Chapter 03 Notes: Cells - The Living Units (Marieb & Hoehn)

Cell Theory

• Cell: the smallest structural and functional living unit.

• Cell Theory: the basic organizing principle of biology: all living things are composed of cells; body’s functions depend on cells working individually and as a group.

• Important notes from transcript:

  • Define cell and cell theory.

  • Continuity of life (from parents to child) has cellular basis.

  • Sperm cells and egg cells are used to illustrate cellular basis of reproduction.

Generalized Cell

• Three basic parts of a general cell:

  • Plasma membrane

  • Cytoplasm

  • Nucleus

• Functions to list under each major region (not expanded in slide, but typically):

  • Plasma membrane: boundary and communication; selective permeability.

  • Cytoplasm: site of metabolic activity; contains cytosol and organelles.

  • Nucleus: genetic control center; houses DNA.

Extracellular Materials

• Outside of cells, classed as:

  • Extracellular fluids (ECFs): body fluids such as interstitial fluid (bathes cells), blood plasma, cerebrospinal fluid (CSF surrounding nervous system organs).

  • Cellular secretions (e.g., saliva, mucus, gastric fluids).

  • Extracellular matrix: glue-like substance that holds cells together.

Plasma Membrane – What Does It Do?

• Purpose: boundary, protection, cell–environment interactions, controls movement of substances into and out of the cell.

• Chemical composition and relation to function:

  • Lipid bilayer as a fundamental barrier: polar (hydrophilic) heads and nonpolar (hydrophobic) tails.

  • Major lipids: phospholipids (bimolecular layer), cholesterol, glycolipids.

  • Proteins: integral (transmembrane) and peripheral.

  • Fluid Mosaic Model: proteins float in a dynamic phospholipid bilayer.

• Glycocalyx:

  • Consists of sugars attached to lipids (glycolipids) and to proteins (glycoproteins).

  • Each cell type has a unique sugar coating used as markers for cell-to-cell recognition and self/non-self identification by the immune system.

  • Functions: biological markers for recognition; helps the immune system distinguish self vs non-self.

Membrane Proteins – Types and Roles

• Integral proteins, peripheral proteins, glycoprotein markers; overview of membrane proteins:

  • Marker proteins (glycoproteins): identification tags for cell recognition.

  • Receptor proteins: binding sites for signal molecules; initiate cellular responses.

  • Enzymes: active sites for catalysis at the membrane surface.

  • Junction proteins: form various junctions between cells.

  • Transport proteins: channels and carriers enabling movement of substances across the membrane.

• Two main components of the cell membrane:

  • 1) Lipids

  • 2) Proteins

• Fluid Mosaic Model implies that protein molecules (… float in bilayer) contribute to membrane dynamics and function.

• What is a glycoprotein? A glycoprotein is a membrane protein with carbohydrate chains attached, contributing to the glycocalyx and receptor functions.

Glycocalyx

• Sugar coating on cell surface composed of carbohydrates attached to lipids (glycolipids) or proteins (glycoproteins).

• Individual cell types have different sugar patterns.

• Functions:

  • Biological markers for cell-to-cell recognition.

  • Helps immune system distinguish self from non-self.

Mechanisms of Membrane Transport

• Cell membranes are selectively permeable: they regulate what enters and leaves.

• Modes of transport:

  • Passive transport (no ATP required): diffusion, facilitated diffusion, osmosis.

  • Active transport (ATP required): primary and secondary active transport.

• Permeability concepts:

  • Freely permeable membranes allow many substances to cross.

  • Selectively permeable membranes permit certain substances to pass while blocking others.

  • Impermeable membranes block passage of most substances.

Permeability of Membranes – Why Selectivity?

• Selectivity depends on:

  • Properties of solutes (size, charge, solubility, shape).

  • Lipids and proteins present in the membrane and their arrangement.

• Charged solutes are less able to pass through the lipid bilayer; lipophilicity and solute characteristics influence transport.

Passive Transport

• Across plasma membranes via:

  • diffusion (directly through the membrane)

  • carrier-mediated transport (facilitated diffusion)

  • channel-mediated transport (facilitated diffusion)

  • osmosis (diffusion of water)

• Concentration gradient: change in concentration over distance; substances tend to move from high to low concentration.

• Equilibrium: net movement stops when concentrations are equal on both sides.

• Three main types of passive transport:

  • Simple diffusion

  • Facilitated diffusion

  • Osmosis

Diffusion (Passive Transport) – Key Concepts

• Diffusion: movement of particles from high to low concentration; no ATP used; particles move down their concentration gradient.

• Diffusion can occur directly through the phospholipid bilayer (simple diffusion) or via protein channels (facilitated diffusion).

• Terms to know:

  • Equilibrium: no net diffusion.

  • Dye in an aquarium analogy: illustrates diffusion toward equilibrium.

• Factors influencing diffusion rates:

  • Distance: shorter distance = faster diffusion.

  • Molecule size: smaller molecules diffuse faster.

  • Temperature: higher temperature = faster diffusion.

  • Concentration gradient: steeper gradient = faster diffusion.

  • Electrical forces: attraction between opposite charges or repulsion between like charges affects diffusion.

Facilitated Diffusion (Passive)

• For lipid-insoluble solutes (e.g., sugars, amino acids) that cannot cross bilayer easily.

• Carriers: binding of substrate induces a conformational change permitting passage; specificity for a chemical.

• Channels: pore-forming proteins that allow specific ions or water to cross; two types:

  • Leakage channels (always open)

  • Gated channels (open/close in response to stimuli)

Osmosis (Passive)

• Osmosis: diffusion of water across a semipermeable membrane.

• Water movement is dictated by solute concentration differences on either side of the membrane.

• Osmolarity measures total solute particle concentration.

• When solutions of different osmolarity are separated by a membrane, osmosis occurs until equilibrium is reached.

• In figure examples:

  • A membrane permeable to both solutes and water can result in equal solute concentrations on both sides with equal volumes.

  • A membrane permeable to water but not solutes results in volume differences due to water movement while solute concentrations remain identical.

• Importance: osmosis affects cell volume and function; water balance is critical for organisms.

Tonicity

• Tonicity is the ability of a solution to cause a cell to gain or lose water.

• Definitions:

  • Isotonic: solution has the same solute concentration as cytosol; no net water movement.

  • Hypertonic: solution has higher solute concentration than cytosol; cells lose water and shrink.

  • Hypotonic: solution has lower solute concentration than cytosol; cells gain water and may lyse.

• Illustrative cases:

  • Isotonic: blood plasma is balanced with plasma cells.

  • Hypertonic: cells lose water and shrink.

  • Hypotonic: cells swell, potentially bursting (lyse).

Summary of Passive Processes

• Simple diffusion: movement of molecules such as O2 through bilayer; energy is kinetic energy.

• Facilitated diffusion: movement of glucose into cells via carrier proteins; no energy used.

• Osmosis: diffusion of water through bilayer or aquaporins; no energy used.

• Energy source for all these processes: kinetic energy.

Active Transport

• Active transport moves substances against their concentration gradient (uphill) using carrier proteins (solute pumps).

• Two main types:

  • Primary active transport

  • Secondary active transport

Primary Active Transport

• Energy source: hydrolysis of ATP causes a conformational change in the transport protein, pumping solutes across the membrane.

• Example: Na⁺/K⁺-ATPase (sodium–potassium pump)

  • Located in all plasma membranes.

  • Involved in both primary and secondary active transport of nutrients and ions.

• Mechanism (Na⁺/K⁺ pump) – stepwise process:
  1) Extracellular Na⁺ binds to the pump protein.
  2) Binding of Na⁺ promotes phosphorylation of the protein by ATP.
  3) Phosphorylation causes a conformational change that expels Na⁺ to the outside.
  4) Extracellular K⁺ binds to the pump protein.
  5) Binding of K⁺ triggers release of the phosphate group.
  6) Pump returns to its original conformation; K⁺ is released inside; cycle repeats.

• Result: creates steep Na⁺ concentration gradient outside the cell and K⁺ gradient inside, fueling other transport processes.

• Important energy accounting: Na⁺/K⁺ pump moves Na⁺ out and K⁺ in with a 3:2 stoichiometry (3 Na⁺ pumped out for every 2 K⁺ pumped in).
  $3\,Na^+\text{ out} : 2\,K^+\text{ in}.$

Secondary Active Transport

• Depends on ion gradients established by primary active transport.

• Energy from ionic gradients is used indirectly to drive transport of other solutes.

• Cotransport systems:

  • Symport: two substances transported in the same direction.

  • Antiport: two substances transported in opposite directions.

• Example: Na⁺-glucose symport uses the Na⁺ gradient to drive glucose uptake into the cell.

• Key concept: the Na⁺-K⁺ pump stores energy by creating a gradient, which is then used by cotransporters.

Vesicular Transport

• Transport of large particles, macromolecules, and fluids via vesicles; requires energy (e.g., ATP).

• Major functions:

  • Exocytosis: secretion out of cell (hormones, neurotransmitters, mucus, wastes).

  • Endocytosis: uptake into cell.

  • Phagocytosis: engulfing large particles; typically for pathogens.

  • Pinocytosis: engulfing fluids.

  • Receptor-mediated endocytosis: uptake of specific ligands via receptor binding.

  • Transcytosis: transport into, across, and out of a cell; vesicular trafficking within a cell.

Receptor-Mediated Endocytosis (Endocytosis – 1)

• Materials bind to receptors on the membrane surface.

• Saturated receptor areas form pockets that pinch off to form endosomes.

• Vesicles formed have a clathrin (protein) coat on the inner membrane surface (coated vesicles).

• Fusion with lysosomes occurs, delivering digestive enzymes to the endocytosed material.

• Ligands may be released from receptors and enter the cytoplasm; vesicle membrane then detaches and recycling begins.

• Pathway can also lead to transcytosis when vesicles move to opposite sides of the cell.

Phagocytosis (Endocytosis – 2)

• Extension of pseudopodia surrounds the object (e.g., bacterium).

• Pseudopodia fuse to form a phagosome.

• Phagosome fuses with a lysosome, whose enzymes digest contents.

• Digested nutrients diffuse into the cytoplasm; residue may be expelled via exocytosis.

Pinocytosis (Endocytosis – 3)

• Small vesicles form to internalize extracellular fluid and dissolved solutes.

• Vesicles may fuse with endosomes and subsequently either recycle membrane components or release contents.

Exocytosis

• Secretory vesicles migrate to the plasma membrane.

• Vesicle membrane proteins (v-SNAREs) bind to plasma membrane SNAREs (t-SNAREs), docking the vesicle.

• Fusion pore forms and vesicle contents are released to the extracellular fluid.

• Examples: hormone secretion, neurotransmitter release, mucus secretion, and waste ejection.

Endocytosis and Transcytosis – Visual Summary

• Coated pits, vesicles, endosomes, and lysosomes participate in the endocytic process; membrane components are recycled.

• Through transcytosis, vesicles can deliver contents to the opposite side of the cell.

Electric Potential Energy and Membrane Potential

• Electric potential energy: energy stored due to separation of positive and negative charges (voltage).

• Voltage (potential difference) is measured in volts (V).

• Resting membrane potential (RMP): the steady-state voltage across cell membranes in resting cells.

• In most cells, K⁺ is higher inside and Na⁺ is higher outside.

• RMP is established and maintained by:

  • Movement of K⁺ down its concentration gradient via leakage channels (out of the cell).

  • A negative charge inside the cell due to trapped anions and the efflux of K⁺.

  • Na⁺-K⁺ ATPase maintains concentration gradients by pumping Na⁺ out and K⁺ in.

• Typical numerical values and concepts:

  • K⁺ concentration gradient drives K⁺ out; Na⁺ concentration gradient drives Na⁺ in/out as per pump activity.

  • A steady negative interior (relative to exterior) is established when the rate of K⁺ efflux equals the rate of K⁺ influx via the pump and leak channels.

  • A common reference value mentioned in slide: negative membrane potential around $V_m \,\approx\; -90\ \text{mV}$.

Intercellular Junctions

• Tight junctions: integral proteins on adjacent cells fuse to form an impermeable junction encircling the cell; prevent fluids and most molecules from passing between cells; create two compartments.

• Desmosomes (anchoring junctions): proteins (cadherins) interlock like teeth of a zipper; plaques anchor cells via keratin filaments; provide mechanical stability and resist tearing.

• Gap junctions: transmembrane proteins (connexons) form tunnels allowing small molecules and ions to pass between cells; enable rapid electrical signaling in cardiac and smooth muscle cells.

Microvilli

• Minute, fingerlike extensions of the plasma membrane.

• Found on absorptive cells (e.g., intestinal and kidney tubule cells).

• Function: increase surface area for absorption.

Organelles within the Cytoplasm – General Organization

• Cytoplasm: all materials inside the cell, excluding the nucleus.

  • Cytosol: intracellular fluid with dissolved nutrients, ions, proteins, and wastes.

  • Organelles: structures with specialized functions.

  • Inclusions: masses of insoluble materials (e.g., glycogen or lipid droplets).

• Cytoskeleton: structural proteins providing shape, strength, and intracellular transport. Three fiber types:

  • Microfilaments (actin)

  • Intermediate filaments

  • Microtubules (tubulin)

Cytoskeleton – Details

• Microfilaments (Actin): provide mechanical support; interact with myosin for muscle contraction; influence cytosol consistency.

• Intermediate filaments: provide tensile strength; stabilize organelle positions; help maintain cell shape.

• Microtubules: large, hollow tubes; attach to centrosome; anchor organelles; move organelles using motor proteins (kinesin, dynein); form spindle apparatus during division; form centrioles and cilia.

• Centrosome and Centrioles: centrosome contains a pair of centrioles; organizes microtubules during cell division.

• Cilia: motile and primary (nonmotile) types; primary cilia act as sensory organelles; motile cilia move fluids across surfaces; e.g., respiratory and reproductive tracts.

• Flagellum: whip-like extension for locomotion (in sperm).

Membranous Organelles

• Endoplasmic Reticulum (ER)

  • Rough ER (RER): has ribosomes; synthesizes proteins and glycoproteins; packages products in transport vesicles to Golgi.

  • Smooth ER (SER): lacks ribosomes; synthesizes lipids; detoxifies harmful substances; stores/releases calcium ions.

• Golgi apparatus: receives vesicles from ER; modifies and packages secretions (hormones, enzymes); adds/removes carbohydrates to/from proteins; renews/modifies plasma membrane; packages enzymes into lysosomes.

• Lysosomes: enzyme-containing vesicles; two types:

  • Primary lysosomes: contain inactive digestive enzymes.

  • Secondary lysosomes: formed when primary lysosomes fuse with damaged organelles and enzymes become active; functions include destroying bacteria and recycling damaged components.

• Peroxisomes: small, enzyme-containing vesicles; break down organic compounds; produce hydrogen peroxide (H₂O₂); catalase converts H₂O₂ to oxygen and water.

• Mitochondria: produce ATP; have smooth outer membrane and highly folded inner membrane (cristae) surrounding the matrix; powerhouse of the cell.

• Ribosomes: synthesize proteins; two types: free ribosomes (produce cytosolic proteins) and fixed ribosomes (attach to rough ER; produce proteins for packaging or membrane insertion).

• Proteasomes: contain proteases to break down damaged proteins for recycling of amino acids.

• Nucleolus: region within nucleus where rRNA synthesis and ribosomal subunit assembly occur.

• Nuclear envelope: double-membrane surrounding nucleus; contains nuclear pores for transport.

• Nuclear pores: large protein complexes spanning the nuclear envelope, allowing controlled exchange of materials.

The Nucleus

• Largest organelle; control center of the cell.

• Nucleus contains:

  • Nuclear envelope (double membrane)

  • Perinuclear space between the layers

  • Nuclear pores for communication with cytoplasm

  • Nucleoplasm and chromatin: DNA plus proteins.

  • Nucleolus: site of rRNA synthesis and ribosomal subunit assembly.

  • Nuclear matrix: protein network within nucleoplasm.

• Organization of DNA inside the nucleus:

  • Chromatin: DNA loosely coiled in non-dividing cells; becomes tightly coiled into chromosomes before division.

  • Nucleosome: DNA wrapped around histone proteins; basic unit of chromatin structure.

• DNA structure:

  • Double helix with base-pairing rules: $A!\leftrightarrow!T$ and $G!\leftrightarrow!C$.

  • Antiparallel strands: one runs 5' to 3', the other 3' to 5'.

• Genes: DNA instructions for one protein; functional unit of heredity.

• The genetic code: DNA -> RNA -> Protein; flow of genetic information.

DNA and Protein Synthesis (Molecular Biology)

• DNA structure and base pairing:

  • Adenine pairs with thymine (A-T) in DNA; Guanine pairs with cytosine (G-C).

  • In RNA, thymine is replaced by uracil (A-U and G-C pairing rules in transcription).

• Transcription (nucleus):

  • DNA code transcribed into pre-mRNA.

  • Pre-mRNA processed into mature mRNA by removing introns and joining exons; addition of 5' cap and 3' poly-A tail.

  • Mature mRNA exits nucleus via nuclear pores into cytoplasm for translation.

• Translation (cytoplasm, ribosomes):

  • Process of converting mRNA codons into a polypeptide chain using tRNA anticodons.

  • Initiation: small ribosomal subunit binds to mRNA; initiator tRNA carrying methionine (AUG) binds to start codon.

  • Formation of functional ribosome: ribosomal subunits join to enclose mRNA and tRNA; ribosome has E, P, and A sites for tRNA binding.

  • Elongation: a second tRNA arrives at the A site; peptide bond forms between amino acids; first tRNA moves to E site and exits; ribosome shifts along mRNA by one codon.

  • Termination: when stop codon is reached; release factor promotes release of completed polypeptide; ribosomal subunits separate; mRNA is freed.

• Codons and anticodons:

  • Codon: sequence of three mRNA bases that code for an amino acid.

  • Anticodon: base triplet on tRNA complementary to a codon.

  • Example: Start codon AUG codes for Methionine.

• Genetic code examples (Table 3-1 conceptually): codons specify amino acids; start codon sets reading frame; stop codons terminate translation. (Note: the transcript includes a table with several codon-to-amino-acid mappings; the key takeaways are start codon AUG = methionine and presence of stop codons UAA, UAG, UGA.)

The Cell Cycle and Mitosis

• Cell cycle phases: Interphase and Mitosis with Cytokinesis.

  • Interphase: G1 (cell growth), S (DNA replication), G2 (preparation for division). Cells may enter G0 (a non-dividing, inactive state).

  • Mitosis: Prophase, Prometaphase, Metaphase, Anaphase, Telophase; followed by Cytokinesis.

• Chromosome structure:

  • Chromosome consists of two sister chromatids held together at the centromere.

  • Centromere: constricted region linking sister chromatids.

  • During mitosis, spindle apparatus and centrosomes organize chromosomes for separation.

• Mitosis and growth: essential for growth and cell replacement; dysregulation can lead to genetic disorders and cancer.

Summary of Key Numerical Relationships and Concepts

• Na⁺/K⁺ ATPase: pumps 3 Na⁺ out and 2 K⁺ in per ATP hydrolyzed, creating gradients essential for secondary transport and RMP stabilization.

  • Stoichiometry: $3\,Na^+\;\text{out} : 2\,K^+\;\text{in}$.

• Resting membrane potential: a typical negative interior potential, influenced by K⁺ leak and Na⁺/K⁺ ATPase activity; example value mentioned: $V_m\approx -90\ \text{mV}$.

• Directionality of transport:

  • Diffusion and osmosis move down their respective gradients (high to low concentrations for solutes; higher to lower water activity for water).

  • Primary active transport uses ATP to move substances against gradients (uphill).

  • Secondary active transport uses energy stored in gradients to move other substances.

• DNA and RNA directions:

  • DNA replication proceeds in the 5' to 3' direction on the new strand templates, with Okazaki fragments on the lagging strand.

  • Transcription uses a DNA template to synthesize RNA (in the 5' to 3' direction for RNA polymerase).

• Codon-anticodon pairing principle and base rules:

  • DNA bases: A with T, G with C.

  • RNA uses U in place of T; transcription produces mRNA from a DNA template; mRNA codons are decoded by tRNA anticodons to assemble amino acids into a polypeptide.

Connections to Foundational Principles and Real-World Relevance

• The cell theory anchors biology in the notion that all functions are carried out by cells; tissues and organs are ultimately products of cellular activities.

• The plasma membrane’s selective permeability and transport mechanisms are fundamental to physiology, including nutrient uptake, waste removal, and cell signaling.

• Membrane potentials underpin nerve impulse transmission, muscle contraction, and numerous cellular processes; Na⁺/K⁺ gradients are central to bioelectricity.

• Vesicular transport (endocytosis/exocytosis) is essential for secretion, nutrient uptake, receptor signaling, and immune responses.

• The nucleus and genetic machinery govern heredity and protein synthesis; understanding transcription and translation is foundational to genetics, molecular biology, and medicine.

• Errors in inheritance, signaling, or cell cycle control underlie diseases such as cancer and congenital disorders.

Notation and Formulas Used in This Course

• Diffusion and transport gradients are described with qualitative and quantitative language; key quantitative relationships include:

  • Transport stoichiometry: $3\,Na^+\text{ out} : 2\,K^+\text{ in}$ for the Na⁺/K⁺ pump.

  • Membrane potential: $V_m$, with typical values around $-90\ \,\text{mV}$ for some cells.

  • Directionality indicators: 5' to 3' for DNA/RNA synthesis directions; concentration gradients for diffusion/osmosis.

  • Antiparallel DNA strands: strands run in opposite 5' to 3' directions.

  • Base pairing rules: $A\leftrightarrow T\,,\; G\leftrightarrow C$ in DNA; in RNA, replacement of T by U (i.e., A-U, G-C base pairs in transcription).

This set of notes captures the major and minor points from the provided transcript, organized into topic-focused sections with key mechanisms, definitions, and the essential numerical relationships that underpin the cellular processes discussed.