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Complete Cell Biology Study Guide

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SHORT QUESTIONS (3 MARKS EACH)

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Q1. Three Organelles Bounded by a Single Membrane and Three by a Double Membrane

Single-membrane organelles

Other examples: peroxisomes, vacuoles, secretory vesicles

Double-membrane organelles

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Q2. Cell Signalling - Definition and Protein Signal Pathway

Definition

• Junqueira's Basic Histology, p. 87

Pathway of a Protein Signal from Outside to Inside the Cell

1. Ligand synthesis and secretion - The signalling cell secretes a protein signal molecule (ligand) by exocytosis into the extracellular environment.
2. Receptor binding - The ligand binds with high affinity to a specific receptor protein on the surface of the target cell. Receptors for protein hormones are integral membrane proteins.
3. Receptor activation - Binding causes a conformational change in the receptor. Most protein signal receptors are either:
   • Receptor tyrosine kinases (RTKs) - dimerize and autophosphorylate on tyrosine residues
   • G-protein-coupled receptors (GPCRs) - activate associated heterotrimeric G proteins
4. Second messenger generation - Activated receptors generate intracellular second messengers (e.g. cAMP, IP3, DAG, Ca2+) that amplify the signal.
5. Protein kinase cascade - Second messengers activate protein kinases (e.g. PKA, PKC, MAPK) which phosphorylate target proteins. Second messenger-independent protein kinases such as MAPK, cyclin-dependent kinase (Cdk), and protein tyrosine kinase also play roles.
6. Cellular response - Phosphorylation events alter the activity of enzymes, structural proteins, and transcription factors, producing the final cellular response (e.g. gene expression, secretion, cell division).

• Histology: A Text and Atlas, p. 143

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Q3. Prokaryotic vs Eukaryotic Cells

Diagrams

        _______________
       /  Capsule       \
      | _______________  |
      ||  Nucleoid      | |
      || (circular DNA) | |
      || Ribosome (70S) | |
      ||________________| |
      |  Cell wall         |
      |  Plasma membrane   |
      |  Flagellum ------> |
       \___________________/
         Pilus

         ___________________________
        /   Smooth ER    Rough ER   \
       |   ___________  ________    |
       |  |           ||Ribosomes|  |
       |  | Nucleus   ||________|  |
       |  | (DNA +    |            |
       |  |  histones)|  Golgi     |
       |  |___________|  apparatus |
       |                           |
       |  Mitochondria  Lysosome   |
       |  Cytoskeleton             |
        \__________________________/
           Plasma membrane (single)

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Q4. Stem Cells - Definition and Advantages

Definition

1. Self-renewal - dividing to produce more stem cells
2. Differentiation - developing into specialized cell types

Advantages of Using Stem Cells

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Q5. Categories of Stem Cells

By Potency

TOTIPOTENT
  │  Can form entire organism including extraembryonic tissues
  │  Example: fertilized egg (zygote), first few blastomeres
  ▼
PLURIPOTENT
  │  Can form any cell of all three germ layers
  │  Cannot form placenta/extraembryonic tissues
  │  Examples: Embryonic Stem Cells (ESCs), iPSCs
  ▼
MULTIPOTENT
  │  Can form multiple cell types within one lineage
  │  Examples: Haematopoietic stem cells (HSCs), mesenchymal stem cells
  ▼
OLIGOPOTENT
  │  Can differentiate into a few cell types
  │  Example: Lymphoid progenitor cells
  ▼
UNIPOTENT
     Can only produce one cell type, but retain self-renewal
     Example: Muscle satellite cells, spermatogonial stem cells

By Origin/Source

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Q6. Advantages and Disadvantages of Induced Pluripotent Stem Cells (iPSCs)

Advantages

Disadvantages

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Q7. Four Membrane Transport Mechanisms

Diagram 1 - Overview of passive mechanisms

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1. Simple Diffusion

• Mechanism: Movement of small, nonpolar, lipophilic (fat-soluble) molecules and gases directly through the lipid bilayer, down their concentration gradient.
• Energy required: None (passive)
• Direction: High concentration → Low concentration
• Examples: O₂, CO₂, N₂, ethanol, steroid hormones
• Key feature: No transport protein needed; continues until equilibrium

2. Facilitated Diffusion

• Mechanism: Movement of ions and polar/charged molecules down their concentration gradient, assisted by membrane transport proteins (channel proteins or carrier proteins).
• Energy required: None (passive); uses kinetic energy of the molecule
• Direction: High concentration → Low concentration
• Two subtypes:
  • Channel-mediated: Ions (Na⁺, K⁺, Ca²⁺, Cl⁻) pass through selective ion channel proteins. Channels may be voltage-gated, ligand-gated, or mechanically gated.
  • Carrier-mediated: Molecules (e.g. glucose) bind to carrier proteins which undergo conformational changes to shuttle them across (e.g. GLUT transporters)
• Examples: Glucose transport into cells, Na⁺ through ion channels

3. Osmosis

• Mechanism: Net movement of water molecules through a selectively permeable membrane from a region of high water concentration (low solute concentration / hypotonic) to a region of low water concentration (high solute concentration / hypertonic).
• Energy required: None (passive)
• Direction: Follows water potential gradient
• Driven by: Osmotic pressure difference across the membrane
• Transport protein: Water channels called aquaporins facilitate rapid water movement across cell membranes
• Key terms:
  • Hypotonic solution → cell swells (gains water)
  • Hypertonic solution → cell shrinks/crenates (loses water)
  • Isotonic solution → no net water movement

4. Active Transport

• Mechanism: Movement of ions and solutes against their concentration or electrochemical gradient, requiring energy (ATP hydrolysis). Carried out by membrane pump proteins (ATPases).
• Energy required: ATP hydrolysis
• Direction: Low concentration → High concentration (against gradient)
• Types:
  • Primary active transport: Pump directly uses ATP (e.g. Na⁺/K⁺-ATPase pump - exports 3 Na⁺ out and imports 2 K⁺ in per ATP cycle, maintaining resting membrane potential)
  • Secondary active transport: Uses the electrochemical gradient established by primary pumps to co-transport another solute (symport or antiport); no direct ATP use
• Examples: Na⁺/K⁺ pump, H⁺ pump, Ca²⁺ pump
• Junqueira's Basic Histology, p. 79-80

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Q8. Endocytosis and Exocytosis

Diagrams

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Endocytosis

• Cell surface extends pseudopodia to surround large particles (bacteria, dead cells)
• The folds fuse to form a phagosome (large vacuole)
• Phagosome merges with a lysosome → phagolysosome → enzymatic digestion
• Performed by macrophages and neutrophils

• Smaller invaginations of the plasma membrane trap extracellular fluid and dissolved contents
• Pinches off as pinocytotic vesicles (~80 nm diameter)
• Vesicles either fuse with lysosomes for digestion, or travel to the opposite membrane surface for transcytosis

• Specific ligands (e.g. LDL, protein hormones, antibodies) bind to cell-surface receptor proteins
• Occupied receptors aggregate in coated pit regions lined with clathrin protein
• The pit invaginates and pinches off as a clathrin-coated vesicle (endosome)
• Clathrin is recycled; the receptor-ligand complex is sorted in the endosomal compartment
• Receptors are often returned to the cell surface (recycling endosomes) while ligands are sent to lysosomes

Exocytosis

• Delivers newly synthesised proteins, lipids, and other macromolecules to outside the cell
• Triggered in many cells by a transient rise in cytosolic Ca²⁺
• Mediated by SNARE proteins which drive membrane fusion
• Maintains plasma membrane integrity by returning endocytosed membrane material

1. Constitutive secretion - products released continuously as soon as synthesised (e.g. collagen to ECM)
2. Regulated secretion - products stored in vesicles and released upon signal (e.g. digestive enzymes from pancreatic acinar cells; neurotransmitters at synapses)

• Junqueira's Basic Histology, p. 82-86

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Q9. Chemical Structure of a Single Phospholipid

            Choline (+ charged)
               |
          Phosphate group (- charged)
               |   ← HYDROPHILIC HEAD
          Glycerol backbone
               |
      ________/ \_________
     |                   |
 Fatty acid 1        Fatty acid 2
 (saturated -        (unsaturated -
  no double bonds)    has C=C kink)
     |                   |
     CH₂                CH₂
     |                   |
     CH₂                CH₂=CH
     |                   |
     ...                 ...     ← HYDROPHOBIC TAILS
     |                   |
     CH₃                CH₃

        CH₃
        |
H₃C—N⁺—CH₃           ← Choline (quaternary ammonium)
        |
        CH₂
        |
        CH₂
        |
    O   |
    ‖   |
HO—P—O—CH₂             ← Phosphate group
    |
    O
    |
    CH₂—O—CO—(CH₂)n—CH₃    ← sn-1 fatty acid (saturated)
    |
    CH—O—CO—(CH₂)m=...—CH₃  ← sn-2 fatty acid (unsaturated)
    |
    CH₂—OH

• Polar head: Phosphate group + alcohol (choline, ethanolamine, serine, or inositol) - hydrophilic, water-loving
• Glycerol backbone: 3-carbon bridge linking head to tails
• Two fatty acid tails: Long hydrocarbon chains - hydrophobic, water-repelling
  • Saturated tail: straight chain (palmitic acid, stearic acid)
  • Unsaturated tail: kinked due to C=C double bond (oleic acid, linolenic acid)

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Q10. Ultrastructure of Animal and Plant Cells

Animal Cell Ultrastructure

Plant Cell Ultrastructure

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LONG QUESTIONS (6 MARKS EACH)

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L1. Fluid Mosaic Model of the Plasma Membrane

Definition and History

Composition

• The backbone of the membrane consists of two layers of phospholipids arranged tail-to-tail
• Hydrophilic heads face outward (toward water - extracellular fluid and cytoplasm)
• Hydrophobic tails face inward (away from water), forming the hydrophobic core
• The bilayer is fluid at body temperature (~37°C), allowing lateral movement of lipids and proteins
• Cholesterol molecules are interspersed among the phospholipids:
  • Reduces membrane fluidity at high temperatures
  • Prevents solidification at low temperatures
  • Maintains optimal membrane flexibility

• Short oligosaccharide chains covalently attached to membrane lipids (glycolipids) and proteins (glycoproteins)
• Located exclusively on the extracellular surface
• Functions: cell recognition, cell adhesion, immune identity (ABO blood groups), receptor binding, protection from mechanical/chemical damage

Labelled Diagram

EXTRACELLULAR SPACE
      │
      │  Carbohydrate chains (Glycocalyx)
      │  ⌇⌇⌇⌇⌇⌇⌇⌇⌇
══════╪══╪══╪═══╪══╪════════════════════════════
● ● ● │  │  │   │  │ ● ● ● ● ● ● ● ● ● ● ● ●    ← Phospholipid heads
║ ║ ║ ┼──┼──┼───┼──┼ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║    ← Fatty acid tails
║ ║ ║ │  │  │   │  │ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║
║ ║ ║ │  │ [G]  │  │ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║
║ ║ ║ [A]  [B]  [C] ║ ║ ║ ║ [Chol]║ ║ ║ ║ ║ ║   ← Integral proteins
║ ║ ║ │           │ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║ ║    & cholesterol
● ● ● │           │ ● ● ● ● ● ● ● ● ● ● ● ●    ← Phospholipid heads
══════╪═══════════╪════════════════════════════
      │           │
   [Peripheral] [Peripheral]
     protein      protein
      │
CYTOPLASM

• [A] = Transmembrane integral protein (e.g. channel/transporter)
• [B] = Transmembrane receptor protein
• [C] = Peripheral protein (inner leaflet, e.g. G protein)
• [G] = Glycoprotein (extracellular carbohydrate chain)
• [Chol] = Cholesterol molecule

Properties of the Fluid Mosaic Model

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L2. Structure and Functions of Subcellular Organelles

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1. Mitochondria

• Bounded by two membranes
• Outer membrane: smooth, contains porins (VDAC channels) that make it permeable to small molecules
• Inner membrane: highly folded into shelf-like projections called cristae - greatly increases surface area for ATP synthesis
  • Contains the electron transport chain proteins (Complexes I-IV) and ATP synthase (Complex V)
• Intermembrane space: between the two membranes; protons are pumped here during oxidative phosphorylation
• Matrix: enclosed by the inner membrane; contains:
  • TCA (Krebs) cycle enzymes
  • Circular mitochondrial DNA (~16,569 base pairs in humans)
  • 70S ribosomes (like bacteria - evidence of endosymbiotic origin)
  • Mitochondria-specific tRNAs and rRNAs

• Primary function: ATP synthesis via oxidative phosphorylation - "powerhouse of the cell"
• Pyruvate oxidation and acetyl-CoA generation
• TCA cycle (citric acid cycle)
• Beta-oxidation of fatty acids
• Calcium homeostasis
• Regulation of apoptosis (release of cytochrome c)
• Heat generation (thermogenesis via uncoupling proteins)

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2. Nucleus

• Largest organelle; bounded by a double membrane (nuclear envelope)
• Outer nuclear membrane: continuous with the rough ER; studded with ribosomes
• Inner nuclear membrane: lined by the nuclear lamina (intermediate filaments that provide structural support)
• Nuclear pores (~3,000-4,000 per nucleus): large protein complexes (~120 nm) that perforate the nuclear envelope and regulate bidirectional traffic of molecules (mRNA out; transcription factors, histones in)
• Nucleoplasm: gel-like interior containing:
  • Chromatin: DNA wrapped around histone octamers (nucleosomes) - heterochromatin (condensed, transcriptionally inactive) and euchromatin (dispersed, transcriptionally active)
  • Nucleolus: dense, spherical sub-region; site of ribosomal RNA (rRNA) synthesis and ribosome assembly; disappears during mitosis

• Stores and protects the genetic information (DNA)
• Transcription (DNA → mRNA)
• Pre-mRNA processing (splicing, capping, poly-A tail addition)
• Ribosome biogenesis (in nucleolus)
• Controls all cell activities - gene expression, cell cycle, differentiation

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3. Chloroplast

• Bounded by two membranes
• Outer membrane: smooth and freely permeable
• Inner membrane: contains protein transporters; selectively permeable
• Intermembrane space: between the two membranes
• Stroma: gel-like interior containing:
  • Circular chloroplast DNA
  • 70S ribosomes
  • Starch granules
  • Calvin cycle enzymes (carbon fixation)
• Thylakoids: flattened, membrane-bound sacs within the stroma, arranged in stacks called grana (singular: granum); connected by lamellae (intergranal thylakoids)
  • Thylakoid membranes contain chlorophyll and other pigments, embedded in Photosystems I and II, and the electron transport chain

• Photosynthesis:
  • Light-dependent reactions (on thylakoid membranes): Capture light energy, split water (O₂ released), generate ATP and NADPH
  • Light-independent reactions / Calvin cycle (in stroma): Use ATP and NADPH to fix CO₂ into glucose (G3P)
• Synthesis of fatty acids, amino acids
• Own DNA and ribosomes allow semi-autonomous function

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4. Golgi Apparatus

• Stack of 4-8 flattened membrane-bound cisternae (like a stack of hollow pancakes)
• Cis face (entry/receiving face): oriented toward the RER; receives vesicles budding from the RER
• Trans face (exit/dispatch face): oriented toward the plasma membrane; buds off secretory vesicles
• Sorted into: cis Golgi network → medial Golgi → trans Golgi network (TGN)

• Post-translational modification of proteins: glycosylation (addition of sugar chains), phosphorylation, sulfation, proteolytic cleavage
• Sorting and packaging of proteins and lipids into vesicles for correct destinations (lysosomes, plasma membrane, secretion)
• Synthesis of complex polysaccharides and glycolipids
• Quality control - proteins that fail quality checks are sent to lysosomes for degradation

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5. Rough Endoplasmic Reticulum (Rough ER)

• Network of membrane-bound flattened sacs (cisternae) and tubules
• Continuous with the outer nuclear membrane
• Cytoplasmic surface is studded with 80S ribosomes (giving the "rough" appearance)

• Protein synthesis: Ribosomes on the RER translate mRNAs encoding secretory, membrane, and lysosomal proteins; the nascent polypeptide is co-translationally inserted into the ER lumen
• Protein folding and modification: Glycosylation (N-linked); disulfide bond formation; chaperone assistance
• Protein quality control: Misfolded proteins are retrotranslocated and degraded (ERAD pathway)
• Vesicle budding: Correctly folded proteins are packaged into COPII-coated vesicles for transport to the Golgi

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6. Smooth Endoplasmic Reticulum (Smooth ER)

• Network of branching tubules; no ribosomes on its surface (hence "smooth")
• Continuous with the rough ER
• Relative amount varies by cell type (abundant in liver, adrenal cortex, gonads, muscle)

• Lipid synthesis: Phospholipids, cholesterol, and triglycerides
• Steroid hormone synthesis: In adrenal cortex, gonads (testosterone, oestrogen, cortisol)
• Drug detoxification: Liver SER - cytochrome P450 enzymes oxidise and conjugate drugs and toxins for excretion
• Calcium storage and release: In skeletal muscle (called sarcoplasmic reticulum) - Ca²⁺ release triggers muscle contraction
• Glycogen metabolism: Glucose-6-phosphatase activity

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7. Lysosomes

• Small (~0.1-1.2 µm), membrane-bound vesicles
• Bounded by a single membrane (the lysosomal membrane)
• Lysosomal membrane contains:
  • ATP-driven H⁺ pump (V-ATPase) maintaining interior at pH ~4.5-5.0
  • Lysosomal membrane proteins (LAMP-1, LAMP-2) that protect it from its own enzymes
• Interior contains ~60 hydrolytic enzymes (acid hydrolases):
  • Proteases (cathepsins), lipases, nucleases, glycosidases, phosphatases
  • All optimally active at acidic pH; safe at cytoplasmic pH ~7.2

• Intracellular digestion: Digest engulfed bacteria (phagolysosomes), worn-out organelles (autophagy), and macromolecules
• Autophagy: Recycling of damaged organelles - they are enclosed in autophagosomes which fuse with lysosomes
• Receptor-mediated endocytosis: Processing of endocytosed ligands
• Antigen processing: In immune cells (present peptides on MHC molecules)
• Bone resorption: Osteoclasts secrete lysosomal enzymes extracellularly to degrade bone matrix

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8. Ribosomes

• Not membrane-bound - no surrounding membrane
• Dense ribonucleoprotein particles made of rRNA + protein
• Two subunits that associate during translation:

• The ribosome has three tRNA binding sites: A site (aminoacyl), P site (peptidyl), E site (exit)

• Protein synthesis (translation): Decode mRNA codons and catalyse peptide bond formation between amino acids
• Free ribosomes (cytoplasm): synthesise proteins destined for the cytoplasm, nucleus, mitochondria, peroxisomes
• Membrane-bound ribosomes (on RER): synthesise secretory proteins, membrane proteins, lysosomal proteins

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• Single membrane: Lysosome, ER, Golgi, vacuole, peroxisome
• Double membrane: Nucleus, mitochondria, chloroplast
• Active transport is the only process that uses ATP and moves substances against their gradient
• Osmosis specifically refers to water movement; aquaporins are the water channels
• iPSCs were discovered by Yamanaka (2006); the main risk is tumourigenicity from c-Myc oncogene
• The fluid mosaic model (Singer & Nicolson, 1972) features lateral fluidity, membrane asymmetry, and lipid rafts
• Ribosomes are the only organelle with no membrane whatsoever