membrane.
• DNA: In addition to the genomic DNA (single chromosome/circular DNA), many bacteria have small circular DNA outside the genomic DNA called plasmids. Plasmid DNA confers unique phenotypic characters, such as resistance to antibiotics. Plasmids are used to monitor bacterial transformation with foreign DNA.
• Organelles: No membrane-bound organelles like in eukaryotes, except for ribosomes.
• Inclusions: Prokaryotes have unique structures called inclusions.
• Mesosome: A specialised differentiated form of cell membrane, characteristic of prokaryotes, formed by infoldings of the cell membrane.

Cell Envelope and its Modifications

Most prokaryotic cells, particularly bacterial cells, have a chemically complex cell envelope. This envelope consists of a tightly bound three-layered structure:

1. Outermost glycocalyx
2. Cell wall
3. Plasma membrane These layers act together as a single protective unit, though each performs distinct functions.

Classification of Bacteria based on Cell Envelope:

• Gram-positive: Take up the Gram stain.
• Gram-negative: Do not take up the Gram stain.

Components of the Cell Envelope:

• Glycocalyx: Varies in composition and thickness; can be a loose sheath (slime layer) or thick and tough (capsule).
• Cell Wall: Determines cell shape and provides strong structural support to prevent the bacterium from bursting or collapsing.
• Plasma Membrane: Selectively permeable and interacts with the outside world, structurally similar to eukaryotic plasma membranes.

Specialised Membranous Structures:

• Mesosome: Formed by extensions of the plasma membrane into the cell, in the form of vesicles, tubules, and lamellae.
  • Functions: Helps in cell wall formation, DNA replication and distribution to daughter cells, respiration, secretion processes, increasing the surface area of the plasma membrane, and enzymatic content.
• Chromatophores: In some prokaryotes (e.g., cyanobacteria), these are other membranous extensions into the cytoplasm that contain pigments.

Bacterial Motility and Surface Structures

Bacterial cells may be motile or non-motile.

• Flagella: Thin filamentous extensions from their cell wall, responsible for motility. A bacterial flagellum has three parts: filament, hook, and basal body. The filament is the longest portion.
• Pili: Elongated tubular structures made of a special protein; do not play a role in motility.
• Fimbriae: Small bristle-like fibres sprouting out of the cell; do not play a role in motility. In some bacteria, they help attach the bacteria to rocks in streams and to host tissues.

Ribosomes and Inclusion Bodies (Prokaryotes)

• Ribosomes: Associated with the plasma membrane. They are about 15 nm by 20 nm in size and are made of two subunits (50S and 30S) which together form 70S prokaryotic ribosomes. Ribosomes are the site of protein synthesis. Several ribosomes can attach to a single mRNA to form a chain called polyribosomes or polysome, translating mRNA into proteins.
• Inclusion bodies: Reserve materials in prokaryotic cells, stored in the cytoplasm. They are not bound by any membrane system and lie free. Examples include phosphate granules, cyanophycean granules, glycogen granules, and gas vacuoles (found in blue-green, purple, and green photosynthetic bacteria).

Eukaryotic Cells

Eukaryotes include all protists, plants, animals, and fungi. Key characteristics of eukaryotic cells:

• Extensive compartmentalisation of cytoplasm through the presence of membrane-bound organelles.
• Possess an organised nucleus with a nuclear envelope.
• Have a variety of complex locomotory and cytoskeletal structures.
• Genetic material is organised into chromosomes.

Differences between Plant and Animal Cells:

Cell Organelles (Eukaryotic)

Cell Membrane

The detailed structure was studied after the advent of the electron microscope in the 1950s. Chemical studies, especially on human red blood cells (RBCs), helped deduce its structure.

• Composition: Mainly composed of lipids and proteins.

  • Lipids: Major lipids are phospholipids arranged in a bilayer. The polar heads are towards the outer sides, and hydrophobic tails are towards the inner part, protecting the nonpolar tails from the aqueous environment. The membrane also contains cholesterol.
  • Proteins: The ratio of protein to lipid varies. Human erythrocyte membrane has approximately 52% protein and 40% lipids. Proteins are classified based on extraction ease:
    • Peripheral proteins: Lie on the surface of the membrane.
    • Integral proteins: Partially or totally buried in the membrane.
  • Carbohydrates: Also present.

• Fluid Mosaic Model: Proposed by Singer and Nicolson (1972), it is widely accepted. According to this model, the quasi-fluid nature of lipids allows lateral movement of proteins within the overall bilayer, a property measured as its fluidity.

• Functions related to fluidity: Cell growth, formation of intercellular junctions, secretion, endocytosis, and cell division.

• Transport of Molecules across the Membrane: One of the most important functions. The membrane is selectively permeable.

  • Passive transport: Movement without energy requirement.
    • Simple diffusion: Neutral solutes move along the concentration gradient (higher to lower concentration).
    • Osmosis: Movement of water by diffusion from higher to lower concentration.
    • Facilitated diffusion: Polar molecules cannot pass through the nonpolar lipid bilayer directly, so they require a carrier protein.
  • Active transport: Energy-dependent process (utilises ATP) to transport ions/molecules against their concentration gradient (lower to higher concentration). Example: Na+/K+ Pump.

Cell Wall

A non-living rigid structure that forms an outer covering for the plasma membrane of fungi and plants.

• Functions: Gives shape to the cell, protects from mechanical damage and infection, helps in cell-to-cell interaction, and provides a barrier to undesirable macromolecules.
• Composition:
  • Algae: Cell walls made of cellulose, galactans, mannans, and minerals like calcium carbonate.
  • Other plants: Consists of cellulose, hemicellulose, pectins, and proteins.
• Primary Wall: The cell wall of a young plant cell, capable of growth, which gradually diminishes as the cell matures.
• Secondary Wall: Formed on the inner side (towards the membrane) as the cell matures.
• Middle Lamella: A layer mainly of calcium pectate which holds or glues different neighbouring cells together.
• Plasmodesmata: Traverses the cell wall and middle lamellae, connecting the cytoplasm of neighbouring cells.

Endomembrane System

A system of membranous organelles whose functions are coordinated.

• Includes: Endoplasmic Reticulum (ER), Golgi complex, Lysosomes, and Vacuoles.
• Excludes: Mitochondria, chloroplasts, and peroxisomes (as their functions are not coordinated with the others).

The Endoplasmic Reticulum (ER)

A network or reticulum of tiny tubular structures scattered in the cytoplasm of eukaryotic cells.

• Compartmentalisation: Divides intracellular space into two distinct compartments: luminal (inside ER) and extraluminal (cytoplasm).
• Rough Endoplasmic Reticulum (RER): Has ribosomes attached to its outer surface. Frequently observed in cells actively involved in protein synthesis and secretion. It is extensive and continuous with the outer membrane of the nucleus.
• Smooth Endoplasmic Reticulum (SER): Lacks ribosomes, appearing smooth. It is the major site for synthesis of lipid. In animal cells, lipid-like steroidal hormones are synthesised in SER.

Golgi Apparatus

First observed by Camillo Golgi (1898).

• Structure: Consists of many flat, disc-shaped sacs or cisternae (0.5µm to 1.0µm diameter) stacked parallel to each other.
• Faces: Concentrically arranged near the nucleus with distinct convex cis or forming face and concave trans or maturing face. The cis and trans faces are entirely different but interconnected.
• Functions:
  • Principally performs the function of packaging materials to be delivered either to intracellular targets or secreted outside the cell.
  • Materials from the ER fuse with the cis face of the Golgi apparatus and move towards the maturing face, explaining its close association with ER.
  • Proteins synthesised by ribosomes on the ER are modified in the cisternae of the Golgi apparatus before release from its trans face.
  • Important site for the formation of glycoproteins and glycolipids.

Lysosomes

Membrane-bound vesicular structures formed by the packaging process in the Golgi apparatus.

• Contents: Very rich in almost all types of hydrolytic enzymes (hydrolases), including lipases, proteases, and carbohydrases. These enzymes are optimally active at acidic pH.
• Function: Capable of digesting carbohydrates, proteins, lipids, and nucleic acids.

Vacuoles

Membrane-bound space found in the cytoplasm.

• Contents: Contains water, sap, excretory products, and other materials not useful for the cell.
• Membrane: Bound by a single membrane called tonoplast.
• Size (in Plants): In plant cells, vacuoles can occupy up to 90% of the volume of the cell.
• Tonoplast function: In plants, it facilitates the transport of many ions and materials against concentration gradients into the vacuole, resulting in significantly higher concentrations inside the vacuole than in the cytoplasm.
• Specific Vacuoles:
  • Contractile vacuole: In Amoeba, important for osmoregulation and excretion.
  • Food vacuoles: Formed in many cells (e.g., protists) by engulfing food particles.

Mitochondria

Typically sausage-shaped or cylindrical, with a diameter of 0.2-1.0 µm (average 0.5 µm) and length of 1.0-4.1 µm.

• Visibility: Not easily visible under the microscope unless specifically stained.
• Number: Variable per cell, depending on physiological activity.
• Structure: Double membrane-bound structure.
  • Outer membrane: Forms the continuous limiting boundary.
  • Inner membrane: Forms numerous infoldings called cristae towards the matrix, which increase the surface area.
  • Compartments: The outer and inner membranes divide the lumen into two aqueous compartments: the outer compartment and the inner compartment.
  • Matrix: The inner compartment is filled with a dense homogeneous substance called the matrix.
• Enzymes: Both membranes have specific enzymes associated with mitochondrial function.
• Functions: They are the sites of aerobic respiration and produce cellular energy in the form of ATP, hence called the ‘power houses’ of the cell.
• Genetic Material: The matrix contains a single circular DNA molecule, a few RNA molecules, ribosomes (70S), and components for protein synthesis.
• Division: Divide by fission.

Plastids

Found in all plant cells and in euglenoids. They are large and bear specific pigments, imparting colours to plants.

• Classification based on pigments:
  • Chloroplasts: Contain chlorophyll and carotenoid pigments, responsible for trapping light energy essential for photosynthesis.
  • Chromoplasts: Contain fat-soluble carotenoid pigments (like carotene and xanthophylls), giving plant parts yellow, orange, or red colour.
  • Leucoplasts: Colourless plastids of varied shapes and sizes, with stored nutrients:
    • Amyloplasts: Store carbohydrates (starch), e.g., in potato.
    • Elaioplasts: Store oils and fats.
    • Aleuroplasts: Store proteins.

Chloroplasts (Detailed):

• Location: Majority found in mesophyll cells of leaves.
• Shape/Size: Lens-shaped, oval, spherical, discoid, or ribbon-like; 5-10 µm long and 2-4 µm wide.
• Number: Varies from 1 per cell (e.g., Chlamydomonas) to 20-40 per cell (in mesophyll).
• Structure: Double membrane bound. The inner chloroplast membrane is relatively less permeable.
  • Stroma: The space limited by the inner membrane. Contains enzymes for carbohydrate and protein synthesis, small, double-stranded circular DNA molecules, and ribosomes (70S, smaller than cytoplasmic 80S ribosomes).
  • Thylakoids: Organised flattened membranous sacs present in the stroma. They are arranged in stacks called grana (singular: granum) or intergranal thylakoids. Chlorophyll pigments are present in the thylakoids.
  • Stroma lamellae: Flat membranous tubules connecting the thylakoids of different grana.
  • Lumen: The space enclosed by the membrane of the thylakoids.

Ribosomes (Eukaryotic)

Granular structures first observed by George Palade (1953).

• Composition: Composed of ribonucleic acid (RNA) and proteins.
• Membrane: Not surrounded by any membrane.
• Type: Eukaryotic ribosomes are 80S.
• Subunits: Each 80S ribosome has two subunits: a larger 60S subunit and a smaller 40S subunit. The ‘S’ (Svedberg’s Unit) stands for the sedimentation coefficient, indirectly measuring density and size.

Cytoskeleton

An elaborate network of filamentous proteinaceous structures in the cytoplasm.

• Components: Consists of microtubules, microfilaments, and intermediate filaments.
• Functions: Involved in mechanical support, motility, and maintenance of the shape of the cell.

Cilia and Flagella

Hair-like outgrowths of the cell membrane.

• Cilia: Small structures that work like oars, causing movement of either the cell or the surrounding fluid.
• Flagella: Comparatively longer and responsible for cell movement. Prokaryotic bacteria also have flagella, but they are structurally different from eukaryotic flagella.
• Structure (Eukaryotic):
  • Covered with plasma membrane.
  • Core (axoneme): Possesses microtubules running parallel to the long axis.
  • Microtubule arrangement: Usually has nine doublets of radially arranged peripheral microtubules and a pair of centrally located microtubules. This is referred to as the 9+2 array.
  • The central tubules are connected by bridges and enclosed by a central sheath. The sheath is connected to one of the tubules of each peripheral doublet by a radial spoke (nine radial spokes in total). The peripheral doublets are also interconnected by linkers.
  • Both cilia and flagella emerge from centriole-like structures called basal bodies.

Centrosome and Centrioles

• Centrosome: An organelle usually containing two cylindrical structures called centrioles. They are surrounded by amorphous pericentriolar materials.
• Centrioles: Lie perpendicular to each other, each with a cartwheel-like organisation.
  • Composition: Made up of nine evenly spaced peripheral fibrils of tubulin protein, with each fibril being a triplet. Adjacent triplets are linked.
  • Hub: The central part of the proximal region of the centriole is proteinaceous and called the hub, connected to the tubules of the peripheral triplets by radial spokes made of protein.
• Functions: Centrioles form the basal body of cilia or flagella and give rise to spindle fibres that form the spindle apparatus during cell division in animal cells.

Nucleus

First described by Robert Brown as early as 1831. The material of the nucleus stained by basic dyes was named chromatin by Flemming.

• Interphase Nucleus: (Nucleus when cell is not dividing) has highly extended and elaborate nucleoprotein fibres called chromatin, nuclear matrix, and one or more spherical bodies called nucleoli.
• Nuclear Envelope: Consists of two parallel membranes with a perinuclear space (10 to 50 nm) between them. It forms a barrier between nuclear materials and cytoplasm. The outer membrane is usually continuous with the endoplasmic reticulum and bears ribosomes.
• Nuclear Pores: Minute interruptions in the nuclear envelope, formed by the fusion of its two membranes. They are the passages for movement of RNA and protein molecules in both directions between the nucleus and the cytoplasm.
• Nucleus Number: Normally one nucleus per cell, but variations exist (e.g., multinucleate syncytium).
• Anucleated Cells: Some mature cells lack a nucleus, e.g., erythrocytes of many mammals and sieve tube cells of vascular plants.
• Nucleoplasm (Nuclear Matrix): Contains the nucleolus and chromatin.
• Nucleolus: Spherical structures within the nucleoplasm, not membrane-bound (content continuous with nucleoplasm). It is the site for active ribosomal RNA synthesis. Larger and more numerous nucleoli are found in cells actively carrying out protein synthesis.
• Chromatin: In interphase, it’s a loose and indistinct network of nucleoprotein fibres. During cell division, it forms structured chromosomes.
  • Composition: Contains DNA, basic proteins called histones, some non-histone proteins, and RNA.
  • A single human cell has approximately two metres of DNA distributed among 46 (23 pairs) chromosomes.

Chromosomes

(Visible only in dividing cells).

• Centromere: Each chromosome essentially has a primary constriction called the centromere.
• Kinetochores: Disc-shaped structures present on the sides of the centromere. The centromere holds two chromatids of a chromosome together.

Classification of Chromosomes based on Centromere Position:

• Metacentric: Middle centromere, forming two equal arms of the chromosome.
• Sub-metacentric: Centromere slightly away from the middle, resulting in one shorter and one longer arm.
• Acrocentric: Centromere situated close to its end, forming one extremely short and one very long arm.
• Telocentric: Terminal centromere.
• Satellite: Sometimes a few chromosomes have non-staining secondary constrictions at a constant location, giving the appearance of a small fragment.

Microbodies

Many membrane-bound minute vesicles containing various enzymes. Present in both plant and animal cells.

Biomolecules (Chapter 9)

How to Analyse Chemical Composition?

• Elemental analysis of living tissue (plant, animal, microbial) yields elements like carbon, hydrogen, oxygen, etc..
• Similar elements are found in non-living matter (e.g., Earth’s crust).
• Key difference: Relative abundance of carbon and hydrogen is higher in living organisms than in Earth’s crust.

Comparison of Elements in Non-living and Living Matter (Table 9.1):

To analyse organic compounds, living tissue is ground in trichloroacetic acid, producing a slurry. Straining the slurry yields two fractions:

1. Filtrate (Acid-soluble pool): Contains thousands of organic compounds with molecular weights ranging from 18 to ~800 daltons (Da). These are generally referred to as micromolecules or simply biomolecules. This pool roughly represents the cytoplasmic composition.
2. Retentate (Acid-insoluble fraction): Contains four types of organic compounds: proteins, nucleic acids, polysaccharides, and lipids. These are generally referred to as macromolecules or biomacromolecules, typically having molecular weights of ten thousand daltons and above. Macromolecules from cytoplasm and organelles become this fraction.

• Note on Lipids: Although lipids have molecular weights not exceeding 800 Da (making them micromolecules), they are found in the acid-insoluble fraction. This is because lipids are arranged into structures like cell membranes. When tissue is ground, cell membranes break into water-insoluble vesicles, which separate with the acid-insoluble pool. Lipids are not strictly macromolecules.

Inorganic elements and compounds are also present in living organisms. By burning dried tissue (ash), inorganic elements like calcium and magnesium are obtained. Inorganic compounds like sulphate and phosphate are found in the acid-soluble fraction.

Representative Inorganic Constituents of Living Tissues (Table 9.2):

From a biological perspective, organic compounds are classified into amino acids, nucleotide bases, fatty acids, etc..

Small Molecular Weight Organic Compounds (Micromolecules)

Amino Acids

Organic compounds containing an amino group and an acidic (carboxyl) group as substituents on the same carbon (the α-carbon), hence called α-amino acids. They are substituted methanes with four substituents: hydrogen, carboxyl group, amino group, and a variable R group.

• Approximately 20 types of amino acids occur in proteins.
• Examples of R groups: hydrogen (glycine), methyl group (alanine), hydroxy methyl (serine).
• Properties: Based on amino, carboxyl, and R functional groups.
  • Acidic: E.g., glutamic acid.
  • Basic: E.g., lysine.
  • Neutral: E.g., valine.
  • Aromatic: E.g., tyrosine, phenylalanine, tryptophan.
• Ionizable nature: The -NH₂ and -COOH groups are ionizable, so the structure of amino acids changes with different pH solutions (can exist in a zwitterionic form).

Lipids

Generally water insoluble.

• Fatty Acids: Have a carboxyl group attached to an R group. The R group can be a methyl, ethyl, or higher number of -CH₂ groups (1 to 19 carbons).
  • Palmitic acid: 16 carbons (including carboxyl carbon).
  • Arachidonic acid: 20 carbon atoms (including carboxyl carbon).
  • Can be saturated (without double bonds) or unsaturated (with one or more C=C double bonds).
• Glycerol: Trihydroxy propane.
• Glycerides: Many lipids have both glycerol and fatty acids, where fatty acids are esterified with glycerol. They can be monoglycerides, diglycerides, and triglycerides.
  • Also called fats (higher melting point) or oils (lower melting point, e.g., gingelly oil, which remains oil in winters).
• Phospholipids: Some lipids contain phosphorous and a phosphorylated organic compound. They are found in cell membranes, e.g., lecithin.
• More complex lipid structures are found in certain tissues, especially neural tissues.

Nitrogen Bases, Nucleosides, and Nucleotides

• Nitrogen Bases: Carbon compounds with heterocyclic rings, some of which are nitrogen bases: adenine, guanine, cytosine, uracil, and thymine.
  • Adenine and Guanine are substituted purines.
  • Cytosine, Uracil, and Thymine are substituted pyrimidines.
• Nucleosides: Nitrogen bases found attached to a sugar. E.g., Adenosine, Guanosine, Thymidine, Uridine, Cytidine.
• Nucleotides: If a phosphate group is also esterified to the sugar of a nucleoside, it forms a nucleotide. E.g., Adenylic acid, Thymidylic acid, Guanylic acid, Uridylic acid, Cytidylic acid. A nucleotide has three chemically distinct components: a heterocyclic compound (nitrogen base), a monosaccharide (sugar), and phosphoric acid or phosphate.
• Nucleic Acids: Like DNA and RNA, consist only of nucleotides. They function as genetic material.
  • The sugar found in polynucleotides is either ribose (a monosaccharide pentose) or 2’ deoxyribose.
  • Deoxyribonucleic acid (DNA): Contains deoxyribose.
  • Ribonucleic acid (RNA): Contains ribose.

Primary and Secondary Metabolites

• Metabolites: Biomolecules like amino acids, sugars, etc..
• Primary Metabolites: Found in animal tissues; have identifiable functions and known roles in normal physiological processes. E.g., amino acids, sugars, fatty acids, nucleotides.
• Secondary Metabolites: Thousands of compounds found in plant, fungal, and microbial cells that are not primary metabolites.
  • Examples: Alkaloids, flavonoids, rubber, essential oils, antibiotics, coloured pigments, scents, gums, spices.
  • Their roles in host organisms are often not fully understood.
  • Many are useful for human welfare (e.g., rubber, drugs, spices, scents, pigments). Some have ecological importance.

Some Secondary Metabolites (Table 9.3):

Biomacromolecules

These are the large molecular weight compounds found in the acid-insoluble fraction, primarily proteins, nucleic acids, and polysaccharides. They are generally polymeric substances.

Average Composition of Cells (Table 9.4):

Proteins

Polypeptides, which are linear chains of amino acids linked by peptide bonds. Each protein is a polymer of amino acids. Since there are 20 types of amino acids, a protein is a heteropolymer (composed of different types of monomers), not a homopolymer (one type of monomer repeating). Dietary proteins are a source of essential amino acids, which our body cannot make and must be supplied through diet.

Functions of Proteins:

• Transport: Transport nutrients across cell membranes.
• Defense: Fight infectious organisms (e.g., Antibodies).
• Hormones: Some act as hormones (e.g., Insulin).
• Enzymes: Many are enzymes (e.g., Trypsin).
• Receptors: Involved in sensory reception (smell, taste, hormones).
• Structural: (e.g., Collagen, intercellular ground substance).
• Glucose Transport: (e.g., GLUT-4 enables glucose transport into cells).

Abundant Proteins:

• Collagen: Most abundant protein in the animal world.
• Ribulose bisphosphate Carboxylase-Oxygenase (RuBisCO): Most abundant protein in the whole of the biosphere.

Polysaccharides

Also known as carbohydrates, these are long chains of sugars. They are polymers made of different monosaccharides as building blocks.

• Cellulose: A polymeric polysaccharide consisting of only one type of monosaccharide, glucose (it is a homopolymer). Plant cell walls are made of cellulose. Paper and cotton fibre are cellulosic. Cellulose does not contain complex helices and cannot hold I₂.
• Starch: A variant of glucose polymer, present as a storehouse of energy in plant tissues. Starch forms helical secondary structures and can hold I₂ molecules in its helical portion, which results in a blue colour with iodine.
• Glycogen: An animal variant of glucose polymer, storing energy. It has a reducing end (right end) and a non-reducing end (left end) and features branches.
• Inulin: A polymer of fructose.
• Complex Polysaccharides: Have amino-sugars and chemically modified sugars (e.g., glucosamine, N-acetyl galactosamine) as building blocks.
  • Chitin: A complex polysaccharide found in the exoskeletons of arthropods. These complex polysaccharides are mostly homopolymers.

Nucleic Acids

Macromolecules found in the acid-insoluble fraction of living tissue. They are polynucleotides.

• Together with polysaccharides and polypeptides, they comprise the true macromolecular fraction of any living tissue or cell.
• Building block: A nucleotide.
• A nucleotide consists of three chemically distinct components:
  1. A heterocyclic compound (nitrogenous base: adenine, guanine, uracil, cytosine, thymine).
  2. A monosaccharide (sugar: ribose or 2’ deoxyribose).
  3. A phosphoric acid or phosphate.
• Deoxyribonucleic acid (DNA): A nucleic acid containing deoxyribose.
• Ribonucleic acid (RNA): A nucleic acid containing ribose.
• DNA and RNA function as genetic material.

Structure of Proteins

Proteins are heteropolymers containing strings of amino acids. Biologists describe protein structure at four levels:

1. Primary Structure: The sequence of amino acids (positional information) in a protein. It is imagined as a line, with the first amino acid called the N-terminal amino acid (left end) and the last amino acid called the C-terminal amino acid (right end).
2. Secondary Structure: Portions of the protein thread are folded into specific forms, such as a helix (only right-handed helices are observed in proteins) or beta-pleated sheets.
3. Tertiary Structure: The long protein chain is folded upon itself like a hollow woolen ball, giving a 3-dimensional view of the protein. This structure is absolutely necessary for the many biological activities of proteins. This folding creates crevices or pockets, one of which is the active site.
4. Quaternary Structure: An assembly of more than one polypeptide or subunits, describing how these individual folded polypeptides are arranged relative to each other. Example: Adult human haemoglobin consists of 4 subunits (two α-type and two β-type).

Enzymes

Almost all enzymes are proteins. Some nucleic acids also behave like enzymes and are called ribozymes.

• Structure: Like other proteins, enzymes possess primary, secondary, and tertiary structures.
• Active Site: A crevice or pocket formed by the tertiary structure into which the substrate fits. Enzymes catalyse reactions at a high rate through their active site.
• Enzyme vs. Inorganic Catalysts:
  • Inorganic catalysts work efficiently at high temperatures and pressures.
  • Enzymes typically get damaged at high temperatures (above ~40°C) as proteins are denatured by heat.
  • However, enzymes from thermophilic organisms (living in extremely high temperatures) are thermally stable and retain catalytic power even at 80°-90°C.

Chemical Reactions and Enzyme Catalysis

• A chemical reaction involves bonds breaking and new bonds forming during transformation.
• Rate of a process: Amount of product formed per unit time. Rates are influenced by temperature, generally doubling or halving for every 10°C change.
• Enzyme-catalysed reactions: Proceed at vastly higher rates than uncatalysed ones.
  • Example: The enzyme carbonic anhydrase speeds up the reaction CO₂ + H₂O → H₂CO₃ by about 10 million times (from ~200 molecules/hour without enzyme to ~600,000 molecules/second with enzyme).
• Metabolic Pathway: A multistep chemical reaction where each step is catalysed by the same enzyme complex or different enzymes. E.g., Glucose to Pyruvic acid involves ten enzyme-catalysed reactions.

How Enzymes Bring About High Rates of Chemical Conversions

The chemical converted into a product is called a substrate (S). Enzymes convert S into a product (P).

• Enzyme-Substrate (ES) complex: The substrate binds to the enzyme at its active site, forming an obligatory and transient ES complex.
• Transition State Structure: While bound to the enzyme active site, the substrate forms a new structure called the transition state structure. The pathway of transformation goes through this high-energy, unstable transition state.
• Activation Energy: The difference in average energy content of the substrate from that of the transition state.
• Enzyme Function: Enzymes work by lowering this activation energy barrier, making the transition from substrate to product easier and faster.

Catalytic Cycle of Enzyme Action

1. Binding: The substrate (S) binds to the active site of the enzyme (E), forming a highly reactive, short-lived enzyme-substrate complex (ES).
2. Induced Fit: The binding of the substrate induces the enzyme to alter its shape, fitting more tightly around the substrate.
3. Catalysis: The active site, now in close proximity, breaks the chemical bonds of the substrate, forming a new enzyme-product complex (EP).
4. Release: The enzyme releases the products (P), and the free enzyme is ready to bind to another substrate molecule and repeat the cycle.

Factors Affecting Enzyme Activity

Enzyme activity can be affected by conditions that alter the protein’s tertiary structure.

• Temperature and pH:
  • Enzymes generally function in a narrow range of temperature and pH.
  • Each enzyme shows highest activity at an optimum temperature and optimum pH.
  • Activity declines both below and above the optimum value.
  • Low temperature preserves the enzyme in a temporarily inactive state.
  • High temperature destroys enzymatic activity because proteins are denatured by heat.
• Concentration of Substrate:
  • As substrate concentration increases, the reaction velocity initially rises.
  • The reaction eventually reaches a maximum velocity (Vmax), which is not exceeded by further increases in substrate concentration. This occurs because the enzyme molecules become fewer than the substrate molecules, leading to saturation of all active sites.
• Specific Chemicals (Inhibitors):
  • Chemicals that bind to the enzyme and shut off its activity are called inhibitors.
  • Competitive inhibitor: Closely resembles the substrate in molecular structure and inhibits activity by competing with the substrate for the enzyme’s substrate-binding site. This prevents the substrate from binding, leading to a decline in enzyme action. Example: Malonate inhibits succinic dehydrogenase because it closely resembles the substrate succinate. Competitive inhibitors are often used in the control of bacterial pathogens.

Classification and Nomenclature of Enzymes

Thousands of enzymes have been classified into 6 classes, each with 4-13 subclasses, and named by a four-digit number based on the type of reactions they catalyse:

1. Oxidoreductases/dehydrogenases: Catalyse oxidoreduction between two substrates (S reduced + S’ oxidised → S oxidised + S’ reduced).
2. Transferases: Catalyse the transfer of a group ‘G’ (other than hydrogen) between a pair of substrates (S-G + S’ → S + S’-G).
3. Hydrolases: Catalyse hydrolysis of ester, ether, peptide, glycosidic, C-C, C-halide, or P-N bonds.
4. Lyases: Catalyse removal of groups from substrates by mechanisms other than hydrolysis, leaving double bonds.
5. Isomerases: Include all enzymes catalysing inter-conversion of optical, geometric, or positional isomers.
6. Ligases: Catalyse the linking together of 2 compounds, e.g., joining C-O, C-S, C-N, P-O bonds.

Co-factors

Non-protein constituents that bind to an enzyme to make it catalytically active. The protein portion of the enzyme in this instance is called the apoenzyme. Catalytic activity is lost when the co-factor is removed, highlighting their crucial role.

Three kinds of cofactors:

1. Prosthetic groups: Organic compounds tightly bound to the apoenzyme. Example: Haem in peroxidase and catalase, which is part of the active site.
2. Co-enzymes: Organic compounds whose association with the apoenzyme is transient, usually occurring during catalysis. They serve as co-factors in many different enzyme-catalysed reactions. Essential chemical components of many coenzymes are vitamins (e.g., nicotinamide adenine dinucleotide (NAD) and NADP contain vitamin niacin).
3. Metal ions: Required by a number of enzymes for activity. They form coordination bonds with side chains at the active site and simultaneously with the substrate. Example: Zinc is a cofactor for the proteolytic enzyme carboxypeptidase.

Cell Cycle and Cell Division (Chapter 10)

All organisms, even the largest, begin life from a single cell. Growth and reproduction are fundamental characteristics of all living organisms. Cells reproduce by dividing into two daughter cells, and these daughter cells can grow and divide, forming new cell populations. This cycle allows a single cell to form large multicellular structures.

Cell Cycle

Cell division is a very important process. During cell division, DNA replication and cell growth also occur. These processes must be coordinated to ensure correct division and the formation of progeny cells with intact genomes.

• The sequence of events by which a cell duplicates its genome, synthesises other cell constituents, and eventually divides into two daughter cells is termed the cell cycle.
• Cell growth (cytoplasmic increase) is a continuous process, but DNA synthesis occurs only during one specific stage.
• Replicated chromosomes are distributed to daughter nuclei through complex, genetically controlled events.

Phases of Cell Cycle

A typical eukaryotic cell cycle (e.g., human cells in culture) lasts approximately 24 hours. This duration varies among organisms and cell types (e.g., yeast: ~90 minutes).

The cell cycle is divided into two basic phases:

1. Interphase
2. M Phase (Mitosis phase)

• M Phase: Represents the phase when actual cell division or mitosis occurs. In a 24-hour human cell cycle, cell division proper lasts only about an hour.
  • It starts with nuclear division (karyokinesis), which corresponds to the separation of daughter chromosomes.
  • It usually ends with the division of cytoplasm (cytokinesis).
• Interphase: The phase between two successive M phases. Though called the “resting phase,” it is the time during which the cell prepares for division by undergoing both cell growth and DNA replication in an orderly manner. Interphase lasts more than 95% of the cell cycle duration.

Interphase is divided into three further phases:

1. G₁ phase (Gap 1):
   • Corresponds to the interval between mitosis and the initiation of DNA replication.
   • During G₁ phase, the cell is metabolically active and continuously grows.
   • Does not replicate its DNA.
   • Most organelle duplication also occurs during this phase.
2. S phase (Synthesis):
   • Marks the period during which DNA synthesis or replication takes place.
   • The amount of DNA per cell doubles (if initial amount is 2C, it increases to 4C).
   • There is no increase in chromosome number (if a cell had 2n chromosomes at G₁, it remains 2n after S phase).
   • In animal cells, DNA replication begins in the nucleus, and the centriole duplicates in the cytoplasm.
3. G₂ phase (Gap 2):
   • Proteins are synthesised in preparation for mitosis.
   • Cell growth continues.
   • Period of cytoplasmic growth.

• Quiescent Stage (G₀): Some cells in adult animals (e.g., heart cells) do not divide or divide only occasionally. These cells exit the G₁ phase and enter an inactive stage called the quiescent stage (G₀). Cells in this stage remain metabolically active but do not proliferate unless called upon based on organism requirements.

M Phase (Mitosis)

This is the most dramatic period of the cell cycle, involving a major reorganisation of virtually all cell components. Mitosis is also called equational division because the number of chromosomes in the parent and progeny cells remains the same. Cell division is a progressive process, so clear-cut lines cannot be drawn between stages.

Karyokinesis (nuclear division) involves the following four stages:

1. Prophase
2. Metaphase
3. Anaphase
4. Telophase

Prophase

The first stage of karyokinesis, following the S and G₂ phases of interphase.

• New DNA molecules formed in S and G₂ are intertwined but become untangled during chromatin condensation.
• Chromosomal material condenses to form compact mitotic chromosomes, which are seen to be composed of two chromatids attached at the centromere.
• The centrosome, duplicated during interphase S phase, begins to move towards opposite poles of the cell. Each centrosome radiates microtubules called asters. The two asters together with spindle fibres form the mitotic apparatus.
• By the end of prophase, golgi complexes, endoplasmic reticulum, nucleolus, and the nuclear envelope disappear.

Metaphase

Marked by the complete disintegration of the nuclear envelope, spreading chromosomes throughout the cytoplasm.

• Condensation of chromosomes is completed, making them clearly observable under the microscope (this is the stage where chromosome morphology is most easily studied).
• A metaphase chromosome is made of two sister chromatids held together by the centromere.
• Kinetochores: Small disc-shaped structures on the surface of centromeres that serve as attachment sites for spindle fibres.
• All chromosomes come to lie at the equator. One chromatid of each chromosome is connected by its kinetochore to spindle fibres from one pole, and its sister chromatid to spindle fibres from the opposite pole.
• The plane of alignment of the chromosomes at metaphase is called the metaphase plate.

Key features of metaphase:

• Spindle fibres attach to kinetochores of chromosomes.
• Chromosomes are moved to the spindle equator and aligned along the metaphase plate through spindle fibres to both poles.

Anaphase

Begins with the simultaneous splitting of each centromere.

• The two daughter chromatids, now referred to as daughter chromosomes, begin their migration towards the two opposite poles.
• As each chromosome moves, its centromere remains directed towards the pole (leading edge), with the arms trailing behind.

Key events of anaphase:

• Centromeres split and chromatids separate.
• Chromatids move to opposite poles.

Telophase

The final stage of karyokinesis.

• Chromosomes that have reached their respective poles decondense and lose their individuality. Each set of chromatin material tends to collect at each of the two poles.

Key events of telophase:

• Chromosomes cluster at opposite spindle poles and their identity is lost as discrete elements.
• Nuclear envelope develops around the chromosome clusters at each pole, forming two daughter nuclei.
• Nucleolus, Golgi complex, and ER reform.

Cytokinesis

The division of the cell’s cytoplasm into two daughter cells. It follows karyokinesis and completes cell division.

• In animal cells: Achieved by the appearance of a furrow in the plasma membrane, which gradually deepens and divides the cytoplasm.
• In plant cells: Undergo cytokinesis by a different mechanism due to their inextensible cell wall.
  • Wall formation starts in the centre of the cell and grows outward to meet the existing lateral walls.
  • The formation of the new cell wall begins with a precursor called the cell-plate, which represents the middle lamella between the walls of two adjacent cells.
• During cytoplasmic division, organelles like mitochondria and plastids get distributed between the two daughter cells.
• In some organisms, karyokinesis is not followed by cytokinesis, resulting in a multinucleate condition (e.g., liquid endosperm in coconut), forming a syncytium.

Significance of Mitosis

• Usually restricted to diploid cells, but occurs in haploid cells in some lower plants and social insects (e.g., male honey bees).
• Results in the production of diploid daughter cells with identical genetic complement.
• Growth of multicellular organisms.
• Restores the nucleo-cytoplasmic ratio, which gets disturbed by cell growth.
• Cell repair: Constantly replaces cells of the upper layer of the epidermis, gut lining, and blood cells.
• Continuous growth in plants: Mitotic divisions in meristematic tissues (apical and lateral cambium) allow plants to grow throughout their life.

Meiosis

The production of offspring by sexual reproduction involves the fusion of two gametes, each with a complete haploid set of chromosomes. Gametes are formed from specialised diploid cells through meiosis.

• Meiosis is a specialised cell division that reduces the chromosome number by half, resulting in the production of haploid daughter cells. It is therefore called reduction division.
• Meiosis ensures the production of the haploid phase in the life cycle of sexually reproducing organisms, while fertilisation restores the diploid phase.
• It occurs during gametogenesis in plants and animals.

Key features of meiosis:

• Involves two sequential cycles of nuclear and cell division: Meiosis I and Meiosis II.
• Involves only a single cycle of DNA replication, which occurs before Meiosis I (in the S phase).
• Meiosis I is initiated after parental chromosomes have replicated to produce identical sister chromatids at the S phase.
• Involves pairing of homologous chromosomes and recombination (crossing over) between non-sister chromatids of homologous chromosomes.
• Four haploid cells are formed at the end of Meiosis II.

Meiotic events are grouped under the following phases:

• Meiosis I: Prophase I, Metaphase I, Anaphase I, Telophase I.
• Meiosis II: Prophase II, Metaphase II, Anaphase II, Telophase II.

Meiosis I

Prophase I

Typically longer and more complex than prophase of mitosis. It is further subdivided into five phases based on chromosomal behaviour:

1. Leptotene: Chromosomes gradually become visible under the light microscope. Compaction of chromosomes continues.
2. Zygotene: Chromosomes start pairing together, a process called synapsis. Such paired chromosomes are called homologous chromosomes.
   • Chromosome synapsis is accompanied by the formation of a complex structure called the synaptonemal complex.
   • The complex formed by a pair of synapsed homologous chromosomes is called a bivalent or a tetrad.
3. Pachytene: The four chromatids of each bivalent chromosome become distinct and clearly appear as tetrads.
   • Characterised by the appearance of recombination nodules, which are the sites where crossing over occurs between non-sister chromatids of the homologous chromosomes.
   • Crossing over is the exchange of genetic material between two homologous chromosomes. It is an enzyme-mediated process involving the enzyme recombinase.
   • Crossing over leads to recombination of genetic material. Recombination between homologous chromosomes is completed by the end of pachytene, leaving chromosomes linked at crossover sites.
4. Diplotene: Recognised by the dissolution of the synaptonemal complex and the tendency of recombined homologous chromosomes to separate from each other, except at the sites of crossovers. These X-shaped structures are called chiasmata. In oocytes of some vertebrates, diplotene can last for months or years.
5. Diakinesis: Marked by the terminalisation of chiasmata. During this phase, chromosomes are fully condensed, and the meiotic spindle is assembled. The nucleolus disappears, and the nuclear envelope breaks down. Diakinesis represents the transition to metaphase.

Metaphase I

The bivalent chromosomes align on the equatorial plate. Microtubules from the opposite poles of the spindle attach to the kinetochore of homologous chromosomes.

Anaphase I

The homologous chromosomes separate, while sister chromatids remain associated at their centromeres.

Telophase I

The nuclear membrane and nucleolus reappear. Cytokinesis follows, resulting in a dyad of cells (two haploid cells). Chromosomes may undergo some dispersion but do not reach the extremely extended state of the interphase nucleus.

• Interkinesis: The stage between the two meiotic divisions. It is generally short-lived, and there is no replication of DNA during this stage. Interkinesis is followed by prophase II.

Meiosis II

Initiated immediately after cytokinesis, usually before chromosomes have fully elongated. Meiosis II resembles a normal mitosis.

Prophase II

The nuclear membrane disappears by the end of this phase. The chromosomes again become compact.

Metaphase II

Chromosomes align at the equator. Microtubules from opposite poles of the spindle attach to the kinetochores of sister chromatids.

Anaphase II

Begins with the simultaneous splitting of the centromere of each chromosome (which was holding the sister chromatids together). This allows the sister chromatids to move toward opposite poles of the cell by shortening of microtubules attached to kinetochores.

Telophase II

Meiosis ends with telophase II. The two groups of chromosomes once again get enclosed by a nuclear envelope. Cytokinesis follows, resulting in the formation of a tetrad of cells (four haploid daughter cells).

Significance of Meiosis

• Conservation of Chromosome Number: It is the mechanism by which the conservation of a specific chromosome number for each species is achieved across generations in sexually reproducing organisms. While the process itself reduces chromosome number by half, fertilisation restores it.
• Genetic Variability: Meiosis increases the genetic variability in the population of organisms from one generation to the next. These variations are very important for the process of evolution.

G.N. Ramachandran

An outstanding figure in the field of protein structure, G.N. Ramachandran (1922 – 2001) was the founder of the ‘Madras school’ of conformational analysis of biopolymers.

• Key Contributions:
  • Discovery of the triple helical structure of collagen, published in Nature in 1954.
  • Analysis of the allowed conformations of proteins through the use of the ‘Ramachandran plot’.
• Background: Born October 8, 1922, in a small town near Cochin, India. His father, a mathematics professor, influenced his interest in mathematics.
• Education: Graduated top-ranking in B.Sc. (Honors) Physics from the University of Madras in 1942. Received a Ph.D. from Cambridge University in 1949.
• Influences: While at Cambridge, he met Linus Pauling and was deeply influenced by Pauling’s publications on models of the α-helix and β-sheet structures, which directed his attention to solving the structure of collagen.
• Death: Passed away at the age of 78, on April 7, 2001.