Cell: Structure and Functions Notes

Biology: The Study of Life

  • Biology is the study of living organisms.
  • Early descriptions focused on the diversity of life forms.
  • Cell theory highlights the unity of life based on cellular organization.

Cell Theory and Living Phenomena

  • Cell theory poses a mystery regarding living phenomena (physiological and behavioral processes).
  • Integrity of cellular organization is essential for demonstrating or observing living phenomena.
  • Physico-chemical approach using cell-free systems helps investigate these processes.
  • This approach describes processes in molecular terms.
  • Analysis of living tissues reveals elements and compounds present.
  • Questions arise about the function of these compounds within the cell.
  • How do these compounds carry out physiological processes (digestion, excretion, memory, defense, recognition)?
  • What is the molecular basis of physiological processes?
  • This approach can explain abnormal processes during disease.
  • This physico-chemical approach is termed ‘Reductionist Biology’.
  • Applies physics and chemistry concepts to understand biology.

G.N. Ramachandran

  • G.N. Ramachandran was a prominent figure in protein structure.
  • Founder of the ‘Madras school’ of conformational analysis of biopolymers.
  • Discovered the triple helical structure of collagen (published in Nature, 1954).
  • Developed the ‘Ramachandran plot’ for analyzing allowed protein conformations.
  • Born on October 8, 1922, near Cochin, India.
  • His father was a mathematics professor who influenced his interest in mathematics.
  • Graduated top of his class in B.Sc. (Honors) Physics from the University of Madras in 1942.
  • Received a Ph.D. from Cambridge University in 1949.
  • Met Linus Pauling at Cambridge and was influenced by his work on α-helix and β-sheet structures.
  • Passed away on April 7, 2001, at the age of 78.

Cell: The Unit of Life

What is a Cell?

  • Living organisms are made of living and non-living things.
  • Living organisms possess a basic unit of life-the cell.
  • Organisms can be unicellular (single cell) or multicellular (many cells).
  • Unicellular organisms:
    • Can exist independently.
    • Perform essential life functions.
  • A complete cell structure is necessary for independent living.
  • The cell is the fundamental structural and functional unit of life.
  • Antonie Von Leeuwenhoek first observed and described a live cell.
  • Robert Brown discovered the nucleus.
  • Microscope and electron microscope advancements revealed cell structural details.

Cell Theory

  • In 1838, Matthias Schleiden (botanist) observed that plants are composed of different kinds of cells forming plant tissues.
  • In 1839, Theodore Schwann (zoologist) reported that animal cells have a thin outer layer (plasma membrane).
  • Schwann concluded that animal and plant bodies are composed of cells and cell products.
  • Schleiden and Schwann formulated the cell theory.
  • Rudolf Virchow (1855) explained that cells divide and new cells form from pre-existing cells (Omnis cellula-e cellula).
  • Virchow modified Schleiden and Schwann's hypothesis to give the cell theory a final shape.
  • Modern Cell Theory:
    • All living organisms are composed of cells and cell products.
    • All cells arise from pre-existing cells.

Overview of the Cell

  • Onion cells (plant cells) have a distinct cell wall and cell membrane.
  • Human cheek cells have an outer membrane.
  • Inside each cell is a nucleus containing chromosomes and DNA.
  • Eukaryotic Cells: Have membrane-bound Nuclei
  • Prokaryotic Cells: Lack a membrane-bound nucleus.
  • Cytoplasm: A semi-fluid matrix occupies the cell volume.
    • The main arena of cellular activities, where chemical reactions occur.
  • Eukaryotic cells contain membrane-bound organelles (endoplasmic reticulum, Golgi complex, lysosomes, mitochondria, microbodies, vacuoles).
  • Prokaryotic cells lack membrane-bound organelles.
  • Ribosomes: Non-membrane bound organelles found in all cells (eukaryotic and prokaryotic).
    • Found in the cytoplasm, chloroplasts (plants), mitochondria, and rough ER.
  • Animal cells contain centrioles (non-membrane bound) which aid in cell division.
  • Cells vary in size, shape, and activity.
  • Mycoplasmas (smallest cells): 0.3 \mu m in length.
  • Bacteria: 3-5 \mu m.
  • Largest isolated single cell: Ostrich egg.
  • Human red blood cells: 7.0 \mu m in diameter.
  • Nerve cells: Some of the longest cells.
  • Cell shapes: Disc-like, polygonal, columnar, cuboid, thread-like, irregular.
  • Cell shape varies with function.

Prokaryotic Cells

  • Represented by bacteria, blue-green algae, mycoplasma, and PPLO (Pleuro Pneumonia Like Organisms).
  • Generally smaller and multiply more rapidly than eukaryotic cells.
  • Vary in shape and size.
  • Four basic bacterial shapes: bacillus (rod-like), coccus (spherical), vibrio (comma-shaped), spirillum (spiral).
  • Prokaryotic cell organization is fundamentally similar despite diverse shapes and functions.
  • Cell Wall: All prokaryotes have a cell wall surrounding the cell membrane except mycoplasma.
  • Cytoplasm: Semi-fluid matrix filling the cell.
  • Nucleus: No well-defined nucleus; genetic material is naked (not enveloped by a nuclear membrane).
  • Genomic DNA: Single chromosome/circular DNA.
  • Plasmids: Small circular DNA outside the genomic DNA.
    • Confer unique phenotypic characters (e.g., antibiotic resistance).
  • Nuclear membrane: Found in eukaryotes, absent in prokaryotes.
  • Organelles: No organelles like eukaryotes, except ribosomes.
  • Inclusions: Unique to prokaryotes.
  • Mesosome: Specialised differentiated form of cell membrane characteristic of prokaryotes.
    • Infoldings of the cell membrane.

Cell Envelope and Modifications

  • Most prokaryotic cells (especially bacteria) have a chemically complex cell envelope.
  • Cell envelope: Tightly bound three-layered structure:
    • Outermost glycocalyx.
    • Cell wall.
    • Plasma membrane.
  • Each layer has a distinct function but acts as a single protective unit.
  • Gram Staining: Bacteria classified into two groups based on cell envelopes and staining:
    • Gram-positive: Take up the gram stain.
    • Gram-negative: Do not take up the gram stain.
  • Glycocalyx: Varies in composition and thickness among bacteria.
    • Slime layer: Loose sheath in some.
    • Capsule: Thick and tough in others.
  • Cell wall:
    • Determines cell shape.
    • Provides structural support to prevent bursting or collapsing.
  • Plasma membrane:
    • Selectively permeable.
    • Interacts with the outside world.
    • Structurally similar to eukaryotic membranes.
  • Mesosome:
    • Formed by extensions of the plasma membrane into the cell.
    • Forms: Vesicles, tubules, and lamellae.
    • Functions: Cell wall formation, DNA replication, distribution to daughter cells, respiration, secretion, increasing surface area, and enzymatic content.
  • Chromatophores: Membranous extensions into the cytoplasm found in some prokaryotes like cyanobacteria, contain pigments.
  • Motility: Bacterial cells may be motile or non-motile.
  • Flagella: Thin filamentous extensions from the cell wall if motile.
    • Vary in number and arrangement.
    • Composed of three parts: filament, hook, and basal body.
    • Filament: Longest portion, extends from the cell surface.
  • Pili and Fimbriae: Surface structures, do not play a role in motility.
    • Pili: Elongated tubular structures made of special protein.
    • Fimbriae: Small bristle-like fibers sprouting out of the cell.
      • Help attach bacteria to rocks in streams and host tissues.

Ribosomes and Inclusion Bodies

  • Ribosomes in prokaryotes are associated with the plasma membrane.
  • Size: Approximately 15 nm by 20 nm.
  • Subunits: Made of two subunits – 50S and 30S, forming 70S prokaryotic ribosomes.
  • Function: Site of protein synthesis.
  • Polyribosomes or Polysomes: Several ribosomes attach to a single mRNA.
    • Ribosomes translate mRNA into proteins.
  • Inclusion bodies:
    • Reserve material stored in the cytoplasm.
    • Not bound by any membrane system.
    • Examples: Phosphate granules, cyanophycean granules, and glycogen granules.
  • Gas vacuoles: Found in blue green, purple, and green photosynthetic bacteria.

Eukaryotic Cells

  • Include all protists, plants, animals, and fungi.
  • Extensive compartmentalization of cytoplasm through membrane-bound organelles.
  • Organized nucleus with a nuclear envelope.
  • Complex locomotory and cytoskeletal structures.
  • Genetic material organized into chromosomes.
  • Not identical: Plant and animal cells differ; plant cells have cell walls, plastids, and a large central vacuole, which are absent in animal cells.
  • Animal cells have centrioles, absent in most plant cells.

Cell Membrane

  • Detailed structure studied after the advent of the electron microscope in the 1950s.
  • Chemical studies (especially on human red blood cells) enabled deducing the plasma membrane structure.
  • Mainly composed of lipids and proteins.
  • Lipids: Phospholipids are arranged in a bilayer.
    • Polar heads face outward, hydrophobic tails face inward.
      • Ensures nonpolar tails of saturated hydrocarbons are protected from the aqueous environment.
  • Contains cholesterol.
  • Contains protein and carbohydrate.
  • Protein and Lipid Ratio:
    • Varies in different cell types.
    • Erythrocyte membrane: Approximately 52% protein and 40% lipids.
  • Membrane Proteins:
    • Integral: Partially or totally buried in the membrane.
    • Peripheral: Lie on the surface of the membrane.

Fluid Mosaic Model

  • Proposed by Singer and Nicolson (1972).
  • Lipid quasi-fluid nature enables lateral movement of proteins within the bilayer.
  • Fluidity: Ability to move within the membrane.
  • Importance of Fluidity: Cell growth, formation of intercellular junctions, secretion, endocytosis, cell division, etc.
  • Function: transport of molecules across it.
  • Selectively permeable.

Passive Transport

  • Many molecules move briefly without energy requirement.
  • Neutral solutes move by simple diffusion along the concentration gradient (higher to lower).
  • Osmosis: Water movement by diffusion (higher to lower concentration).
  • Since polar molecules cannot pass through the nonpolar lipid bilayer, they require a carrier protein of the membrane to facilitate their transport across the membrane.

Active Transport

  • A few ions or molecules are transported against concentration gradient (lower to higher concentration).
  • Energy-dependent process (ATP is utilised).
  • Example: Na^+/K^+ Pump.

Cell Wall

  • Non-living rigid structure forming an outer covering for the plasma membrane in fungi and plants.
  • Functions: Gives shape, protects from mechanical damage and infection, aids cell-to-cell interaction, provides a barrier to undesirable macromolecules.
  • Composition:
    • Algae: Cellulose, galactans, mannans, and minerals like calcium carbonate.
    • Plants: Cellulose, hemicellulose, pectins, and proteins.
  • Primary Wall:
    • In young plant cells.
    • Capable of growth.
  • Secondary Wall:
    • Formed on the inner side of the cell as it matures.
  • Middle Lamella:
    • Layer mainly of calcium pectate.
    • Holds neighboring cells together.
  • Plasmodesmata: Traverses the cell wall and middle lamellae, connecting the cytoplasm of neighboring cells.

Endomembrane System

  • Many membranous organelles are considered together due to coordinated functions.
  • Includes: Endoplasmic reticulum (ER), Golgi complex, lysosomes, and vacuoles.
  • Does not include: Mitochondria, chloroplasts, and peroxisomes (functions not coordinated with the above components).
Endoplasmic Reticulum (ER)
  • Network of tiny tubular structures scattered in the cytoplasm of eukaryotic cells.
  • Divides the intracellular space into two compartments: luminal (inside ER) and extra-luminal (cytoplasm).
  • Rough Endoplasmic Reticulum (RER):
    • Has ribosomes attached to the outer surface.
    • Involved in protein synthesis and secretion.
    • Continuous with the outer membrane of the nucleus.
  • Smooth Endoplasmic Reticulum (SER):
    • Lacks ribosomes, appears smooth.
    • Major site for lipid synthesis.
    • In animal cells, synthesizes lipid-like steroidal hormones.
Golgi Apparatus
  • Observed by Camillo Golgi (1898) as densely stained reticular structures near the nucleus.
  • Consists of flat, disc-shaped sacs or cisternae of 0.5\mum to 1.0\mum diameter.
  • Cisternae are stacked parallel to each other; varied numbers are present in a Golgi complex.
  • Cis and Trans Faces: Concentrically arranged cisternae near the nucleus with distinct convex cis (forming) face and concave trans (maturing) face.
    • The cis and trans faces of the organelle are entirely different, but interconnected.
  • Function: Principal function is packaging materials for intracellular targets or secretion.
  • Vesicle Formation: Vesicles from the ER fuse with the cis face and move toward the trans face.
  • Association with ER: The Golgi apparatus remains in close association with the endoplasmic reticulum.
  • Protein Modification: Numerous proteins synthesized by ribosomes on the endoplasmic reticulum are modified in the cisternae before release from the trans face.
  • Glycoproteins and Glycolipids: Important site of formation of glycoproteins and glycolipids.
Lysosomes
  • Membrane-bound vesicular structures formed by packaging in the Golgi apparatus.
  • Enzymes: Rich in hydrolytic enzymes (hydrolases – lipases, proteases, carbohydrases).
  • Optimal Activity: Active at acidic pH.
  • Function: Capable of digesting carbohydrates, proteins, lipids, and nucleic acids.
Vacuoles
  • Membrane-bound space in the cytoplasm.
  • Contents: Water, sap, excretory products, and other materials not useful for the cell.
  • Tonoplast: Bounded by a single membrane called the tonoplast.
  • Plant Cells: Vacuoles can occupy up to 90% of the cell volume.
  • Tonoplast Function: Facilitates the transport of ions and materials against concentration gradients into the vacuole.
  • Concentration: Significantly higher in the vacuole than in the cytoplasm.
  • Contractile Vacuole: In Amoeba, important for osmoregulation and excretion.
  • Food Vacuoles: In some cells (e.g., protists), formed by engulfing food particles.

Mitochondria

  • Not easily visible under a microscope unless specifically stained.
  • Number per cell: Variable, depending on the physiological activity of the cells.
  • Shape and Size: Considerable variability observed.
    • Typically sausage-shaped or cylindrical.
    • Diameter: 0.2-1.0 \mu m (average 0.5 \mu m).
    • Length: 1.0-4.1 \mu m.
  • Structure: Double membrane-bound:
    • Outer membrane.
    • Inner membrane (divides the lumen into two aqueous compartments: outer and inner).
  • Matrix: Inner compartment filled with a dense homogeneous substance.
  • Outer Membrane: Forms the continuous limiting boundary of the organelle.
  • Cristae:
    • Infoldings of the inner membrane towards the matrix.
    • Increase surface area.
  • Membrane Enzymes: Both membranes have specific enzymes associated with mitochondrial function.
  • Aerobic Respiration: The sites of aerobic respiration.
  • ATP Production: Produce cellular energy in the form of ATP; called ‘power houses’ of the cell.
  • Matrix Contents: Single circular DNA molecule, a few RNA molecules, ribosomes (70S), and components for protein synthesis.
  • Division: Mitochondria divide by fission.

Plastids

  • Found in all plant cells and in euglenoids.
  • Easily observed under the microscope because they are large.
  • Pigments: Bear specific pigments, imparting specific colors to plants.
  • Types:
    • Chloroplasts.
    • Chromoplasts.
    • Leucoplasts.
  • Chloroplasts:
    • Contain chlorophyll and carotenoid pigments.
    • Responsible for trapping light energy essential for photosynthesis.
  • Chromoplasts:
    • Contain fat-soluble carotenoid pigments (carotene, xanthophylls, etc.).
    • Give parts of the plant yellow, orange, or red color.
  • Leucoplasts:
    • Colorless plastids of varied shapes and sizes with stored nutrients.
    • Amyloplasts: Store carbohydrates (starch), e.g., potato.
    • Elaioplasts: Store oils and fats.
    • Aleuroplasts: Store proteins.
  • Chloroplasts in Green Plants:
    • Found in mesophyll cells of the leaves.
    • Shape: Lens-shaped, oval, spherical, discoid, or ribbon-like.
    • Variable length: 5-10 \mu m
    • Variable width: 2-4 \mu m
    • Number per cell: Varies from 1 (Chlamydomonas) to 20-40 (mesophyll cells).
  • Structure:
    • Double membrane-bound.
    • Inner membrane is less permeable.
    • Stroma: Space limited by the inner membrane.
    • Thylakoids: Organized flattened membranous sacs located in the stroma.
    • Grana (singular: granum): Stacks of thylakoids like piles of coins.
    • Stroma Lamellae: Flat membranous tubules connecting thylakoids of different grana.
    • Lumen: Space enclosed by the thylakoid membrane.
    • Stroma Contents: Enzymes for carbohydrate and protein synthesis.
    • DNA: Small, double-stranded circular DNA molecules.
    • Ribosomes.
    • Chlorophyll pigments: Present in thylakoids.
    • Ribosomes: Smaller (70S) than cytoplasmic ribosomes (80S).

Ribosomes

  • Granular structures observed under the electron microscope by George Palade (1953).
  • Composition: Ribonucleic acid (RNA) and proteins.
  • Membrane: Not surrounded by any membrane.
  • Types: Eukaryotic ribosomes are 80S; prokaryotic ribosomes are 70S.
  • Subunits: Each ribosome has two subunits (larger and smaller).
    • 80S Ribosomes: 60S and 40S subunits.
    • 70S Ribosomes: 50S and 30S subunits.
  • Svedberg's Unit (S): Stands for the sedimentation coefficient; a measure of density and size.

Cytoskeleton

  • Elaborate network of filamentous proteinaceous structures in the cytoplasm.
  • Components: Microtubules, microfilaments, and intermediate filaments.
  • Functions: Mechanical support, motility, maintenance of cell shape.

Cilia and Flagella

  • Hair-like outgrowths of the cell membrane.
  • Cilia (Singular: cilium): Small structures that work like oars, moving the cell or surrounding fluid.
  • Flagella (Singular: flagellum): Comparatively longer, responsible for cell movement.
  • Prokaryotic Bacteria: Also possess flagella, but structurally different from eukaryotic flagella.
  • Structure:
    • Covered with plasma membrane.
    • Axoneme: Core containing microtubules running parallel to the long axis.
      • 9+2 Array: Axoneme usually has nine doublets of radially arranged peripheral microtubules and a pair of centrally located microtubules.
      • Central Tubules: Connected by bridges and enclosed by a central sheath.
      • Radial Spoke: Connects central sheath to one tubule of each peripheral doublet (nine radial spokes).
      • Linkers: Peripheral doublets are interconnected by linkers.
  • Basal Bodies: Both cilium and flagellum emerge from centriole-like structures called basal bodies.

Centrosome and Centrioles

  • Centrosome: Organelle usually containing two cylindrical structures called centrioles.
  • Pericentriolar Material: Centrioles are surrounded by amorphous pericentriolar materials.
  • Arrangement: Centrioles are perpendicular to each other.
  • Structure: Cartwheel-like organisation.
    • Nine evenly spaced peripheral fibrils of tubulin protein.
    • Each peripheral fibril is a triplet.
    • Adjacent triplets are linked.
    • Hub: Central proteinaceous part in the proximal region of the centriole.
    • Radial Spokes: Connect the hub with tubules of the peripheral triplets.
      Basal Body and Spindle Fibres: Centrioles form the basal body of cilia or flagella and spindle fibres that give rise to the spindle apparatus during cell division in animal cells.

Nucleus

  • Described by Robert Brown (1831).
  • Chromatin: Nuclear material stained by basic dyes, named by Flemming.
  • Interphase Nucleus (non-dividing cell):
    • Contains nucleoprotein fibres (chromatin), nuclear matrix, and nucleoli (singular: nucleolus).
  • Nuclear Envelope: Two parallel membranes with a perinuclear space (10-50 nm) forming a barrier between the nucleus and cytoplasm.
  • Outer Membrane: Continuous with the endoplasmic reticulum and bears ribosomes.
    Nuclear Pores: Interruptions in the nuclear envelope formed by the fusion of the two membranes; passages for RNA and protein movement between the nucleus and cytoplasm.
  • Number: Usually one nucleus per cell, but variations exist.
  • Mature Cells: Some lack a nucleus (e.g., erythrocytes of mammals, sieve tube cells of vascular plants).
  • Nuclear Matrix or Nucleoplasm: Contains nucleolus and chromatin.
  • Nucleoli: Spherical structures within the nucleoplasm.
    • Site for active ribosomal RNA synthesis.
    • Larger and more numerous in cells actively carrying out protein synthesis.

Chromosomes

  • During cell division, structured chromosomes appear instead of the nucleus.
  • Composition: DNA, basic proteins (histones), non-histone proteins, and RNA.
  • Human Cell: Approximately two meters of DNA thread distributed among 46 chromosomes (23 pairs).
  • Structure (visible only in dividing cells):
    • Primary Constriction or Centromere: Essential constriction on the chromosome.
    • Kinetochores: Disc-shaped structures on the sides of the centromere.
    • Centromere: Holds two chromatids of a chromosome.
  • Chromosome Classification (based on centromere position):
    • Metacentric: Middle centromere forming two equal arms.
    • 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

  • Non-staining secondary constrictions at a constant location on some chromosomes, giving the appearance of a small fragment.

Microbodies

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