Discovery of the Cell

• The term cell was first used by Robert Hooke (1665) when he observed a thin section of cork under a simple microscope.
• He noticed tiny empty compartments resembling a honeycomb structure and called them cells.
• However, Hooke only observed dead plant cells (cell walls); he did not see the internal structures of living cells.

Why is this discovery important?
Hooke’s observation laid the groundwork for modern cell biology. Although he only saw dead cell walls, his findings encouraged future scientists to investigate living cells.

Cell Theory Development

Cell Theory was formulated by Schleiden and Schwann in the 19th century, stating that:

1. All living organisms are made up of cells.
2. The cell is the basic unit of structure and function in living beings.

Later, Rudolf Virchow (1855) added an important principle:
3. All cells arise from pre-existing cells. (Omnis cellula e cellula)

➡ Why is cell theory revolutionary?
Before the cell theory, people believed in spontaneous generation (the idea that life arises from non-living matter). Cell theory proved that life originates from pre-existing life.

Protoplasm Theory (1861)

• Introduced by De Bary and Schultze, stating that protoplasm is the fundamental substance of life.
• Protoplasm consists of:
  • Cytoplasm (fluid matrix inside the cell)
  • Nucleus (controls genetic information)

Strasburger (1884) further established that the nucleus is responsible for inheritance.

➡ Why is this important?
This theory emphasized that life processes occur inside the protoplasm, shifting focus from the cell wall (which Hooke observed) to the living content of cells.

Size of Cells

Cells come in various sizes, from microscopic bacteria to large eggs.

➡ Why do cell sizes vary?

• Smaller cells (like bacteria) have a high surface-area-to-volume ratio, which allows efficient nutrient exchange.
• Larger cells (like the ostrich egg) contain nutrients for early embryonic development.

Microscopic Resolution and Cell Observation

• Human Eye Resolving Power: 100 µm (can only see large cells)
• Light Microscope: 0.3 µm (3000 Å)
• Electron Microscope: 0.25 Å (can see even organelles)

➡ Why do we need electron microscopes?
Light microscopes allow us to see cell structure, but electron microscopes help us study organelles like mitochondria, ribosomes, and chromosomes in detail.

Structural Organization of the Cell

Cells consist of three main parts:

1. Cell Boundaries (Protection and Regulation)
   • Cell wall (only in plant cells; provides rigidity)
   • Cell membrane (present in all cells; controls material exchange)
2. Cytoplasm (Houses Organelles)
   • Membrane-bound organelles:
     • Mitochondria (Powerhouse of the cell)
     • Endoplasmic Reticulum (ER) (Protein & lipid synthesis)
     • Golgi Complex (Processing and packaging)
     • Lysosomes (Digestion of waste)
     • Plastids (Chloroplasts in plants for photosynthesis)
     • Peroxisomes (Detoxification)
   • Membrane-less organelles:
     • Ribosomes (Protein synthesis)
     • Centrioles (Cell division)
     • Microtubules (Cell shape & movement)
3. Nucleus (Control Center)
   • Contains DNA (genetic material)
   • Regulates cell activities
   • Responsible for inheritance

Differences Between Plant and Animal Cells

structured comparison of Prokaryotic and Eukaryotic Cells based on different characteristics:

Key Differences Summary:

1. Prokaryotic cells are simpler, smaller, and lack membrane-bound organelles.
2. Eukaryotic cells are more complex, larger, and have a well-defined nucleus and organelles.
3. Prokaryotes reproduce by binary fission, while eukaryotes divide by mitosis or meiosis.
4. Prokaryotic respiration occurs on the plasma membrane, whereas eukaryotic respiration takes place in mitochondria.

Structure and function of cell organelles

Cell Wall (Only in Plant Cells)

• Definition: A non-living, thick protective layer outside the plasma membrane, present in plant cells but absent in animal cells.
• Composition: Mainly cellulose (a carbohydrate) but also contains lignin, hemicellulose, and pectin.
• Function: Provides mechanical strength, rigidity, and permeability.
• Lignin: A complex polymer (coniferyl alcohol) that gives rigidity.
  • Non-lignified cells: Parenchyma, Collenchyma, Sieve tubes.
  • Lignified cells: Sclerenchyma, Vessels, Tracheids.
  • Classroom stain for lignified cells: Safranin.

Types of Cell Walls

• Middle Lamella: Rich in pectin, acts as a cementing material between plant cells.
• Primary Cell Wall: Composed of cellulose, hemicellulose, and pectin.
• Secondary Cell Wall: Present in some cells, contains cellulose and lignin (e.g., sclerenchyma, vessels, and tracheids).
• Based on Secondary Wall Thickness:
  • Thin or absent: Parenchyma.
  • Moderate thickness: Collenchyma (mechanical support due to cellulose).
  • Thick secondary wall with lignin: Sclerenchyma, vessels, and tracheids.

Protoplasm (Living part of the cell)

• Definition: Includes all living components of a cell, including the cytoplasm and nucleus.
• Discovery: J.E. Purkinje (1830-37) introduced the term “protoplasm.”
• Huxley’s Definition: “Protoplasm is the physical basis of life.”
• Composition:
  • 80-90% Water.
  • Colloidal in nature (heterogeneous).
  • Proteins (60-70%) are the major dry constituents.

Nucleus (Control Center of the Cell)

• Discovery: Robert Brown (1833).
• Structure:
  • Surrounded by a double membrane called the nuclear envelope, which has pores for transport.
  • Inside, there is a nuclear sap (karyolymph) where chromatin and the nucleolus are present.
• Chromatin: A tangled mass of DNA + Protein, condenses into chromosomes during cell division.
• Exceptions:
  • No true nucleus in bacteria and cyanobacteria (they have nucleoid instead).
  • No nucleus in mature mammalian RBCs and sieve tube cells in phloem.

Nucleolus (Ribosome Factory)

• Discovery: Fontana (1781).
• Composition: Rich in RNA, but also contains DNA.
• Function: Synthesis of ribosomal RNA (rRNA).
• Location: Attached to a specific site on a chromosome called the nucleolar organizer.
• RNA Polymerases:
  • RNA Polymerase I → Synthesizes rRNA in the nucleolus.
  • RNA Polymerase II → Synthesizes HnRNA (precursor to mRNA) in nucleoplasm.
  • RNA Polymerase III → Synthesizes tRNA and small RNA.

Chromosome

• First observed by: Strasburger in 1875 as fine threads.
• Named by: Waldeyer in 1888 (Chroma = color, Soma = body) using basic dye.
• Function: Chromosomes are the carriers of hereditary units (genes).
• Chromosome number in species:
  • Humans: 2n = 46
  • Rice: 2n = 24
  • Prokaryotes: Have a single circular chromosome (sometimes described as rod-shaped).

Chemical Composition of Chromatin

• Chromatin → Nucleoprotein
  • Nucleic Acid + Protein
    • DNA
    • RNA
    • Histones
    • Non-histones

Nucleic Acid Composition

• Nucleic acid is a polymer of nucleotides.
• Nucleotide = Sugar + Nitrogenous Base + Phosphate
• Nucleoside = Sugar + Base
• Nucleotide = Nucleoside + Phosphoric Acid

Nitrogenous Bases

• Ring-structured bases:
  • Purines (Two Rings): Adenine (A), Guanine (G)
  • Pyrimidines (Single Ring): Thymine (T), Uracil (U), Cytosine (C)

DNA Model

• Proposed by: Watson & Crick in 1953 (Book: Double Helix).
• Wilkins: Used X-ray diffraction to study DNA structure.

Mitochondria (“Powerhouse of the Cell”)

• Function: Generates energy in the form of ATP (~ energy currency).
• Discovery:
  • First identified by: Altman (1886) as Bioplast (suggested its role in respiration).
  • Term “Mitochondria” given by: C. Benda (1898).
  • First observed by: Kolliker (1853).

Mitochondrial Functions

• Site of aerobic respiration (Krebs cycle).
• Site of glycolysis: Hyaloplasm (not cytoplasm).
• Electron Transport Chain (ETC) occurs on Oxysomes (F1 particles / Elementary particles) located on the inner mitochondrial membrane.
• Enzymes are confined in the perimitochondrial space, with reactions occurring on the inner membrane.

Mitochondrial DNA & RNA

• Contains 0.02% DNA, 3-4% RNA, and ribosomes.
• Semi-autonomous organelle: Can synthesize some of its own proteins.

Plastids (Discovered by Schimper, 1885)

Types of Plastids

1. Chloroplasts: Green plastids responsible for photosynthesis.
2. Chromoplasts: Red, yellow, brown, or orange plastids (Chromo = color).
3. Leucoplasts: Colorless plastids primarily for food storage.

Functions of Leucoplasts

• Amyloplast: Stores starch.
• Elaioplast: Stores oils.
• Aleuronoplast (Proteinoplast): Stores proteins.

Chloroplasts:

• Contain pigment chlorophyll.
• Outer membrane and Inner membrane
• Stroma: The homogenous matrix in which grana are embedded.
• Grana: Stacks of membrane-bound, flattened, discoid sacs containing chlorophyll molecules.
• Starch grains, Lipid droplets, DNA
• Grana Lamellae:
  • Contain Thylakoids → Quantasomes → Pigment Lamellae
  • Site of Light reaction → Grana/Thylakoids/Quantasomes
  • Dark reaction → Stroma/Matrix
• Chloroplast contains:
  • DNA (0.5%), RNA (3-4%), and Ribosomes → Capable of independent protein synthesis → Semi-autonomous body of the cell.
• Called the kitchen of the cell due to its role in photosynthesis.

Chloroplast and Pigments

Chloroplast: Contains pigments such as chlorophyll and carotenoids.

Types of Pigments in Chloroplast

1. Chlorophyll (Soluble in organic solutions)

1. • Chlorophyll a: Blue-black, Chemical formula: C₅₅H₇₂O₅N₄Mg
   • Chlorophyll b: Green-black, Chemical formula: C₅₅H₇₀O₆N₄Mg
   • Chlorophyll a & b in green plants: 65%

2. Carotenoids (Carotene & Xanthophyll)

1. • Carotene: Yellowish-orange, Chemical formula: C₄₀H₅₆
   • Xanthophyll: Yellow, Chemical formula: C₄₀H₅₆O₂
   • Carotene & Xanthophyll together form carotenoid pigments.
   • Carotene content in plants: 6%
   • Xanthophyll content in plants: 29%

3. Chromoplast

1. • Contains only carotenoid pigments (Carotene & Xanthophyll).

4. Sap Pigments

1. • Found in vacuoles (e.g., Anthocyanins)
   • Soluble in water
   • Present in flower petals and beets

Functions of Chloroplast:

• Site of photosynthesis (Light reaction occurs in Grana/Thylakoids/Quantasomes).
• Dark reaction occurs in Stroma/Matrix.
• Known as the kitchen of the cell due to food production.

Endoplasmic Reticulum (ER)

• A network of double membranes running through the cytoplasm.
• Origin: Derived from nuclear membrane.
• First observed by Porter (1948).
• Two types:
  1. Rough ER (RER): Has ribosomes → Protein synthesis.
  2. Smooth ER (SER): Lacks ribosomes → Lipid synthesis, detoxification.

Functions of ER:

1. Structural support for cell (endoskeleton).
2. Increased metabolic surface area.
3. Intracellular transport of proteins.
4. Formation of cell plate and nuclear membrane during cell division.
5. Protein synthesis (on ribosomes of Rough ER).
6. Lipid secretion (SER) → Forms cell membrane (membrane biogenesis).
7. Transmission of impulses in animals.
8. Detoxification of poisons & drugs (SER).

Ribosomes (RNA Particles)

• Discovered by Claude (1943), later termed “ribosomes” by R.B. Robert (1958).
• Palade (1956) isolated ribosomes and reported detailed structure.

Composition:

• RNA (40-60%)
• Protein (60-40%)

Types of RNA in Ribosomes:

1. mRNA (Messenger RNA) → 5-10% of total RNA.
2. tRNA (Transfer RNA / Soluble RNA) → 10-15% of total RNA (Smallest).
3. rRNA (Ribosomal RNA) → 80% of total RNA, provides site for protein synthesis.

Two major steps of protein synthesis:

1. Transcription → Genetic information transfer from DNA to mRNA.
2. Translation → Conversion of nucleic acid language into proteins.

Structure of Ribosome:

• Prokaryotic Ribosomes: 70S (Subunits: 30S + 50S)
• Eukaryotic Ribosomes: 80S (Subunits: 40S + 60S)
• Higher Mg²⁺ concentration → Promotes ribosome assembly.
• Lower Mg²⁺ concentration → Dissociates ribosome subunits.

Golgi Complex (Dictyosome in Plants)

• Discovered by Camillo Golgi (1898).
• Formed from the ER.
• Composed of flattened sacs (cisternae), vesicles, and granules.

Functions:

1. Storage, modification, and packaging of proteins (from ribosomes).
2. Formation of cell plate during cell division.
3. Addition of sugars to proteins → Synthesizes polysaccharides.
4. Lysosome formation → Stores digestive enzymes.

Lysosomes

• Discovered by De Duve (1955).
• Found mainly in animal cells but also in some plants (e.g., Neurospora).
• Formed directly from Golgi Complex & indirectly from ER.
• Contain digestive enzymes synthesized in RER.

Functions:

1. Intracellular digestion → Breakdown of large molecules.
2. Defense mechanism → Destroys bacteria & viruses.

Centrosome:

The centrosome is an essential structure found near the nucleus, mainly in animal cells but also in some other organisms such as Chlamydomonas, certain fungi, and Gymnosperms. It consists of two centrioles located at right angles to each other. During mitosis, the centrosomes play a crucial role by moving to opposite poles of the cell and producing astral rays (microtubules), which are involved in the formation of the spindle apparatus, guiding the chromosomes to opposite poles during cell division.

Ergastic Substances:

Ergastic substances refer to non-living inclusions within cells, often stored in vacuoles or other compartments. These substances include:

• Starch, sugars, organic acids, fats, oils, and pigments. These substances are not involved in the immediate metabolic processes but can serve as energy reserves, structural components, or protectants against environmental stress.

Genetic Material – DNA & RNA:

Both DNA and RNA are classified as nucleic acids and are essential for the storage, transfer, and expression of genetic information in organisms. The discovery of nucleic acids is attributed to Friedrich Miescher in 1868 when he isolated them from white blood cells.

Structure of DNA:

The DNA molecule, as described by James Watson and Francis Crick in 1953, has the following features:

1. Double helix structure: Two polynucleotide strands wound around each other.
2. Sugar-phosphate backbone: The outer structure of each strand is made of sugar and phosphate groups.
3. Base pairing: The internal bases of the helix are purines (Adenine – A, Guanine – G) and pyrimidines (Cytosine – C, Thymine – T).
   • Adenine always pairs with Thymine (A-T) via two hydrogen bonds.
   • Guanine always pairs with Cytosine (G-C) via three hydrogen bonds.
4. Complementary strands: The two strands of DNA run in opposite directions (anti-parallel) and are complementary, meaning the sequence of bases in one strand dictates the sequence of the other strand.
5. Base-pairing rules (known as Chargaff’s rule):
   • The amount of A = T, and C = G in a DNA molecule.
   • These base-pairing rules are fundamental for accurate DNA replication and function.

The Structure of RNA: RNA, unlike DNA, is usually single-stranded, though in some cases, it can be double-stranded. RNA molecules are often much shorter than DNA molecules and play a key role in the synthesis of proteins.

• RNA types:
  • mRNA (messenger RNA): Carries genetic information from DNA to the ribosome for protein synthesis.
  • tRNA (transfer RNA): Helps in the translation process by carrying amino acids to the ribosome.
  • rRNA (ribosomal RNA): A major component of ribosomes that aids in protein synthesis.

RNA vs. DNA:

• • DNA has the sugar deoxyribose, while RNA contains ribose.
  • DNA uses Thymine (T) as one of its bases, whereas RNA uses Uracil (U) instead of Thymine.
  • DNA is typically double-stranded, whereas RNA is usually single-stranded.

Genetic Code:

The genetic code is the set of rules that determines how the information in DNA and RNA is translated into the sequence of amino acids that make up proteins. The code is universal across almost all organisms and is made up of sequences of three nucleotide bases, called codons, each coding for a specific amino acid.

RNA and Virus Genetics:

RNA is not only essential in living organisms but also serves as genetic material in many viruses. Some RNA viruses (e.g., Influenza virus, Poliovirus) utilize RNA as their genetic material instead of DNA. In these cases, the RNA functions as the genetic blueprint of the virus. Interestingly, RNA viruses can replicate their genetic material through a process called RNA-dependent RNA synthesis, where an RNA template is used to create new RNA molecules.

• Genetic RNA in viruses can be single or double-stranded, and it generally follows the base-pairing rules similar to DNA in the case of double-stranded RNA.

Types of RNA Viruses:

1. Plant Viruses: Example – Turnip Yellow Mosaic Virus (single-stranded RNA).
2. Animal Viruses: Examples include Influenza virus, Poliomyelitis virus (single-stranded RNA).
3. Bacteriophages: Example – MS.2 (single-stranded RNA).

Summary of DNA vs. RNA: