Chapter 4: Cells and Microscopy Review
Exam next Wednesday; Monday's class will be a review for that exam.
Reminder to bring a Scantron form next Wednesday; about 50 bubbles on front and 50 on back.
You will have a worksheet today; grades for in-class work and worksheet will be posted in Canvas by the end of the week.
Chapter 4: there is a SmartBook homework in Connect; dates will be updated today after activation.
If you haven’t activated Connect yet, set up accounts this afternoon; the instructor will email when the homework opens (date adjusted).
SmartBook homework format:
As you work through chapter topics, it asks you to answer questions and rate your confidence.
If you answer correctly, you get more questions on that topic or move on to the next topic after mastery.
If you’re not mastering a topic, more questions are provided on that topic.
There is not a fixed number of questions or a fixed time; outcomes depend on performance.
It’s due the day before the noon exam (Tuesday night next week).
Start early: you can complete a few topics now and return later to continue.
Grading notes: there will be a worksheet with answers posted for self-check; another worksheet option can be requested for more practice.
The instructor will remind you about specific chapters ahead of the exam; plan ahead for study questions.
Cells, cell theory, and microscopy
We begin with looking at cells and the universal features across organisms.
Key focus: what all cells share and how they differ across domains (Bacteria, Archaea, Eukarya).
Cell size tendency: cells are small; surface area-to-volume ratio is crucial for exchange with the environment.
Surface area-to-volume intuition:
To maximize exchange, cells increase surface area while keeping volume manageable.
If a cell grows too large, energy demand for maintenance and exchange rises disproportionately.
A helpful relation for spherical cells: the ratio is \text{S/V} = \frac{S}{V} = \frac{4\pi r^2}{\frac{4}{3}\pi r^3} = \frac{3}{r}, showing that increasing radius reduces the surface-area-to-volume ratio.
Visual examples of cell shapes to maximize surface area without huge volume:
Neuron (nerve cell): very flat in the center with long, thin extensions increasing surface area.
Root hair cells: filamentous extensions to increase surface area.
Red blood cells: biconcave shape increasing surface area relative to volume.
Amoebae: highly adaptable shapes with protrusions to increase contact area.
Shared cell features across all cells:
Genetic information inside a centralized location, varies by organism (nucleus in eukaryotes; nucleoid region in prokaryotes).
Ribosomes present in all cells for protein synthesis; composed of two subunits that assemble into a full ribosome.
Cytoplasm: gel-like interior space; all cells have cytoplasm.
Plasma membrane (cell membrane): surrounds the cell, often a phospholipid bilayer; separates the interior from the environment.
Not all cells have a cell wall; all have a plasma membrane.
Prokaryotic vs. eukaryotic distinctions (domain-level perspective):
Prokaryotes include Bacteria and Archaea; both are generally small (roughly 10x smaller than typical human cells).
Prokaryotes commonly have shapes: rod (bacillus), spiral (spirillum), and spherical (coccus).
Prokaryotes store genetic information in the nucleoid region with circular DNA; ribosomes are present; cell walls are common.
Prokaryotes have cell walls containing peptidoglycan in Bacteria; Archaea cell walls have different materials and distinct lipids.
Bacteria vs. Archaea distinctions often used to separate their domains: peptidoglycan presence, lipid composition, and extreme-environment tolerance (archaea often extremophiles).
Archaea can survive in extreme environments (extremophiles) with high temperature, salinity, or pH in conditions where bacteria typically do not.
Eukaryotes (Domain: Eukarya) and the four kingdoms in this domain: plants, animals, fungi, protists.
Eukaryotic cells are typically 10–100x larger than prokaryotic cells; cytoplasm contains more diverse membrane-bound organelles.
All eukaryotes have membrane-bound organelles; examples include nucleus, mitochondria, chloroplasts (in plants/algae), endoplasmic reticulum, Golgi apparatus, lysosomes, peroxisomes, vacuoles, etc.
Eukaryotes have a cytoskeleton that supports cell shape and transport; include microfilaments (actin), intermediate filaments, and microtubules.
Plant cells have cell walls made of cellulose; chloroplasts enable photosynthesis; rigid shape due to the wall.
Animal cells lack cell walls but have cytoskeletal support and other organelles.
Prokaryotes: Bacteria and Archaea
Similarities between Bacteria and Archaea:
Both are prokaryotic: lack a nucleus; have genetic material in a nucleoid region; small size.
Both have ribosomes and lack membrane-bound organelles like mitochondria or chloroplasts.
Both typically have a cell wall; shapes include rod, spiral, and spherical.
Both have flagella or cilia-like structures for movement in some species.
Key differences between Bacteria and Archaea:
Cell wall composition: Bacteria commonly use peptidoglycan (peptidoglycan can be on the exterior or sandwiched); Archaea lack peptidoglycan and have unique lipids and wall structures.
Gram staining relevance: peptidoglycan location affects Gram stain results (Gram-positive vs Gram-negative) and antibiotic susceptibility.
Antibiotic sensitivity varies by wall structure; some antibiotics target peptidoglycan synthesis.
Environmental tolerance: Archaea include many extremophiles, enabling survival in extreme conditions; some bacteria lack such adaptation.
Gram stain concept (brief, per transcript):
Gram-positive bacteria have peptidoglycan exposed, absorb purple stain, appear purple.
Gram-negative bacteria have peptidoglycan not exposed or thinner, absorb less dye, appear pink/red.
This staining guides antibiotic choice in clinical settings; not all antibiotics target both types equally.
Eukaryotes: Cell organization and organelles
Overall features of eukaryotic cells:
Size: generally larger than prokaryotes; contains multiple membrane-bound organelles.
Nucleus: houses genetic material; site of transcription; contains the nuclear envelope with pores for macromolecule transport.
Endomembrane system: nucleus, rough and smooth endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vesicles; coordinates protein and lipid processing and transport.
Cytoskeleton: network of filaments providing shape, organization, and transport tracks for vesicles.
Energy-producing organelles: mitochondria (and, in plants/algae, chloroplasts).
Endomembrane system (functional flow):
DNA is transcribed in the nucleus to mRNA.
mRNA exits the nucleus via nuclear pores and is translated by ribosomes on the rough ER to form proteins.
Proteins are packaged into transport vesicles after being processed by the ER.
Vesicles fuse with the Golgi apparatus, where proteins are further processed, sorted, and packaged for delivery.
Final cargo is shipped via vesicles to appropriate destinations inside or outside the cell.
Lipids and other molecules (e.g., glucose, calcium) are supplied by the smooth ER and other stores to the Golgi and onward.
Nucleus details:
DNA in eukaryotes is organized as chromatin; transcription occurs in the nucleus; mRNA produced there exits to cytoplasm for translation.
Nuclear envelope contains nuclear pores for selective exchange with cytoplasm.
Endoplasmic reticulum (ER):
Rough ER: ribosomes on surface; synthesizes proteins; proteins packaged into transport vesicles for export.
Smooth ER: lacks ribosomes; synthesizes lipids; involved in carbohydrate metabolism and calcium storage/release.
Golgi apparatus:
Structure: cisternae (flattened, cup-shaped sacs).
Functions: modify, sort, and package proteins and lipids; ships via vesicles to final destinations; acts like a logistical hub (FedEx analogy).
Lysosomes:
Digestive organelles containing hydrolytic enzymes; break down macromolecules, damaged organelles, and invading bacteria.
High lysosome content in immune cells.
Tay-Sachs disease example: a single lysosomal enzyme deficiency leads to lipid accumulation, especially affecting the nervous system; often fatal by age ~5.
Vacuoles (plants) and other microbodies:
Vesicular compartments with storage and degradative roles; plant vacuoles store acids and contribute to turgor pressure.
Peroxisomes and glycosomes (collectively microbodies): break down toxins and biomolecules; liver-rich in these organelles for processing fats and amino acids.
Mitochondria:
The powerhouse of the cell; convert chemical energy from nutrients into usable ATP.
Double membrane with inner membrane folds (cristae).
Contain their own circular DNA and ribosomes, highlighting endosymbiotic origins.
Chloroplasts (plants and some algae):
Sites of photosynthesis; contain thylakoids arranged in granum; stroma is the surrounding fluid.
Have their own DNA and ribosomes; like mitochondria, chloroplasts are evidence for endosymbiotic origin.
Internal thylakoids are the sites of light-dependent reactions; chlorophyll gives plants their green color.
Endosymbiotic theory (origin of organelles):
Mitochondria and chloroplasts likely originated as free-living bacteria engulfed by ancestral eukaryotic cells.
Over time, these endosymbionts became organelles, providing energy and photosynthetic capabilities to the host cell.
Cytoskeleton (cell support and movement):
Microfilaments (actin): support cell shape; essential for muscle contraction and dynamic movements; actin is the main protein in microfilaments.
Intermediate filaments: provide structural support and resilience.
Microtubules: largest filaments; provide tracks for vesicle transport and form structural components like centrioles and the mitotic spindle.
Cilia and flagella: hair-like and whip-like projections aiding movement; built from cytoskeletal elements; organized by the centrosome.
Centrosomes organize the cytoskeleton and are involved in organizing microtubules during cell division.
Cell walls and membranes:
Most plant, fungal, and some protist cells have a cell wall; bacteria and archaea also have cell walls, but with different chemistry.
Plant cell walls are made of cellulose and contribute to rigid, defined cell shapes.
All cells have a plasma (cell) membrane; walls (when present) lie outside the membrane and provide structural support.
Protists and examples (context in chapter)
Protists are a diverse group within Eukarya; examples include Amoeba (shape-shifting single-celled organism) and Paramecium.
Protists are covered briefly in this chapter; deeper treatment occurs in the next semester and related lab activities.
Health, disease, and practical implications
Tay-Sachs disease example illustrates how a single lysosomal enzyme deficiency can have catastrophic consequences for the nervous system.
Understanding cell structure and organelle function informs medical treatment strategies (e.g., antibiotic targeting based on cell wall composition in bacteria).
Endomembrane system and protein trafficking are fundamental to cell health; disruptions can lead to severe cellular dysfunctions.
Practical exam preparation and study strategy
Start SmartBook chapter four topics early; use the adaptive questions to identify mastery gaps.
Review and reattempt topics as needed; ensure you understand the flow from nucleus to ER to Golgi and beyond.
Practice with the in-class worksheet and optional extra practice worksheets to reinforce understanding.
Use the cell theory framework to anchor understanding of domain differences and organelle functions.
Correlate structure with function when studying cytoskeleton, organelles, and the endomembrane system.
Connections to foundational principles and real-world relevance
The cell theory (Schleiden and Schwann; later refinements by Virchow) underpins modern biology: all living things are composed of cells, the cell is the basic unit of life, and new cells arise from existing cells.
Endomembrane system demonstrates cellular organization and compartmentalization essential for complex life.
Endosymbiotic theory explains the origin of organelles and highlights evolutionary processes that shaped eukaryotic complexity.
Understanding Gram staining, peptidoglycan, and archaeal cell walls informs clinical decision-making and antibiotic use.
The balance of surface area and volume in cells provides a foundational concept for understanding how cells optimize exchange with their environment.
Quick reference: key terminology recap
Nucleus, chromatin, nuclear envelope, nuclear pores
Rough ER, Smooth ER, ribosomes
Golgi apparatus, cisternae
Lysosome, vacuole, peroxisome, microbody
Mitochondrion, chloroplast, thylakoids, granum, stroma
Endomembrane system
Cytoskeleton: microfilaments (actin), intermediate filaments, microtubules
Cilia, flagella, centrosomes
Cell membrane (plasma membrane), cell wall
Prokaryotes: Bacteria, Archaea; Gram-positive vs Gram-negative
Eukaryotes: Eukarya; plants, animals, fungi, protists
Endosymbiosis
Tay-Sachs disease (lysosomal enzyme deficiency)