Plant cell: Introduction and Functions of Cell Organelles - Agrobotany

Cell Biology

Cell Biology (Cytology) studies the structure, function, and behavior of cells—the basic structural, functional, and genetic units of life. It links genetics, molecular biology, biochemistry, physiology, and development, forming a core of modern life sciences.

Introduction

Cells carry out metabolism, maintain homeostasis, store and transmit genetic information, and coordinate responses. Understanding cellular organization explains organismal growth, development, disease, and evolution.

Historical Background

• 1665 – Robert Hooke: Observed cork and coined “cell”.
• 1674 – Anton van Leeuwenhoek: Saw living cells (protozoa, bacteria, sperm) with simple microscopes.
• 1838–39 – Schleiden & Schwann: Proposed the cell theory for plants and animals.
• 1855 – Rudolf Virchow: “Omnis cellula e cellula” – cells arise from pre-existing cells.

Cell Theory

1. All living organisms are composed of one or more cells.
2. The cell is the basic structural and functional unit of life.
3. All cells arise from pre-existing cells.
4. Cells contain hereditary information (DNA) passed to daughter cells.
5. Metabolic and energy transformations occur within cells.

Types of Cells

Feature	Prokaryotes	Eukaryotes
Domains / Examples	Bacteria, Archaea (e.g., E. coli)	Protists, Fungi, Plants, Animals (e.g., human cells)
Nucleus	No true nucleus; DNA in nucleoid	True nucleus with nuclear envelope
Organelles	No membrane-bound organelles	Membrane-bound organelles present
Genome	Single circular chromosome; plasmids	Linear chromosomes with histones
Size	~1–10 µm	~10–100 µm

Cell Structure

1) Plasma Membrane

Flexible boundary composed of a phospholipid bilayer with embedded proteins (fluid mosaic model). Functions include selective permeability, transport, cell–cell recognition, signal transduction, and protection.

2) Cytoplasm

Semi-fluid matrix (cytosol) containing organelles and cytoskeleton; site of many metabolic pathways.

3) Nucleus (Eukaryotes)

• Nuclear envelope with pores regulates traffic.
• Chromatin (DNA + proteins) organizes genetic material.
• Nucleolus synthesizes rRNA and assembles ribosomal subunits.

4) Cell Organelles

• Mitochondria: ATP production via cellular respiration; contain their own DNA.
• Endoplasmic Reticulum (ER): Rough ER (ribosomes) for protein synthesis; Smooth ER for lipid synthesis and detoxification.
• Golgi Apparatus: Modifies, sorts, and packages proteins/lipids into vesicles.
• Lysosomes: Hydrolytic enzymes for intracellular digestion and autophagy.
• Peroxisomes: Oxidative reactions; detoxify hydrogen peroxide via catalase.
• Chloroplasts (plants): Photosynthesis; contain chlorophyll and their own DNA.
• Ribosomes: Sites of protein synthesis (free or ER-bound).
• Cytoskeleton: Microtubules, microfilaments, and intermediate filaments for shape, transport, and division.
• Vacuoles: Storage; large central vacuole in plant cells maintains turgor.

Cell Division

Mitosis (Somatic Cells)

• Outcome: Two genetically identical diploid daughter cells.
• Phases: Prophase → Metaphase → Anaphase → Telophase; followed by cytokinesis.
• Role: Growth, tissue repair, asexual reproduction (in some organisms).

Meiosis (Germ Cells)

• Outcome: Four genetically diverse haploid cells.
• Divisions: Meiosis I (reductional) and Meiosis II (equational).
• Genetic diversity: Crossing over and independent assortment.

Cell Communication & Signaling

• Autocrine: Signals act on the same cell that secretes them.
• Paracrine: Local signaling to nearby cells.
• Endocrine: Hormones travel via bloodstream to distant targets.
• Direct contact: Gap junctions (animals) and plasmodesmata (plants).
• Signal transduction: Receptors (GPCRs, RTKs, ion channels) trigger intracellular cascades.

Applications of Cell Biology

• Disease mechanisms: Cancer (cell-cycle dysregulation), genetic disorders, infections.
• Regenerative medicine: Stem cells, tissue engineering.
• Biotechnology: Genetic engineering, recombinant proteins, CRISPR workflows.
• Pharmacology: Target discovery, screening, and mechanism-of-action studies.
• Agriculture: Plant tissue culture, crop improvement, GM/GE traits.

Plant Cell Wall

The plant cell wall is a rigid, extracellular structure surrounding the plasma membrane. It provides shape, protection, and mechanical support while regulating growth and enabling communication between cells.

Introduction

The plant cell wall is unique to plants and some algae. It is non-living but dynamic, secreted by the protoplast, and allows plants to grow upright without a skeletal system.

Historical Note

Robert Hooke (1665) first described the cell wall while observing cork cells. Initially thought to be living, it was later recognized as a non-living protective structure.

Characteristics

• Present in plants, fungi, algae, and some prokaryotes (composition varies).
• Main components: cellulose, hemicellulose, pectin, proteins, and lignin.
• Non-living but metabolically active and remodeled during growth.
• Located outside the plasma membrane.

Functions

• Provides rigidity and mechanical support.
• Maintains cell shape and prevents bursting under turgor pressure.
• Acts as a protective barrier against pathogens and stress.
• Facilitates cell-to-cell adhesion and communication (plasmodesmata).
• Regulates growth and stores ions/signaling molecules.

Structure of Cell Wall

1) Middle Lamella

First layer formed during cell division; rich in pectin (Ca and Mg pectates). Acts as a cement between adjacent cells.

2) Primary Cell Wall

Formed after middle lamella; thin, flexible, and extensible. Contains cellulose microfibrils, hemicellulose, pectins, and proteins. Present in all cells, allows cell expansion.

3) Secondary Cell Wall

Deposited inside the primary wall after cell growth stops. Thick, rigid, and lignified, providing strength and impermeability. Found in specialized cells like xylem vessels, fibers, and tracheids.

Chemical Composition

• Cellulose: β-1,4-linked glucose forming microfibrils for tensile strength.
• Hemicellulose: Branched polysaccharides binding cellulose fibrils.
• Pectin: Galacturonic acid-rich heteropolysaccharide; adhesion in middle lamella.
• Lignin: Aromatic polymer imparting rigidity and decay resistance.
• Proteins: Extensins, expansins, and enzymes for wall remodeling.
• Cutin/Suberin: Lipid-based compounds in specialized walls for waterproofing.

Specialized Structures

• Plasmodesmata: Cytoplasmic connections between adjacent cells.
• Pits: Thin regions in secondary walls allowing water flow between xylem cells.
• Cuticle: Waxy cutin layer on epidermal cells reducing water loss.

Deposition Patterns of Secondary Wall

Secondary wall thickening shows various patterns depending on function:

• Annular (rings)
• Spiral
• Scalariform (ladder-like)
• Reticulate (net-like)
• Pitted

Primary vs Secondary Cell Wall

Feature	Primary Cell Wall	Secondary Cell Wall
Formation	During cell growth	After cell growth stops
Thickness	Thin, flexible	Thick, rigid
Composition	Cellulose, hemicellulose, pectin, proteins	Cellulose, hemicellulose, lignin
Function	Permits expansion	Provides strength & support
Examples	Parenchyma cells	Xylem vessels, fibers

Functions in Plant Physiology

• Cell elongation through primary wall expansion.
• Transport via pits in xylem walls.
• Defense through lignified secondary walls.
• Symplastic communication via plasmodesmata.
• Storage of ions, carbohydrates, and signals.

Applications

• Agriculture: Crop improvement for strength or digestibility.
• Industry: Paper, cotton, and textile production.
• Biofuels: Lignocellulosic biomass as renewable energy.
• Biotechnology: Enzymatic modification of wall composition.

The Endoplasmic Reticulum (ER) is a complex membranous network found in eukaryotic cells. It plays a central role in the synthesis, folding, modification, and transport of proteins and lipids. The ER is an extensive organelle that spreads throughout the cytoplasm and is continuous with the nuclear envelope.

Structure of Endoplasmic Reticulum

The ER is made up of a network of membranous tubules and flattened sacs called cisternae. Its structure provides a large surface area for biochemical activities and transport. The ER membrane is continuous with the nuclear membrane, ensuring direct communication between the nucleus and cytoplasm.

Types of Endoplasmic Reticulum

1. Rough Endoplasmic Reticulum (RER)

• RER has ribosomes attached to its cytoplasmic surface, giving it a "rough" appearance under a microscope.
• It is primarily involved in the synthesis and folding of proteins, particularly those destined for secretion, membrane insertion, or organelle targeting.
• Proteins synthesized on RER undergo modifications such as glycosylation before transport.

2. Smooth Endoplasmic Reticulum (SER)

• SER lacks ribosomes and has a smooth appearance.
• It is involved in lipid and steroid hormone synthesis, carbohydrate metabolism, and detoxification of harmful substances.
• SER plays a key role in calcium ion storage and release, especially in muscle cells (sarcoplasmic reticulum).

Functions of Endoplasmic Reticulum

• Protein synthesis: RER provides a site for the synthesis and initial folding of proteins.
• Lipid synthesis: SER synthesizes phospholipids, cholesterol, and steroids for membranes and hormones.
• Detoxification: SER detoxifies drugs, alcohol, and metabolic by-products, particularly in liver cells.
• Calcium storage: ER regulates intracellular calcium levels, crucial for muscle contraction and cell signaling.
• Transport: ER forms transport vesicles that carry proteins and lipids to the Golgi apparatus for further processing.

Specialized Forms of ER

• Sarcoplasmic Reticulum: A specialized form of ER found in muscle cells, responsible for calcium storage and release during contraction.
• Transitional ER: The region of the ER where transport vesicles bud off to deliver proteins to the Golgi apparatus.

Significance of Endoplasmic Reticulum

The ER is vital for maintaining cellular homeostasis. It ensures proper protein folding and quality control, prevents the accumulation of misfolded proteins, and regulates lipid composition of membranes. Malfunction of the ER is linked with diseases such as diabetes, neurodegenerative disorders (e.g., Alzheimer's), and cancer.

Golgi Body (Golgi Apparatus)

The Golgi body is a stack of flattened membrane-bound sacs called cisternae, typically organized into a cis (entry), medial, and trans (exit) face. It receives cargo from the endoplasmic reticulum and prepares it for its final destination.

Key Points

• Modification: Glycosylation, sulfation, and proteolytic processing of proteins and lipids.
• Sorting & Packaging: Sorts cargo into coated vesicles (e.g., clathrin-coated) for delivery to lysosomes, plasma membrane, or secretion.
• Lysosome Formation: Generates primary lysosomes and tags hydrolases with mannose-6-phosphate.
• Secretion: Central to constitutive and regulated secretory pathways.

Mitochondria

Mitochondria are double-membrane organelles responsible for cellular energy production. The outer membrane is relatively permeable; the inner membrane forms cristae to maximize the surface area for oxidative phosphorylation. The internal compartment is the matrix, containing enzymes, mtDNA, and ribosomes.

Key Points

• ATP Production: Site of the TCA cycle, electron transport chain, and oxidative phosphorylation.
• Semi-autonomous: Possess their own circular DNA and 70S ribosomes; replicate by fission.
• Metabolic Roles: Involved in fatty acid oxidation, amino acid metabolism, and heme synthesis steps.
• Cell Signaling: Regulate apoptosis via cytochrome c release; buffer and signal Ca²⁺.

Nucleus

The nucleus is a double-membrane-bound organelle that functions as the cell’s control center. It stores hereditary material (DNA) and regulates gene expression, growth, metabolism, and cell division.

Structure

1) Nuclear Envelope

• Double membrane surrounding the nucleus; outer membrane is continuous with rough ER.
• Perinuclear space lies between inner and outer membranes.
• Supported internally by the nuclear lamina (lamin A/C, lamin B) for shape and chromatin organization.

2) Nuclear Pores (Nuclear Pore Complex, NPC)

• Large protein assemblies that perforate the envelope.
• Mediate selective transport: proteins/RNAs in and out via importins/exportins and Ran-GTP cycle.

3) Nucleoplasm

• Gel-like matrix containing nucleotides, ions, enzymes for DNA replication and transcription.

4) Chromatin

• DNA wrapped around histones forming nucleosomes.
• Euchromatin: loosely packed, transcriptionally active.
• Heterochromatin: densely packed, transcriptionally inactive.
• Condenses into visible chromosomes during cell division.

5) Nucleolus

• Dense, non-membranous region; site of rRNA transcription and ribosomal subunit assembly.
• Composed of fibrillar center, dense fibrillar component, and granular component.

Functions

• Genetic storage: Houses DNA and associated proteins.
• Gene expression control: Transcription, RNA processing (capping, splicing, polyadenylation).
• Ribosome biogenesis: Nucleolus forms rRNA and assembles ribosomal subunits.
• Cell cycle regulation: Coordinates DNA replication, repair, and chromosome segregation.
• Signal integration: Responds to cellular signals to modulate transcriptional programs.

Dynamics & Variations

• Cell cycle: Envelope disassembles in open mitosis (most animals) and reassembles in telophase.
• Number: Most cells are mononucleate; some are anucleate (mammalian RBCs) or multinucleate (skeletal muscle fibers).
• Nuclear bodies: Cajal bodies, PML bodies—sites for RNA/protein processing and regulation.

Clinical/Applied Notes

• Laminopathies: Mutations in lamins cause muscular dystrophies, progeroid syndromes.
• Cancer: Altered nuclear size/shape (pleomorphism), nucleolar hypertrophy correlate with malignancy.
• Diagnostics: Karyotyping and FISH assess chromosomal abnormalities.

Ribosome

Ribosomes are small, non-membrane-bound molecular machines composed of ribosomal RNA (rRNA) and proteins. They are the primary sites of protein synthesis in all living cells.

Structure

• Made of two subunits: a small subunit and a large subunit (assembly of rRNA + ribosomal proteins).
• Prokaryotic ribosomes: 70S (30S + 50S). Eukaryotic ribosomes: 80S (40S + 60S).

Location

• Free in the cytosol (synthesize proteins for cytosolic use).
• Bound to the rough endoplasmic reticulum (synthesize secretory, lysosomal, and membrane proteins).
• Also present in mitochondria and chloroplasts (70S-like), reflecting their endosymbiotic origin.

Function

• Translate mRNA codons into a polypeptide chain by facilitating tRNA binding and peptide bond formation.
• Ensure accuracy of translation and help fold nascent polypeptides (often together with chaperones).

Clinical/Applied Note

• Some antibiotics (e.g., tetracycline, chloramphenicol, streptomycin) target prokaryotic ribosomes to inhibit bacterial protein synthesis while sparing eukaryotic ribosomes.

Plastids

Plastids are double-membrane-bound organelles found in the cells of plants and algae. They are responsible for processes such as photosynthesis, storage of food, and synthesis of various molecules. Plastids are unique because they have their own DNA and ribosomes, allowing them to produce some of their own proteins.

Main Characteristics of Plastids

• Present in plant cells and algae, absent in animal cells.
• Double-membrane structures with an internal matrix called stroma.
• Contain their own DNA and 70S ribosomes, enabling semi-autonomous function.
• Can differentiate into various types based on function.

Types of Plastids

1. Chloroplasts

Chloroplasts are green plastids that contain the pigment chlorophyll, which is essential for photosynthesis. They capture light energy and convert it into chemical energy (glucose). Chloroplasts have an internal system of membranes called thylakoids, arranged into stacks called grana.

2. Chromoplasts

Chromoplasts are plastids that contain pigments other than chlorophyll, such as carotenoids (yellow, orange, and red pigments). They are responsible for the coloration of flowers, fruits, and aging leaves, which helps in pollination and seed dispersal.

3. Leucoplasts

Leucoplasts are colorless plastids primarily involved in storage and biosynthetic functions. They are usually found in non-photosynthetic tissues like roots, tubers, and seeds. Types of leucoplasts include:

• Amyloplasts: Store starch.
• Elaioplasts: Store oils and fats.
• Aleuroplasts: Store proteins.

Functions of Plastids

• Photosynthesis (in chloroplasts).
• Synthesis and storage of food materials like starch, proteins, and fats.
• Provide coloration to plant parts, aiding in reproduction processes.
• Play a role in various biosynthetic activities such as production of amino acids, fatty acids, and hormones.

Vacuoles

Vacuoles are membrane-bound compartments found in eukaryotic cells. They are especially large and prominent in plant cells, where a single central vacuole can occupy up to ~90% of the cell volume. The vacuole is enclosed by a membrane called the tonoplast and contains cell sap — a watery solution of ions, sugars, organic acids, pigments, and sometimes defensive compounds.

Structure

• Tonoplast: Single membrane surrounding the vacuole; contains transporters and proton pumps (e.g., V-ATPase) that regulate ion gradients and pH.
• Cell sap: Fluid inside vacuole (water, salts, sugars, organic acids, secondary metabolites, pigments).
• Size & number: Typically one large central vacuole in plant cells; several small vacuoles may be present in young cells or in animal cells.

Major Functions

• Storage: Stores water, nutrients, ions, pigments (anthocyanins), and secondary metabolites (alkaloids, phenolics).
• Turgor & support: Maintains cell turgidity by osmotic water uptake; provides mechanical support to non-woody tissues.
• Homeostasis: Regulates cytosolic pH, ionic composition, and osmotic balance via tonoplast transporters.
• Waste sequestration & detoxification: Isolates harmful substances and heavy metals in an inactive form.
• Digestion & recycling: Contains hydrolytic enzymes in some cells for breakdown of macromolecules (vacuolar autophagy-like functions).
• Defense & deterrence: Stores bitter or toxic compounds to deter herbivores and pathogens.
• Coloration: Stores pigments (e.g., anthocyanins) that contribute to flower and fruit color.

Specialized Types & Examples

• Central vacuole (plants): Large storage and turgor-maintaining compartment in mature plant cells.
• Contractile vacuole (protists): Expels excess water to maintain osmotic balance in freshwater protozoa.
• Storage vacuoles: Seed protein storage vacuoles or pigment vacuoles in petal cells.
• Lytic vacuoles: Functionally similar to lysosomes in plants for degradation of cellular material.

Role in Development & Physiology

• Drives cell expansion: Vacuolar enlargement allows rapid cell growth with minimal cytoplasm synthesis.
• Seed germination: Vacuoles mobilize stored reserves and help re-establish turgor in emerging seedlings.
• Stress responses: Vacuoles sequester salts and toxic molecules during salt, drought, or heavy-metal stress.

Notes

• Vacuolar transport is energized by proton pumps (V-ATPase, V-PPase) that acidify the lumen and power secondary transporters.
• Vacuole composition is dynamic and changes with cell type, developmental stage, and environmental conditions.

Glyoxysome

Glyoxysomes are specialized peroxisomes found mainly in the fat‑storing tissues of germinating seeds (for example, castor bean and sunflower). They contain enzymes of the glyoxylate cycle and are essential for converting stored lipids into carbohydrates that fuel seedling growth before photosynthesis begins.

Key Features

• Organellar type: Specialized form of peroxisome found in plants (especially oil seeds) and some fungi.
• Main enzymes: Isocitrate lyase (ICL) and malate synthase (MS), which define the glyoxylate cycle.
• Primary role: Convert fatty acids → acetyl‑CoA → C₄ compounds (e.g., succinate) that are used for gluconeogenesis to form sugars.
• Association with other organelles: Work closely with mitochondria (for respiration and TCA cycle intermediates) and cytosol (for gluconeogenesis).
• Temporal occurrence: Prominent during seed germination when mobilizing storage lipids; may decline as chloroplasts develop and photosynthesis begins.

The Glyoxylate Cycle (Brief)

• Isocitrate → glyoxylate + succinate (via isocitrate lyase).
• Glyoxylate + acetyl‑CoA → malate (via malate synthase).
• Succinate is exported to mitochondria, converted through TCA intermediates to provide carbon skeletons for gluconeogenesis.

Physiological Significance

• Enables seedlings to produce sugars from fats when light-driven photosynthesis is not yet available.
• Critical for establishment of oil‑rich seeds and early growth of seedlings.
• Biotechnological interest for modifying seed oil mobilization and improving seedling vigor.

Short summary: Glyoxysomes are peroxisome derivatives that run the glyoxylate cycle, allowing germinating seeds to convert stored fats into sugars needed for early growth.

Peroxisome

Peroxisomes are small, single-membrane-bound organelles found in most eukaryotic cells. They contain oxidative enzymes (e.g., catalase, various oxidases) that metabolize toxic compounds and participate in lipid metabolism.

Key Features

• Single membrane bound; 0.1–1.0 µm in diameter.
• Contain enzymes for oxidation reactions that generate hydrogen peroxide (H₂O₂).
• Have catalase to decompose H₂O₂ into water and oxygen, protecting the cell from oxidative damage.
• Formed by growth and division of preexisting peroxisomes or by budding from the ER.

Main Functions

• Detoxification: Breakdown of hydrogen peroxide and other harmful compounds.
• Fatty acid metabolism: β-oxidation of very-long-chain fatty acids (shorter products are transferred to mitochondria).
• Plasmalogen synthesis: Important in myelin production (in animals).
• Photorespiration: In plants, peroxisomes (glyoxysomes in seeds) participate in photorespiratory pathways and glyoxylate cycle functions.

Clinical/Physiological Notes

• Peroxisomal disorders (e.g., Zellweger spectrum) result from defects in peroxisome biogenesis and cause severe developmental and metabolic problems.
• Essential for cellular redox balance and lipid homeostasis.

Lysosome

Lysosomes are membrane-bound organelles found in most eukaryotic cells. They contain a suite of hydrolytic enzymes (proteases, lipases, nucleases, glycosidases) that function optimally at an acidic pH (~5).

Key Features

• Single membrane-bound vesicles filled with acid hydrolases.
• Maintain an acidic lumen using proton pumps (v-ATPases).
• Formed by budding from the Golgi apparatus or via endosomal maturation.

Main Functions

• Intracellular digestion: Break down macromolecules delivered by endocytosis, phagocytosis, and autophagy.
• Autophagy: Degrade damaged organelles and recycle cellular components.
• Defense: Destroy pathogens in phagocytic cells.
• Regulated cell death: Contribute to autolysis and certain forms of programmed cell death.

Clinical/Physiological Notes

• Lysosomal storage diseases (e.g., Tay–Sachs, Gaucher) are caused by defective lysosomal enzymes leading to substrate accumulation.
• Lysosome dysfunction is linked to neurodegeneration, immune defects, and aging-related diseases.

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Sphaerosome (Sperosome)

Sphaerosomes (sometimes spelled “sperosomes” in older literature) are small, single-membrane organelles in plant cells that are rich in lipids and involved in lipid storage and metabolism—especially abundant in oil seeds.

Key Features

• Bound by a single membrane and contain lipid droplets or oil bodies.
• Originate from the endoplasmic reticulum; contain enzymes like lipases and esterases.
• Common in seed storage tissues and developing embryos of oil-rich seeds.

Main Functions

• Lipid storage: Store triacylglycerols and other neutral lipids as energy reserves for germination.
• Lipid metabolism: Serve as sites for lipid mobilization and associated enzymatic activity.
• Support seedling growth: Supply carbon and energy during germination before photosynthesis begins.

Notes

• Sphaerosomes are distinct from glyoxysomes (which run the glyoxylate cycle) but often act in concert during seed germination.
• Terminology varies in older texts—“sperosome” appears occasionally, but sphaerosome is the preferred modern term.

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