Eukaryotes

Characteristics of Eukaryotic Cells

Eukaryotes are organisms whose cells contain a nucleus and various membranous organelles. They arose approximately 2.7 billion years ago and are typically larger than prokaryotes, ranging from 10 to 100 μm.

• Nucleus: Surrounded by a double membrane (envelope) with pores and ribosomes. Contains inner lamina, matrix, nucleolus, and chromosomes (DNA coiled with histones).

• Cellular Replication: Includes interphase (DNA duplication), mitosis (division of duplicated chromosomes), and cytokinesis (cellular division).

• Mitosis Stages: Prophase (chromosomes condense, nuclear envelope degrades), prometaphase (chromosomes sort), metaphase (align), anaphase (separate), telophase (decondense, nuclei reform).

• Meiosis: Produces four haploid gametes through two divisions (2n → n → n).

Organelles and Functions

Eukaryotic cells contain specialized organelles for various functions.

• Mitochondrion, Chloroplast, Hydrogenosome: Endosymbionts providing energy; have multiple membranes, circular DNA, and ribosomes.

• Endoplasmic Reticulum: Rough ER (ribosomes for protein synthesis), Smooth ER (Ca2+ storage, lipid production).

• Golgi Apparatus: Glycosylation and sorting of proteins.

• Lysosomes: Acidic hydrolase digestion; fuse with phagosomes/endosomes.

• Endocytosis: Includes phagocytosis (engulfing targets), pinocytosis (membrane recycling), and receptor-mediated endocytosis (clathrin-dependent).

• Cytoskeleton: Microtubules, microfilaments, intermediate filaments for motility, transport, and rigidity; flagella and cilia (9+2 microtubule arrangement).

Fungi

Fungi are eukaryotic organisms including molds and yeast.

• Cell Wall: Composed of chitin, β-glucans, mannoproteins, and sometimes cellulose.

• Cell Membrane: Contains ergosterols.

• Hyphae: Septate (divided) or aseptate (continuous); form macroscopic mycelium.

• Spores: Sporangiospores (from sporangium), conidiospores (from vegetative cells).

• Pathogenicity: Mycoses (infections), mycotoxins, allergens; dimorphism (mold in cold, yeast in heat).

Protists

Protists are diverse eukaryotes, often unicellular, with vegetative trophozoites and dormant cysts.

• Cercozoans: Foraminiferans (calcium shells), radiolarians (silica shells).

• Stramenopiles: Diatoms (silicon frustule), oomycetes (water molds), brown/golden algae.

• Alveolates: Ciliates (Balantidium), dinoflagellates (red tides, neurotoxins), apicomplexans (Plasmodium, Toxoplasma).

• Parabasalids: Hydrogenosome, anoxic (Trichomonas).

• Diplomonads: Bi-nucleate (Giardia).

• Euglenozoa: Single mitochondrion, flagella (Euglena, Trypanosoma).

• Amoebozoa: Amoeba, slime molds.

Helminths

Helminths are parasitic worms, including flatworms (Platyhelminthes) and roundworms (Aschelminthes).

• Flatworms: Often segmented, suckers, monoecious, lack or have rudimentary GI tract. Includes cestodes (tapeworms, e.g., Taenia) and trematodes (flukes, e.g., Clonorchis).

• Roundworms: Cylindrical, teeth, dioecious, complete GI tract. Includes nematodes (Ascaris, Enterobius).

Microbial Genetics

Genes and Genomes

Microbial genetics studies the structure and function of genes and genomes.

• Gene: Functional segment of DNA; allelic variants (dominant/recessive).

• Genome: Sum of all genetic elements.

DNA Structure and Replication

• DNA: Double helix, antiparallel strands, phosphate-deoxyribose backbone, base pairs (A=T, C≡G).

• Replication: DNA polymerase builds 5'→3'; primase generates RNA primers; leading and lagging strands (Okazaki fragments); ligase seals gaps; gyrase unwinds DNA; helicase separates strands; SSB stabilizes single-stranded DNA.

• Bacterial Replication: Bidirectional, θ (theta) structure.

Central Dogma

• DNA → RNA → Protein: Fundamental flow of genetic information.

Transcription

• Initiation: Promoter, RNA polymerase, transcription factors.

• Elongation: RNA polymerase builds RNA 5'→3' (U replaces T, ribose sugars).

• Termination: Rho proteins or stem-loop (hairpin).

• Processing (Eukaryotes): mRNA cap, tail, splicing (introns removed).

Translation

• tRNA: Cloverleaf structure, anticodon loop, amino acid binding.

• Aminoacyl-tRNA synthetases: Attach amino acids to tRNA.

• Genetic Code: Universal and redundant (codons).

• Ribosome: Small and large subunits, catalytic rRNA, proteins; E-P-A sites.

• Initiation: 16S rRNA binds mRNA, tRNAmet binds start codon (AUG), large subunit attaches.

• Elongation: tRNA cycles A→P→E, peptide grows amino→carboxyl terminus.

• Termination: Release factors bind stop codon, hydrolysis, ribosome dissociation.

• Polyribosomes: Multiple ribosomes translate mRNA simultaneously.

Gene Expression Regulation

• Operons: Trp operon (corepressor activates repressor), Lac operon (inducer inactivates repressor).

• Regulation: DNA accessibility, transcriptional, post-transcriptional, translational, post-translational, RNA/protein half-lives.

Horizontal Gene Transfer

• Transformation: Uptake of DNA from surroundings.

• Transduction: DNA transfer via bacteriophage.

• Conjugation: Exchange via F plasmid or Hfr.

• Transposition: Jumping elements (transposons).

Mutations

• Point Mutations: Base substitution (silent, nonsense, missense).

• Frameshift: Base additions or deletions.

• UV Damage: Thymine dimers, error-prone excision repair.

Molecular Biology Techniques

• Restriction Endonucleases: Create compatible ends for cloning.

• Plasmid Vectors: Used in transformation.

• RFLP Mapping: Restriction fragment length polymorphism.

• Sequencing: Determining DNA sequence.

• PCR: Polymerase chain reaction for DNA amplification.

Virology

Virus Structure and Classification

Viruses are obligate intracellular parasites, ranging from 20–300 nm, relying on host metabolism.

• Naked Virus: Nucleocapsid (capsid proteins surround nucleic acid); symmetry can be helical, icosahedral, or complex.

• Enveloped Virus: Lipids/proteins surround nucleocapsid.

• Baltimore & Temin Classification: Based on genome and replication mode:

  • I: dsDNA

  • II: +ssDNA

  • III: dsRNA

  • IV: +ssRNA

  • V: –ssRNA

  • VI: +ssRNA-RT

  • VII: dsDNA-RT

Viral Gene Expression and Life Cycle

• Gene Expression: Must produce viral +ssRNA; encode capsid, envelope proteins, polymerases, RNA replicases, reverse transcriptase.

• Host-derived: Metabolic enzymes, lipid membranes, ribosomes, tRNA, rRNA.

• Life Cycle: Adsorption (viral protein + host receptor), penetrance/uncoating, synthesis (DNA virus in nucleus, RNA virus in cytoplasm), assembly, release (exocytosis/cellular lysis).

Cytopathic Effects and Infection Phases

• Cytopathic Effects: Inclusion bodies, membrane fusion (syncytia), lysis.

• Phases: Lysogenic (integration, dormancy), lytic (replication, release), chronic latent (periodic lytic), oncogenic (tumorigenesis).

Bacteriophage

• Temperate: Lytic and lysogenic integration as prophage.

• Lysogenic Conversion: Phage genes add pathogenicity (toxins: diphtheria, cholera, botulinum).

Virus Cultivation and Pathogens

• Cultivation: Chicken eggs (pocks), cell culture (PFU), in vivo (animal models).

• Pathogens: Common cold, flu, hepatitis, chicken pox, herpes, rabies, Ebola, dengue fever, AIDS, etc.

Prions, Satellite Viruses, and Viroids

• Prions: Proteinaceous infectious particles; cause diseases like BSE and Creutzfeldt-Jakob.

• Satellite Viruses: Depend on another virus for replication (e.g., Hepatitis D).

• Viroids: Smallest infectious organisms; ssRNA, no capsid.

Treatments

• Antibiotics: Ineffective against viruses.

• Antivirals: Disrupt viral replication/assembly.

• Vaccination: Attenuated viruses used for immunization.