Cell Structure and Function

Cellular Study Tools & Diagnostic Techniques

• Diagnostic & Analytical Methods:

  • Microscopy: Light, fluorescence, dark field, confocal, scanning electron microscopy (SEM), and atomic force microscopy (AFM; resolution $0.1\,\text{nm}$).

  • Molecular & Biochemical Tools: Cell culture (e.g., HeLa, microbes), biochemical fractionation, electrophoresis, chromatography, gene isolation, recombinant DNA, monoclonal antibodies, immunogold labeling, immunohistochemistry, autoradiography, and mathematical models.

  • Clinical Imaging: Ultrasound, X-rays, computerized tomography (CT), and magnetic resonance imaging (MRI).

• Tissue Preparation & Stains:

  • Steps: Fixation, decalcification/dehydration, embedding, sectioning, and staining.

  • Stains: Hematoxylin (basic), Eosin, Methylene blue, toluidine blue, Alcian blue, and Periodic stain (Iodine for carbohydrates/polysaccharides).

  • Special nuclear stains and markers: Osmium, Thallium, Silver, Tritiated Actinomycin D, and Fluorodeoxyuridine.

Cellular Pathology & Clinical Context

• Etiology of Cell Sickness and Death:

  • Congenital diseases: Present from birth.

  • Acquired diseases: Including cancers.

  • Other causes: Traumatic injuries, infections, autoimmune disorders, idiopathic causes (unknown origins), and degenerative diseases (e.g., Alzheimer's disease).

• Cellular Diversity: Key variables across cell types include service, signals, sizes, shape, span, structure, and surface.

Nuclear Structure, Chromatin & Chromosomes

• Nuclear Composition:

  • Houses the human DNA genome consisting of $2.85 \times 10^9$ nucleotide pairs.

  • Components include the nucleolus, nucleoplasm, chromatin fibers, polysomes, polymerases, ribosomal precursor elements, histone and non-histone proteins, nucleolini/vacuoles, and the nuclear envelope with nuclear pore complexes.

  • Nuclear Pore Complex (NPC): Composed of an FG Nups layer (Phenylalanine-Glycine repeats), scaffold layer, membrane layer, nuclear basket, cytoplasmic filaments, cytoplasmic ring, nuclear ring, and nuclear filaments.

• Chromatin States & Terminology:

  • Chromosome: Thread-like structure carrying genetic information.

  • Chromatid: One of two identical strands of a replicated chromosome.

  • Chromatin: Protein, RNA, and DNA complex forming eukaryotic chromosomes.

  • Euchromatin: Loosely packed, active transcriptionally; contains all active genes.

  • Heterochromatin: Tightly packed, dense ($100\,\text{\AA}$ thick fibrils), transcriptionally inert/inactive.

• Nucleosome Architecture & Packaging:

  • Core octamer contains pairs of histones H2A, H2B, H3, and H4, wrapped by $146\,\text{bp}$ of DNA. Histone H1 acts as a linker protein outside the core.

  • Histone Tail Modifications: Acetylation, methylation, phosphorylation, ubiquitination (small ubiquitin), tetradecanoyl transferase activity, ADP-ribosylation, and citrullination; modified by "writers," "readers," and "erasers."

  • Hierarchical Packaging Levels: DNA double helix ($2\,\text{nm}$) $\rightarrow$ "Beads-on-a-string" nucleosomes ($11\,\text{nm}$) $\rightarrow$ Packed nucleosome fiber ($30\,\text{nm}$) $\rightarrow$ Extended section ($300\,\text{nm}$) $\rightarrow$ Condensed metaphase section ($700\,\text{nm}$) $\rightarrow$ Entire metaphase chromosome ($1400\,\text{nm}$).

• Chromosome Features & Genetics:

  • Features: P arm (short), Q arm (long), centromere, telomeres, chromatids, genes, alleles, and replication origins.

  • Karyotype: Total of $46$ chromosomes (autosomals and sex chromosomes).

  • Expression: Females possess two X chromosomes per cell with only one expressed (via X-inactivation/imprinting); males express one X and one Y.

Protein Synthesis & Endomembrane System

• Endoplasmic Reticulum (ER):

  • Rough ER (Ergastoplasm): Involved in protein synthesis, transcription processing, pre-mRNA modification, and bidirectional coatomer traffic with the Golgi apparatus. Utilizes $40\text{--}50$ distinct tRNAs, signal peptides, recognition particles, and docking proteins.

  • Smooth ER: Dedicated to lipid, steroid, and fat synthesis.

• Ribosomes & Translation:

  • Consist of two subunits ($30\text{S}$ and $50\text{S}$ in prokaryotes / $30/50$).

  • Stages: Initiation (formation of transitional complex with starting codon AUG), Elongation (tRNAs add amino acids), and Termination (release factor recognizes stop codon UAG; polypeptide released).

  • Free polyribosomes synthesize cytoplasmic proteins; bound polyribosomes synthesize proteins segregated into the rough ER lumen.

• Golgi Apparatus & Secretion:

  • Consists of stacked cisternae with a cis face (receiving) and trans face (shipping).

  • Modifies proteins post-translationally with enzymes and packages cargo.

  • Forms the secretory pathway alongside the ER and plasma membrane, utilizing Vesicular Tubular Carriers (VTC) and the Trans-Golgi Network (TGN).

Genetic Mutations & Clinical Disorders

• Chromosomal Alterations:

  • Nullisomy (incompatible with life), monosomy, disomy, microdeletions, and trisomy.

  • Conditions: Angelman's syndrome (microdeletion), Prader-Willi syndrome (microdeletion), Down syndrome, Edwards syndrome, and Patau syndrome.

• Types of Gene Mutations:

  • Silent Mutation: Single base change with no effect on amino acid sequence.

  • Missense Mutation: Single base substitution altering amino acid sequence.

  • Example: Sickle Cell Anemia (HbSS), a mutation in the beta-globin gene replacing glutamic acid with valine at position 6 (DNA: CCT GAG GAG $\rightarrow$ CCT GTG GAG; RNA: CCU GUG GAG).

  • Nonsense Mutation: Generates a premature stop codon, producing a truncated protein fragment.

  • Frameshift Mutation: Insertion or deletion altering the reading frame; linked to Crohn's disease and various cancers.

• Trinucleotide Repeat Expansion:

  • Huntington's Disease: Mapped to chromosome 4, caused by expanded CAG repeats (greater than $35$) coding for glutamine sequences.