Chapter 4
Think-Pair-Share: Opening Questions
Are all living things made of cells?
Five things you know about cells in general (as listed):
Basic unit of life
Cells come from pre-existing cells (Cell Theory)
Two types: Prokaryotes and Eukaryotes
Cells divide (binary fission in Prokaryotes; mitosis or meiosis in Eukaryotes)
Cells can have organelles (Eukaryotes)
Cells can be specialized
Introduction to Cells: History and Cell Theory
Early cell observation: cells first observed under a microscope in 1665 by Robert Hooke.
Pioneers in cell theory: Mathias Schleiden (1838) and Theodor Schwann (1839).
Schleiden and Schwann proposed the Cell Theory.
Cell Theory (core principles):
All organisms are composed of cells
Cells are the smallest living things
Cells arise only from pre-existing cells
All cells today represent a continuous line of descent from the first living cells
Cell Size and Diffusion (Limitations)
Most cells are relatively small because diffusion of substances in and out of cells is essential for function.
Rate of diffusion is affected by several factors:
Surface area available
Temperature
Concentration gradient
Distance
Surface Area-to-Volume Ratio and Cell Design
An organism made of many small cells has advantages over one made of fewer, larger cells due to SA:V considerations.
As a cell’s size increases, its volume grows more rapidly than its surface area.
Some cells overcome diffusion limitations by becoming long and narrow (e.g., neurons).
Microscopy and Resolution
Most cells are too small to be seen with the naked eye; typical cell diameter < 50\,\mu m.
Resolution: the minimum distance two points must be apart to be distinguished as two points.
Naked eye resolution: objects must be separated by roughly 100\,\mu m to be resolved as two objects.
Prokaryotic vs. Eukaryotic Cells (Overview)
Prokaryotic cells:
Include Bacteria and Archaea
Lack a membrane-bound nucleus
DNA located in the nucleoid
Have a cell wall outside the plasma membrane
Contain ribosomes
Eukaryotic cells: plants, animals, fungi, and protists
Contain a membrane-bound nucleus and membrane-bound organelles
Have compartmentalized cytoplasm and an endomembrane system
Basic structural similarities between cell types include:
Nucleoid or nucleus where DNA is located
Cytoplasm (semifluid matrix of organelles and cytosol)
Ribosomes (protein synthesis)
Plasma membrane (phospholipid bilayer)
Prokaryotic Cells: Structure and Features
Two domains: Archaea and Bacteria
Key features:
No membrane-bound nucleus
DNA in nucleoid region
Cell wall outside the plasma membrane
Ribosomes present
Some prokaryotes contain specialized organelles or infoldings (e.g., magnetosomes, infoldings of the plasma membrane that aggregate reactions).
Prokaryotic cells are typically small and simple; first appearance around 3.5\,\text{BYA}; unicellular.
Archaea: cell walls lack peptidoglycan and exhibit diversity in membrane lipids; different from bacteria.
Bacteria: include rod-shaped examples; show various external structures (fimbriae, capsule, pili, flagella).
Prokaryotic Cell Exterior and Internal Organization
External features often include:
Glycocalyx (capsule) for protection and adhesion
Pili for attachment or DNA transfer
Flagella for locomotion (rotary motion)
Internal features include:
Nucleoid containing bacterial chromosome
Ribosomes for protein synthesis
Plasma membrane; cell wall
Prokaryotic cells may show microcompartments (bacterial microcompartments) that are bounded by a protein shell (40–400 nm) and serve to isolate metabolic processes or store substrates.
Cytoskeleton-like elements exist in prokaryotes and influence cell shape in conjunction with the cell wall.
Bacterial cell walls are primarily composed of peptidoglycan and are critical for protection, shape, and antibiotic susceptibility.
Archaea differ in cell wall composition and membrane lipid structure (saturated hydrocarbons attached to glycerol at both ends).
Prokaryotic Flagella
Present in some prokaryotes; allow locomotion via rotary motion; can be one or multiple if present.
Eukaryotic Cells: Overview and Key Features
Eukaryotic cells possess a membrane-bound nucleus and a compartmentalized cytoplasm with membrane-bound organelles.
Hallmark: compartmentalization via membrane-bound organelles and an endomembrane system.
Eukaryotic cells also possess a cytoskeleton for support and maintenance of cellular structure.
Two broad cell types: Animal cells and Plant cells (with unique features in each).
Animal and Plant Cells: Idealized Structures
Animal cell features ( Structures labeled in pink on diagrams ):
Nuclear envelope
Lysosome
Ribosomes (free or attached to rough ER)
Golgi apparatus
Vesicle
Plasma membrane
Nucleus (DNA location)
Endoplasmic Reticulum (ER): rough and smooth variants
Mitochondrion
Cytoskeleton
Cytoplasm
Flagellum (in some cells)
Plant cell features ( Structures labeled in green on diagrams ):
Chloroplast
Mitochondrion
Nuclear envelope and nucleus
Endoplasmic Reticulum (ER): rough and smooth
Ribosomes
Cytoskeleton
Golgi apparatus
Vesicle
Cytoplasm
Central vacuole
Plasma membrane
Cell wall
Cell wall of adjoining cell (plasmodesmata in plant cells)
Nucleus and Chromatin
Nucleus is the repository of genetic information in most eukaryotic cells.
The nucleolus is the region where ribosomal RNA (rRNA) synthesis occurs.
The nuclear envelope consists of two phospholipid bilayers and contains nuclear pores that regulate traffic between the nucleus and cytoplasm.
In eukaryotes, DNA is organized into multiple linear chromosomes; chromatin is composed of DNA wrapped around proteins.
Ribosomes
The cell’s protein synthesis machinery.
Found in all cell types across all three domains.
Composed of ribosomal RNA (rRNA) + proteins; complexed with mRNA and tRNA during translation.
Ribosomes can be free in the cytoplasm or attached to the endoplasmic reticulum (rough ER).
Ribosome structure includes a large and small subunit (as shown in typical figures).
Endomembrane System
A network of membranes throughout the cytoplasm that divides the cell into functional compartments.
A fundamental distinction between eukaryotes and prokaryotes.
Major components include:
Nuclear envelope
Endoplasmic reticulum (ER)
Golgi apparatus
Lysosomes
Vacuoles
Plasma membrane
These components are either continuous or connected via transfer by vesicles.
Protein production pathway (cis → trans Golgi):
Transcription in the nucleus produces RNA from DNA.
Translation at ribosomes produces proteins.
Proteins may be processed in the ER and Golgi and then trafficked via vesicles to the plasma membrane or extracellular space.
Endoplasmic Reticulum (ER)
Rough ER (RER):
Ribosomes bound to the membrane give a rough appearance.
Synthesis of proteins to be secreted, sent to lysosomes, or integrated into the plasma membrane.
Smooth ER (SER):
Lacks bound ribosomes.
Involves a variety of metabolic functions including lipid synthesis and storage.
The ratio of RER to SER depends on cell function.
Golgi Apparatus
Flattened stacks of interconnected membranes (Golgi bodies).
Functions include packaging and distribution of molecules synthesized at one location and used at another within the cell or exported outside the cell.
Has cis (receiving) and trans (shipping) faces.
Vesicles transport molecules to the appropriate destination.
Lysosomes and Other Microbodies
Lysosomes:
Membrane-bounded digestive vesicles that arise from the Golgi apparatus.
Contain hydrolytic enzymes that catalyze breakdown of macromolecules.
Fuse with target to initiate breakdown; recycle old organelles or digest cells/foreign matter via phagocytosis.
Microbodies (e.g., peroxisomes):
Contain enzymes for oxidation of fatty acids and other metabolic reactions; produce hydrogen peroxide as by-product and detoxify via catalase.
Vacuoles:
Plant cells commonly have a central vacuole; other types include storage vacuoles in plants and contractile vacuoles in some fungi/protists.
Mitochondria and Chloroplasts
Mitochondria:
Present in all eukaryotic cells; bound by membranes with an inner membrane folded into cristae.
Matrix contains enzymes for oxidative metabolism; have their own DNA.
Chloroplasts:
Present in plant cells and some other eukaryotes; surrounded by two membranes and contain chlorophyll for photosynthesis.
Thylakoids are membranous sacs; grana are stacks of thylakoids; have their own DNA.
Endosymbiosis Theory:
Proposes that mitochondria and chloroplasts evolved from symbiotic relationships where a prokaryote was engulfed by another cell.
Modern evidence shows similarities between mitochondria/chloroplasts and free-living prokaryotes (e.g., DNA and ribosomes).
Origins (illustrated in figures):
Modern eukaryotes likely arose from an ancestral endosymbiotic event with proteobacteria (mitochondria) and cyanobacteria (chloroplasts).
The Cytoskeleton
Network of protein fibers found in all eukaryotic cells; supports cell shape, organizes internal components, and enables movement.
Three main types of fibers:
Microfilaments (actin filaments): support movement and shape changes (contraction, crawling, pinching).
Microtubules: largest cytoskeletal elements; made of α- and β-tubulin; facilitate movement within the cell and cell movement.
Intermediate filaments: intermediate in size; very stable and not easily broken down; provide mechanical support.
Visual representations show the cytoskeleton interacting with the plasma membrane and organelles.
Centrosomes, Centrioles, and Microtubule Organization
Centrosomes: region surrounding centrioles in almost all animal cells; microtubule-organizing center (MTOC).
Centrioles: often present in animal cells as a pair; plants and fungi typically lack centrioles.
Role in organizing microtubules during cell division and in maintaining cell structure.
Cell Movement and the Cytoskeleton
Cell movement driven by rearrangements of actin filaments and microtubules.
Some cells crawl using actin (microfilaments).
Eukaryotic flagella and cilia possess a 9 + 2 arrangement of microtubules (nine doublets around two central microtubules).
Cilia are shorter and more numerous than flagella.
Flagella and Cilia Structure
Internal structure includes components of the cytoskeleton and motor proteins that enable beating patterns.
Flagella and cilia enable locomotion and movement of substances across cell surfaces.
Eukaryotic Cell Walls and Extracellular Matrix (ECM)
Eukaryotic cell walls are present in plants, fungi, and some protists, and differ chemically and structurally from prokaryotic walls.
Plant/fungal walls:
Plants: cellulose-based (cell walls); may have primary and secondary walls.
Fungi: chitin-based walls.
Animals lack cell walls but have an extracellular matrix (ECM) consisting of a complex mix of glycoproteins (e.g., collagen) secreted into the extracellular space.
ECM interacts with cells via integrins to link ECM to the cytoskeleton and influence cell behavior.
Table 4.3: Comparison of Prokaryotic, Animal, and Plant Cells
Exterior structures:
Cell wall: Prokaryote present; Animal absent; Plant present
Cell membrane: Present in all three
Flagella/cilia: Prokaryotes may have flagella; Animal: may have flagella/cilia (9+2); Plant: absent except in sperm of some species (9+2)
Interior structures:
Endoplasmic reticulum: Prokaryotes absent; Animal and Plant usually present
Ribosomes: Present in all
Microtubules: Absent in Prokaryotes; Present in Animal and Plant
Centrioles: Absent in Prokaryotes; Present in Animal; Absent in Plant
Golgi apparatus: Absent in Prokaryotes; Present in Animal and Plant
Nucleus: Absent in Prokaryotes; Present in Animal and Plant
Mitochondria: Absent in Prokaryotes; Present in Animal and Plant
Chloroplasts: Absent in Prokaryotes and Animal; Present in Plant
Chromosomes: Prokaryotes typically single circular DNA; Eukaryotes multiple linear chromosomes
Lysosomes: Absent in Prokaryotes; Present in Animal; Plant usually lacks lysosomes in a typical sense or has vacuoles with similar function
Vacuoles: Absent or small in Prokaryotes; Usually present in Plant; Animal vacuoles vary
Cell-to-Cell Interactions and Junctions
Cells carry surface markers that identify cell type and state.
Glycolipids and glycoproteins serve as tissue-specific cell surface markers.
MHC (Major Histocompatibility Complex) proteins enable recognition of self vs. non-self by the immune system.
Cells communicate and adhere via various junctions:
Adhesive junctions: mechanically attach cytoskeletons of neighboring cells or connect to the ECM (includes adherens junctions, desmosomes, and hemidesmosomes).
Septate or tight junctions: seal gaps between adjacent cells to prevent leakage.
Communicating junctions: allow direct chemical or electrical signaling between adjacent cells (gap junctions); plasmodesmata in plants.
Plasmodesmata (Plant-Specific Intercellular Connections)
Plasmodesmata are openings through plant cell walls that connect cytoplasm of adjacent cells.
Function similarly to gap junctions in animal cells by allowing transport and communication between cells.
Syllabus and Course Logistics (Notes for Context)
AI usage policy: Use of AI in course is not permitted.
Lecture and lab attendance are graded and mandatory.
All tasks accessed and submitted via Blackboard (LMS).
Chapter 1 Connect Tutorial, Chapter 1 Smartbook, and Chapter assignments; Chapter 4 Smartbook and Chapter assignments; Chapter 5 Smartbook and Chapter assignments.
Smartbook = Pre-Lecture Assignment; Chapter Assignment = Post-Lecture Assignment.
Deadlines: Ch. 1, 4, & 5 assignments due Friday, August 29, 2025, at 11:59 pm.
Questions
If you have questions, refer to the slide deck or instructor prompts for clarification.