Unit 1: Cellular Organization; Cytoskeleton and Function of Intracellular Organelles - Subjective Questions

All cells, whether prokaryotic or eukaryotic, share a set of universal features that reflect their descent from a common ancestor:

• Plasma membrane: Every cell is bounded by a lipid bilayer membrane that separates the internal cytoplasm from the external environment and regulates transport.
• Genetic material (DNA): All cells store hereditary information in DNA using the same four nucleotides (A, T, G, C).
• Universal genetic code: The same codon-to-amino-acid assignments are used across nearly all organisms.
• Transcription and translation machinery: All cells use RNA polymerase to transcribe DNA into RNA and ribosomes to translate mRNA into protein.
• Common metabolic pathways: Processes like glycolysis and ATP-based energy currency are shared widely.
• Cytoplasm: A semi-fluid internal matrix where metabolic reactions occur.

Evidence for common origin: The near-universality of the genetic code, the shared macromolecular machinery, and identical basic biochemistry strongly suggest that all life descended from a single Last Universal Common Ancestor (LUCA). It is statistically improbable that these highly specific systems arose independently multiple times.

Cells are composed primarily of water and organic macromolecules built from smaller subunits. The chemical organization includes:

1. Water (~70%): The universal solvent; medium for biochemical reactions.

2. Carbohydrates: Made of monosaccharides (e.g., glucose).

• Provide energy (glucose, glycogen, starch)
• Structural roles (cellulose in plants, chitin)

3. Lipids: Hydrophobic molecules.

• Membrane formation (phospholipids)
• Energy storage (triglycerides)
• Signaling (steroids)

4. Proteins: Polymers of amino acids joined by peptide bonds.

• Enzymes, structural support, transport, signaling
• Four levels of structure: primary, secondary, tertiary, quaternary

5. Nucleic acids: Polymers of nucleotides.

• DNA stores genetic information
• RNA in expression and catalysis

Bonding: Macromolecules are held together by covalent bonds (backbone) and stabilized by non-covalent interactions (hydrogen bonds, ionic bonds, van der Waals, hydrophobic interactions). These weak interactions collectively determine molecular shape and function.

The fluid mosaic model, proposed by Singer and Nicolson (1972), describes the cell membrane as a dynamic structure.

Key features:

• The membrane is a phospholipid bilayer with hydrophilic heads facing outward and hydrophobic tails facing inward.
• Proteins are embedded within (integral/transmembrane) or attached to the surface (peripheral), forming a mosaic.
• Components are not static — lipids and many proteins diffuse laterally, giving the membrane its fluid nature.
• Cholesterol modulates fluidity in animal cells.
• Carbohydrates attach to lipids (glycolipids) and proteins (glycoproteins) on the outer surface.

Supporting evidence:

• Frye-Edidin experiment (1970): Fusion of mouse and human cells showed intermixing of membrane proteins, proving lateral mobility.
• Freeze-fracture electron microscopy revealed proteins embedded within the bilayer.
• FRAP (Fluorescence Recovery After Photobleaching) demonstrated lateral diffusion of labeled lipids.

The model explains membrane asymmetry, selective permeability, and dynamic behavior.

Compartmentalization refers to the division of the eukaryotic cell interior into distinct membrane-bound regions called organelles, each with a specialized function.

Basis of compartmentalization:

• Internal membranes create separate aqueous compartments (e.g., nucleus, ER, Golgi, lysosomes, mitochondria).
• Each compartment maintains a unique chemical environment (pH, ion concentration, enzyme sets).

Advantages:

• Segregation of incompatible reactions: For example, lysosomal digestive enzymes are kept away from the cytosol to prevent self-damage.
• Increased efficiency: Concentrating enzymes and substrates in a small volume speeds up reactions.
• Specialized microenvironments: Lysosomes maintain acidic pH (~4.5); mitochondria maintain proton gradients.
• Regulation and control: Processes can be independently regulated.
• Increased membrane surface area: Internal membranes provide sites for reactions (e.g., inner mitochondrial membrane for the electron transport chain).

Compartmentalization allows eukaryotic cells to achieve greater complexity and metabolic sophistication than prokaryotes.

The cytoskeleton is a dynamic network of protein filaments extending throughout the cytoplasm that provides shape, mechanical support, and enables movement.

Three main components:

1. Microfilaments (Actin filaments):

• Diameter ~7 nm; thinnest
• Composed of actin monomers forming a double helix
• Roles: cell shape, muscle contraction, cytokinesis, cell migration

2. Intermediate filaments:

• Diameter ~10 nm
• Composed of diverse proteins (keratin, vimentin, lamins)
• Rope-like, most stable; provide mechanical strength and tensile support

3. Microtubules:

• Diameter ~25 nm; thickest, hollow tubes
• Composed of α- and β-tubulin dimers
• Roles: intracellular transport, chromosome segregation (spindle), form cilia and flagella
• Organized from the centrosome (MTOC)

Organization: These filaments are highly dynamic, undergoing continuous assembly and disassembly, and interact with motor proteins (myosin, kinesin, dynein) and accessory proteins to perform their functions.

Prokaryotic vs. Eukaryotic cells:

Summary: Prokaryotes are simpler and lack internal compartmentalization, whereas eukaryotes exhibit extensive compartmentalization with a defined nucleus and specialized organelles.

The nucleus is the control center of the eukaryotic cell, housing the genetic material.

Structure:

• Nuclear envelope: A double membrane (outer and inner) that separates nucleoplasm from cytoplasm; the outer membrane is continuous with the ER.
• Nuclear pores: Protein complexes (nuclear pore complexes) that regulate the movement of molecules between nucleus and cytoplasm.
• Nucleoplasm: The gel-like interior containing chromatin and nucleolus.
• Chromatin: DNA associated with histone proteins; condenses into chromosomes during division.
• Nucleolus: A dense region where ribosomal RNA (rRNA) synthesis and ribosome subunit assembly occur.
• Nuclear lamina: A meshwork of intermediate filaments (lamins) supporting the inner membrane.

Functions:

• Stores and protects genetic information (DNA).
• Site of DNA replication and transcription.
• Controls gene expression and cellular activities.
• Assembles ribosomal subunits in the nucleolus.
• Regulates transport via nuclear pores.

Mitochondria are the powerhouses of the cell, generating ATP through oxidative phosphorylation.

Structure:

• Outer membrane: Smooth, permeable to small molecules (contains porins).
• Inner membrane: Folded into cristae to increase surface area; impermeable, houses the electron transport chain (ETC) and ATP synthase.
• Intermembrane space: Region between the two membranes where protons accumulate.
• Matrix: Innermost compartment containing enzymes of the citric acid cycle, mitochondrial DNA, and ribosomes.

Structure–function relationship:

• The extensive cristae maximize the area for ATP-generating machinery.
• The impermeable inner membrane allows a proton gradient to be maintained.

Chemiosmotic mechanism (Peter Mitchell):

• Electrons pass through the ETC complexes, pumping H⁺ from the matrix into the intermembrane space.
• This creates an electrochemical proton-motive force.
• Protons flow back into the matrix through ATP synthase, driving the synthesis of ATP:
  

Mitochondria also contain their own DNA, supporting the endosymbiotic theory of their origin.

The endoplasmic reticulum (ER) is an extensive network of membranous tubules and flattened sacs (cisternae) continuous with the nuclear envelope.

Rough ER (RER):

• Studded with ribosomes on its cytoplasmic surface.
• Functions:
  • Synthesis of secretory and membrane proteins
  • Protein folding and initial glycosylation
  • Quality control of proteins

Smooth ER (SER):

• Lacks ribosomes.
• Functions:
  • Lipid and steroid synthesis
  • Detoxification of drugs and poisons (especially in liver)
  • Ca²⁺ storage (e.g., sarcoplasmic reticulum in muscle)
  • Carbohydrate metabolism

Key differences:

Overall: The ER is central to the biosynthesis and transport of proteins and lipids, feeding products into the Golgi apparatus.

The Golgi apparatus (Golgi complex/body) is a stack of flattened membranous sacs called cisternae involved in processing and packaging.

Structure:

• Consists of 4–8 stacked, curved cisternae.
• Has distinct polarity:
  • Cis face (forming face): Receives vesicles from the ER.
  • Trans face (maturing face): Ships processed vesicles toward the plasma membrane.
  • Medial cisternae: Between the two.

Functions:

• Modification of proteins and lipids: glycosylation, phosphorylation, sulfation.
• Sorting and packaging of molecules into vesicles.
• Synthesis of certain polysaccharides.
• Formation of lysosomes and secretory vesicles.

Role in the secretory pathway:

1. Proteins synthesized in the RER are transported to the cis Golgi in transport vesicles.
2. Molecules move through the cisternae (cis → medial → trans), being progressively modified.
3. At the trans face, sorted products are packaged into vesicles.
4. Vesicles are directed to lysosomes, the plasma membrane (secretion via exocytosis), or other destinations.

The Golgi acts as the cell's central processing and shipping station.

Lysosomes are membrane-bound organelles containing hydrolytic enzymes for intracellular digestion.

Structure:

• Single-membrane-bound spherical vesicles.
• Contain over 40 hydrolytic enzymes (acid hydrolases) — proteases, lipases, nucleases, glycosidases.
• Maintain an acidic internal pH (~4.5) via a membrane H⁺ (proton) pump.
• The enzymes work optimally at acidic pH, protecting the cytosol if enzymes leak.

Functions:

• Intracellular digestion of macromolecules.
• Autophagy: Digestion of worn-out organelles.
• Phagocytosis: Digestion of engulfed particles/pathogens.
• Autolysis: Self-destruction of the cell (programmed cell death) — hence called suicide bags.

Lysosomal storage disorders:

• Genetic mutations cause deficiency of a specific lysosomal enzyme.
• Undigested substrates accumulate inside lysosomes, impairing cell function.
• Examples: Tay-Sachs disease (hexosaminidase A deficiency), Gaucher's disease, Pompe disease.

These disorders demonstrate the essential role of lysosomes in cellular maintenance.

Peroxisomes are small, single-membrane-bound organelles involved in oxidative metabolism.

Structure:

• Spherical vesicles bounded by a single membrane.
• Contain oxidative enzymes such as catalase and oxidases.
• Often contain a crystalline core of enzymes.

Functions:

• Oxidation of fatty acids (β-oxidation).
• Breakdown of hydrogen peroxide: oxidases produce , which catalase then decomposes:
  
• Detoxification of harmful substances (e.g., ethanol in liver).
• Synthesis of plasmalogens (membrane lipids) and bile acids.
• In plants, glyoxysomes (specialized peroxisomes) convert fats to carbohydrates.

Differences from lysosomes:

Peroxisomes handle oxidative reactions, whereas lysosomes handle degradation.

Chloroplasts are plastids found in plant and algal cells that carry out photosynthesis.

Structure:

• Outer and inner membranes: Double-membrane envelope.
• Stroma: Fluid matrix containing enzymes for the Calvin cycle, chloroplast DNA, and ribosomes.
• Thylakoids: Flattened membranous sacs containing chlorophyll and photosynthetic pigments.
• Grana: Stacks of thylakoids (singular: granum).
• Lamellae: Membranes connecting the grana.

Structure–function relationship in photosynthesis:

1. Light reactions (thylakoid membranes):

• Chlorophyll absorbs light energy.
• Water is split, releasing .
• ATP and NADPH are produced via the electron transport chain and chemiosmosis.

2. Dark reactions / Calvin cycle (stroma):

• is fixed into carbohydrates using ATP and NADPH.
  

The large thylakoid surface area maximizes light capture, while the stroma provides space for carbon fixation. Chloroplasts contain their own DNA, supporting the endosymbiotic theory.

The cell wall is a rigid external structure providing shape, support, and protection. Its composition varies across organisms.

Plant cell wall:

• Primary component: cellulose (β-1,4-linked glucose) microfibrils.
• Also contains hemicellulose, pectin, and lignin (in secondary walls).
• Layers: middle lamella, primary wall, and secondary wall.
• Functions: rigidity, prevents excess water uptake, structural support.

Fungal cell wall:

• Main component: chitin (polymer of N-acetylglucosamine).
• Also contains glucans and glycoproteins.

Bacterial cell wall:

• Main component: peptidoglycan (murein) — chains of sugars cross-linked by peptides.
• Gram-positive: Thick peptidoglycan layer.
• Gram-negative: Thin peptidoglycan plus an outer lipopolysaccharide membrane.

Common functions:

• Maintain cell shape
• Provide mechanical strength
• Protect against osmotic lysis
• Regulate cell expansion

Animal cells notably lack a cell wall, relying on the extracellular matrix and cytoskeleton for support.

Plastids are double-membrane-bound organelles unique to plants and algae, involved in synthesis and storage. They arise from proplastids and can interconvert.

Main types of plastids:

1. Chloroplasts (green):

• Contain chlorophyll.
• Site of photosynthesis.

2. Chromoplasts (colored):

• Contain carotenoid pigments (red, orange, yellow).
• Give color to flowers and fruits, aiding in pollination and seed dispersal.

3. Leucoplasts (colorless):

• Involved in storage. Subtypes:
  • Amyloplasts: store starch
  • Elaioplasts: store lipids/oils
  • Proteinoplasts: store proteins

Common features:

• Bounded by a double membrane.
• Contain their own DNA and ribosomes (semi-autonomous).
• Support the endosymbiotic theory.

Interconversion: Plastids are interconvertible — e.g., chloroplasts become chromoplasts as fruits ripen. This flexibility allows plants to adapt to different physiological needs.

Vacuoles are membrane-bound fluid-filled sacs found in plant, fungal, and some animal cells.

Structure:

• Bounded by a single membrane called the tonoplast.
• Filled with cell sap — a solution of water, ions, sugars, enzymes, and pigments.
• In mature plant cells, a single large central vacuole occupies up to 90% of cell volume.

Functions:

• Turgor pressure: Water uptake creates internal pressure that keeps plant cells rigid and provides mechanical support.
• Storage: Stores nutrients, ions, waste products, and pigments (e.g., anthocyanins).
• pH and ion homeostasis.
• Degradation: Contains hydrolytic enzymes (lysosome-like function in plants).
• Defense: Stores toxic compounds against herbivores.

Importance of the central vacuole:

• Maintains turgidity, essential for plant support and growth.
• Loss of turgor leads to wilting.
• Allows the cell to grow in size economically by filling with water rather than cytoplasm.
• Contributes to storage and homeostasis, making it essential for plant survival.

The cytoskeleton drives various forms of cell motility through its filaments and associated motor proteins.

1. Cilia and Flagella (microtubule-based):

• Built on the 9+2 axoneme arrangement: nine outer microtubule doublets surrounding two central singlets.
• The motor protein dynein causes adjacent doublets to slide past one another.
• Because doublets are anchored, sliding is converted into bending, producing beating movements.
• Cilia: short, numerous, beat in a coordinated whip-like motion.
• Flagella: long, few, produce wave-like undulations (e.g., sperm movement).

2. Amoeboid movement (actin-based):

• Driven by actin filament assembly and disassembly.
• The cell extends pseudopodia by polymerizing actin at the leading edge.
• Sol–gel transitions of cytoplasm and myosin motor activity drive forward crawling (e.g., macrophages, amoeba).

3. Muscle contraction:

• Actin (thin) and myosin (thick) filaments slide past each other via the sliding filament mechanism, powered by ATP.

Motor proteins:

• Myosin moves along actin.
• Kinesin and dynein move along microtubules.

Thus, the cytoskeleton, together with motor proteins and ATP, generates diverse and precise cellular movements.

The three cytoskeletal filaments differ in size, composition, and roles:

Key points:

• Microfilaments are best for movement and shape changes.
• Intermediate filaments provide durable mechanical support and resist tension.
• Microtubules organize intracellular transport and cell division.

Together they form an integrated network essential for cell structure and function.

The selectively permeable plasma membrane regulates transport by several mechanisms.

1. Passive transport (no energy required):

• Moves substances down the concentration gradient.
• Simple diffusion: Small nonpolar molecules (, ) pass directly through the bilayer.
• Facilitated diffusion: Ions and polar molecules move through channel or carrier proteins.
• Osmosis: Diffusion of water through the membrane / aquaporins.

2. Active transport (requires energy):

• Moves substances against the concentration gradient using ATP.
• Primary active transport: Directly uses ATP (e.g., Na⁺/K⁺ pump, which pumps 3 Na⁺ out and 2 K⁺ in).
• Secondary active transport (co-transport): Uses the gradient created by primary transport (symport/antiport).

3. Bulk transport (vesicular):

• Endocytosis: Uptake of material (phagocytosis, pinocytosis, receptor-mediated).
• Exocytosis: Release of material via vesicle fusion.

Passive vs. Active:

These processes maintain the cell's internal environment and ion balance.

The endosymbiotic theory, popularized by Lynn Margulis, proposes that mitochondria and chloroplasts originated from free-living prokaryotes that were engulfed by an ancestral host cell.

The theory:

• Mitochondria arose from an aerobic α-proteobacterium engulfed by a primitive eukaryotic host.
• Chloroplasts arose from a photosynthetic cyanobacterium engulfed similarly.
• Instead of being digested, these prokaryotes formed a symbiotic relationship, eventually becoming permanent organelles.

Supporting evidence:

• Double membrane: Consistent with engulfment by phagocytosis (inner membrane = original bacterium; outer = host vesicle).
• Own circular DNA: Both organelles have their own genome, resembling bacterial DNA.
• 70S ribosomes: Similar to bacterial ribosomes, not the 80S of eukaryotic cytoplasm.
• Independent replication: They divide by binary fission, like bacteria.
• Size and structure: Comparable to prokaryotic cells.
• Sensitivity to antibiotics: Their protein synthesis is inhibited by antibacterial antibiotics.
• Molecular similarity: Their rRNA sequences resemble those of bacteria.

Significance: This theory explains the semi-autonomous nature of these organelles and represents a key event in the evolution of complex eukaryotic cells.