Chapter Notes

What is a Cell?

All living things, from the smallest bacteria to the largest animals, are made of cells. The cell is the fundamental structural and functional unit of all living organisms. This means it's the basic building block of life and the smallest unit capable of performing all the essential functions of life.

• Unicellular Organisms: These are living things made of just a single cell, like bacteria or amoeba. A single cell can exist independently and carry out all necessary life processes.
• Multicellular Organisms: These are complex organisms, like plants and humans, composed of many cells that work together.

Key Discoveries

• Antonie Von Leeuwenhoek: The first person to see and describe a live cell.
• Robert Brown: Later discovered the nucleus within the cell.
• The Electron Microscope: The invention and improvement of microscopes, especially the electron microscope, allowed scientists to see the detailed structures inside a cell.

Cell Theory

The Cell Theory is a foundational principle in biology that helps us understand the unity among all diverse life forms. It was developed through the work of several scientists.

• Matthias Schleiden (1838): A German botanist who observed that all plants are composed of different kinds of cells.
• Theodore Schwann (1839): A German zoologist who studied animal cells and noted they have a thin outer layer, now known as the plasma membrane. He also observed that plant cells have a unique feature: a cell wall. Schwann proposed that the bodies of both animals and plants are made of cells and their products.
• Rudolf Virchow (1855): He explained that new cells are formed from the division of pre-existing cells. His famous statement was Omnis cellula-e cellula.

Schleiden and Schwann formulated the initial cell theory, and Virchow's contribution gave it its final shape.

The modern Cell Theory states:

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 can be broadly categorized into two main types based on their internal structure: prokaryotic and eukaryotic.

• Eukaryotic Cells: These cells have a membrane-bound nucleus, which contains the genetic material (DNA) organized into chromosomes. They also have other distinct, membrane-bound structures called organelles (like mitochondria and endoplasmic reticulum). Plant and animal cells are eukaryotic.
• Prokaryotic Cells: These cells lack a membrane-bound nucleus. Their genetic material is located in the cytoplasm. Bacteria are prokaryotic.

Common Features of Cells

• Cytoplasm: A semi-fluid matrix that fills the cell's volume. It's the main arena for cellular activities and chemical reactions that keep the cell alive.
• Ribosomes: These are non-membrane-bound organelles found in all cells (both prokaryotic and eukaryotic). They are responsible for making proteins.

Differences Between Plant and Animal Cells

• Plant cells have a rigid cell wall outside the cell membrane, plastids (like chloroplasts for photosynthesis), and a large central vacuole.
• Animal cells lack these structures but have centrioles, which are involved in cell division and are absent in almost all plant cells.

Diversity in Cells

Cells show great variety in size, shape, and function.

• Size: Mycoplasmas are the smallest cells (only $0.3 \mu \text{m}$ long), while the largest isolated single cell is an ostrich egg. Human red blood cells are about $7.0 \mu \text{m}$ in diameter.
• Shape: Cells can be disc-like (red blood cells), polygonal, columnar, thread-like (nerve cells), or irregular. The shape of a cell is often related to the function it performs.

Prokaryotic Cells

Prokaryotic cells are simpler and generally smaller than eukaryotic cells. They also multiply much more rapidly.

• Examples: Bacteria, blue-green algae, mycoplasma, and PPLO (Pleuro Pneumonia Like Organisms).
• Basic Shapes of Bacteria:
  • Bacillus: Rod-like
  • Coccus: Spherical
  • Vibrio: Comma-shaped
  • Spirillum: Spiral

Key Features of Prokaryotic Cells

• Cell Wall: Surrounds the cell membrane in most prokaryotes (exception: mycoplasma).
• No Well-defined Nucleus: The genetic material is not enclosed by a nuclear membrane. It is often a single, circular DNA molecule found in a region of the cytoplasm.
• Plasmids: Many bacteria have small, circular DNA molecules called plasmids in addition to their main genomic DNA. Plasmids can carry genes for unique traits, such as resistance to antibiotics.
• No Membrane-Bound Organelles: Prokaryotes lack organelles like mitochondria or Golgi apparatus. Their only organelles are ribosomes.
• Mesosome: A specialized structure formed by infoldings of the plasma membrane. This is a characteristic feature of prokaryotes.

Cell Envelope and its Modifications

Most prokaryotic cells have a chemically complex cell envelope consisting of three tightly bound layers that act as a single protective unit.

1. Glycocalyx (Outermost Layer): Varies in thickness and composition. It can be a loose sheath called the slime layer or a thick, tough layer called the capsule.
2. Cell Wall: Determines the cell's shape and provides structural support, preventing the cell from bursting.
3. Plasma Membrane (Innermost Layer): It is selectively permeable, controlling what enters and leaves the cell.

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

Membrane Structures and Appendages

• Mesosome: Formed by extensions of the plasma membrane into the cell as vesicles, tubules, and lamellae.
  • Functions: Helps in cell wall formation, DNA replication, distribution to daughter cells, respiration, and secretion processes.
• Chromatophores: In some prokaryotes like cyanobacteria, these are membranous extensions containing pigments for photosynthesis.
• Flagella: Thin, filamentous extensions from the cell wall that enable movement (motility). A bacterial flagellum has three parts: filament, hook, and basal body.
• Pili and Fimbriae: Surface structures that do not play a role in motility.
  • Pili: Elongated tubular structures made of a special protein.
  • Fimbriae: Small, bristle-like fibers that help bacteria attach to surfaces like rocks or host tissues.

Ribosomes and Inclusion Bodies

• Ribosomes: In prokaryotes, ribosomes are associated with the plasma membrane.
  • They are about 15 nm by 20 nm in size.
  • They are 70S ribosomes, made of a 50S and a 30S subunit.
  • They are the site of protein synthesis. Multiple ribosomes can attach to a single mRNA to form a polysome, which translates the mRNA into proteins.
• Inclusion Bodies: These are storage bodies for reserve materials found free in the cytoplasm. They are not bound by any membrane.
  • Examples: Phosphate granules, cyanophycean granules, glycogen granules, and gas vacuoles (found in photosynthetic bacteria).

Eukaryotic Cells

Eukaryotes include all protists, plants, animals, and fungi. Their cells are characterized by extensive compartmentalization of the cytoplasm due to the presence of membrane-bound organelles.

Key Features of Eukaryotic Cells

• Organized Nucleus: The genetic material (DNA) is enclosed within a nuclear envelope.
• Membrane-Bound Organelles: Cytoplasm contains various organelles like the endoplasmic reticulum, Golgi complex, lysosomes, mitochondria, and vacuoles.
• Cytoskeleton: A complex network of protein filaments that provides structural support and aids in movement.
• Chromosomes: The genetic material is organized into linear structures called chromosomes.

Cell Membrane

The detailed structure of the plasma membrane was revealed by the electron microscope. Chemical studies, especially on human red blood cells (RBCs), showed it's composed mainly of lipids and proteins.

• Composition:
  • Lipids: The major lipids are phospholipids, arranged in a bilayer. The polar heads face the outer, aqueous sides, while the hydrophobic tails face the inner part, away from water. The membrane also contains cholesterol.
  • Proteins: The ratio of protein to lipid varies. In human RBCs, it's about 52% protein and 40% lipids. Proteins can be:
    • Peripheral proteins: Lie on the surface of the membrane.
    • Integral proteins: Partially or totally buried within the membrane.

Fluid Mosaic Model

Proposed by Singer and Nicolson (1972), this is the most widely accepted model for the cell membrane.

• It describes the membrane as having a "quasi-fluid" nature, meaning the lipids can move, which allows proteins to move laterally within the bilayer.
• This fluidity is crucial for functions like cell growth, secretion, endocytosis, and cell division.

Transport Across the Membrane

The plasma membrane is selectively permeable.

• Passive Transport: Movement of molecules across the membrane without any energy requirement.
  • Simple Diffusion: Neutral solutes move from a higher concentration to a lower concentration.
  • Osmosis: The movement of water by diffusion across the membrane.
• Facilitated Transport: Polar molecules cannot pass through the lipid bilayer directly. They require a carrier protein in the membrane to help them cross.
• Active Transport: Movement of ions or molecules against their concentration gradient (from lower to higher concentration). This process requires energy, which is supplied by ATP.
  • Example: The $\text{Na}^+ / \text{K}^+$ Pump.

Cell Wall

A non-living, rigid structure found outside the plasma membrane of fungi and plant cells.

• Functions:
  • Gives shape to the cell.
  • Protects the cell from mechanical damage and infection.
  • Helps in cell-to-cell interaction.
  • Provides a barrier to undesirable large molecules.
• Composition:
  • Algae: Cellulose, galactans, mannans, and minerals like calcium carbonate.
  • Other Plants: Cellulose, hemicellulose, pectins, and proteins.
• Structure:
  • Primary wall: In a young plant cell, this wall is capable of growth.
  • Secondary wall: Forms on the inner side of the cell as it matures.
  • Middle lamella: A layer made mainly of calcium pectate that glues neighboring cells together.
  • Plasmodesmata: Channels that traverse the cell wall and middle lamella, connecting the cytoplasm of adjacent cells.

Endomembrane System

This is a group of membranous organelles whose functions are coordinated.

• Includes: Endoplasmic reticulum (ER), Golgi complex, lysosomes, and vacuoles.
• Not Included: Mitochondria, chloroplasts, and peroxisomes are not part of this system because their functions are not coordinated with the others.

The Endoplasmic Reticulum (ER)

A network of tiny tubular structures scattered in the cytoplasm. The ER divides the intracellular space into two compartments: luminal (inside the ER) and extra-luminal (cytoplasm).

• Rough Endoplasmic Reticulum (RER): Has ribosomes attached to its outer surface. RER is extensive in cells actively involved in protein synthesis and secretion. It is continuous with the outer membrane of the nucleus.
• Smooth Endoplasmic Reticulum (SER): Appears smooth because it lacks ribosomes. SER is the major site for synthesis of lipids. In animal cells, it synthesizes lipid-like steroidal hormones.

Golgi Apparatus

First observed by Camillo Golgi (1898), this organelle consists of flat, disc-shaped sacs called cisternae stacked parallel to each other.

• The cisternae are arranged with a distinct convex cis face (forming face) and a concave trans face (maturing face).
• Function: The principal role is packaging materials to be delivered to other intracellular targets or secreted outside the cell.
  • Vesicles from the ER fuse with the cis face and move towards the trans face.
  • Proteins from the RER are modified in the cisternae before being released from the trans face.
  • It is an important site for the formation of glycoproteins and glycolipids.

Lysosomes

These are membrane-bound vesicular structures formed by the packaging process in the Golgi apparatus.

• They are rich in hydrolytic enzymes (lipases, proteases, carbohydrases) that are active at an acidic pH.
• These enzymes are capable of digesting carbohydrates, proteins, lipids, and nucleic acids.

Vacuoles

A membrane-bound space in the cytoplasm, enclosed by a single membrane called the tonoplast.

• It contains water, sap, excretory products, and other materials not useful to the cell.
• In Plant Cells: The vacuole can occupy up to 90% of the cell's volume. The tonoplast transports ions and other materials into the vacuole against their concentration gradient.
• In Amoeba: The contractile vacuole is important for osmoregulation and excretion.
• In Protists: Food vacuoles are formed by engulfing food particles.

Mitochondria

Mitochondria (singular: mitochondrion) are typically sausage-shaped or cylindrical organelles.

• Structure:
  • It is a double membrane-bound structure.
  • The outer membrane is a continuous boundary.
  • The inner membrane is folded into numerous infoldings called cristae, which increase the surface area.
  • The inner compartment is filled with a dense substance called the matrix.
• Function: Mitochondria are the sites of aerobic respiration. They produce cellular energy in the form of ATP, earning them the name 'power houses' of the cell.
• Semiautonomous Nature: The matrix contains a single circular DNA molecule, RNA molecules, and 70S ribosomes. Mitochondria can synthesize some of their own proteins and divide by fission.

Plastids

Plastids are large organelles found in all plant cells and in euglenoides. They contain specific pigments, giving color to different parts of the plant.

• Types of Plastids:
  1. Chloroplasts: Contain chlorophyll and carotenoid pigments. They trap light energy for photosynthesis.
  2. Chromoplasts: Contain fat-soluble carotenoid pigments like carotene and xanthophylls. They give plants yellow, orange, or red colors.
  3. Leucoplasts: Colorless plastids that store nutrients.
     • Amyloplasts: Store starch (e.g., in potato).
     • Elaioplasts: Store oils and fats.
     • Aleuroplasts: Store proteins.

Structure of Chloroplasts

• Most are found in the mesophyll cells of leaves. They are lens-shaped, oval, or spherical.
• Like mitochondria, they are double membrane-bound. The inner membrane is less permeable.
• Stroma: The space enclosed by the inner membrane. It contains enzymes for synthesizing carbohydrates and proteins.
• Thylakoids: Organized, flattened membranous sacs within the stroma. Chlorophyll pigments are located in the thylakoids.
• Grana (singular: granum): Stacks of thylakoids, resembling piles of coins.
• Stroma Lamellae: Flat tubules connecting the thylakoids of different grana.
• Semiautonomous Nature: The stroma also contains small, double-stranded circular DNA and 70S ribosomes.

Ribosomes

Ribosomes are granular, non-membranous structures composed of ribonucleic acid (RNA) and proteins. They were first observed by George Palade (1953).

• Types of Ribosomes:
  • Eukaryotic ribosomes are 80S. They consist of a 60S and a 40S subunit.
  • Prokaryotic ribosomes are 70S. They consist of a 50S and a 30S subunit.
• 'S': Stands for Svedberg's Unit, a measure of sedimentation coefficient, which reflects density and size.

Cytoskeleton

An elaborate network of filamentous proteinaceous structures in the cytoplasm.

• Components: Microtubules, microfilaments, and intermediate filaments.
• Functions:
  • Mechanical support.
  • Motility (movement).
  • Maintenance of cell shape.

Cilia and Flagella

Cilia (singular: cilium) and flagella (singular: flagellum) are 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.

• Structure: Both are covered with plasma membrane. Their core, the axoneme, contains microtubules running parallel to the long axis.
  • The arrangement of microtubules is called the 9+2 array: nine doublets of peripheral microtubules and a pair of central microtubules.
  • The central tubules are connected by bridges and enclosed by a central sheath.
  • Each peripheral doublet is connected to the central sheath by a radial spoke. There are nine radial spokes.
• Basal Bodies: Both cilia and flagella emerge from a centriole-like structure called the basal body.

Centrosome and Centrioles

The centrosome is an organelle found in animal cells, usually containing two cylindrical structures called centrioles.

• The centrioles lie perpendicular to each other and are surrounded by amorphous pericentriolar materials.
• Structure: Each centriole has an organization like a cartwheel.
  • It is made of nine evenly spaced peripheral fibrils of tubulin protein. Each fibril is a triplet.
  • The central part is a proteinaceous hub, connected to the peripheral triplets by radial spokes.
• Functions:
  • Centrioles form the basal bodies of cilia and flagella.
  • They form the spindle fibers that create the spindle apparatus during cell division in animal cells.

Nucleus

The nucleus was first described by Robert Brown in 1831. It contains the cell's genetic material and controls its activities.

• Nuclear Envelope: A double membrane that separates the nucleus from the cytoplasm.
  • The space between the two membranes is the perinuclear space.
  • The outer membrane is often continuous with the endoplasmic reticulum and has ribosomes on it.
  • Nuclear Pores: Interruptions in the envelope formed by the fusion of the two membranes. They regulate the movement of RNA and protein molecules between the nucleus and cytoplasm.
• Nucleoplasm (or Nuclear Matrix): The fluid inside the nucleus, containing the nucleolus and chromatin.
• Nucleolus (plural: nucleoli): A spherical, non-membrane-bound structure within the nucleoplasm.
  • It is the site of active ribosomal RNA (rRNA) synthesis.
  • Cells actively involved in protein synthesis have larger and more numerous nucleoli.
• Chromatin: A loose network of nucleoprotein fibers seen in a non-dividing (interphase) nucleus.
  • It consists of DNA, basic proteins called histones, some non-histone proteins, and RNA.
  • During cell division, chromatin condenses to form distinct, structured chromosomes.

Chromosomes

Chromosomes are visible only in dividing cells.

• Structure: Each chromosome has a primary constriction called the centromere. On the sides of the centromere are disc-shaped structures called kinetochores. The centromere holds the two chromatids of a chromosome together.
• Types of Chromosomes (based on centromere position):
  1. Metacentric: Centromere is in the middle, forming two equal arms.
  2. Sub-metacentric: Centromere is slightly away from the middle, resulting in one shorter and one longer arm.
  3. Acrocentric: Centromere is situated close to one end, forming one extremely short and one very long arm.
  4. Telocentric: Centromere is at the terminal end.
• Satellite: Sometimes, a chromosome has a non-staining secondary constriction at a constant location, which gives the appearance of a small fragment called a satellite.

Microbodies

These are many membrane-bound, minute vesicles that contain various enzymes. They are present in both plant and animal cells.