1. Biomolecules and Cell Biology

Biomolecules

1.1 Carbohydrates

Definition: Organic compounds composed of carbon, hydrogen, and oxygen, generally with the empirical formula C_n(H₂O)_n.

Classification and Examples:

• Monosaccharides: Simple sugars; e.g., α‑D‑glucose (blood sugar), fructose (fruit sugar).
• Disaccharides: Two monosaccharides linked by a glycosidic bond; e.g., sucrose (glucose+fructose, table sugar), lactose (glucose+galactose, milk sugar).
• Polysaccharides: Long chains of monosaccharides; e.g., starch (plant storage, amylose & amylopectin), glycogen (animal storage, highly branched), cellulose (plant cell wall, β‑1,4‑linked glucose).

Functions: Primary energy source (glucose oxidation yields ATP), structural support (cellulose in plant walls, chitin in fungi/arthropods), and storage (starch, glycogen).

1.2 Proteins

Definition: Polymers of amino acids joined by peptide bonds (‑CO‑NH‑) forming polypeptides.

Amino Acid Structure: Central α‑carbon bonded to an amino group (‑NH₂), carboxyl group (‑COOH), hydrogen, and a variable side chain (R‑group).

Peptide Bond Formation: Condensation reaction: R₁‑CH(NH₂)‑COOH + H₂N‑CH(R₂)‑COOH → R₁‑CH(NH₂)‑CO‑NH‑CH(R₂)‑COOH + H₂O.

Levels of Protein Structure:

1. Primary: Linear sequence of amino acids.
2. Secondary: Local folding into α‑helices (stabilized by H‑bonds every 4th residue) or β‑pleated sheets (H‑bonds between strands).
3. Tertiary: Overall 3‑D shape of a single polypeptide, stabilized by disulfide bridges, ionic bonds, hydrophobic interactions, and H‑bonds.
4. Quaternary: Association of multiple polypeptide subunits (e.g., hemoglobin: α₂β₂).

Functions: Enzymatic catalysis, structural support (collagen, keratin), transport (hemoglobin, membrane carriers), defense (antibodies, clotting factors), signaling (hormones, receptors).

1.3 Lipids

Definition: Hydrophobic or amphipathic molecules soluble in organic solvents; include fats, oils, waxes, phospholipids, and steroids.

Types and Examples:

Functions: Energy storage (fat yields ~9 kcal/g), insulation and protection (subcutaneous fat, myelin), major component of cell membranes (phospholipid bilayer, cholesterol modulates fluidity), precursors for hormones and vitamin D.

1.4 Nucleic Acids

Definition: Polymers of nucleotides that store and transmit genetic information.

Nucleotide Structure: Phosphate group + pentose sugar (ribose in RNA, deoxyribose in DNA) + nitrogenous base (adenine, guanine, cytosine, thymine (DNA) or uracil (RNA)).

Base Pairing Rules (Watson‑Crick): Adenine pairs with thymine (A‑T) via two hydrogen bonds; guanine pairs with cytosine (G‑C) via three hydrogen bonds. In RNA, uracil replaces thymine (A‑U).

DNA: Double‑helix, antiparallel strands, major repository of genetic code; functions: storage of hereditary information, replication, transcription.

RNA: Usually single‑stranded; types: mRNA (messenger, carries code to ribosome), tRNA (transfer, brings amino acids), rRNA (ribosomal, structural and catalytic). Functions: transfer of genetic information, protein synthesis, regulation.

1.5 Minerals

Definition: Inorganic elements required in trace or larger amounts for physiological processes.

Macro‑minerals (required >100 mg/day): Calcium (Ca²⁺), Phosphorus (P as phosphate), Potassium (K⁺).

Micro‑minerals (trace, required <100 mg/day): Iron (Fe²⁺/Fe³⁺), Zinc (Zn²⁺), Copper (Cu²⁺), etc.

Functions:

• Calcium: bone/teeth structure, blood clotting, muscle contraction, nerve signaling.
• Phosphorus: component of ATP, nucleic acids, phospholipids, bone mineral.
• Potassium: maintains membrane potential, enzyme activation, osmolarity.
• Iron: part of hemoglobin (O₂ transport), cytochromes (electron transport).
• Zinc: cofactor for >300 enzymes (DNA polymerase, carbonic anhydrase), immune function.
• Copper: cofactor for cytochrome c oxidase, lysyl oxidase (cross‑linking collagen).

1.6 Enzymes

Definition: Biological catalysts, almost exclusively proteins, that increase reaction rates without being consumed.

Models of Enzyme Action:

• Lock‑and‑Key: Enzyme active site is a rigid complement to substrate.
• Induced‑Fit: Binding induces conformational change, improving fit and catalytic efficiency.

Factors Affecting Activity:

• pH: Each enzyme has optimal pH (e.g., pepsin pH 2, trypsin pH 8). Deviations alter ionization of active‑site residues.
• Temperature: Rate increases with temperature up to optimum (~37 °C for human enzymes); denaturation occurs beyond.
• Substrate Concentration: Follows Michaelis‑Menten kinetics: V = (Vmax [S]) / (Km + [S]), where Vmax is maximal rate and Km is substrate concentration at ½ Vmax.

Enzyme Classes (by reaction type):

1.7 Water

Definition: Polar molecule (H₂O) with high dielectric constant, essential as solvent.

Key Properties:

• Universal Solvent: Dissolves ionic and polar substances (salts, sugars, amino acids).
• Cohesion & Adhesion: Hydrogen bonding gives high surface tension, capillary action (important in xylem).
• High Specific Heat: Buffers temperature changes in organisms.
• High Heat of Vaporization: Evaporative cooling (sweating).

Roles in Biochemistry: Medium for metabolic reactions, participant in hydrolysis (e.g., peptide bond cleavage) and dehydration synthesis (e.g., peptide bond formation), reactant in photosynthesis (6 CO₂ + 6 H₂O → C₆H₁₂O₆ + 6 O₂).

Cell

2.1 Introduction of Cell

Cell Theory (Schleiden, Schwann, Virchow):

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 by division.

Prokaryotic vs. Eukaryotic Cells:

2.2 Detailed Structure of Eukaryotic Cells

Cell Wall

Composition: Primarily cellulose microfibrils embedded in a matrix of hemicellulose and pectin (plants). Provides rigidity, shape, and protection against osmotic lysis.

Cell Membrane

Phospholipid Bilayer: Amphipathic molecules arrange with hydrophilic heads outward and hydrophobic tails inward, forming a fluid mosaic.

Fluid Mosaic Model: Proteins (integral, peripheral) float within the lipid bilayer, enabling transport, signaling, and enzymatic activities.

Transport Mechanisms: Passive (simple diffusion, facilitated diffusion via channels/carriers) and active (ATP‑driven pumps, e.g., Na⁺/K⁺‑ATPase).

Mitochondria

Structure: Double membrane; inner membrane folded into cristae increasing surface area; matrix contains enzymes for Krebs cycle.

Function: Site of oxidative phosphorylation; produces ATP via electron transport chain and chemiosmosis. Semi‑autonomous: possesses circular DNA, ribosomes, and divides independently.

Plastids (Plant Cells)

• Chloroplasts: Site of photosynthesis; contain thylakoid membranes (photosystems I & II) stacked into grana; stroma houses Calvin‑Benson cycle enzymes.
• Chromoplasts: Synthesize and store pigments (carotenoids) giving color to flowers/fruits.
• Leucoplasts: Non‑pigmented; specialize in storage (amyloplasts – starch, proteinoplasts – proteins, elaioplasts – lipids).

Endoplasmic Reticulum (ER)

Rough ER: Studded with ribosomes; site of synthesis of secretory and membrane proteins; nascent polypeptides enter lumen for folding and glycosylation.

Smooth ER: Lacks ribosomes; involved in lipid synthesis, steroid hormone production, detoxification (e.g., cytochrome P450 enzymes), and calcium storage.

Golgi Apparatus (Golgi Bodies)

Structure: Stacked flattened cisternae; receives vesicles from ER, modifies (glycosylation, phosphorylation), sorts, and packages proteins/lipids into vesicles for secretion or lysosomal delivery.

Lysosomes

Content: Acidic lumen (pH ≈ 4.5) containing hydrolytic enzymes (proteases, nucleases, lipases).

Functions: Intracellular digestion (autophagy), degradation of worn‑out organelles, apoptosis, defense against pathogens (phagolysosome formation).

Ribosomes

Size: 80S in eukaryotes (60S large subunit + 40S small subunit); 70S in prokaryotes.

Function: Site of translation; mRNA decoded to synthesize polypeptide chains.

Nucleus

Components: Nuclear envelope (double membrane with pores), nucleoplasm, nucleolus (site of rRNA transcription and ribosome assembly), chromatin (DNA‑protein complex), chromosomes.

Chromosomes

Structure: Consist of two sister chromatids joined at the centromere.

Centromere Types (based on position):

• Metacentric – centromere middle, arms equal.
• Submetacentric – off‑center, arms unequal.
• Acrocentric – near one end, very short p‑arm.
• Telocentric – at terminal end (rare in humans).

Cilia and Flagella

Axoneme: 9+2 microtubule arrangement (nine doublet pairs surrounding two central singlets). Powered by dynein arms; responsible for locomotion (e.g., sperm flagella) and moving fluid across epithelial surfaces (cilia in respiratory tract).

Cell Inclusions

Non‑living substances stored in the cytoplasm: starch grains (amyloplasts), lipid droplets, protein granules, crystals (e.g., calcium oxalate), pigments.

Cell Division

3.1 Concept of Cell Cycle

The cell cycle is an ordered series of events leading to cell duplication.

Phases:

• G₁ (Gap 1): Cell growth, synthesis of proteins and organelles.
• S (Synthesis): DNA replication; each chromosome duplicated.
• G₂ (Gap 2): Preparation for mitosis; synthesis of mitotic proteins.
• M (Mitosis): Nuclear division (karyokinesis) followed by cytokinesis.

Interphase: G₁ + S + G₂ (cell spends ~90% of time here).

Checkpoint Regulation: Critical control points ensure fidelity:

• G₁ checkpoint (restriction point) – evaluates size, nutrients, growth factors, DNA damage.
• G₂ checkpoint – verifies DNA replication completeness and damage.
• M checkpoint (spindle assembly checkpoint) – ensures all kinetochores attached to spindle microtubules before anaphase.

Regulatory Proteins: Cyclins fluctuate in concentration; Cyclin‑Dependent Kinases (CDKs) are activated upon cyclin binding, phosphorylating target proteins to drive cycle progression (e.g., Cyclin D/CDK4‑6 in G₁, Cyclin E/CDK2 at G₁/S, Cyclin A/CDK2 in S, Cyclin B/CDK1 at G₂/M).

3.2 Types of Cell Division

Amitosis

Direct splitting of the nucleus and cytoplasm without chromosome condensation or spindle formation. Observed in some bacteria, protozoa, and certain specialized mammalian cells (e.g., liver hepatocytes). Results in unequal distribution of genetic material.

Mitosis

Equational division producing two genetically identical diploid daughter cells.

Stages:

1. Prophase: Chromatin condenses into visible chromosomes; nucleolus disappears; mitotic spindle begins to form from centrosomes.
2. Metaphase: Chromosomes align at the metaphase plate (equatorial plane); spindle fibers attach to kinetochores.
3. Anaphase: Sister chromatids separate and are pulled toward opposite poles by shortening kinetochore microtubules.
4. Telophase: Chromatids reach poles, decondense; nuclear envelopes reform; nucleoli reappear; cytokinesis begins (contractile actin‑myosin ring in animal cells, cell plate formation in plant cells).

Outcome: Two daughter cells each with the same chromosome number as the parent (2n → 2n).

Meiosis

Reduction division generating four haploid gametes from one diploid precursor; essential for sexual reproduction.

Meiosis I (Reductional): Homologous chromosomes segregate.

1. Prophase I: Chromosome pairing (synapsis), crossing over (chiasmata formation) between non‑sister chromatids.
2. Metaphase I: Tetrads align at metaphase plate.
3. Anaphase I: Homologs separate; sister chromatids remain attached.
4. Telophase I: Two haploid cells formed (each chromosome still consists of two chromatids).

Meiosis II (Equational): Similar to mitosis but without prior DNA replication.

1. Prophase II: Chromosomes condense.
2. Metaphase II: Chromosomes align singly.
3. Anaphase II: Sister chromatids separate.
4. Telophase II: Four haploid cells produced.

Sources of Genetic Variation:

• Crossing over (recombination) during Prophase I.
• Independent assortment of homologous chromosomes during Metaphase I.
• Random fertilization.

3.3 Significance of Cell Division

• Growth: Increase in cell number contributes to organismal size.
• Repair: Replaces damaged or dead cells (e.g., skin epithelium, gut lining).
• Reproduction: Mitosis underlies asexual reproduction; meiosis produces gametes for sexual reproduction.
• Genetic Variation: Meiosis and recombination generate diversity essential for evolution and adaptation.
• Maintenance of Chromosome Number: Alternating mitosis (keeps ploidy constant) and meiosis (halves then restores via fertilization) ensures species‑specific chromosome complement across generations.