Chapter 7: Inside the Cell

Prokaryote

A tiny, simple cell with no special room for its DNA. The DNA just floats inside. SCENARIO: Like a one-room cabin where your toys, bed, and kitchen are all in the same open space.

Eukaryote

A bigger cell with lots of little rooms inside, including a special room (the nucleus) for its DNA. Plants, animals, and fungi are made of these. SCENARIO: Like a big house with a bedroom, kitchen, and bathroom, each with its own door.

Transmission electron microscope

A super-powerful microscope that shoots tiny particles through very thin slices of a cell to see the smallest parts. SCENARIO: Like a magic magnifying glass that lets you see the rooms inside a dollhouse through its walls.

Plasma membrane

The thin, soft skin around every cell that decides what gets in and out. SCENARIO: Like a bouncer at a party door who only lets certain guests inside.

Cytoplasm

Everything inside the cell's skin (except the nucleus in eukaryotes). SCENARIO: Like everything inside a snow globe: the water, glitter, and little house.

Cytosol

The watery jelly inside the cell that the parts float in. SCENARIO: Like the water in a fish tank that the fish and plants sit in.

Chromosome

A long string of DNA that holds all the cell's instructions. SCENARIO: Like a giant cookbook with every recipe the cell will ever need.

Gene

One instruction on the DNA for making something. SCENARIO: Like one recipe in the cookbook, such as "how to make chocolate chip cookies."

Central dogma

The path instructions follow: DNA to RNA to protein. SCENARIO: Mom's cookbook (DNA) stays safe, you copy one recipe onto a card (RNA), then bake the cookies (protein).

Supercoiling

Twisting DNA tightly so a very long strand fits in a tiny cell. SCENARIO: Like twisting a rubber band over and over until it bunches into a tiny knot.

Nucleoid

The area in a prokaryote where the DNA hangs out, with no wall around it. SCENARIO: Like the corner of your room where you pile your toys, but there is no toy box.

Plasmid

A small bonus loop of DNA with extra helpful instructions. SCENARIO: Like a small emergency booklet you only read when something unusual happens, like a storm.

Ribosome

A tiny machine that reads instructions and builds proteins. SCENARIO: Like a little chef who reads the recipe card and cooks the meal.

Cytoskeleton

A network of protein strings and sticks that gives the cell its shape and moves things around. SCENARIO: Like the poles and ropes that hold up a tent and keep it from flopping over.

Photosynthesis

Using sunlight to make food (sugar). SCENARIO: Like a solar-powered kitchen that cooks meals using sunshine.

Organelle

A little room inside a cell with its own special job. SCENARIO: Like the different rooms in a school: the cafeteria, library, and gym.

Cell wall

A hard, strong layer outside the membrane that protects the cell and keeps its shape. SCENARIO: Like a hard shell on a turtle or a crab.

Osmosis

Water moving across a membrane toward the side with more stuff dissolved in it. SCENARIO: Like a dry sponge soaking up water when you drop it in a bowl.

Peptidoglycan

The strong sugar-and-protein material that most bacterial cell walls are made of. SCENARIO: Like the bricks used to build a bacteria's wall.

Prokaryotic flagellum

A long tail that spins like a propeller to push a bacterium through water. SCENARIO: Like the spinning motor on the back of a little toy boat.

Fimbriae

Tiny sticky hairs that let bacteria grab onto things. SCENARIO: Like Velcro on your shoes that sticks to things, which helps germs stick to your body and make you sick.

Surface-area-to-volume ratio

How much outside skin a cell has compared to how much inside space. Big cells have less skin for their size. SCENARIO: A tiny ice cube melts fast, but a giant ice block melts slowly because less of it touches the air.

Compartmentalization

Splitting the cell into separate rooms so jobs don't get in each other's way. SCENARIO: Keeping paint in the art room and food in the kitchen so you never mix them up.

Nucleus

The cell's control center that holds the DNA. SCENARIO: Like the principal's office where all the important school records are kept.

Nuclear envelope

The double wall around the nucleus. SCENARIO: Like a castle with two walls to protect the treasure inside.

Nuclear pore

Holes in the nuclear envelope that let things in and out. SCENARIO: Like the doors and windows in the castle walls.

Nuclear lamina

A net of protein strings lining the inside of the nucleus to keep it strong. SCENARIO: Like the metal frame inside a play tent that keeps its shape.

Nucleolus

A spot inside the nucleus where ribosome parts are made. SCENARIO: Like the workshop in the principal's office where they build new chefs.

Endoplasmic reticulum (ER)

A big maze of folded membranes that makes and handles proteins and fats. SCENARIO: Like a giant factory connected right next to the principal's office.

Rough ER

The part of the ER covered in ribosomes that makes proteins. SCENARIO: Like a bumpy factory floor covered with chefs cooking proteins.

Smooth ER

The part of the ER with no ribosomes that makes fats and cleans up poisons. SCENARIO: Like the smooth, quiet part of the factory that makes oils and cleans spills.

Lumen

The empty space inside a sac or tube in the cell. SCENARIO: Like the inside of a straw where the juice goes.

Golgi apparatus

A stack of flat sacs that finishes, packs, and ships proteins. SCENARIO: Like a post office that wraps presents and sends them to the right address.

Cisternae

The flat pancake-like sacs that make up the Golgi. SCENARIO: Like a stack of pancakes on a plate.

Cis face

The side of the Golgi that receives packages from the ER. SCENARIO: Like the front door of the post office where packages come in.

Trans face

The side of the Golgi that sends packages out. SCENARIO: Like the back door of the post office where delivery trucks leave.

Lysosome

A little bag of digestive juices that breaks down old stuff so it can be reused. SCENARIO: Like a recycling bin that chews up old toys into pieces to build new ones.

Acid hydrolases

The digestive enzymes inside lysosomes that only work in sour (acidic) conditions. SCENARIO: Like special scissors that only cut when dipped in lemon juice, so they are safe if they spill out.

Proton pump

A tiny pump that pushes acid particles into a lysosome to keep it sour. SCENARIO: Like someone squeezing lemon juice into a bucket to keep it sour.

Endomembrane system

The team of the ER, Golgi, and lysosomes working together to make and ship things. SCENARIO: Like the factory, post office, and recycling center all working as one team in a town.

Vacuole

A big storage bag, mostly in plant cells, that holds water and other stuff. SCENARIO: Like a water balloon inside the cell that keeps a plant standing up tall. When it's empty, the plant droops.

Peroxisome

A small room that does chemical clean-up and breaks down things like alcohol. SCENARIO: Like a science lab with safety goggles, where dangerous chemicals are handled safely.

Catalase

An enzyme in peroxisomes that turns dangerous hydrogen peroxide into safe water and oxygen. SCENARIO: Like a firefighter who puts out a small fire before it can spread.

Mitochondrion

The cell's power plant that makes energy (ATP) from food. SCENARIO: Like a battery charger that turns your snack into energy to run and play.

ATP

The cell's energy money that it spends to do work. SCENARIO: Like tokens at an arcade. You need them to play any game.

Cristae

The folds inside a mitochondrion that give it more space to make energy. SCENARIO: Like folding a long towel into a small drawer so more fits inside.

Mitochondrial matrix

The fluid inside the inner membrane of a mitochondrion. SCENARIO: Like the juice inside a grape.

Chloroplast

The part of a plant cell that uses sunlight to make sugar. SCENARIO: Like a tiny solar panel kitchen inside a leaf.

Thylakoid

Flat discs inside a chloroplast that catch sunlight. SCENARIO: Like tiny solar panels shaped like coins.

Granum (grana)

A stack of thylakoids. SCENARIO: Like a stack of coins on a table.

Stroma

The fluid around the grana where sugar gets made. SCENARIO: Like the kitchen counter space around the solar panels where the cooking happens.

Endosymbiosis theory

The idea that mitochondria and chloroplasts were once free bacteria that got swallowed by a bigger cell and stayed to help. SCENARIO: Like a stray puppy that walked into your house, never left, and became part of the family.

Extracellular matrix (ECM)

A mesh of proteins and sugars outside animal cells that holds them together. SCENARIO: Like the glue and string holding popsicle sticks together in a craft project.

Differential centrifugation

Spinning broken-up cells really fast to separate their parts by size and weight. SCENARIO: Like a spinning ride where heavy kids slide out first and light kids stay in the middle.

Live-cell imaging (GFP)

Tagging cell parts with glowing markers to watch them move in living cells. SCENARIO: Like putting glow sticks on your friends at night so you can see where they run.

Nuclear pore complex

The big protein gate in each nuclear pore that controls traffic. SCENARIO: Like a security gate at an airport that checks everyone going in and out.

mRNA (messenger RNA)

A copy of a gene's instructions that leaves the nucleus to tell ribosomes what to build. SCENARIO: Like a note from the principal sent to the cafeteria saying what to cook today.

Nucleoplasmin

A protein found only in the nucleus that scientists used to discover how proteins get in. SCENARIO: Like the student with a hall pass that helped teachers figure out how the pass system works.

Nuclear localization signal (NLS)

A short "zip code" on a protein that says "send me into the nucleus." SCENARIO: Like a sticker on a letter that says "Deliver to the Principal's Office."

Nuclear transport proteins

Helper proteins that carry big molecules through the nuclear pores. SCENARIO: Like delivery trucks that carry packages through the castle gate.

Secretory pathway

The route proteins take to leave the cell: ER, then Golgi, then vesicle, then out. SCENARIO: Like a toy going from the factory, to the gift wrap station, to the delivery truck, to your house.

Vesicle

A tiny bubble made of membrane that carries stuff around the cell. SCENARIO: Like a soap bubble with a toy inside floating to a friend.

Pulse-chase experiment

Marking a batch of new proteins for a short time, then watching where they travel. SCENARIO: Like dropping a little food coloring into a stream and watching where the color flows.

Signal hypothesis

The idea that proteins going to the ER have a special tag at the front that sends them there. SCENARIO: Like kids wearing a red bracelet getting walked straight to the art room.

ER signal sequence

The "send me to the ER" tag at the start of a protein. SCENARIO: Like the red bracelet that tells the teacher "take me to the art room."

Signal recognition particle (SRP)

A helper that grabs the ER tag, pauses protein building, and brings the ribosome to the ER. SCENARIO: Like a hall monitor who sees your red bracelet, says "stop," and walks you to the art room.

SRP receptor

The spot on the ER where the SRP docks. SCENARIO: Like a lock on the art room door that only the hall monitor's key can open.

Translocon

A channel in the ER membrane that the growing protein threads through. SCENARIO: Like a tunnel slide that the protein slides down into the ER.

Chaperone proteins

Helpers that make sure new proteins fold into the right shape. SCENARIO: Like a teacher helping you fold your paper airplane the right way.

Glycosylation

Adding sugar chains to a protein. SCENARIO: Like putting sprinkles on a cupcake before sending it off.

Glycoprotein

A protein with sugar chains attached. SCENARIO: Like a cupcake that already has its sprinkles on.

Mannose-6-phosphate

A special tag that tells the Golgi "send this protein to the lysosome." SCENARIO: Like an address label that says "Recycling Center."

Exocytosis

A vesicle joining with the cell's skin and dumping its stuff outside the cell. SCENARIO: Like opening your front door and throwing a ball out into the yard.

Endocytosis

The cell's skin folding inward to bring stuff from outside into the cell. SCENARIO: Like a mouth closing around a bite of food.

Receptor-mediated endocytosis

The cell grabs specific things with hooks on its surface, then pulls them inside. SCENARIO: Like a claw machine that only picks up the teddy bears, not the other prizes.

Early endosome

The first drop-off station for things brought into the cell; it gets more and more sour. SCENARIO: Like the mudroom where you drop your stuff when you first come in the house.

Late endosome

A more mature, more sour endosome that receives digestive enzymes and turns into a lysosome. SCENARIO: Like the mudroom slowly turning into the laundry room where things get cleaned up.

Phagocytosis

A cell wrapping around and swallowing a whole particle or smaller cell. SCENARIO: Like Pac-Man gobbling up a dot.

Phagosome

The bubble that forms around something a cell swallowed. SCENARIO: Like a lunchbox holding the food Pac-Man just ate.

Autophagy

A cell wrapping up its own broken parts to recycle them. SCENARIO: Like cleaning your room and putting broken toys in a bag for recycling.

Autophagosome

The bubble that wraps broken parts during autophagy. SCENARIO: Like the recycling bag holding your broken toys.

Actin filament (microfilament)

The thinnest cytoskeleton string, made of actin, that helps cells move and keep shape. SCENARIO: Like the thin strings on a puppet that make it move.

Polarity (plus and minus ends)

Having two different ends. The plus end grows faster than the minus end. SCENARIO: Like a pencil with a sharp end and an eraser end. They look different and do different jobs.

Motor protein

A protein that uses ATP to move along cytoskeleton tracks. SCENARIO: Like a toy train that uses batteries to drive along its track.

Myosin

A motor protein that walks along actin to make muscles and cells move. SCENARIO: Like a sailor pulling a rope hand over hand.

Cytokinesis

The final step of cell division where the cell pinches in half. SCENARIO: Like tightening a belt around a balloon until it splits into two balloons.

Cytoplasmic streaming

The flow of cytoplasm around a big cell to move things. SCENARIO: Like a lazy river at a water park carrying floaties around in a circle.

Cell crawling

A cell moving by growing actin forward to push its edge out. SCENARIO: Like an inchworm stretching out its front to scoot forward.

Intermediate filament

A medium-sized, rope-like fiber that only gives strength and support. SCENARIO: Like the strong ropes that hold down a bouncy house so it doesn't blow away.

Keratin

A type of intermediate filament that makes skin strong and forms hair and nails. SCENARIO: Like the tough stuff your fingernails are made of.

Lamin

A type of intermediate filament that forms the net inside the nucleus. SCENARIO: Like the frame that keeps the principal's office from caving in.

Microtubule

The biggest cytoskeleton fiber, a hollow tube that acts like a road and a support pole. SCENARIO: Like highways that delivery trucks drive on, or tent poles that hold up a tent.

Tubulin

The protein building blocks of microtubules, which come in pairs. SCENARIO: Like LEGO bricks that snap together to build a tube.

Microtubule-organizing center (MTOC)

The place where microtubules start growing. SCENARIO: Like a bus station where all the bus routes begin.

Centrosome

The MTOC in animal cells, found near the nucleus. SCENARIO: Like the main bus station downtown.

Centriole

A small barrel of 9 groups of 3 microtubules; two of them sit in the centrosome. SCENARIO: Like two small barrels sitting at the bus station.

Kinesin

A motor protein that walks along microtubules toward the plus end (outward), carrying vesicles. SCENARIO: Like a tiny mail carrier walking on a tightrope, carrying a package out to the edge of town.

Dynein

A motor protein that walks toward the minus end (inward) and makes cilia and flagella bend. SCENARIO: Like a mail carrier walking the other way, back toward the post office.

Eukaryotic flagellum

A long whip-like tail made of microtubules that swishes back and forth to move the cell. SCENARIO: Like a tadpole swishing its tail to swim.

Cilium (cilia)

Short hair-like parts, often lots of them, that beat to move a cell or push stuff past it. SCENARIO: Like a crowd doing "the wave" at a stadium.