Anna ch 2

cyto

Terminology / concept

Cytology

Cell

Eukaryotic cell

Three major cell regions

Intracellular

Extracellular

Organelle

Structure–function relationship

anatomical meaning , function , where it fits?

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Cytology	Study of cells. cyto- = cell; -ology = study of	This entire chapter is microscopic anatomy at the cellular level.	Anatomy → microscopic anatomy → cytology → cell
Cell	Smallest living structural and functional unit of the body.	Obtains nutrients, synthesizes molecules, eliminates waste, maintains itself, and can reproduce when appropriate.	Tissues are built from cells.
Eukaryotic cell	Cell containing a membrane-enclosed nucleus. Human cells are eukaryotic.	Separates DNA into a nuclear compartment while many cellular reactions occur in the cytoplasmic compartment. The professor uses the presence of a nucleus as the defining distinction for this course.	Cell → nuclear compartment + cytoplasmic compartment
Three major cell regions	Plasma membrane + cytoplasm + nucleus	The basic map she should use whenever looking at a cell diagram or micrograph.	Plasma membrane → Cytoplasm → Nucleus
Intracellular	Inside the cell.	Used constantly to describe locations/processes.	extracellular environment → membrane → intracellular environment
Extracellular	Outside the cell.	Extracellular fluid surrounds cells.	Extracellular fluid → plasma membrane → cytoplasm
Organelle	Specialized subcellular structure; literally a “little organ.”	Different organelles perform different jobs. Different cell types contain different amounts of them depending on function.	Cytoplasm → organelles → specialized functions
Structure–function relationship	Cell shape and organelle abundance vary with what the cell does.	Very important anatomy principle: function predicts anatomy. Example: high-energy cells → many mitochondria; protein-secreting cells → abundant RER/Golgi. The textbook explicitly tests these relationships.	Cell function → required machinery → characteristic cellular anatomy

Terminology / concept

Plasma membrane / cell membrane / plasmalemma

Unit membrane

Phospholipid

Hydrophilic

Hydrophobic

Polar

Nonpolar

Phospholipid bilayer

Fluid mosaic model

Cholesterol

Integral protein

Transmembrane protein

Peripheral protein

Glyco-

Glycolipid

Glycoprotein

Glycocalyx / cell coat

Receptor

Selective permeability

pm flow

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Plasma membrane / cell membrane / plasmalemma	Thin flexible outer boundary of the cell. -lemma = layer/sheath in the terminology emphasized by the professor.	Separates intracellular from extracellular fluid; controls passage, receives signals, participates in recognition and anchors cells/cytoskeleton.	Extracellular fluid → PLASMA MEMBRANE → cytoplasm
Unit membrane	Professor’s term for the common basic lipid-bilayer organization of biological membranes.	Plasma membrane and many organelle membranes share the phospholipid-bilayer principle, although their exact proteins/lipids differ.	Phospholipids → bilayer → plasma membrane / organelle membrane
Phospholipid	Membrane lipid with a polar hydrophilic head + two nonpolar hydrophobic fatty-acid tails.	Amphipathic nature causes phospholipids to arrange themselves into bilayers in water.	hydrophilic head — hydrophobic tails
Hydrophilic	“Water loving”; attracted to/interacts with water.	Phospholipid heads face the watery cytoplasm and extracellular fluid.	Water ↔ head
Hydrophobic	“Water fearing”; avoids water.	Phospholipid tails point inward, away from water, creating the membrane’s hydrophobic core.	head → **tails
Polar	Molecule/region with separated electrical charge that interacts with water.	Phospholipid head is polar.	polar → hydrophilic
Nonpolar	Lacks strong separated electrical charges; generally poorly interacts with water.	Fatty-acid tails are nonpolar.	nonpolar → hydrophobic
Phospholipid bilayer	Two layers of phospholipids arranged tail-to-tail.	Fundamental membrane barrier. Hydrophobic interior helps exclude many charged/water-soluble molecules.	water → heads → tails : tails → heads → water
Fluid mosaic model	Membrane viewed as a flexible lipid bilayer in which proteins and other molecules are embedded and can move laterally.	Fluid = components can move within membrane. Mosaic = mixture of lipids, proteins, carbohydrates. Professor emphasizes that the membrane can remain intact while components move.	phospholipid bilayer + proteins + carbohydrates → fluid mosaic membrane
Cholesterol	Lipid interspersed among phospholipids.	In Marieb, increases membrane rigidity and decreases permeability to water/water-soluble substances.	phospholipids + cholesterol → membrane properties
Integral protein	Protein embedded firmly in the bilayer.	May act as receptor, carrier, channel, enzyme, adhesion molecule.	bilayer → embedded protein
Transmembrane protein	Integral protein extending completely through the membrane.	Can create a connection/pathway between extracellular and intracellular environments.	outside → transmembrane protein → inside
Peripheral protein	Protein attached to a membrane surface rather than buried across the bilayer.	Can provide structural support and connect membrane with cytoskeleton.	membrane → peripheral protein → cytoskeleton
Glyco-	Word root meaning sugar/carbohydrate.	Helps decode glycolipid, glycoprotein, glycocalyx.	glyco = sugar
Glycolipid	Membrane lipid + carbohydrate chain.	Contributes to external glycocalyx and cell recognition.	membrane lipid → sugar extends outside
Glycoprotein	Membrane protein + carbohydrate chain.	Important in recognition, adhesion, receptors/signaling.	membrane protein → sugar extends outside
Glycocalyx / cell coat	Carbohydrate-rich coating on the external membrane surface formed by glycoproteins + glycolipids.	Different cell types have distinctive carbohydrate patterns, helping cells bind to and recognize one another.	glycolipids + glycoproteins → glycocalyx → recognition
Receptor	Usually membrane protein with a specific binding site for a signaling molecule.	Converts information outside the cell into a cellular response; membrane receptors are part of intercellular communication.	signal → receptor binds → cellular response
Selective permeability	Ability of membrane to allow certain substances to cross more readily than others.	Central function of plasma membrane; makes different intracellular and extracellular compositions possible.	membrane composition → determines what enters/leaves

Phospholipids form the barrier→ proteins provide specialized functions→ carbohydrates provide recognition→ cholesterol modifies membrane properties

Why can the membrane do so many different jobs?

same basic phospholipid bilayer + different inserted/attached molecules = different membrane functions.

The professor emphasizes that membranes share a basic structure but can differ greatly according to which proteins and lipids are added or anchored.

membrane transport

Concentration gradient

Diffusion

Simple diffusion

Osmosis

Aquaporin

Facilitated diffusion

Channel protein

Ion channel

Carrier / transport protein

Active transport

ATP

Passive transport concept

Bulk / vesicular transport

Vesicle

Invagination

Endocytosis

Phagocytosis

Pseudopod / pseudopodium

Phagosome

Pinocytosis

Receptor-mediated endocytosis

Clathrin

Coated pit / coated vesicle

Receptor recycling

Exocytosis

v-SNARE

t-SNARE

Secretion

Excretion

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Concentration gradient	Difference in concentration of a substance between two regions.	Provides the driving force for diffusion.	HIGH concentration → LOW concentration
Diffusion	Net movement down a concentration gradient.	Does not require the cell to directly spend ATP.	high → low
Simple diffusion	Substance passes directly through lipid bilayer.	Used particularly by small uncharged/lipid-soluble molecules.	high → bilayer directly → low
Osmosis	Diffusion of water across a membrane.	Water movement specifically. The textbook explicitly asks this in Chapter 2 review.	water high → membrane → water low
Aquaporin	Membrane channel specialized for passage of water.	Allows much more rapid water movement through membranes. Professor specifically introduces aquaporins.	water → aquaporin → water
Facilitated diffusion	Passive transport through a specific integral membrane protein.	Still moves down concentration gradient; no ATP required for the movement itself.	high → channel/carrier → low
Channel protein	Transmembrane protein containing a selective passage.	Allows selected water-soluble or charged substances to cross.	solute → protein pore → other side
Ion channel	Channel selective for ions.	Channel size/shape allows selectivity; not every molecule passes through every channel. Professor emphasizes this specificity.	ion → appropriate channel → across membrane
Carrier / transport protein	Protein that binds a substance and changes configuration to move it through membrane.	Can participate in facilitated diffusion or active transport depending on direction/energy use.	molecule binds → protein changes shape → molecule crosses
Active transport	Protein-mediated movement against a concentration gradient.	Requires energy; professor emphasizes ATP-driven protein conformational changes.	low → HIGH + ATP
ATP	Adenosine triphosphate; major immediately usable cellular energy molecule.	Powers active transport and many other cellular processes.	ATP → energy released → cellular work
Passive transport concept	Transport without direct cellular ATP expenditure.	Includes simple diffusion, osmosis and facilitated diffusion.	high → low
Bulk / vesicular transport	Movement of large materials by membrane-bound vesicles.	Used when material is too large to simply pass through membrane transport proteins.	membrane bends/fuses → vesicle moves cargo
Vesicle	Small membrane-bound sac.	Carries substances between compartments or into/out of cell.	membrane → buds → vesicle → destination
Invagination	Inward folding of a membrane.	First physical step in many forms of endocytosis.	membrane → bends inward → pit
Endocytosis	Vesicular movement into the cell. endo = in/within	Plasma membrane folds inward and pinches off around extracellular material.	outside → invagination → vesicle → inside
Phagocytosis	“Cell eating”; endocytosis of large particles.	Cells form pseudopods around material; commonly associated with protective phagocytic cells.	particle → pseudopods → phagosome → lysosome
Pseudopod / pseudopodium	Temporary cell projection; “false foot.”	Surrounds material during phagocytosis and can participate in amoeboid movement.	membrane/cytoskeleton extends → surrounds object
Phagosome	Vesicle containing material engulfed by phagocytosis.	Typically combines with lysosome so contents can be digested.	particle → phagosome + lysosome → digestion
Pinocytosis	“Cell drinking”; uptake of extracellular fluid and dissolved solutes.	Nonspecific sampling using small vesicles in the textbook description.	extracellular fluid → tiny vesicle → cytoplasm
Receptor-mediated endocytosis	Selective uptake after extracellular material binds specific membrane receptors.	Allows cells to concentrate particular substances rather than indiscriminately engulfing fluid.	ligand → receptor → coated pit → coated vesicle
Clathrin	Intracellular coat protein emphasized by professor during receptor-mediated endocytosis.	Clathrin molecules aggregate beneath membrane and help curve membrane into a coated pit/vesicle.	receptor binding → clathrin coat → pit → vesicle
Coated pit / coated vesicle	Membrane region/vesicle with associated coat proteins.	Promotes selective receptor-mediated uptake.	receptor-ligand → coated pit → coated vesicle
Receptor recycling	Return of endocytosis receptors to plasma membrane.	Receptors can be reused rather than permanently lost.	endocytic vesicle → receptor separates → recycled to membrane
Exocytosis	Vesicular movement out of the cell. exo = out	Vesicle fuses with plasma membrane and releases contents outside. Major secretion pathway.	vesicle → membrane fusion → contents outside
v-SNARE	Vesicle-associated SNARE protein shown in the book’s exocytosis figure.	Recognizes/binds appropriate target membrane machinery.	vesicle v-SNARE ↔ t-SNARE membrane
t-SNARE	Target/plasma-membrane SNARE in the book’s exocytosis figure.	Helps dock/fuse vesicle with target membrane.	v-SNARE + t-SNARE → fusion → pore
Secretion	Release/movement of a substance from a cell into another body compartment.	May be useful product rather than “waste,” e.g. mucus or hormone.	Golgi → secretory vesicle → exocytosis → secretion
Excretion	Elimination from the body/region.	Professor distinguishes it from secretion: secretion can remain within the body; excretion leaves it.	cellular/body waste → outside body

Transport different materials

what needs to cross the membrane

small+ lipid soluble

water

water soluble / charged materials

moving against gradient

very large material

endocytosis

very large solid

fluid

specific receptor bound cargo

Small + lipid soluble
→ simple diffusion

Water
→ osmosis, often through aquaporins

Water-soluble/charged + going high → low
→ facilitated diffusion

Moving against gradient
→ active transport + ATP

Very large material
→ vesicular transport
→ INTO = endocytosis
→ OUT = exocytosis

And endocytosis:

large solid → phagocytosis
fluid → pinocytosis
specific receptor-bound cargo → receptor-mediated endocytosis

cell junctions

Cell junction

Tight junction

Desmosome

Cadherin

Gap junction / nexus

Connexon

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Cell junction	Specialized protein connection between neighboring cells.	Allows cells in tissues to seal, anchor or communicate with one another.	cell membrane ↔ junction ↔ neighboring cell membrane
Tight junction	Junction where neighboring membranes are tightly linked along a region.	Creates a seal that restricts passage between cells. Professor compares repeated junctions to stitching fabric together.	cell A ║ SEAL ║ cell B
Desmosome	Strong point-like anchoring junction connected to cytoskeletal intermediate filaments.	Resists pulling/mechanical stress; professor compares it to a rivet.	intermediate filament → desmosome ↔ desmosome ← intermediate filament
Cadherin	Adhesion protein discussed by professor as part of strong cell-cell attachment at desmosomes.	Helps link neighboring cells.	cell A → cadherin ↔ cadherin ← cell B
Gap junction / nexus	Channel junction between neighboring cells.	Allows ions and other small molecules to pass directly cell-to-cell, enabling communication/electrical coupling.	cytoplasm A → channel → cytoplasm B
Connexon	Hollow protein channel unit composing a gap junction.	Connexons of neighboring cells align to form continuous passage.	connexon A ↔ connexon B → gap junction

Tight junction = SEAL

Desmosome = STRENGTH

Gap junction = SIGNAL/COMMUNICATION

cell membrane projections

Terminology / concept

Microvillus

Microvilli

Actin core of microvillus

Cilium

Cilia

9 + 2 arrangement

Dynein

Flagellum

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Microvillus	One short fingerlike extension of plasma membrane.	Increases membrane surface area.	plasma membrane → folds outward → microvillus
Microvilli	Plural of microvillus; many closely packed projections.	More surface area means room for more channels/transporters → enhanced absorption/transport.	more membrane → more transport machinery → more absorption
Actin core of microvillus	Microfilaments inside microvillus.	Provides internal structural support to the projection.	membrane projection → actin microfilaments inside
Cilium	Singular, longer hairlike motile membrane projection.	Moves extracellular material along cell surface.	cell → one cilium
Cilia	Plural; numerous coordinated motile projections.	Coordinated beating moves mucus/fluid like a conveyor belt.	ATP-powered beat → fluid/mucus moves
9 + 2 arrangement	Internal ciliary organization: 9 peripheral microtubule doublets surrounding 2 central microtubules.	Characteristic architecture of motile cilia taught by professor.	cilium → membrane surrounding 9+2 microtubules
Dynein	Microtubule motor protein in cilia.	ATP-dependent dynein activity produces movement/bending.	ATP → dynein → microtubule movement → cilium beats
Flagellum	Long cilia-like motile projection; sperm is the major human example discussed.	Propels the cell itself rather than moving material over a surface.	microtubule machinery → flagellum → cell movement

Microvilli → increase SURFACE AREA

Cilia → MOVE material

And internally:

Microvilli → actin

Cilia → microtubules + dynein

Cytoplasm

Terminology / concept

Cytoplasm

Cytosol

Cytoplasmic organelle

Cytoplasmic inclusion

Lipid droplet

Glycosome

Glycogen

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Cytoplasm	Everything between plasma membrane and nucleus.	Site of most cellular activities.	plasma membrane → CYTOPLASM → nucleus
Cytosol	Jellylike fluid portion of cytoplasm.	Contains water, ions and enzymes; organelles/inclusions are suspended in it.	cytoplasm = cytosol + organelles + inclusions
Cytoplasmic organelle	Specialized functional structure in cytoplasm.	Metabolic machinery of the cell.	cytosol → organelles
Cytoplasmic inclusion	nonpermanent/ Temporary stored material.	Not equivalent to a metabolically active organelle.	cytoplasm → storage material
Lipid droplet	Non-membrane-bound drop of stored fat.	Energy/nutrient storage; can resemble lysosome in size but lacks surrounding membrane.	nutrients → fat → lipid droplet
Glycosome	Cytoplasmic inclusion containing glycogen and enzymes involved in glycogen metabolism.	Stores carbohydrate energy as glycogen.	glucose → glycogen → glycosome
Glycogen	Branched storage polymer of glucose.	Stored carbohydrate fuel.	glucose units → glycogen storage

Ribosomes and the endomembrane/protein-processing system

distinguishes free ribosomes from RER-bound ribosomes based on the destination of the proteins they make.

Terminology / concept

Ribosome

rRNA

Free ribosome

Bound ribosome

Endoplasmic reticulum / ER

Rough ER / RER

Cistern / cisternae

Smooth ER / SER

Calcium storage in SER

Transport vesicle

Golgi apparatus

Cis face

Trans face

Secretory vesicle / secretory granule

Endomembrane relationship

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Ribosome	Dense nonmembranous particle with large + small subunit, composed of rRNA and proteins.	Site of translation/protein synthesis.	mRNA → ribosome → protein
rRNA	Ribosomal RNA.	Structural/functional RNA making up much of ribosome.	nucleolus → rRNA → ribosomal subunits
Free ribosome	Ribosome floating in cytosol.	Produces proteins primarily used within cytosol.	mRNA → free ribosome → cytosolic protein
Bound ribosome	Ribosome attached to rough ER during protein production.	Produces proteins destined for secretion, membranes, and endomembrane pathways.	mRNA → RER ribosome → secreted/membrane protein
Endoplasmic reticulum / ER	Extensive membranous network of sacs and tubes; literally “network within cytoplasm.”	Major intracellularproduction/processing system.	nuclear envelope ↔ ER → Golgi
Rough ER / RER	ER with ribosomes attached to cytosolic surface; much of it consists of flattened cisterns.	Synthesizes proteins for secretion/membranes; textbook also calls it a major	nucleus → mRNA → ribosome/RER → protein
Cistern / cisternae	Fluid-filled flattened membranous cavity/cavities.	Structural units of rough ER and Golgi.	RER/Golgi → flattened sacs
Smooth ER / SER	Tubular ER lacking ribosomes.	Lipid metabolism/synthesis, steroid hormone production, detoxification of lipid-soluble drugs, Ca²⁺ storage.	lipids/steroids/detox/Ca²⁺
Calcium storage in SER	SER stores Ca²⁺ and keeps resting cytosolic Ca²⁺ relatively low.	Released Ca²⁺ can participate in events such as muscle contraction and glandular secretion.	SER Ca²⁺ store → release → cellular response
Transport vesicle	Small membrane sac carrying products from one organelle to another.	Transfers products from RER to Golgi, among other destinations.	RER → transport vesicle → Golgi
Golgi apparatus	Stack of approximately 3–10 disc-shaped membrane cisterns.	Modifies, sorts and packages products received from RER.	RER → Golgi → destinations
Cis face	Convex receiving side of Golgi.	Receives transport vesicles from RER.	RER → vesicle → CIS Golgi
Trans face	Concave shipping side of Golgi.	New vesicles bud away toward final destinations.	cis → Golgi processing → TRANS → vesicle
Secretory vesicle / secretory granule	Golgi-derived vesicle containing a product for secretion.	Travels toward plasma membrane and releases product by exocytosis.
Endomembrane relationship	Nuclear envelope, ER, Golgi, vesicles, lysosomes and plasma membrane are structurally/functionally connected through membrane production and vesicle trafficking.	Helps explain why membrane-bound protein processing is a pathway, not isolated organelles.	nuclear envelope ↔ RER → vesicle → Golgi → vesicle → membrane/lysosome

Secreted-protein pathway

DNA in nucleus→ transcription→ mRNA→ nuclear pore→ RER-bound ribosome→ protein enters RER→ transport vesicle→ cis Golgi→ modification/sorting→ trans Golgi→ secretory vesicle→ plasma membrane→ exocytosis

Lysosomes and peroxisomes

Lysosome

Acid hydrolase

Autodigestion/recycling concept

Phagosome–lysosome relationship

Peroxisome

Oxidase

Free radical

Hydrogen peroxide / H₂O₂

Catalase

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Lysosome	Membranous sac containing digestive enzymes/acid hydrolases.	Intracellular digestion; destroys ingested substances and deteriorated cellular components.	material → lysosome → digestion/recycling
Acid hydrolase	Digestive enzyme functioning in lysosome.	Breaks down macromolecules.	lysosome → hydrolysis → smaller components
Autodigestion/recycling concept	Lysosomes can digest worn cellular structures as well as incoming material.	Explains lysosome as cellular recycling center.	damaged organelle → lysosome → recycled components
Phagosome–lysosome relationship	Phagosome carrying engulfed material joins lysosomal digestive machinery.	Connects membrane transport with organelle function.	phagocytosis → phagosome → lysosome → digestion
Peroxisome	Small membrane-bound organelle containing oxidative enzymes.	Detoxification and other oxidative metabolic processes.	toxic/reactive molecule → peroxisome
Oxidase	Enzyme in peroxisomes that oxidizes substrates and can form hydrogen peroxide.	Helps neutralize reactive substances.	substrate → oxidase → H₂O₂
Free radical	Highly reactive molecule produced during metabolism or exposure to damaging agents.	Can damage proteins, membranes and DNA.	metabolism → free radicals → cellular damage unless controlled
Hydrogen peroxide / H₂O₂	Reactive peroxide produced during some peroxisomal reactions.	Must itself be detoxified.	oxidase → H₂O₂ → catalase
Catalase	Important peroxisomal enzyme.	Breaks hydrogen peroxide down to safer products; textbook emphasizes this function.	H₂O₂ → catalase → H₂O + O₂

Lysosome = DIGEST

Peroxisome = DETOXIFY/OXIDIZE

Mitochondria

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Mitochondrion	Singular organelle; generally rod/thread/bean-shaped with two membranes.	Main site of ATP production.	nutrients → mitochondrion → ATP
Mitochondria	Plural.	Number varies with cellular energy requirement. Muscle/high-metabolic-demand cells contain many.	higher energy demand → more mitochondria
Outer mitochondrial membrane	Outer boundary membrane.	Encloses mitochondrion.	cytoplasm → outer membrane
Inner mitochondrial membrane	Membrane internal to outer membrane, heavily folded.	Contains important energy-producing machinery.	outer membrane → inner membrane
Crista / cristae	Fold/folds of inner mitochondrial membrane.	Increase inner-membrane surface area for energy-producing machinery.	more folds → more membrane surface area → greater ATP machinery capacity
Mitochondrial matrix	Innermost compartment enclosed by inner membrane.	Contains mitochondrial components involved in energy metabolism.	inner membrane/cristae → matrix
ATP production	Principal functional association of mitochondria.	Immediate link she should make if shown a mitochondrion.	food-energy pathways → mitochondrion → ATP
Mitochondrial DNA	Mitochondria contain some of their own genetic material.	One observation supporting their unusual/semi-autonomous evolutionary history.	mitochondrion → own DNA
Endosymbiotic concept	Professor explains mitochondria as thought to derive evolutionarily from bacteria engulfed by ancestral cells.	Basic evidence emphasized: bacterial resemblance, own DNA, replication characteristics.	ancestral cell + engulfed bacterium → mitochondrion
Structure–function link	Inner membrane folds extensively because important energy-production proteins are membrane associated.	Very anatomy-style question: why cristae? → increased surface area.	cristae ↑ → membrane surface ↑ → energy machinery ↑

cytoskeleton

cytoskeleton is not one structure. It contains three major protein-fiber systems with different anatomy and jobs

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Cytoskeleton	Internal network of nonmembranous protein rods/fibers through cytosol.	Gives shape, mechanical support, organizes organelles and enables movement.	cytoplasm → cytoskeletal framework
Microfilament / actin filament	Thinnest major cytoskeletal fiber; made of actin.	Contraction, cell movement, cytokinesis, membrane changes, support of microvilli.	actin → movement/contraction
Actin	Protein making microfilaments.	Interacts with myosin to generate force.	actin + myosin → force
Myosin	Motor protein interacting with actin.	Produces contractile movement.	actin ↔ myosin → contraction
Pseudopod movement	Cell extension/retraction involving cytoskeletal rearrangement.	Supports amoeboid movement and phagocytosis.	cytoskeleton rearranges → pseudopod
Intermediate filament	Tough fiber intermediate in diameter between microfilament and microtubule.	Most stable cytoskeletal element; resists tensile/pulling forces.	mechanical stress → intermediate filaments resist
Tensile strength	Resistance to being pulled apart.	Major defining property of intermediate filaments.	pulling force → intermediate filament → structural integrity
Microtubule	Largest major cytoskeletal element; hollow tube made of tubulin.	Cell shape, organelle positioning, intracellular tracks, mitotic spindle, cilia/flagella.	centrosome → microtubules radiate through cell
Tubulin	Protein subunit composing microtubules.	Tubulin assembly/disassembly changes microtubule length.	tubulin units ↔ microtubule
Dynamic microtubule behavior	Microtubules can assemble and disassemble.	Lets cell rapidly reorganize its internal framework.	tubulin added → grows; removed → shrinks
Intracellular transport track	Microtubules act as routes along which cargo can move.	Positions/moves mitochondria, vesicles and other organelles.	cargo + motor protein → microtubule track → destination
Kinesin	Microtubule-associated motor protein.	Professor describes kinesin “walking” vesicular cargo along microtubules.	vesicle → kinesin → microtubule → movement
Dynein	Another microtubule-associated motor protein.	Involved in intracellular transport and particularly emphasized in cilia.	microtubule + dynein → movement
Centrosome	Nonmembranous microtubule-organizing region near nucleus.	Site from which many microtubules originate; organizes mitotic spindle.	nucleus nearby → centrosome → microtubules
Centrosome matrix	Cloudlike protein material forming outer part of centrosome.	Anchors/seeds microtubule growth.	centrosome matrix → microtubules radiate
Centriole	Barrel-shaped structure inside centrosome.	Involved in organization of mitotic apparatus and formation of cilia/flagella bases.	centrosome → pair of centrioles
9 triplets	Each centriole contains nine groups of three microtubules.	Important structural recognition point.	centriole cross-section → 9 × 3

cytoskeleon comparison

microfilaments

intermediate filaments

microtubules

Microfilaments
→ smallest
→ actin
→ movement/contraction

Intermediate filaments
→ middle
→ strongest/stable
→ resist tension

Microtubules
→ largest
→ tubulin tubes
→ shape + intracellular transport + spindle + cilia

Nucleus

nuclear anatomy chart

Nucleus

Anucleate

Nuclear envelope

Outer nuclear membrane

Nuclear lamina

Nuclear pore / nuclear pore complex

Nucleoplasm

Nucleolus

Nucleus vs nucleolus

nuclear anatomy is nuclear envelope → pores → nucleoplasm → chromatin → nucleolus.

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Nucleus	Large membrane-enclosed cellular compartment containing most cellular DNA.	Controls cellular activity largely through gene expression.	cytoplasm → NUCLEUS → genetic information
Anucleate	Having no nucleus.	Mature red blood cells are a textbook human example.	specialized exception
Nuclear envelope	Double membrane surrounding nucleus.	Separates nucleoplasm from cytoplasm and regulates exchange.	cytoplasm → nuclear envelope → nucleoplasm
Outer nuclear membrane	Outer of the two nuclear-envelope membranes.	Continuous with rough ER and can have ribosomes on its external surface.	nuclear envelope ↔ RER
Nuclear lamina	Network of intermediate-filament proteins (lamins) lining inner nuclear membrane.	Supports and maintains nuclear shape.	inner envelope → lamina → nuclear support
Nuclear pore / nuclear pore complex	Protein-lined opening where inner/outer nuclear membranes join.	Allows regulated transport of large molecules such as RNA and proteins.	nucleus ↔ pore ↔ cytoplasm
Nucleoplasm	Jellylike fluid within nucleus.	Suspends chromatin and nucleolus; nuclear equivalent conceptually to cytosol.	nuclear envelope → nucleoplasm → chromatin/nucleolus
Nucleolus	Dense, dark-staining nonmembranous region inside nucleus.	Produces rRNA and assembles large/small ribosomal subunits.	DNA genes → nucleolus → rRNA → ribosome subunits → nuclear pore
Nucleus vs nucleolus	Nucleus = entire DNA-containing compartment; nucleolus = structure inside nucleus.	Textbook explicitly warns students not to confuse them.	cell → nucleus → nucleolus

DNA, chromatin, and chromosome anatomy

DNA

Nucleotide

Sugar-phosphate backbone

Adenine / A

Thymine / T

Cytosine / C

Guanine / G

Complementary base pairing

Double helix

Histone

Nucleosome

Chromatin

Extended chromatin

Euchromatin

Condensed chromatin

Heterochromatin

Chromatid

Chromosome

Sister chromatids

Centromere

Kinetochore

Telomere

Telomerase

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
DNA	Deoxyribonucleic acid; double-helical genetic molecule.	Stores genetic information.	nucleus → DNA
Nucleotide	Basic nucleic-acid subunit consisting of sugar + phosphate + nitrogenous base.	Nucleotides link to form DNA/RNA chains.	nucleotide → nucleotide → nucleic-acid strand
Sugar-phosphate backbone	Alternating sugar and phosphate portion forming sides of DNA/RNA chain.	Supports ordered sequence of bases.	sugar—phosphate—sugar—phosphate
Adenine / A	DNA/RNA nitrogenous base.	DNA pairing partner for thymine.	A ↔ T in DNA
Thymine / T	DNA base.	Pairs with adenine.	A ↔ T
Cytosine / C	DNA/RNA base.	Pairs with guanine.	C ↔ G
Guanine / G	DNA/RNA base.	Pairs with cytosine.	C ↔ G
Complementary base pairing	Specific association between bases on opposite DNA strands.	Professor emphasizes A–T and C–G as basis of stable double-stranded DNA and replication.	strand 1 ↔ complementary strand 2
Double helix	Two DNA strands twisted around each other.	Stable long-term genetic-information structure.	two complementary strands → double helix
Histone	DNA-packaging protein.	DNA wraps around histones to compact it.	DNA → histones
Nucleosome	DNA wrapped around a cluster of eight histone proteins.	Basic chromatin packaging unit; looks like “beads on a string.”	DNA → histone octamer → nucleosome
Chromatin	DNA + associated proteins, especially histones.	Form in which nuclear genetic material is organized.	DNA + histones → chromatin
Extended chromatin	Loosely packed chromatin.	Active DNA regions; transcription can occur.	loose DNA → accessible → transcription
Euchromatin	Professor’s term for lighter, more extended/uncoiled chromatin regions.	Generally associated with more active/accessed DNA.	light → loose → active
Condensed chromatin	Tightly coiled chromatin during nondivision.	Relatively inactive/inaccessible.	packed DNA → stored/inactive
Heterochromatin	Professor’s term for darker, densely packed chromatin regions.	Appears dark in electron micrographs; corresponds conceptually to condensed material emphasized in lecture.	dark → dense → less active
Chromatid	Highly condensed DNA-protein structure; in a duplicated chromosome, each identical longitudinal copy is a sister chromatid.	Enables orderly segregation of replicated DNA.	chromatin coils → chromatid
Chromosome	Maximally compact DNA-protein structure visible during division; duplicated metaphase chromosome consists of two sister chromatids.	Packaging prevents genetic material from tangling/breaking during segregation.	chromatin → tighter coiling → chromosome
Sister chromatids	Two duplicated copies of one chromosome joined together before separation.	Separate during anaphase.	replicated chromosome = chromatid + chromatid
Centromere	Constricted region holding sister chromatids together.	Important site for chromosome segregation.	chromatid ↔ centromere ↔ chromatid
Kinetochore	Protein structure located at chromosome centromere.	Attachment site for kinetochore spindle microtubules.	centromere → kinetochore ← spindle microtubule
Telomere	Repeating DNA at chromosome ends.	Protects chromosome ends; shortens with repeated replication and is discussed in aging.	chromosome END → telomere
Telomerase	Enzyme that can extend telomeric DNA.	Prevents/limits telomere shortening in certain cells; textbook notes germ-line and cancer-cell relevance.	telomerase → adds repeats → telomere length maintained

DNA packaging flow

DNA double helix→ wraps around histones→ nucleosomes→ extended chromatin→ further coiling→ condensed chromatin→ looped/packed further→ chromatid→ two sister chromatids→ duplicated chromosome

DNA RNA Protein

Terminology / concept

Gene

RNA

Uracil / U

mRNA / messenger RNA

tRNA / transfer RNA

rRNA / ribosomal RNA

Transcription

RNA polymerase

Translation

Amino acid

Triplet / codon concept

how protein made flow chart

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Gene	Segment of DNA carrying information for a functional product; professor focuses on protein-coding genes.	Determines which protein can be produced.	DNA → gene → RNA → product
RNA	Ribonucleic acid; generally single-stranded in the professor’s introductory comparison.	Functions in expression/translation of genetic information.	DNA information → RNA intermediates
Uracil / U	RNA base used in place of thymine.	Professor’s quick recognition rule: T suggests DNA; U suggests RNA.	RNA: A, U, C, G
mRNA / messenger RNA	RNA carrying copied genetic instructions from nucleus to ribosome.	Delivers protein-production message.	DNA → mRNA → nuclear pore → ribosome
tRNA / transfer RNA	RNA that participates in translation by bringing amino-acid information/cargo to ribosome.	Helps convert nucleotide code into amino-acid sequence.	mRNA codon ↔ tRNA → amino acid
rRNA / ribosomal RNA	RNA forming major part of ribosome.	Produced in nucleolus; contributes to protein synthesis machinery.	nucleolus → rRNA → ribosome
Transcription	Copying DNA information into RNA.	Occurs in nucleus in this introductory model.	DNA → mRNA
RNA polymerase	Enzyme emphasized by professor that reads DNA to synthesize RNA.	Performs transcription.	DNA + RNA polymerase → RNA
Translation	Process in which ribosome uses mRNA information to assemble amino acids into protein.	Actual protein-synthesis step.	mRNA → ribosome + tRNA → protein
Amino acid	Building block of proteins.	Ribosome links amino acids into a chain.	amino acid + amino acid → protein
Triplet / codon concept	Genetic information is read in groups of three bases; professor explains each three-base instruction in relation to amino-acid coding.	Provides code relating nucleic-acid sequence to protein sequence.	3 bases → amino-acid instruction

DNA→ transcription→ mRNA→ nuclear pore→ cytoplasm→ ribosome→ tRNA helps decode message→ translation→ amino acids linked→ protein

where does the protein go after being made

2 ways

Stay in cytosol
→ free ribosome

Be secreted / become membrane protein
→ RER-bound ribosome
→ RER
→ Golgi
→ vesicle
→ destination

cell life cycle

flow chart

Terminology / concept	Anatomical meaning / structure	Function + important information	Where it fits / flow
Cell life cycle / cell cycle	Sequence of changes from formation of a cell until it divides.	Coordinates growth, DNA duplication and division.	G₁ → S → G₂ → M
Interphase	Nondividing portion of cycle: G₁ + S + G₂.	Cell spends most of its life here; carries out normal activity and prepares for division.	G₁ → S → G₂
G₁ phase	First growth phase.	Cell grows and performs normal functions.	division ends → G₁
S phase	DNA synthesis phase.	DNA is replicated.	G₁ → S: DNA copied
G₂ phase	Second growth/preparation phase.	Final preparation for cell division.	S → G₂ → M
DNA replication	Creation of another DNA copy before division.	Ensures each daughter cell can receive equivalent genetic information.	DNA → replicate → two copies
Helicase	DNA-unwinding enzyme mentioned in professor’s extended replication explanation.	Separates DNA strands so replication machinery can work.	double helix → helicase → separated strands → copies
Checkpoint	Regulatory point where progression through cycle may be halted/permitted.	Professor emphasizes checkpoints because uncontrolled progression connects to cancer.	G₁/S or G₂/M decision → continue/stop
Mitotic / M phase	Phase in which cell division occurs.	Includes nuclear division and cytoplasmic division.	M = mitosis + cytokinesis
Mitosis	Division of the nucleus.	Distributes replicated chromosomes into two daughter nuclei.	prophase → metaphase → anaphase → telophase
Mitotic spindle / spindle apparatus	Microtubule machinery used to position and separate chromosomes.	Links cytoskeleton directly to chromosome segregation.	centrosomes → spindle microtubules → chromosomes
Spindle pole	Opposite ends of mitotic spindle.	Chromosomes ultimately segregate toward opposite poles.	pole ← chromosomes → pole
Aster	Star-shaped microtubule array radiating from centrosome during mitosis.	Part of mitotic microtubule organization.	centrosome → aster
Kinetochore microtubule	Spindle microtubule attached to chromosome kinetochore.	Pulls chromosomes during segregation.	pole → microtubule → kinetochore
Nonkinetochore microtubule	Spindle microtubule not attached to chromosome.	Interacts with opposite spindle microtubules to help move poles apart.	pole → microtubules ↔ microtubules ← pole
Prophase	First mitotic phase. Chromatin condenses; chromosomes become visible; nucleolus disappears; centrosomes separate; spindle develops; nuclear envelope breaks down.	Prepares compact chromosomes for movement.	chromatin → chromosomes + spindle
Metaphase	Chromosomes align at middle/equator of cell.	Ensures each sister chromatid is correctly attached before separation.	chromosome chromosome chromosome → middle
Metaphase plate	Imaginary plane at cell equator where centromeres align.	Defining visual feature of metaphase.	pole — metaphase plate — pole
Anaphase	Sister chromatids separate; each becomes an independent daughter chromosome and moves toward opposite pole.	Physically distributes duplicated DNA.	sister chromatids → apart → opposite poles
Daughter chromosome	Former sister chromatid after separation.	Becomes part of daughter nucleus.	sister chromatid separates → daughter chromosome
Telophase	Final mitotic phase; chromosomes reach poles and uncoil; nuclear envelopes and nucleoli re-form; spindle disappears.	Restores two nuclei.	chromosomes at poles → new nuclei form
Cytokinesis	Division of cytoplasm/cell.	Separates one parent cell into two daughter cells.	mitosis → cytokinesis → 2 cells
Contractile ring	Ring of actin microfilaments involved in cytokinesis.	Contracts and pinches plasma membrane inward.	actin ring contracts → cleavage furrow
Cleavage furrow	Indentation formed as animal cell membrane pinches inward during cytokinesis.	Deepens until cell separates.	membrane indentation → separation

G₁ cell grows→S DNA replicates → G₂ prepare to divide
→ PROPHASE chromosomes condense + spindle forms→ METAPHASE chromosomes line up in middle→ ANAPHASE sister chromatids separate→TELOPHASE two nuclei re-form→CYTOKINESIS cytoplasm divides→2 daughter cells

difference game

Cytoplasm vs cytosol

Nucleus vs nucleolus

Chromatin vs chromosome

Chromatid vs chromosome

Centrosome vs centromere

Centriole vs centrosome

Microvilli vs cilia

RER vs SER

Lysosome vs peroxisome

Diffusion vs active transport

Endocytosis vs exocytosis

Phagocytosis vs pinocytosis

Secretion vs excretion

Terms	Difference she needs to know	Flow / association
Cytoplasm vs cytosol	Cytoplasm = cytosol + organelles + inclusions. Cytosol = fluid component only.	cytoplasm = cytosol + contents
Nucleus vs nucleolus	Nucleus contains genetic material; nucleolus is inside nucleus and produces rRNA/ribosomal subunits.	cell → nucleus → nucleolus
Chromatin vs chromosome	Chromatin is DNA-protein material; chromosome is highly condensed organization of that material during division.	DNA → chromatin → chromosome
Chromatid vs chromosome	A duplicated chromosome has two sister chromatids; after separation each chromatid becomes a chromosome.	chromosome duplication → 2 chromatids → separation → chromosomes
Centrosome vs centromere	Centrosome = cellular microtubule-organizing region. Centromere = chromosome region joining sister chromatids.	centroSOME = cell structure; centroMERE = chromosome
Centriole vs centrosome	Centriole = barrel-shaped microtubule structure; centrosome = region containing pair of centrioles + matrix.	centrosome → centrioles
Microvilli vs cilia	Microvilli increase surface area; cilia move external material.	microvilli = absorption; cilia = motion
RER vs SER	RER has ribosomes → protein production. SER lacks ribosomes → lipids/steroids, detoxification, Ca²⁺.	rough = ribosomes = protein
Lysosome vs peroxisome	Lysosome digests; peroxisome performs oxidative detoxification.	lysis = break down; peroxide = detox
Diffusion vs active transport	Diffusion follows gradient; active transport moves against gradient using energy.	high→low vs low→high + ATP
Endocytosis vs exocytosis	Endocytosis brings material in; exocytosis sends material out.	ENDO = IN; EXO = OUT
Phagocytosis vs pinocytosis	Phago = eating large particles; pino = drinking extracellular fluid.	eat vs drink
Secretion vs excretion	Secretion releases product from cell/into another compartment; excretion eliminates it from body.	cell → secrete; body → excrete

cell specialization : predict anatomy from function

Cell/function

Protein-secreting cell

Steroid-hormone-producing cell

Highly contractile muscle cell

High-energy kidney/muscle-type cell

Phagocytic white blood cell

Detoxifying liver-type cell

Cell resisting mechanical stress

Cell specializing in absorption

Cell moving mucus/fluid over its surface

textbook explicitly tests: different cell types have different organelle abundance because their functions differ.

Cell/function	What should be abundant?	Why / flow
Protein-secreting cell	RER + Golgi + secretory vesicles; substantial ATP demand	protein synthesis → processing → secretion
Steroid-hormone-producing cell	Smooth ER	cholesterol/lipids → SER → steroid
Highly contractile muscle cell	Actin microfilaments + myosin; many mitochondria	ATP + contractile proteins → movement
High-energy kidney/muscle-type cell	Many mitochondria	energy demand ↑ → mitochondria ↑
Phagocytic white blood cell	Lysosomes	particle engulfed → phagosome → lysosomal digestion
Detoxifying liver-type cell	SER and/or peroxisomes depending on substance/process	toxin → detoxification machinery
Cell resisting mechanical stress	Intermediate filaments	pulling force → stable tensile fibers
Cell specializing in absorption	Microvilli	surface area ↑ → transport surface ↑
Cell moving mucus/fluid over its surface	Cilia	coordinated beating → material transported

Terminology / concept

Cell differentiation

Gene expression

Cell specialization

Aging / cellular aging

Mitochondrial theory of aging

Antioxidant

Telomere shortening

Apoptosis

Necrosis

Hyperplasia

Hypertrophy

Dysplasia

They are lower priority than membrane/organelles/nucleus, but they are part of Chapter 2.

Terminology / concept	Meaning / function	Where it fits
Cell differentiation	Process by which cells become specialized in structure/function despite possessing the same basic genome. Different signals lead to different patterns of gene expression.	same DNA → different genes ON/OFF → different cell types
Gene expression	Use of genetic information to produce functional products, leading to cellular characteristics.	DNA → RNA/protein → phenotype/function
Cell specialization	Different cell types develop anatomy suited to their jobs.	differentiation → specialized cells
Aging / cellular aging	Chapter discusses accumulated free-radical damage, genetic influences and loss of division capacity as possible contributors.	metabolism/time → accumulated cellular effects
Mitochondrial theory of aging	Free-radical damage involving highly metabolically active mitochondria may progressively impair energy production.	mitochondrial metabolism → radicals → damage
Antioxidant	Substance that limits oxidative/free-radical damage; textbook discusses vitamins C/E in this context.	free radicals → antioxidant defense
Telomere shortening	Telomeres shorten with repeated DNA replication in many cells; critically short telomeres can limit division.	division → telomere shorter → eventual stop signal
Apoptosis	Programmed, controlled cell death; cell shrinks and is removed without the inflammatory leakage characteristic of necrosis.	controlled signal → orderly cell death
Necrosis	Uncontrolled cell death from injury/disease; cells swell/burst and can promote inflammation.	damage → cell rupture → inflammation
Hyperplasia	Increase in number of cells due to increased proliferation.	more cell division → more cells
Hypertrophy	Increase in size of cells, causing tissue/organ enlargement.	cells get bigger → larger tissue
Dysplasia	Abnormal change in cell size, shape or arrangement associated with chronic irritation/inflammation in the text.	abnormal cellular organization

Last comparison worth memorizing

Hyperplasia = more cells

Hypertrophy = bigger cells

and

Apoptosis = controlled cell death

Necrosis = uncontrolled injury-related cell death

The Chapter 2 related-clinical-terms section explicitly makes these distinctions.

mega review

cell flow chart (ribosome , RER, SER, golgi, lysosome, peroxisome, mitochondrion, cytoskeleton)

where is nucleus? flow chart

DNA

cell division

CELL→ surrounded by PLASMA MEMBRANE→ phospholipid bilayer + cholesterol + proteins + glycocalyx→ controls TRANSPORT / SIGNALING / RECOGNITION→ membrane can form junctions, microvilli, cilia→ inside is CYTOPLASM→ cytosol + organelles + inclusions→ organelles include:

Ribosome → protein synthesis
RER → secreted/membrane proteins
SER → lipid/steroid + detox + Ca²⁺
Golgi → modify/sort/package
Lysosome → digest
Peroxisome → detoxify
Mitochondrion → ATP
Cytoskeleton → shape/movement/transport

inside cytoplasm sits NUCLEUS→ nuclear envelope + pores + nucleoplasm→ nucleolus → ribosome production→ chromatin → genetic material

Then:

DNA→ transcription→ mRNA→ nuclear pore→ ribosome→ translation→ PROTEIN

And when cell divides:

G₁ → S → G₂→ Prophase → Metaphase → Anaphase → Telophase→ Cytokinesis