Chapter 4: A Tour of the Cell

A comprehensive vocabulary review of Chapter 4: A Tour of the Cell, covering light and electron microscopy, cell dimensions and geometry, prokaryotic vs. eukaryotic architecture, the endomembrane system, energy-converting organelles, the cytoskeleton, cell motility, the extracellular matrix, cell junctions, and plant cell walls.

Light microscope (LM)

An optical microscope that uses visible light and glass lenses to magnify specimens.

Magnification

An increase in an object's image size compared with its actual size.

Resolution

A measure of image clarity; the ability to distinguish two nearby points as separate.

Optical resolution limits

The smallest details optical tools can distinguish:

• Human eye: down to $0.1\,\text{mm}$

• Light microscope: down to about $0.2\,\mu\text{m}$ (magnifies up to $1{,}000\times$)

Cell theory

A fundamental biological theory stating that:

• All living things are composed of cells

• All cells come from preexisting cells

Electron microscope (EM)

A powerful microscope that focuses a beam of electrons to view cellular details down to $2\,\text{nm}$.

Cell ultrastructure

The complex internal anatomy and fine architectural detail of a cell revealed by electron microscopy.

Scanning electron microscope (SEM)

An electron microscope used to study cell surfaces:

• Scans an electron beam over gold-coated samples
• Produces detailed, three-dimensional surface images

Transmission electron microscope (TEM)

An electron microscope used to study internal cell architecture:

• Passes an electron beam through thin, metal-stained slices
• Reveals internal organelles and fine structures

Comparative micrographs of Paramecium and Toxoplasma

Different microscopy methods used to observe organisms:

• Light microscopy (LM): Views general shape and living cells
• Scanning electron microscopy (SEM): Views external surfaces and cilia
• Transmission electron microscopy (TEM): Views thin internal cross sections

Differential interference contrast microscopy

An optical light microscopy technique that amplifies density differences to make living cells appear three-dimensional.

Surface-to-volume ratio

The geometric relationship between cell area and volume:

• Volume expands faster than surface area as a cell grows
• Limits cell size to ensure enough membrane area for nutrient and waste exchange

Plasma membrane

A flexible outer boundary that encloses the cell:

• Separates the living cell from its surroundings
• Regulates what enters and leaves the cell

Phospholipid bilayer

A two-layer sheet of phospholipids forming the foundation of cell membranes:

• Hydrophilic heads face outward toward water
• Hydrophobic tails face inward away from water

Membrane transport proteins

Proteins embedded in the phospholipid bilayer:

• Form open channels for ions and polar molecules
• Pump specific substances across the membrane using energy

Prokaryotic cells

Small, simple cells that lack a membrane-enclosed nucleus:

• Represent Earth's earliest life forms
• Store DNA in an open nucleoid region
• Make up domains Bacteria and Archaea

Eukaryotic cells

Complex cells that contain membrane-bound compartments:

• House genetic material inside a true nucleus
• Contain specialized organelles to carry out cellular tasks
• Make up domain Eukarya

Three domains of life

The three major evolutionary classifications of life:

• Bacteria (prokaryotes)
• Archaea (prokaryotes)
• Eukarya (eukaryotes)

Cytosol and cytoplasm

The internal fluid and spaces of a cell:

• Cytosol: Jellylike fluid suspending cellular components
• Cytoplasm: Entire cell interior in prokaryotes, or the area between the nucleus and plasma membrane in eukaryotes

Chromosomes

Structures composed of DNA and proteins that carry a cell's genes.

Ribosomes

Tiny cellular structures that build proteins:

• Read genetic codes from mRNA
• Assemble amino acids into polypeptides

Nucleoid

The non-membrane-bounded region in a prokaryotic cell where circular DNA is located.

Bacterial cell wall

A rigid layer outside the prokaryotic plasma membrane:

• Protects the cell
• Maintains cell shape
• Prevents the cell from bursting

Capsule

A sticky, jellylike outer coat on some prokaryotes:

• Glues cells to surfaces
• Helps cells stick together in a colony

Fimbriae

Short surface projections on bacteria:

• Attach bacteria to surfaces
• Help cells adhere to host tissues

Prokaryotic flagella

Long surface appendages that rotate to propel bacteria through liquids.

Generalized prokaryotic cell structure

The standard anatomical layout of a bacterium:

• Interior: Nucleoid region and ribosomes
• Envelope: Plasma membrane, cell wall, and capsule
• Surface: Fimbriae and flagella

Penicillin

An antibiotic that kills bacteria:

• Prevents the synthesis of bacterial cell walls
• Leaves host eukaryotic cells unharmed because they lack cell walls

Helicobacter pylori

A flagellated, rod-shaped bacterium that causes stomach ulcers in humans.

Organelles

Membrane-enclosed compartments ('little organs') in eukaryotic cells that perform specific functions.

Cellular metabolism

The collective chemical activities and reactions taking place within a cell.

Four functional categories of eukaryotic structures

The four main functional groups of eukaryotic cell components:

• Genetic control (nucleus and ribosomes)
• Manufacturing, distribution, and breakdown (ER, Golgi, lysosomes, vacuoles, peroxisomes)
• Energy processing (mitochondria and chloroplasts)
• Structural support, movement, and communication (cytoskeleton, cell wall, junctions)

Nucleus

The command center of a eukaryotic cell:

• Houses genetic instructions (DNA)
• Directs protein synthesis
• Enclosed by a double membrane with pores

Chromatin

The diffuse, uncoiled mass of DNA and proteins present in the nucleus when a cell is not dividing.

Nuclear envelope and pores

A double membrane enclosing the nucleus:

• Controls entry and exit of large molecules through protein pores
• Connects directly to the endoplasmic reticulum

Nucleolus

A dense structure inside the nucleus:

• Synthesizes ribosomal RNA ($\text{rRNA}$
• Assembles ribosomal subunits

Ribosomal RNA (rRNA)

A type of RNA produced in the nucleolus that joins with proteins to form ribosomes.

Messenger RNA (mRNA)

An RNA molecule transcribed from DNA that carries protein-making instructions to ribosomes.

Free ribosomes

Ribosomes floating freely in the cytosol:

• Produce proteins that function inside the cytosol (like metabolic enzymes)

Bound ribosomes

Ribosomes attached to the rough ER or nuclear envelope:

• Produce proteins destined for membranes, organelles, or export from the cell

Endomembrane system

A connected network of internal eukaryotic membranes:

• Synthesizes, packages, and transports cellular materials
• Includes nuclear envelope, ER, Golgi, lysosomes, vacuoles, and plasma membrane

Vesicles

Tiny membrane sacs that transport substances and transfer membrane between organelles.

Endoplasmic reticulum (ER)

A large membranous network continuous with the nuclear envelope:

• Manufactures lipids and proteins
• Dispatches products in transport vesicles

Smooth endoplasmic reticulum

A ribosome-free region of the endoplasmic reticulum:

• Synthesizes lipids, including steroids and phospholipids
• Detoxifies drugs and poisons in liver cells
• Stores and releases calcium ions in muscle cells

Rough endoplasmic reticulum

A ribosome-studded region of the endoplasmic reticulum:

• Modifies and folds secretory proteins
• Manufactures new membrane phospholipids and proteins
• Packages products into transport vesicles

Detoxification in the smooth ER

The breakdown of harmful substances in liver cells:

• Uses enzymes to process drugs and alcohol
• Proliferates with repeated chemical exposure, increasing tolerance

Calcium ion regulation in the smooth ER

The management of calcium levels in muscle cells:

• Pumps calcium ions into the ER interior for storage
• Releases calcium into cytosol to trigger muscle contraction

Secretory protein

A protein designed to be released outside the cell (such as insulin):

• Synthesized on rough ER ribosomes
• Transported in vesicles to the Golgi and plasma membrane for export

Glycoprotein

A molecule formed when short carbohydrate chains attach to a protein inside the rough ER.

Transport vesicle

A small membrane-bound bubble that carries proteins and lipids between cell components.

Golgi apparatus

A stack of flattened membranous sacs:

• Receives vesicles from the ER
• Modifies proteins and glycoproteins
• Sorts and ships finished molecules to specific cellular destinations

Camillo Golgi

An Italian scientist who discovered the Golgi apparatus in 1898 using a specialized light microscope staining technique.

Receiving and shipping faces of the Golgi

The two functional sides of a Golgi stack:

• Receiving side: Fuses with transport vesicles arriving from the ER
• Shipping side: Buds off vesicles containing sorted, finished products

Molecular tags (Golgi sorting)

Chemical labels (like phosphate groups) added in the Golgi to target molecules for specific locations.

Lysosome

A membrane-enclosed sac of digestive enzymes:

• Breaks down food particles from food vacuoles
• Destroys harmful bacteria engulfed by immune cells
• Recycles damaged organelles and cell molecules

Food vacuole

A membrane sac formed by engulfing food particles:

• Fuses with lysosomes for digestion
• Releases nutrients into the cytosol

Autophagy (lysosomal recycling)

The cell's self-cleaning and recycling process:

• Encloses damaged organelles in a membrane
• Fuses with a lysosome to dismantle contents and reuse organic molecules

Lysosomal storage diseases (Tay-Sachs disease)

Inherited conditions where lysosomes lack specific hydrolytic enzymes:

• Causes undigested material to build up and impair cells
• In Tay-Sachs, missing lipid enzymes cause destructive lipid buildup in brain cells

Vacuoles

Large membrane-bound vesicles:

• Store nutrients, water, and wastes
• Help plant cells expand and maintain rigidity
• Digest materials in certain organisms

Contractile vacuole

A specialized organelle in freshwater protists:

• Collects excess water via radiating spoke channels
• Expels water through a central hub to keep the cell from bursting

Central vacuole

A large organelle found in plant cells:

• Absorbs water to help the cell enlarge
• Stores vital nutrients and pigments
• Safely stockpiles cellular waste products and poisons

Defensive compounds in plant vacuoles

Poisons or bitter chemicals (like nicotine and caffeine) stored in plant vacuoles to deter herbivores.

Peroxisome

A metabolic compartment outside the endomembrane system:

• Breaks down fatty acids for cellular energy
• Detoxifies harmful compounds in the liver
• Converts toxic hydrogen peroxide ($H_2O_2$) by-product into water ($H_2O$)

Mitochondria

The energy-producing organelles of eukaryotic cells:

• Carry out cellular respiration
• Convert food energy into usable ATP

Cellular respiration

A metabolic process that extracts energy from food:

• Uses oxygen ($O_2$) and releases carbon dioxide ($CO_2$)
• Synthesizes ATP for cellular activities

Intermembrane space (mitochondria)

The narrow, fluid-filled space between the outer and inner membranes of a mitochondrion.

Mitochondrial matrix

The fluid compartment inside the inner mitochondrial membrane:

• Houses mitochondrial DNA and ribosomes
• Contains enzymes that catalyze cellular respiration reactions

Cristae

Infoldings of the inner mitochondrial membrane:

• Greatly increase membrane surface area
• Boost the mitochondrion's ability to produce ATP

Chloroplasts

The photosynthesizing organelles of plants and algae:

• Capture solar energy using chlorophyll
• Convert carbon dioxide and water into energy-rich sugars

Photosynthesis

The biological process that converts solar energy into chemical energy stored in glucose molecules.

Stroma

The thick fluid within a chloroplast's inner membrane:

• Holds chloroplast DNA and ribosomes
• Contains enzymes that catalyze sugar synthesis

Thylakoids

Flattened, interconnected sacs inside a chloroplast:

• Contain light-absorbing chlorophyll pigments
• Function as solar power packs to trap light energy

Granum

A stack of thylakoids resembling a pile of poker chips inside a chloroplast.

Chlorophyll

The green, light-absorbing pigment embedded in thylakoid membranes that captures sunlight for photosynthesis.

Endosymbiont theory

An evolutionary theory stating that mitochondria and chloroplasts originated as small prokaryotes that took up residence inside larger host cells.

Cytoskeleton

A dynamic network of protein fibers in eukaryotic cells:

• Provides mechanical support and maintains cell shape
• Acts as tracks for moving vesicles and organelles
• Aids in whole-cell movement and locomotion

Motor proteins

Proteins that interact with the cytoskeleton to power the movement of organelles, vesicles, and whole cells.

Microtubules

Thick, hollow tubes made of tubulin proteins:

• Maintain cell shape
• Serve as tracks for organelle transport
• Guide chromosome movement during cell division
• Form the structural core of cilia and flagella

Tubulin

A globular protein that polymerizes into hollow microtubule tubes and can disassemble to be reused.

Centrosome and centrioles

The microtubule-organizing center near the animal cell nucleus:

• Contains a pair of centrioles composed of microtubule rings
• Directs the assembly of microtubules

Intermediate filaments

Sturdy, ropelike cytoskeletal fibers ($10\,\text{nm}$ thick):

• Reinforce cell shape
• Permanently anchor organelles like the nucleus

Microfilaments (actin filaments)

The thinnest cytoskeletal fibers ($7\,\text{nm}$ thick):

• Support cell shape just inside the plasma membrane
• Drive muscle contraction and amoeboid cell crawling

Actin

A globular protein that links into twisted double chains to form microfilaments.

Myosin

A motor protein that interacts with actin filaments to produce muscle contractions and crawling movements.

Cilia

Short, numerous cell appendages made of microtubules:

• Propel protists through water

• Sweep mucus and trapped debris over tissue surfaces (like the trachea)

Flagella (eukaryotic)

Long, whip-like cell appendages (usually one or a few per cell):

• Propel cells through fluid with undulating motions

• Power the swimming movement of sperm

9 + 2 pattern

The structural arrangement of microtubules in eukaryotic cilia and flagella:

• Nine outer microtubule doublets

• Two single microtubules in the center

Basal body

A microtubule-based cytoplasmic structure that anchors cilia and flagella in the cell.

Dyneins

Motor proteins attached along microtubule doublets in cilia and flagella:

• Use ATP to 'walk' along neighboring doublets
• Cause the doublets to bend, producing movement

Primary cilium

A nonmotile sensory cilium found on almost all vertebrate cells:

• Acts as an antenna to receive external environmental signals
• Lacks the central pair of microtubules

Primary ciliary dyskinesia (PCD)

An inherited genetic disorder where cilia and flagella lack motor proteins:

• Causes chronic respiratory tract infections
• Causes male infertility due to immotile sperm

Extracellular matrix (ECM)

An external mesh of glycoproteins secreted by animal cells:

• Holds cells together in tissues
• Protects and supports the plasma membrane
• Relays signals from outside to regulate cell behavior

Collagen

The most abundant glycoprotein in the animal extracellular matrix:

• Forms strong structural fibers
• Accounts for about $40\%$ of all protein in the human body

Integrins

Transmembrane proteins that link the ECM to the cytoskeleton:

• Span the plasma membrane
• Transmit signals between the cell exterior and interior

Tight junctions

Watertight seals between neighboring animal cells:

• Knit plasma membranes tightly together with proteins

• Prevent fluids from leaking across cell layers (e.g., in the digestive tract)

Anchoring junctions

Rivet-like junctions that fasten animal cells together into strong sheets:

• Anchored by intermediate filaments in the cytoplasm

• Prevent tearing in tissues subject to stretch (like skin and muscle)

Gap junctions

Communicating channels between neighboring animal cells:

• Form open pores for ions and small molecules to flow directly

• Coordinate activities like heart muscle contractions

Plant cell wall

A rigid extracellular structure made of cellulose:

• Protects the plant cell

• Maintains cell shape

• Provides skeletal support to keep plants upright on land

Pectins and lignin

Structural polymers found in plant cell walls:

• Pectins: Sticky polysaccharides that glue neighboring cell walls together

• Lignin: Rigid molecules that harden secondary walls in wood

Plasmodesmata

Open cytoplasmic channels through adjacent plant cell walls:

• Connect neighboring plant cells

• Allow water, nutrients, and chemical signals to pass freely throughout plant tissues