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Chapter 3: The Cellular Level of Organization

The Plasma Membrane

  • A flexible yet sturdy barrier surrounding the cytoplasm (plasmalemma) that encloses the cell’s contents.

  • Composed primarily of a lipid bilayer (phospholipids, cholesterol, glycolipids).

  • Lipids are amphipathic: polar hydrophilic heads and nonpolar hydrophobic tails; this drives bilayer formation with tails inward and heads outward.

  • Permeability and function shaped by membrane proteins embedded or attached to the bilayer.

  • Functions: contact with other cells, selective entry/exit of substances, presence of channels and transporters, enzymes, cell-identity markers, and linkage to cytoskeleton.

  • Adds a dynamic, fluid surface that participates in signaling and transport beyond a simple barrier.

Structures of a Cell (Overview of major components)

  • Cytoplasm and its two major components: cytosol and organelles.

  • Organelles include lysosomes, peroxisomes, mitochondria, endoplasmic reticulum (RER and SER), Golgi complex, secretory vesicles, ribosomes, proteasomes, cytoskeleton, centrosome with centrioles, cilia, flagella, vesicles, etc.

  • Nucleus contains chromatin (DNA + histones), nuclear envelope with nuclear pores, and nucleolus (ribosome synthesis).

  • Plasma membrane underlies all cytoplasmic activities and interfaces with the extracellular environment.

Cytoplasm and Cytosol

  • Cytosol: intracellular fluid portion; site of many metabolic reactions.

  • Organelles: specialized structures with characteristic shapes and functions.

  • The cytoskeleton provides structural support and enables movement; three main filament types: microfilaments, intermediate filaments, microtubules.

Cytoskeleton: Three Filament Types

  • Microfilaments (actin and myosin): thin; support cell shape, enable movement and mechanical support for microvilli.

  • Intermediate filaments: thicker than microfilaments; provide mechanical strength and structural integrity.

  • Microtubules: largest; organize cell shape, move organelles and chromosomes during division; form cilia and flagella; originate from centrosomes.

Centrosome and Centrioles

  • Centrosome consists of a pair of centrioles and the pericentriolar matrix.

  • Pericentriolar matrix contains tubulins used for microtubule growth and mitotic spindle formation.

  • Centrosomes organize the cytoskeleton and direct chromosome movement during cell division.

Cilia and Flagella

  • Cilia: numerous, short, hairlike projections; move fluids over cell surfaces; contain 20 microtubules per basal body arrangement.

  • Flagella: longer; propagate a beating motion (e.g., sperm tail) to propel the cell.

  • Basal body anchors cilia/flagella to the plasma membrane.

Ribosomes

  • Sites of protein synthesis; composed of large and small subunits.

  • Contain ribosomal RNA (rRNA) and proteins.

  • Can be free in the cytosol or attached to rough endoplasmic reticulum (RER).

Endoplasmic Reticulum (ER)

  • Network of membranous sacs and tubules; two forms:

    • Rough ER (RER): studded with ribosomes; synthesizes glycoproteins and phospholipids; initial processing of proteins; forms transport vesicles; proteins may be secreted, become part of membranes, or reside in organelles.

    • Smooth ER (SER): lacks ribosomes; synthesizes fatty acids and steroids; inactivates/detoxifies drugs; involved in glucose-6-phosphate metabolism and stores/releases calcium ions in muscle cells.

Golgi Complex

  • System of 3–20 flattened sacs (saccules) with a cis (entry) face and a trans (exit) face.

  • Functions:

    • Receives proteins from RER at the cis face.

    • Modifies, sorts, and packages proteins (glycoproteins, glycolipids, lipoproteins) within yeast-type diagrams.

    • Exits as secretory vesicles, membrane vesicles, or transport vesicles to destinations (including lysosomes or plasma membrane).

Lysosomes

  • Membrane-bound vesicles filled with digestive enzymes; acidic.

  • Digest final products of digestion into usable forms (glucose, fatty acids, amino acids).

  • Responsible for autophagy (digestion of worn-out organelles) and autolysis (destruction of injured cells).

Peroxisomes

  • Small, enzyme-containing vesicles; contain oxidases and catalase.

  • Break down fatty acids and detoxify harmful substances (e.g., hydrogen peroxide).

  • New peroxisomes bud from preexisting ones.

Proteasomes

  • Barrel-shaped proteolytic complexes that degrade unneeded or faulty proteins by proteolysis into small peptides.

Mitochondria

  • Primary site of aerobic cellular respiration; produce most of the cell’s ATP.

  • Structure includes outer membrane, inner membrane with cristae, and matrix.

  • Semi-autonomous; contain their own DNA and replicate by division.

  • Number per cell varies with energy needs.

Nucleus

  • Enclosed by a nuclear envelope with pores; continuous with rough ER.

  • Communicates with cytoplasm via nuclear pores; contains:

    • Nuclear matrix, nucleoli (ribosome production), chromatin (DNA-histone complex).

    • Chromosomes carry genes that govern cellular structure and function.

Gene Expression: Overview

  • The main job of most cells is to synthesize proteins.

  • DNA stores instructions for all proteins; not all are expressed at once.

  • A gene is expressed when the cell makes the protein it codes for.

  • Proteins are made through two main steps: transcription and translation.

The Genetic Code and Protein Synthesis

  • Genetic information storage uses a triplet code: each DNA base triplet (codon in RNA) codes for a specific amino acid.

  • A gene contains all triplets needed to code for a specific polypeptide.

  • Transcription: copying DNA information into RNA; occurs in the nucleus.

  • Translation: assembling amino acids into a protein using mRNA codons; occurs on a ribosome outside the nucleus.

Transcription (DNA → RNA)

  • Initiation: RNA polymerase binds to a promoter on the gene.

  • Elongation: RNA polymerase synthesizes a complementary RNA strand from the DNA template.

  • Termination: transcription ends at a terminator sequence; pre-mRNA is produced.

  • RNA types produced from DNA template:

    • Messenger RNA (mRNA): directs protein synthesis.

    • Ribosomal RNA (rRNA): part of ribosomes.

    • Transfer RNA (tRNA): carries amino acids to ribosome during translation.

  • Base pairing rules: in DNA, A pairs with T and G pairs with C. In RNA, A pairs with U (uracil) instead of T.

  • Transcription occurs in the nucleus.

Translation (RNA → Protein)

  • Occurs on a ribosome (cytoplasm or on RER).

  • mRNA binds to ribosome; tRNA brings amino acids in the order dictated by mRNA codons.

  • Ribosome has A (aminoacyl), P (peptidyl), and E (exit) sites for tRNA binding and peptide bond formation.

  • Initiation: initiator tRNA bearing methionine binds to start codon on mRNA.

  • Elongation: successive tRNAs bring amino acids; peptide bonds form; ribosome shifts along mRNA by one codon.

  • Termination: stop codon reaches the A site; translation ends and the completed polypeptide is released.

  • Anticodons on tRNA pair with codons on mRNA during translation.

DNA Replication (Overview)

  • The process of copying the DNA double helix prior to cell division: new strands are complementary to the old strands.

  • Involves base-pairing rules and formation of hydrogen bonds between complementary bases.

Cell Division: Mitosis and Cytokinesis (Somatic Cell Division)

  • Mitosis produces two genetically identical diploid cells; follows interphase (growth and DNA replication).

  • Interphase components:

    • G1: cell growth and organelle replication; most cellular components synthesized.

    • S: DNA replication.

    • G2: growth and preparation for mitosis; centrosomes replicated.

  • Mitosis stages:

    • Prophase: chromatin condenses into chromosomes; nuclear envelope breaks down; centrosomes move to poles; spindle apparatus forms.

    • Metaphase: chromosomes align at the metaphase plate; spindle fibers attach to kinetochores.

    • Anaphase: sister chromatids separate and move to opposite poles.

    • Telophase: chromosomes de-condense; nuclear envelope re-forms; spindle breaks down.

  • Cytokinesis: cytoplasm divides; forms two separate daughter cells; cleavage furrow pinches the cell membrane inwards.

Reproductive Cell Division: Meiosis (Gonads)

  • Meiosis produces four haploid gametes; two successive divisions (Meiosis I and Meiosis II) with genetic variation.

  • Meiosis I:

    • Prophase I: sister chromatids pair; crossing over (recombination) may occur, exchanging segments between homologous chromosomes.

    • Metaphase I: tetrads line up at the metaphase plate.

    • Anaphase I: homologous chromosomes separate; sister chromatids remain attached.

    • Telophase I: chromosomes may arrive at poles; cytoplasm divides.

  • Meiosis II resembles mitosis (no replication between divisions) and yields four haploid gametes.

  • Genetic variation arises from crossing over and independent assortment of chromosomes.

Mitosis vs Meiosis: Quick Comparison

  • Starting cell: Mitosis 2n (diploid, replicated), Meiosis I starts with 2n (diploid) and ends with n (haploid).

  • Chromosome behavior: Mitosis maintains chromosome number; Meiosis reduces chromosome number by half.

  • Key events: Mitosis has sister chromatids separation in Anaphase; Meiosis I features homologous chromosome separation and crossing over (tetrads formation).

  • End products: Mitosis yields two identical diploid cells; Meiosis yields four genetically diverse haploid gametes.

Cellular Diversity and Connections to Physiology

  • Cells vary in size, shape, and function to meet tissue-specific roles.

  • The integrated function of organelles supports metabolism, signaling, protein synthesis, energy production, detoxification, and growth.

  • Understanding transport, signaling, and division is essential for grasping organ system physiology and pathology.

Key Equations and Numeric Details (as in slides)

  • Golgi complex contains 3 ext{ to }20 flattened sacs (saccules).

  • Cilia contain 20 microtubules in their axoneme arrangement.

  • Important base-pairing rules:

    • In DNA: A ext{ pairs with } T and G ext{ pairs with } C.

    • In RNA: A ext{ pairs with } U, and G ext{ pairs with } C.

  • An electrochemical gradient combines both a concentration gradient and an electrical gradient across the plasma membrane.

  • Osmotic concepts:

    • Water moves from areas of higher water concentration to lower water concentration (i.e., from lower solute concentration to higher solute concentration).

    • Hydrostatic pressure balance with osmotic pressure determines net water movement.

  • Transport categories (summary):

    • Passive (no energy): diffusion (simple), facilitated diffusion (channel- and carrier-mediated), osmosis.

    • Active (energy required): primary active transport, secondary active transport, vesicular transport (endocytosis, exocytosis, transcytosis).

Connections to Foundational Principles

  • Structure governs function: organelle structure underpins role in metabolism, synthesis, and energy production.

  • Gradients and transport are fundamental for cellular homeostasis and signaling.

  • Gene expression links genome to phenotype through transcription and translation, enabling cell specialization and response to the environment.

  • Cell cycle control ensures growth, maintenance, and reproduction while maintaining genetic integrity.

Practical and Ethical Considerations

  • Biomedical relevance: defects in membranes, transport mechanisms, organelle function, or gene expression can lead to disease; understanding these basics informs diagnostics and therapies.

  • Research and teaching implications: visualizing cellular processes (e.g., diffusion vs. osmosis, mitosis vs meiosis) is essential for accurate interpretation of cell biology in health and disease.

Recap of Core Concepts

  • The plasma membrane is a dynamic, selectively permeable barrier composed of a phospholipid bilayer with embedded proteins.

  • Transport across the membrane occurs via passive (diffusion, osmosis, facilitated diffusion) and active (primary/secondary, vesicular) mechanisms.

  • The cytoplasm contains cytosol and organelles, with the cytoskeleton providing structure and movement.

  • Organelles coordinate synthesis, packaging, energy production, detoxification, and protein turnover.

  • The nucleus stores genetic information and coordinates gene expression through transcription and translation.

  • Mitosis and meiosis describe two fundamental cell division programs with distinct outcomes and genetic consequences.

  • Understanding these processes provides a foundation for interpreting physiology, pathology, and therapeutic interventions.