Study guide: A Tour of the Cell

📋 Course Outline

1. Cell Principles and Microscopy
2. Cell Fractionation and Cell Types
3. Nucleus and Ribosomes
4. The Endomembrane System
5. Mitochondria, Chloroplasts, and Peroxisomes
6. Cytoskeleton and Cell Motility
7. Extracellular Structures and Junctions

📖 1. Cell Principles and Microscopy

★ Must-know

• All organisms are made of cells, the simplest collection of matter that can live, and all cells descend from earlier cells.

📌 Magnification is the ratio of an image’s size to an object’s real size, whereas resolution is image clarity or the minimum distance at which two points remain distinguishable.

• Light microscopes use visible light and glass lenses, can magnify effectively to about 1,000 times, and generally cannot resolve most organelles.

📌 Scanning electron microscopes image specimen surfaces with a three-dimensional appearance, whereas transmission electron microscopes pass electrons through specimens to study internal structure.

Further detail

• Most cells are between 1 and 100 μm in diameter, so they are visible only under a microscope.

• Electron microscopes produce black-and-white images that may be artificially stained and cannot examine live cells because specimen preparation kills them.

💡 Memory Hook

Magnification enlarges; resolution distinguishes nearby points.

📖 2. Cell Fractionation and Cell Types

★ Must-know

• Only organisms in the domains Bacteria and Archaea have prokaryotic cells; protists, fungi, animals, and plants have eukaryotic cells.

• All cells have:

  • a plasma membrane
  • cytosol
  • chromosomes carrying genes
  • ribosomes that make proteins

📌 Prokaryotic cells lack a nucleus and membrane-bound organelles, with DNA in a nucleoid, whereas eukaryotic cells enclose DNA in a nuclear envelope and contain membrane-bound organelles.

Further detail

• A plasma membrane is a selective barrier that permits sufficient exchange of oxygen, nutrients, and waste, and biological membranes generally consist of a phospholipid bilayer.

• Cell size is constrained by the need to contain enough DNA and organelles while maintaining effective transport and exchange with extracellular fluid.

• When cell dimensions increase by a factor of n, surface area increases by $n^2$ while volume increases by $n^3$, making the surface-to-volume ratio important.

📖 3. Nucleus and Ribosomes

🔑 Key Concepts & Definitions

• Ribosome: Particles made of ribosomal RNA and protein that synthesize proteins.

★ Must-know

• The nucleus contains most of a eukaryotic cell’s genes and is enclosed by a double-membrane nuclear envelope whose pores regulate molecular entry and exit.

• In the nucleus, DNA and proteins form chromatin, which condenses to form discrete chromosomes.

📌 Free ribosomes synthesize proteins in the cytosol, whereas bound ribosomes are attached to the outside of the endoplasmic reticulum or nuclear envelope.

Further detail

• The nuclear lamina, a protein structure, helps maintain the shape of the nucleus.

• The nucleolus is the site of ribosomal RNA synthesis.

📖 4. The Endomembrane System

🔑 Key Concepts & Definitions

• Endoplasmic reticulum: An extensive membrane network of tubules and sacs called cisternae, continuous with the nuclear envelope and accounting for more than half of total membrane in many eukaryotic cells.
• Lysosome: A membranous sac of hydrolytic enzymes that digests proteins, fats, polysaccharides, and nucleic acids in an acidic environment of about pH 5.

★ Must-know

• The endomembrane system comprises:
  • the nuclear envelope
  • the endoplasmic reticulum
  • the Golgi apparatus
  • lysosomes
  • vacuoles
  • the plasma membrane

📌 Smooth ER lacks ribosomes and synthesizes lipids, metabolizes carbohydrates, detoxifies drugs and poisons, and stores calcium; rough ER bears ribosomes and synthesizes glycoproteins and cellular membranes.

• The Golgi apparatus receives ER products at its cis face, modifies and sorts them, and ships materials in transport vesicles from its trans face.

Further detail

• Secretory proteins leave the rough ER packaged inside transport vesicles.

• During phagocytosis, a cell engulfs material into a food vacuole, which fuses with a lysosome for digestion; autophagy recycles the cell’s own organelles and macromolecules.

• Contractile vacuoles in many freshwater protists pump excess water out of cells to maintain an adequate concentration of salts and other molecules.

💡 Memory Hook

ER → Golgi → vesicles: modify, sort, and ship.

📖 5. Mitochondria, Chloroplasts, and Peroxisomes

🔑 Key Concepts & Definitions

• Mitochondrion: Has a smooth outer membrane and an inner membrane folded into cristae, which increase membrane surface; the inner membrane separates the intermembrane space from the matrix, where some cellular-respiration steps occur.
• Chloroplast: A plastid containing chlorophyll and other molecules involved in photosynthesis, with thylakoids stacked into grana inside the stroma.

★ Must-know

• Mitochondria are sites of cellular respiration, which generates ATP, while chloroplasts in plants and algae are sites of photosynthesis.

• Mitochondria and chloroplasts have double membranes, their own DNA, and proteins synthesized by free ribosomes, and they are not part of the endomembrane system.

• The endosymbiont theory proposes that mitochondria descended from oxygen-using non-photosynthetic prokaryotes and chloroplasts from photosynthetic prokaryotes.

Further detail

• Peroxisomes are single-membrane oxidative organelles whose enzymes transfer hydrogen from compounds to oxygen, producing hydrogen peroxide that catalase converts to water.

💡 Memory Hook

Mitochondria convert energy, chloroplasts capture light, and peroxisomes oxidize molecules.

📖 6. Cytoskeleton and Cell Motility

🔑 Key Concepts & Definitions

• Cytoskeleton: A network of fibers throughout the cytoplasm that organizes cell structures and activities and anchors many organelles.

★ Must-know

• The cytoskeleton supports cell shape, interacts with motor proteins to produce motility, guides vesicle movement, and can be rapidly dismantled and reassembled to change cell shape.

📌 Microtubules are the thickest cytoskeletal fibers, intermediate filaments have an intermediate diameter, and microfilaments are the thinnest.

• Microtubules are hollow tubulin rods about 25 nm in diameter, assembled from 13 protofilaments, and provide cell form, guide organelle movement, and separate chromosomes during cell division.

📌 Cilia are short and usually numerous, beating with power and recovery strokes, whereas flagella are longer, usually one or a few per cell, and propel cells with undulating waves.

• Eukaryotic cilia and flagella have a membrane-sheathed 9+2 microtubule core, are anchored by basal bodies with a 9+0 arrangement, and bend through dynein-driven sliding constrained by protein cross-links.

Further detail

• In animal cells, the centrosome near the nucleus is the microtubule-organizing center and contains a pair of centrioles, each made of nine microtubule triplets.

• Microfilaments are solid actin rods about 7 nm in diameter that bear tension, support the cell cortex, and form the core of intestinal microvilli.

• Actin and myosin interactions drive muscle contraction, amoeboid movement through pseudopodia, and cytoplasmic streaming in plant cells.

• Intermediate filaments are 8–12 nm fibers that support cell shape, anchor organelles, and bear tension, and include keratins, neurofilaments, and the nuclear lamina.

📖 7. Extracellular Structures and Junctions

🔑 Key Concepts & Definitions

• Extracellular matrix: A network of proteoglycans containing glycoproteins such as collagen and fibronectin, which bind to plasma-membrane receptors called integrins and support, adhere, enable movement, and regulate cells.

★ Must-know

• Plant cell walls protect cells, maintain their shape, and prevent excessive water uptake; they consist of cellulose fibers embedded in polysaccharides and proteins such as pectin and lignin.

📌 Tight junctions press neighboring cell membranes together to prevent extracellular-fluid leakage, desmosomes fasten cells into strong sheets, and gap junctions provide cytoplasmic channels between adjacent animal cells.

Further detail

📌 A plant primary cell wall is relatively thin and flexible, the pectin-rich middle lamella between adjacent primary walls attaches cells, and some cells have a secondary wall between the primary wall and plasma membrane.

• Plasmodesmata are channels through plant cell walls that allow water, small solutes, and sometimes proteins and RNA to pass between adjacent cells.

• A macrophage destroys bacteria through coordinated action involving the cytoskeleton, lysosomes, and plasma membrane.

💡 Memory Hook

Plant walls support and protect; animal ECM supports, adheres, and regulates.

📊 Synthesis Tables

Eukaryotic Cytoskeletal Fibers

Fiber	Structure	Key roles
Microtubules	Hollow tubulin rods; 25 nm diameter	Cell form, organelle movement, chromosome separation
Microfilaments	Solid actin rods; 7 nm diameter	Tension, cell cortex, contraction and motility
Intermediate filaments	Fibers 8–12 nm in diameter	Cell shape, organelle anchoring, tension