The Cell: Structure, Organelles and Division

1. Discovery of the Cell and the Cell Theory

1.1 Historical landmarks

1.2 The cell theory

As formulated by Schleiden and Schwann and completed by Virchow, the cell theory states:

• All living organisms are composed of cells and the products of cells.
  

• The cell is the basic structural and functional unit of life: the smallest unit capable of independent existence. (70th BPSC CCE)
  

• All cells arise from pre-existing cells by division.

• Viruses, viroids and prions are acellular; they lack a cellular organisation and reproduce only inside a host cell. They are therefore not covered by the theory.
  

• Coenocytic and syncytial structures (Rhizopus, Vaucheria, striated muscle fibres and the liquid endosperm of coconut) contain many nuclei in a continuous mass of cytoplasm without cell boundaries.
  

• Mature mammalian red blood cells and sieve tube elements lack a nucleus; mature RBCs also lack most organelles.
  

• Bacteria and cyanobacteria lack a well-defined nucleus and membrane-bound organelles, so the "typical cell" described by the theory does not fit them.
  

2. Cell Size, Shape and Number

• Shape varies with function: Discoidal (RBC), spherical, polygonal, columnar, spindle-shaped (muscle), branched with long processes (nerve).
  

• Number: Organisms may be
  1. Unicellular (Amoeba, bacteria, Chlamydomonas) or
  2. multicellular.
  

• Cell size is limited by the surface area to volume ratio and by the capacity of the nucleus to control the cytoplasm.
  

3. Prokaryotic Cells

Represented by bacteria, cyanobacteria (blue-green algae), mycoplasma and PPLO. They multiply rapidly and are generally smaller than eukaryotic cells.

The four basic bacterial shapes are:
1. Bacillus (rod),
2. Coccus (spherical),
3. Vibrio (comma) and
4. Spirillum (spiral).

3.1 The cell envelope

The three-layered prokaryotic envelope

Read the explanation ↗

Most prokaryotes have a chemically complex three-layered envelope, tightly bound and functioning as a unit:

• Glycocalyx- the outermost layer. It may be a loose sheath called a slime layer, or a thick and tough capsule. Capsules protect against phagocytosis and desiccation, and contribute to virulence.

• Cell wall: made of peptidoglycan (murein); determines the shape of the cell and provides strong structural support to prevent bursting or collapse.

• Plasma membrane: selectively permeable; structurally similar to that of eukaryotes.

Gram staining (Christian Gram): bacteria that retain the stain are Gram-positive; those that do not are Gram-negative. The difference lies in the thickness of the peptidoglycan layer and the presence of an outer lipopolysaccharide membrane in Gram-negative cells, and it has major consequences for antibiotic sensitivity.

4. Eukaryotic Cells

Found in protists, plants, animals and fungi. Their defining features are a true nucleus bounded by a nuclear envelope, and membrane-bound organelles, which permit compartmentalisation of function.

4.1 Prokaryotic and eukaryotic cells compared

4.2 Plant and animal cells compared

5. Cell Wall

General Characteristics

• Cell wall: A non-living rigid structure forming an outer covering for the plasma membrane in fungi and plants.

• Functions: Protects cell, Maintains shape, and Prevents osmotic lysis.

• Animal cells: Completely lack a cell wall.

Cell Wall Composition by Organism Group

6. Plasma Membrane and Transport

6.1 Chemical composition

• Membrane composition: composed primarily of lipids (chiefly phosphoglycerides) and proteins (71st BPSC CCE).
  

• The ratio of protein to lipid varies greatly: human RBC membrane has about 52 per cent protein and 40 per cent lipid.
  
  

6.2 Models of membrane structure

• Fluid Mosaic Model: Universally accepted model, proposed by Singer and Nicolson in 1972.
  

• Structure: Proteins float within a continuous two-dimensional liquid phospholipid bilayer.
  

6.3 Transport across the membrane

Membrane transport: direction and ATP

Read the explanation ↗

Osmosis is a passive transport process where water moves from lower solute concentration to higher solute concentration across a selectively permeable membrane.

7. The Endomembrane System

The organelles whose functions are coordinated are considered together as the endomembrane system:
1. Endoplasmic reticulum,
2. Golgi complex,
3. Lysosomes and
4. Vacuoles.
5. Mitochondria,
6. Chloroplasts and
7. Peroxisomes are excluded because their functions are not coordinated with these.

7.1 Endoplasmic reticulum

• The endoplasmic reticulum (ER) is like a transport system inside a cell. It is a network of tiny tubes that helps make and move proteins and fats around the cell.

• There are two types:

  • Rough ER: Has ribosomes on it and makes proteins.
    

  • Smooth ER: Has no ribosomes and makes Lipid and steroid synthesis, drug detoxification: helps remove harmful substances.

7.2 Golgi apparatus

• Discovered by Camillo Golgi in 1898 in nerve cells; also called the dictyosome in plants.
  

• Consists of many flat, disc-shaped sacs or cisternae, 0.5–1.0 µm in diameter, stacked parallel and concentrically arranged near the nucleus.
  

• Functions:

  • The principal site of packaging and dispatch of materials;

  • Modification of proteins, especially glycosylation;

  • Formation of glycolipids and glycoproteins;

  • Formation of lysosomes; and,

  • In plant cells, synthesis of the polysaccharides of the cell wall.
    

• Aptly called the "post office" or the "traffic police" of the cell.

7.3 Lysosomes

• Discovered by Christian de Duve; membrane-bound vesicular structures formed by the packaging activity of the Golgi apparatus.
  

• Contain almost fifty hydrolytic enzymes (lipases, proteases, carbohydrases and nucleases) all of which are optimally active at acidic pH (about 5), maintained by proton pumps in the lysosomal membrane.
  

• Types: primary (freshly formed, enzymes inactive), secondary or digestive vacuole (formed by fusion with a food vacuole), residual body (containing undigested material), and autophagic vacuole (digesting the cell's own worn-out organelles).
  

• Enzyme nature: Lysosomes contain hydrolytic enzymes; most enzymes are proteins. (67th BPSC CCE)

• Functions:

  • Intracellular digestion;

  • Destruction of foreign material;

  • Autophagy and Autolysis: the self-destruction of the cell, which has earned lysosomes the name "suicide bags of the cell".

  • Also important in metamorphosis (resorption of the tadpole's tail).

7.4 Vacuoles

• A vacuole is like a storage bag inside a cell.

• A membrane-bound space in the cytoplasm containing water, sap, excretory products and other materials not useful to the cell.

• Bounded by a single membrane called the tonoplast.

• In the plant cell the vacuole may occupy up to 90 per cent of the cell volume and is responsible for turgidity.

• The tonoplast facilitates the transport of ions against the concentration gradient, so the vacuole may hold a higher concentration of ions than the cytoplasm.

• In Amoeba the contractile vacuole is important in osmoregulation and excretion; many protists have food vacuoles formed by engulfing food particles.

8. Mitochondria: The Powerhouse of the cell

• First observed by Richard Altmann (1890) as "bioblasts" and named mitochondria by Carl Benda (1897).
  

• Shape and size: usually cylindrical or sausage-shaped
  

• Number varies with the physiological activity of the cell.
  

• Active cells: High numbers in muscle and nerve cells for energy demands.
  

• Structure: A double membrane:

  • The outer membrane is smooth and forms a continuous limiting boundary; it is permeable to small molecules (porins).
    

  • The inner membrane forms a number of infoldings called cristae towards the matrix, which greatly increase the surface area. It is selectively permeable.
    

  • The two membranes divide the organelle into two aqueous compartments, the outer (intermembrane) compartment and the inner compartment or matrix.
    

  • The inner membrane bears stalked particles: F₀-F₁ particles, also called oxysomes or elementary particles: which carry out ATP synthesis.
    

• Matrix contents:

  • A single circular DNA molecule,

  • A few RNA molecules,

  • 70S ribosomes and

  • The components required to synthesise proteins.
    
    Mitochondria therefore divide by fission and are described as semi-autonomous organelles.
    

• Function:

  • The site of aerobic respiration- the Krebs cycle in the matrix and the electron transport chain and oxidative phosphorylation on the inner membrane.
    

  • They produce cellular energy in the form of ATP, and are therefore called the "powerhouses of the cell".

9. Plastid Family and Chloroplast

Found in all plant cells and in euglenoids. They bear specific pigments and are classified into three types.

Structure of the chloroplast

• Bounded by a double membrane; the space inside is the stroma.
  

• The stroma contains a number of organised flattened membranous sacs called thylakoids. Thylakoids are arranged in stacks called grana (singular granum), and flat membranous tubules called stroma lamellae connect the thylakoids of different grana.
  

• The space inside a thylakoid is the lumen.
  

• The light reactions occur on the thylakoid membranes;

• The dark reactions (carbon fixation) occur in the stroma.
  

• The stroma also contains circular DNA, 70S ribosomes and enzymes - so chloroplasts too are semi-autonomous.

Semi-autonomous organelles: Why DNA and RNA enable self-replication

• Replication: Mitochondria and chloroplasts duplicate independently via binary fission.

• Dependence: Rely on nuclear DNA for most structural proteins and enzymes.

The presence of DNA alone does not allow self-replication; requires both DNA and RNA with 70S ribosomes. (68th BPSC CCE)

THE ENDOSYMBIOTIC THEORY (Lynn Margulis)

• Mitochondria and chloroplasts both possess a double membrane, their own circular DNA, 70S ribosomes, and the ability to divide independently by fission: all features of prokaryotes.
  

• The endosymbiotic theory proposes that they originated as free-living prokaryotes (an aerobic bacterium and a cyanobacterium respectively) that were engulfed by an ancestral eukaryotic cell and retained in a mutually beneficial relationship. This is the standard explanation for why they are semi-autonomous.

10. Ribosomes: Protein Factories

• First observed under the electron microscope by George Palade (1953).
  

• Granular structures, not surrounded by any membrane - the only major organelle without a membrane.
  

• Composed of ribosomal RNA (rRNA) and proteins, in two unequal subunits that associate only in the presence of Mg²⁺.
  

• Ribosome types:

  • 80S (60S + 40S) in eukaryotic cytoplasm;

  • 70S (50S + 30S) in prokaryotes, mitochondria, and chloroplasts.
    

• "S" is the Svedberg unit, a measure of the sedimentation coefficient, which depends on both size and shape.
  

• Found free in the cytoplasm (proteins for use within the cell) or attached to the Rough Endoplasmic Reticulum (proteins for export or for membranes).
  

• Several ribosomes translating a single mRNA form a polysome.
  

• Function: The site of protein synthesis : the "Protein Factories" of the cell.

11. Cytoskeleton, Cilia, Flagella and Centrioles

11.1 Cytoskeleton

The cytoskeleton is a network of protein fibres inside the cell. It gives the cell shape, support and movement., of three kinds:

• Microtubules : Hollow tubes made of tubulin. They help form spindle fibres, cilia, flagella and centrioles.

• Microfilaments: Very thin fibres made of actin. They help in cell contraction and movement of cytoplasm.

• Intermediate filaments: Provide tensile strength. Give the cell strength and support

11.2 Cilia and flagella

• Cilia and flagella are hair-like structures that come out from the cell.
  

• Cilia are small and numerous and work like oars, moving the cell or the surrounding fluid.
  

• Flagella are longer and fewer and are responsible for cell movement.
  

• Both are covered with the plasma membrane. The core, called the axoneme, possesses a number of microtubules running parallel to the long axis.

11.3 Centrosome and centrioles

• TThe centrosome is an organelle found mainly in animal cells. It usually contains two centrioles.
  

• The two centrioles are arranged at right angles (90°) to each other.

• Functions:T

  • The centrioles form the basal body of cilia and flagella, and

  • Give rise to the spindle apparatus during cell division in animal cells.
    

12. The Nucleus and Chromosomes

12.1 Structure and Functions

• Control centre: Directing growth, metabolism, and division.
  

• First described by Robert Brown (1831); the stainable material was called chromatin by Flemming.
  

• Biological membranes: Nuclear membrane and plasma membrane are composed of proteins and lipids. (71st BPSC CCE)
  

• Number of nuclei: usually one; some cells are anucleate (mature mammalian RBC, sieve tube cells) and some multinucleate (Rhizopus, striated muscle fibres).

Components of the nucleus

12.2 Chromatin and chromosomes

• Chromatin is an material inside nucleus (an interphase network of nucleoprotein fibres).
  

• It’s made up of: DNA, histones, non-histone proteins and RNA.
  

• When the cell is not dividing (Interphase), DNA is present as a loose network called chromatin.
  

• During division it condenses into chromosomes.
  

• Chromatin = Loose DNA
  
  Chromosome = Condensed/tightly packed DNA
  

• Types of Chromatin:
  Euchromatin: Loosely packed, lightly stained, transcriptionally active. Heterochromatin: Densely packed, darkly stained, transcriptionally inactive.
  

• Nucleosome model: A nucleosome is the basic repeating unit of chromatin.

  • Think of DNA as a long thread wrapped around a spool.

  • DNA is negatively charged.

  • Histone proteins are positively charged.

  • DNA wraps around a group of 8 histone proteins, called a histone octamer.

  • The octamer contains:

    • 2 × H2A

    • 2 × H2B

    • 2 × H3

    • 2 × H4

About 200 base pairs of DNA are associated with each nucleosome.

Parts and types of a chromosome

• Every chromosome has a primary constriction or centromere, on the sides of which are disc-shaped structures called kinetochores, to which the spindle fibres attach. Some chromosomes have a secondary constriction with a small terminal fragment called the satellite.

13. Microbodies

• Membrane-bound minute vesicles containing various enzymes, present in both plant and animal cells.
  

• Peroxisomes:

  • Contain oxidases and catalase;
    

  • carry out oxidation reactions producing hydrogen peroxide, which catalase then breaks down.
    

  • Involved in photorespiration in plants and in the detoxification of alcohol in liver cells.
    

• Glyoxysomes- Found in germinating fatty seeds; site of the glyoxylate cycle, converting stored fats into carbohydrates.
  

• Sphaerosomes- Associated with the synthesis and storage of lipids in plant cells.

14. Enzymes and the chemistry inside the cell

14.1 What an enzyme is, why it is called a biocatalyst, and why almost all of them are proteins

• Biocatalyst: Produced by living organisms to speed up reactions without being consumed.

• Lowers activation energy so metabolic reactions occur rapidly at body temperature.

• Chemically, almost all enzymes are proteins made of long amino acid chains. (67th BPSC Re-Exam)

14.2 Substrate, active site, and models of enzyme action

Mechanism of Action

• Substrate: Reactant molecule acted upon by an enzyme.

• Active Site: Specific enzyme region where substrate binds to form temporary enzyme-substrate complex.

Models of Enzyme Action

14.3 Temperature and pH: factors affecting enzyme activity

Temperature Effects

• Optimum Temperature: 37 °C (98.6 °F) for most human enzymes.

• Cold Temperatures: Temporarily deactivate enzyme activity.

• High Temperatures: Permanently alter protein structure causing denaturation.

Optimum pH for Digestive Enzymes

Extreme pH changes break ionic and hydrogen bonds, permanently altering active site shape and causing denaturation.

14.4 Ribozymes and the RNA exception

Discovery of Non-Protein Catalysts

1980s: Thomas Cech and Sidney Altman discover catalytic RNA molecules called ribozymes.

Ribozyme Functions

• Composed of RNA rather than amino acids or proteins.

• Catalyze joining of amino acids during protein synthesis in ribosomes.
  

15. The Cell Cycle

• The cell cycle is the series of steps a cell goes through to grow, copy its DNA, and divide into two new cells (daughter cells).
  

• It has two broad phases:

  • Interphase: Cell grows and prepare for division.

  • M phase: Cell divides

    

The eukaryotic cell cycle. Interphase (G₁, S and G₂) occupies more than 95 per cent of the cycle; the M phase lasts less than an hour in a typical human cell. Cells that stop dividing leave the cycle at G₁ and enter the quiescent G₀ stage.

15.1 Phases

In S phase, the amount of DNA doubles (2C to 4C), but the total chromosome count stays 2n.

• Points to note:

  • A typical human cell cycle lasts about 24 hours, of which interphase occupies more than 95 per cent; interphase is therefore not a "resting phase" but a period of intense preparatory activity.

  • In yeast the cycle is completed in about 90 minutes.

15.2 The G₀ or quiescent stage

• Some cells stop dividing and leave the cell cycle after G1. These cells are still metabolically active, but they do not normally divide.

• Heart cells → usually permanently in G0

• Nerve cells → usually permanently in G0

• Liver cells → can return to the cell cycle when needed

• G0 = Cell is alive and working, but not dividing.

15.3 Regulation of the cell cycle

• The cell cycle is controlled by proteins called:

  • Cyclins

  • CDKs (Cyclin-dependent kinases)
    

• Think of them as the control system/traffic lights of the cell cycle.
  

• A CDK is inactive on its own and becomes active only when bound to its cyclin; the concentration of each cyclin rises and falls at a specific point in the cycle.
  

15.4 Checkpoints

• Checkpoints make sure everything is correct before the cell moves to the next stage.

1. G1/S checkpoint

• Is the cell big enough?

• Are there enough nutrients?

• Is the DNA undamaged?

2. G2/M checkpoint

• Has DNA been copied correctly?
  

3. M checkpoint (spindle checkpoint)

• Are all chromosomes properly attached to spindle fibres?
  

Why are checkpoints important?

They prevent cells with serious problems from dividing.

Cancer: If these controls fail because of mutations in genes such as p53, cells may divide uncontrollably, which can lead to cancer.

REMEMBER:

Cell Cycle = Grow → Copy DNA → Prepare → Divide

Phases:
G1 = Grow
S = DNA Synthesis
G2 = Prepare
M = Divide
G0 = Not dividing

Checkpoints = Safety checks

Checkpoint failure → Uncontrolled cell division → Cancer

16. Mitosis

• Produce two genetically identical diploid (2n) daughter cells.

• Also called equational division, because the daughter cells receive the same number of chromosomes as the parent.

• It occurs in somatic cells (and in the diploid cells of plants, and in haploid cells of some organisms).

• The division occurs in phases:

  • karyokinesis (nuclear division) followed by

  • cytokinesis (cytoplasmic division).

16.1 Karyokinesis (Nuclear division)

16.2 Cytokinesis (Cytoplasmic division)

• Cytokinesis means division of the cytoplasm after the nucleus has divided.
  

• In an animal cell:

  • A cleavage furrow (groove) appears in the cell membrane.

  • The furrow becomes deeper and deeper. It finally divides the cell into two daughter cells.

  • The furrow is made by a contractile ring of actin and myosin.

  • Division happens from outside → inside

• In a plant cell:

  • The wall makes furrowing impossible.
    Instead:

  • A cell plate forms at the centre of the cell.

  • It grows outwards until it reaches the existing cell walls - that is, centrifugally.

  • The cell plate becomes the middle lamella between the two daughter cells.

  • Plant cell = Cell plate = Centre → Outside

16.3 Significance of mitosis

• Produces daughter cells that are genetically identical to the parent cell - the basis of growth.

• Maintains the same chromosome number generation after generation in somatic tissue.

• Restores the nucleo-cytoplasmic ratio, which becomes disturbed as the cell grows.

• Enables repair and replacement of worn-out cells - epidermis, gut lining, blood cells.

• In plants, permits continuous growth throughout life through meristematic tissue.

• The basis of asexual reproduction and of vegetative propagation.

17. Meiosis

• A Meiosis is a special type of cell division that produces sex cells (gametes) such as sperm and eggs.

• The main purpose is to reduce the chromosome number by half.

The most important idea:

• 1 diploid cell (2n) → 4 haploid cells (n)

• There are 2 divisions: Meiosis I and Meiosis II.

• But DNA is copied only once, before Meiosis I.

17.1 Meiosis I (= Reduction division)

• Meiosis I is called the reduction division because the chromosome number is reduced by half.

Prophase I: the longest and most complex stage, divided into five sub-stages

Leptotene → Zygotene → Pachytene → Diplotene → Diakinesis


The important event in Prophase I is that homologous chromosomes pair up and exchange genetic material through crossing over.

The remaining stages of meiosis I

• Metaphase I: Homologous pairs in the middle

• Anaphase I: Homologues separate, sisters stay together.

• Telophase I: 2 cells formed

• Interkinesis: This is the short period between Meiosis I and Meiosis II, there is no replication of DNA (DNA was already copied before Meiosis I).

17.2 Meiosis II (= Equational division)

• Similar to a normal mitosis and is equational.

• Prophase II: the nuclear membrane disappears again; the chromosomes become compact.

• Metaphase II: chromosomes align at the equator; spindle fibres attach to the kinetochores of the sister chromatids.

• Anaphase II: the centromeres split and the sister chromatids separate, moving to opposite poles.

• Telophase II: nuclear envelopes reform, chromosomes decondense, cytokinesis follows, producing four haploid daughter cells in a tetrad.

  

Outcome of mitosis and meiosis from a diploid parent cell (2n = 4). Mitosis yields two genetically identical diploid cells; meiosis, through one round of DNA replication followed by two divisions, yields four genetically distinct haploid cells.

17.3 Significance of meiosis

• Maintains the chromosome number of a species across generations: gametes are haploid, so fertilisation restores the diploid number.

• Introduces genetic variation through crossing over in pachytene and the independent assortment of maternal and paternal chromosomes at metaphase I.

• This variation is the raw material of evolution and of natural selection.

• Essential for sexual reproduction and gamete formation.
  

18. Mitosis and Meiosis Compared

Where each happens in the body, and the chromosome count after each

Body Location & Fertilization

• Mitosis location: Somatic cells (skin, liver, bone) for growth, repair, and asexual reproduction.

• Meiosis location: Germ cells (testes, ovaries, anthers, ovules) for gamete production.

• Fertilization: Haploid sperm (23) fuses with haploid egg (23) to restore 46 chromosomes in zygote.

19. Applied Notes

• Cancer:

  • Arises from a failure of cell-cycle control: uncontrolled cell division (mitosis) and may spread by metastasis.

  • In tumour suppressor genes such as p53, the "guardian of the genome", are typically involved.
    

• Apoptosis: Programmed cell death that removes unwanted/damaged cells.
  

• Necrosis: Abnormal/pathological cell death.
  

• Lysosomal storage disorders result from the deficiency of a single lysosomal enzyme, for example Tay-Sachs disease, Gaucher's disease and Pompe's disease.
  

• Mitochondrial inheritance is maternal, i.e. Mitochondrial DNA is mainly inherited from the mother.
  

• Non-disjunction: Failure of chromosomes to separate → abnormal chromosome number, giving rise to conditions such as Down syndrome (trisomy 21), Turner syndrome (45, XO) and Klinefelter syndrome (47, XXY).
  

• Antibiotics and the 70S ribosome: Bacteria have 70S ribosomes; drugs like tetracycline and streptomycin inhibit bacterial protein synthesis.
  

• Colchicine: Blocks tubulin/spindle formation, causing metaphase arrest; used in karyotyping and plant breeding.

20. Glossary

21. Rapid Revision: Facts and Numbers

• Cell: The fundamental structural and functional unit of life discovered by Robert Hooke (1665) in cork, while Anton van Leeuwenhoek (1674) first observed living cells.

• Cell Theory: Formulated by Schleiden (1838) and Schwann (1839), and completed by Rudolf Virchow (1855) with the principle *Omnis cellula e cellula* (cells arise from pre-existing cells).

• Cell Membrane: A selectively permeable membrane described by Singer and Nicolson's Fluid Mosaic Model (1972), composed primarily of proteins and lipids.

• Cell Wall: Absent in animals, but present in plants (cellulose), fungi (chitin), and bacteria (peptidoglycan).

• Nucleus: The principal control centre discovered by Robert Brown (1831), containing chromatin (DNA and histones) and the nucleolus for rRNA synthesis.

• Mitochondria: Known as the powerhouse of the cell, generating energy as ATP through aerobic respiration across inner membrane folds called cristae.

• Chloroplast: A double-membrane plastid containing chlorophyll in thylakoid grana and stroma that carries out photosynthesis.

• Semi-autonomous Organelles: Mitochondria and chloroplasts replicate independently because they contain their own circular DNA, RNA, and 70S ribosomes.

• Organelles: Includes ribosomes (protein synthesis), Rough ER (protein processing), Smooth ER (lipid synthesis), Golgi body (packaging), lysosomes (hydrolytic digestion), and vacuoles (storage).

• Enzymes: Biological catalysts that lower activation energy; almost all enzymes are proteins, except catalytic RNA molecules called ribozymes.

• Mitosis: Equational division occurring in somatic cells, producing two identical diploid daughter cells for growth and repair.

• Meiosis: Reductional division occurring in germ cells, producing four haploid daughter cells with genetic variation introduced by crossing over in pachytene of Prophase I.