Unit 2 Beta

Cell Structure and Function: the one-page sheet

2.1 Cell Structure and Function

Every cell has a membrane, cytoplasm, DNA and ribosomes. Eukaryotic cells add a nucleus and membrane-bound organelles that split the work: the rough ER builds proteins for export, the smooth ER makes lipids and detoxifies, the Golgi modifies and packages, lysosomes digest, vacuoles store, mitochondria make ATP and chloroplasts capture the energy of sunlight. Each structure's shape fits its job, from the folded inner membranes of mitochondria to the ribosome-studded surface of the rough ER.

Prokaryotes (bacteria and archaea) have DNA in the cytoplasm, ribosomes and a cell membrane, but no nucleus and no membrane-bound organelles. Eukaryotes keep their DNA in a nucleus and divide the cytoplasm into membrane-bound organelles.
Ribosomes are in every cell. They are made of rRNA and protein, and they build proteins. Free ribosomes make proteins for the cytosol; ribosomes on the rough ER make proteins for membranes, lysosomes and export.
The smooth ER makes lipids and, in liver cells, breaks down drugs and toxins. The Golgi complex modifies, sorts and packages proteins. Lysosomes digest worn-out parts and engulfed material with enzymes that work best in acid.
Mitochondria and chloroplasts each have a double membrane and their own DNA and ribosomes. Their folded inner membranes (cristae, thylakoids) pack in more membrane for the proteins that capture energy.
A plant cell's central vacuole stores water and presses the cytoplasm against the cell wall, keeping the cell firm. The cytoskeleton gives shape and carries vesicles along microtubule tracks.

The instructions are copied into mRNA, which leaves the nucleus through a nuclear pore. The ribosome threads the growing protein into the ER, where it folds and may have sugars added. A vesicle carries the protein to the Golgi complex and merges with it. The protein is packaged into a new vesicle bound for the cell membrane. The vesicle reaches the cell membrane, merges with it, and releases the protein outside the cell.

cell: The smallest unit that can carry out all the processes of life. Every cell is bounded by a membrane and contains cytoplasm, DNA and ribosomes. Cell theory says all living things are made of cells and all cells come from earlier cells.
prokaryote: A cell, or a single-celled organism, whose DNA is not enclosed in a nucleus and which has no membrane-bound organelles. Bacteria and archaea are prokaryotes. Most are about 0.1 to 5 µm across.
bacteria: A large group of prokaryotes. Bacteria have a cell membrane, cytoplasm, ribosomes and DNA but no nucleus, and most have a cell wall.
eukaryote: A cell, or an organism made of such cells, whose DNA is enclosed in a nucleus and which has membrane-bound organelles. Animals, plants, fungi and protists are eukaryotes. Most eukaryotic cells are about 10 to 100 µm across.
fungi: Eukaryotes such as yeasts, molds and mushrooms. Fungal cells have a cell wall made of chitin and take in food from their surroundings.
organelle: A structure inside a cell that does a particular job. In eukaryotes many organelles are wrapped in their own membrane (membrane-bound organelles), such as the nucleus, ER, Golgi complex, lysosomes and mitochondria.
cytoplasm: Everything inside the cell membrane except the nucleus. The cytosol is its fluid part, a watery solution of ions, small molecules and proteins in which the organelles sit.
nucleus: The organelle that holds a eukaryotic cell's DNA. It is wrapped in a double membrane, the nuclear envelope, crossed by nuclear pores. The nucleolus inside it makes rRNA and assembles ribosome pieces.
chromosome: One long DNA molecule, packed with proteins. Chromatin is the DNA-protein material of chromosomes; in a eukaryote it sits in the nucleus.
rRNA: Ribosomal RNA: the RNA that, together with proteins, makes up ribosomes. It is made in the nucleolus.
ribosome: The structure, made of rRNA and protein, that links amino acids into a protein by reading mRNA. Found in all cells. Free ribosomes float in the cytosol and make proteins for the cytosol; bound ribosomes sit on the rough ER and make proteins for membranes, lysosomes or export.
mRNA: Messenger RNA: a copy of a gene's instructions, made in the nucleus, that leaves through nuclear pores and is read by ribosomes to build a protein.
gene expression: Using a gene's instructions to make its product: the gene is copied into mRNA, and ribosomes read the mRNA to build a protein (protein synthesis).
endomembrane system: The set of membranes in a eukaryotic cell that work together and pass material between them in vesicles: the nuclear envelope, ER, Golgi complex, lysosomes, vacuoles and the cell membrane.
endoplasmic reticulum: Endoplasmic reticulum: a network of membrane sacs and tubes that runs through the cytoplasm and joins the nuclear envelope. It comes in two forms, rough and smooth.
rough ER: ER studded with bound ribosomes. It builds proteins that go to membranes, to lysosomes or out of the cell, threading them into the ER as they are made.
smooth ER: ER without ribosomes. It makes lipids, such as phospholipids and steroids, and in liver cells it breaks down drugs and other toxins (detoxification).
Golgi complex: Golgi complex: a stack of flattened membrane sacs that receives proteins from the ER in vesicles, modifies them (for example by adding or trimming sugars), sorts them and packages them into vesicles for their destinations.
vesicle: A small sac of membrane that carries material inside a cell, for example from the ER to the Golgi or from the Golgi to the cell membrane.
secretory pathway: The route a protein takes to leave the cell: built on the rough ER, carried in a vesicle to the Golgi, modified and packaged there, then carried in a vesicle that fuses with the cell membrane and releases it (secretion).
apoptosis: Programmed cell death: a cell's orderly self-destruction, in which it takes itself apart in a controlled way.
lysosome: A membrane sac full of hydrolytic (digestive) enzymes that work best in its acidic interior. It breaks down large molecules, worn-out organelles and engulfed material, and helps in programmed cell death.
vacuole: A large membrane sac that stores water and other materials. A plant cell's central vacuole can fill most of the cell and keeps it firm; a food vacuole forms when a cell engulfs food.
mitochondrion: The organelle where cellular respiration makes most of a eukaryotic cell's ATP. It has a smooth outer membrane and a folded inner membrane, and its own DNA and ribosomes.
chloroplast: The organelle in plants and algae where photosynthesis takes place. It has a double membrane, stacks of thylakoids inside, and its own DNA and ribosomes.
double membrane: Two membranes, one inside the other, around mitochondria, chloroplasts and the nucleus. In a mitochondrion the intermembrane space lies between the outer and inner membranes.
cristae: The folds of a mitochondrion's inner membrane. They pack more membrane, and more of the proteins that make ATP, into the same space.
mitochondrial matrix: The fluid inside a mitochondrion's inner membrane. It holds the mitochondrion's DNA, ribosomes and many enzymes of cellular respiration.
thylakoid: A flattened membrane sac inside a chloroplast; stacks of thylakoids are called grana. Thylakoid membranes capture the energy of sunlight.
stroma: The fluid inside a chloroplast that surrounds the thylakoids. Sugars are built there.
mitochondrial DNA: The small DNA molecules inside mitochondria and chloroplasts, separate from the DNA in the nucleus. They carry genes for some of the organelle's own proteins.
cytoskeleton: A network of protein fibers through the cytoplasm that gives the cell its shape, anchors organelles and moves things. Microtubules are tracks for vesicles; microfilaments (actin) help the cell change shape and move; intermediate filaments resist pulling.
flagellum: A long whip-like structure that moves a cell (plural flagella). Cilia are shorter, numerous projections that beat to move a cell or move fluid past it.

2.2 Cell Size

As an object grows, its volume grows faster than its surface, so its surface area-to-volume ratio falls. Cells exchange materials and heat across their surface, and diffusion is slow over long distances, so a high ratio is needed for fast exchange. That limits cell size and explains the thin, folded shapes of exchange surfaces such as microvilli, root hairs and alveoli. In endotherms the same geometry means small animals lose heat fast for their mass and have a higher metabolic rate per gram than large animals.

For a cube with side s, surface area = 6s² and volume = s³. For a sphere, surface area = 4πr² and volume = 4/3 πr³. Doubling the size multiplies surface by 4 but volume by 8, so the ratio halves.
Diffusion is the net spreading of particles down their concentration gradient, from more crowded to less crowded, powered by their own motion. It is quick across a few micrometers and very slow across centimeters.
Small cells and thin, folded exchange surfaces (microvilli, root hairs, alveoli) keep the surface area-to-volume ratio high. Flattening a shape raises the ratio too: a thin slab exchanges far faster than a cube of the same volume.
Endotherms keep warm with heat from their own cellular respiration; ectotherms rely on outside heat. Small endotherms lose heat fast for their size, so their metabolic rate per gram is much higher than that of large endotherms.

Its surface area grows with the square of its size, but its volume grows with the cube, so its surface area-to-volume ratio falls. Each unit of surface must serve more volume, and exchange per unit of volume slows. Materials reach the center too slowly, which limits how large a cell can grow. They add surface without adding much volume, raising the surface area-to-volume ratio. Each gram must burn more fuel to replace the heat, so small endotherms have higher metabolic rates per gram than large ones.

adaptation: An inherited feature that helps organisms survive and reproduce where they live, such as the root hairs of plants or the thin ears of a desert fox. How adaptations arise is taught in Unit 7.
endotherm: An animal, such as a bird or mammal, that keeps its body warm mainly with heat released by its own cellular respiration. An ectotherm, such as a lizard or fish, gets most of its body heat from its surroundings, so its body temperature follows theirs.
diffusion: The net spreading of particles from where they are more concentrated to where they are less concentrated, driven by their own random motion, with no energy input from the cell. It is fast over short distances and slow over long ones.
concentration gradient: A difference in the concentration of a substance between two places. Particles diffusing from high to low concentration are said to move down their gradient.
surface area: The total area of the outside of an object. For a cell, it is the area of the cell membrane, through which every material enters or leaves.
surface area-to-volume ratio: Surface area divided by volume. It falls as an object gets bigger, because surface area grows with the square of its size and volume with the cube. A high ratio means more surface for exchange per unit of volume.
surface area of a cube: Cube with side s: surface area 6s², volume s³. Sphere with radius r: surface area 4πr², volume 4/3 πr³. Cylinder with radius r and height h: volume πr²h, surface area 2πrh + 2πr².
limits on cell size: The upper limit on how big a cell can get: as it grows, its volume (which uses materials and makes wastes) outgrows the surface through which they are exchanged, and its center gets too far from the surface for diffusion to keep up.
exchange surface: A surface specialized for moving materials in or out, usually thin and folded to give a large area: root hairs in roots, villi and microvilli in the small intestine, alveoli in the lungs.
heat loss and body size: Heat leaves a body through its surface. Smaller animals have more surface per unit of volume, so they lose heat faster for their size than larger animals do.
metabolic rate: How fast an organism uses energy, often measured as oxygen used or heat given off per unit of time. Per gram of body mass, small endotherms have much higher metabolic rates than large ones.

2.3 Plasma Membrane

The plasma membrane is a phospholipid bilayer: hydrophilic heads face the water on each side and hydrophobic tails meet in the middle. Proteins sit in or on it and do most of its jobs: moving substances, receiving signals as receptors, and, with carbohydrate chains attached, letting cells recognize each other. Its lipids and proteins slide sideways, which is why it is called a fluid mosaic. Temperature, unsaturated fatty acids and cholesterol together keep it fluid enough to work.

The fluid mosaic model: a fluid phospholipid bilayer with a patchwork of proteins in it. "Fluid" because lipids and proteins slide sideways; "mosaic" because many kinds of proteins are scattered through it.
Membrane proteins are integral (embedded, often crossing the whole bilayer) or peripheral (loosely attached to one surface). They move substances across, act as receptors for signaling molecules, join cells, and act as enzymes.
Glycoproteins and glycolipids carry carbohydrate chains on the outside of the cell. These chains are identity tags used in cell recognition.
Fluidity rises with temperature and with the share of unsaturated (kinked) tails. Cholesterol buffers it: it restrains movement when warm and prevents tight packing when cold.

They form a bilayer, heads facing the water on each side and tails hidden in the middle. Lipids and many proteins can slide sideways, so the membrane behaves like a fluid. They stay embedded in the bilayer, and many cross it to touch both sides. Glycoproteins and glycolipids carry them on the outer surface, where other cells can recognize them. The membrane's fluidity changes, and with it how well its proteins can move and work.

plasma membrane: The membrane that surrounds a cell and separates its inside from its surroundings: a phospholipid bilayer with proteins, cholesterol (in animal cells) and carbohydrates attached to some lipids and proteins.
membrane protein: A protein in or on a membrane. Integral (embedded) proteins sit in the bilayer, and transmembrane proteins cross it completely; peripheral proteins are attached loosely to one surface. They move substances across, receive signals, join cells and act as enzymes.
fluid mosaic model: The accepted model of membrane structure: a fluid phospholipid bilayer in which lipids and many proteins slide sideways, with a patchwork (mosaic) of different proteins scattered through it.
membrane fluidity: How freely the lipids and proteins of a membrane move. Higher temperature and more unsaturated (kinked) fatty acid tails raise fluidity; cholesterol keeps it within a working range, restraining movement when warm and preventing tight packing when cold.
glycoprotein: A protein with a carbohydrate chain attached; a glycolipid is a lipid with one. On the outer surface of the plasma membrane these chains act as identity tags that let cells recognize each other (cell recognition).
receptor: A protein that a particular signaling molecule binds, which changes the cell's activity. Receptors for molecules that cannot cross the membrane sit in the plasma membrane with their binding site facing outside.
signaling molecule: A molecule that carries a message to a cell by binding a receptor, such as a hormone like insulin. A cell responds to a signal only if it has the matching receptor.

2.4 Membrane Permeability

The plasma membrane is selectively permeable. Small nonpolar molecules diffuse straight through the hydrophobic core of the bilayer (simple diffusion). Polar molecules cross slowly, and ions hardly at all, unless the membrane carries transport proteins that give them a route; most water crosses through aquaporins. Outside the membrane, the cell walls of plants, fungi and bacteria give support and protect the cell from bursting when water moves in.

A membrane is selectively permeable: it lets some substances through easily and holds others back. That lets a cell keep its insides different from its surroundings.
Simple diffusion through the bilayer works for small nonpolar molecules (O₂, CO₂, N₂) and lipid-soluble ones such as steroid hormones. Charge matters more than size: tiny ions cross a bare bilayer more slowly than large uncharged sugars.
Ions and large polar molecules cross at useful rates only through transport proteins. Water can slip through the bilayer slowly, but most water crosses through aquaporins.
The cell wall (cellulose in plants, chitin in fungi, peptidoglycan in bacteria) lies outside the plasma membrane. It gives shape and protects the cell from bursting when water moves in, but it does not control which molecules enter.

Small nonpolar molecules such as O₂ and CO₂ dissolve in it and diffuse straight across: simple diffusion. Small polar molecules such as water cross slowly, and large polar ones such as glucose hardly at all. The hydrophobic core keeps ions out almost entirely, even very small ones like Na⁺. Those substances cross far faster, so which proteins a cell makes decides much of what it lets in and out. The wall pushes back on the cell and keeps it from bursting.

simple diffusion: Diffusion of a substance straight through the phospholipid bilayer, with no protein involved. Small nonpolar molecules such as O₂, CO₂ and N₂, and lipid-soluble molecules such as steroids, cross this way.
selective permeability: The property of a membrane that lets some substances cross easily and others hardly at all (it is selectively permeable). It comes from the hydrophobic core of the bilayer and the particular transport proteins the membrane carries.
transport protein: A membrane protein that gives a particular ion or polar molecule a route across the membrane, so it can cross far faster than through the bilayer alone. Aquaporins are one example.
aquaporin: A transport protein that lets water molecules cross a membrane rapidly, in single file through a narrow pore. A little water crosses the bilayer directly, but most crosses through aquaporins.
peptidoglycan: The material of most bacterial cell walls: long sugar chains cross-linked by short chains of amino acids into one tough mesh around the cell. Penicillin blocks the cross-linking.
cell wall support: The cell walls of plants, fungi and most prokaryotes give the cell its shape and resist stretching. When water moves into the cell and it swells, the wall presses back and protects it from bursting.

2.5 Membrane Transport

Substances cross membranes in three ways. Passive transport moves them down their concentration gradient using only their own motion, until a dynamic equilibrium is reached. Active transport uses ATP and transport proteins to move them against their gradient, which is the only way a cell can build up a substance inside. Bulk transport moves large particles and packages in vesicles: endocytosis brings them in and exocytosis sends them out. Selective permeability and active transport together let a cell keep its internal environment different from the outside.

Passive transport: down the gradient (high to low), no ATP. The energy comes from the particles' own motion. It stops having a net effect at dynamic equilibrium, when crossings in each direction balance.
Active transport: against the gradient (low to high), using energy, usually from ATP, and a transport protein. Only active transport can build up or keep a substance at a higher concentration inside than outside.
Bulk transport moves large particles or large amounts in vesicles. Endocytosis takes material in: phagocytosis (particles), pinocytosis (fluid), receptor-mediated endocytosis (particular molecules bound to receptors). Exocytosis releases material, adding the vesicle's membrane to the cell surface.
Selective permeability plus active transport let a cell keep an internal environment different from its surroundings. Keeping internal conditions within a working range is called homeostasis.

It moves down its gradient by passive transport, driven by its own motion, with no energy from the cell. Molecules still cross both ways, but at equal rates: a dynamic equilibrium with no net change. A transport protein uses energy from ATP to move it against its gradient: active transport. The cell holds an internal environment different from the outside, part of homeostasis. The cell moves it in vesicles: the membrane folds in to take it (endocytosis) or a vesicle fuses with the membrane to release it (exocytosis).

homeostasis: Keeping internal conditions, such as the concentrations of ions and water, within a range that lets the cell or body work, even when outside conditions change. How the body senses and corrects changes is taught in Unit 4.
passive transport: Movement of a substance across a membrane down its concentration gradient, from higher to lower concentration, with no energy input from the cell. Simple diffusion through the bilayer and diffusion through transport proteins are both passive.
active transport: Movement of a substance across a membrane against its concentration gradient, from lower to higher concentration, using energy, usually from ATP, and a transport protein. It lets a cell build up or keep substances at concentrations different from its surroundings.
endocytosis: Taking material into a cell by folding the plasma membrane inward around it and pinching off a vesicle. Phagocytosis engulfs large particles such as bacteria; pinocytosis takes in droplets of fluid; receptor-mediated endocytosis takes in particular molecules after they bind surface receptors.
exocytosis: Releasing material from a cell: a vesicle fuses with the plasma membrane and empties its contents outside, and its membrane becomes part of the plasma membrane. Cells secrete proteins such as insulin and digestive enzymes this way.
bulk transport: Moving large particles or large amounts of material across the plasma membrane inside vesicles, by endocytosis (in) or exocytosis (out). It uses energy.
dynamic equilibrium: The state reached when a substance's concentration is the same on both sides of a membrane: its molecules keep crossing in both directions, but at equal rates, so there is no net change.
internal environment: The conditions inside a cell, which differ from the outside. Selective permeability slows leaks, and active transport keeps moving substances back, so a cell can keep, for example, far more K⁺ inside than outside.

2.6 Facilitated Diffusion

Ions and polar molecules need transport proteins to cross the hydrophobic bilayer. Channels form tunnels, often gated so the cell controls when they open; carriers bind and change shape, so their uptake rate levels off once every carrier is busy. Both are facilitated diffusion: passive, down the gradient. Pumps such as the sodium-potassium pump spend ATP to move ions against their gradients (3 Na⁺ out, 2 K⁺ in). The resulting electrochemical gradients, including a negative membrane potential, store energy the cell uses later.

Facilitated diffusion is still diffusion: the substance moves down its gradient and no ATP is spent. The protein only provides a path through the bilayer.
Channels are tunnels (fast, millions of ions per second). Carriers bind and change shape (slower, and they max out when every carrier is busy). Pumps spend ATP to push substances against their gradient.
An ion feels two pushes: its concentration difference and the charge difference across the membrane. Together they make its electrochemical gradient. For Na⁺ entering a cell, both push inward.
A gradient is stored energy. The pump spends ATP to build the Na⁺ and K⁺ gradients; nerve signals, and other transport you will meet in topic 2.8, spend that stored energy.

Ions and polar molecules such as glucose cannot dissolve in it, so they barely cross the membrane on their own. That ion streams through, from the side where it is crowded to the side where it is scarce, with no ATP spent: facilitated diffusion. The cell controls when ions flow, so an ion rush can serve as a signal. Uptake speeds up as the outside concentration rises, until every carrier is busy; then the rate levels off at a ceiling. Na⁺ stays crowded outside and K⁺ crowded inside, and slightly more positive charge leaves than enters. The inside of the cell is negative (a membrane potential, about −70 mV in a resting nerve cell): an electrochemical gradient that stores energy for later work.

facilitated diffusion: Passive movement of a substance across a membrane through a specific transport protein, a channel or a carrier, from where it is more concentrated to where it is less concentrated. No ATP is used.
channel protein: A transport protein that forms a water-filled tunnel through the membrane. Each channel lets one kind of ion, or water in the case of aquaporins, pass straight through, down its gradient and very fast.
gated channel: A channel protein that opens and closes. A ligand-gated channel opens when a signaling molecule binds to it; a voltage-gated channel opens when the charge difference across the membrane changes.
carrier protein: A transport protein that binds a specific molecule on one side of the membrane, changes shape, and releases it on the other side. Because each carrier handles a few molecules at a time, transport stops speeding up once every carrier is busy.
protein pump: A transport protein that uses energy, usually from ATP, to move ions or molecules against their concentration gradient, from where they are scarce to where they are crowded. Pumps carry out active transport.
sodium-potassium pump: The pump in animal cell membranes that uses one ATP to move three sodium ions (Na⁺) out of the cell and two potassium ions (K⁺) in, keeping Na⁺ high outside and K⁺ high inside.
electrochemical gradient: The combined push on an ion from two sources: the difference in its concentration across a membrane and the difference in electrical charge. Both can point the same way (Na⁺ entering a cell) or opposite ways.
membrane potential: The difference in electrical charge across a cell membrane. In most animal cells the inside is negative compared with the outside, about −70 millivolts in a resting nerve cell. It stores energy, like a small battery.

2.7 Tonicity and Osmoregulation

Osmosis is the net movement of water across a membrane toward the side with more non-crossing solute, from higher to lower water potential (Ψ = Ψs + Ψp; pure water in an open container is 0). Compared with a cell, a hypotonic solution makes it gain water, a hypertonic one makes it lose water, and an isotonic one causes no net change. Animal cells burst or shrivel; plant cells become turgid against their walls or plasmolyze. Organisms osmoregulate with contractile vacuoles, kidneys and control of their own solute levels.

Hypotonic, isotonic and hypertonic are comparisons. A solution is hypertonic to something. Always say what you are comparing.
Water moves toward more solute, which is the same as saying from higher to lower water potential.
Water potential: Ψ = Ψs + Ψp. Pure water in an open container is 0. Solutes make Ψs negative; pressure from a cell wall makes Ψp positive.
Only solutes that cannot cross the membrane set tonicity. A solute that crosses spreads out evenly and stops mattering.
Count particles, not molecules: salt (NaCl) splits into two ions, so it lowers water potential about twice as much as the same amount of sugar.

That solution has a lower water potential: a lower tendency for water to leave it. Water moves by osmosis from the side with higher water potential (fewer solutes, hypotonic) to the side with lower water potential (more solutes, hypertonic). It swells and may burst; in a hypertonic solution it loses water and shrivels; in an isotonic solution it stays the same. Pressure builds inside (turgor), raising the cell's water potential until net water entry stops: the cell is firm, not burst. Turgor drops (the cell goes flaccid), and with more loss the membrane pulls away from the wall: plasmolysis. They osmoregulate: contractile vacuoles bail water out, kidneys adjust how much water leaves, and cells control their solute levels.

osmosis: The net movement of water across a selectively permeable membrane, from the side with fewer dissolved solutes (higher water potential) to the side with more solutes (lower water potential).
tonicity: How a solution would change a cell's volume by osmosis, judged by comparing the concentrations of solutes that cannot cross the membrane on the two sides.
hypotonic: Describes a solution with a lower concentration of non-crossing solutes than the cell it is compared with. A cell in a hypotonic solution gains water.
hypertonic: Describes a solution with a higher concentration of non-crossing solutes than the cell it is compared with. A cell in a hypertonic solution loses water.
isotonic: Describes a solution with the same concentration of non-crossing solutes as the cell. Water moves in and out at equal rates, so there is no net change in volume.
osmolarity: The total concentration of all dissolved solute particles in a solution. A salt that splits into two ions in water counts twice.
water potential: A measure of how likely water is to move out of a region, written Ψ (psi). It is the sum of solute potential and pressure potential, and water moves from higher to lower water potential. Pure water in an open container has Ψ = 0.
solute potential: The part of water potential set by dissolved solutes, written Ψs. It is zero for pure water and becomes more negative as more solute is added, because solutes hold water molecules and lower their freedom to move.
pressure potential: The part of water potential set by physical pressure, written Ψp. It is zero in an open container, positive when water is pushed on (as inside a firm plant cell), and negative when water is pulled (as in the xylem).
turgor pressure: The pressure of a plant cell's contents pushing outward against its cell wall after water has entered. It makes plant cells firm (turgid) and holds up soft stems and leaves.
flaccid: Limp. A plant cell is flaccid when its contents no longer press against the wall, as happens in an isotonic solution.
plasmolysis: The shrinking of a plant cell's contents away from its cell wall as the cell loses water in a hypertonic solution.
cytolysis: The bursting of a cell. An animal cell with no cell wall can swell and burst (cytolysis) when it takes in too much water in a hypotonic solution.
crenation: The shriveling of an animal cell, such as a red blood cell, into a spiky shape as it loses water in a hypertonic solution.
osmoregulation: The control of water and solute balance in an organism, so its cells stay at a workable volume and solute concentration even when its surroundings differ.
contractile vacuole: A vacuole in some single-celled freshwater organisms, such as Paramecium, that collects the extra water entering by osmosis and squeezes it out of the cell, using energy.
kidney: An organ of vertebrates that filters the blood and adjusts how much water and which solutes leave the body in urine, a main organ of osmoregulation.

2.8 Mechanisms of Transport

Cells move substances by simple diffusion, facilitated diffusion, active transport and bulk transport, chosen by size, charge or polarity and gradient direction. Primary active transport spends ATP directly (the sodium-potassium pump, the proton pump) and builds ion gradients. Cotransport spends those gradients: a symporter such as the sodium-glucose cotransporter lets Na⁺ flow in and carries glucose in against its gradient; an antiporter moves the second substance the opposite way. If the pump stops, the gradient runs down and cotransport stops with it.

Primary active transport spends ATP directly. Cotransport (secondary active transport) spends a gradient that a primary pump built.
Symport: both substances cross the same way (Na⁺ and glucose in). Antiport: opposite ways (Na⁺ in, Ca²⁺ out).
Stop the pump and the cotransporter fails too, after a delay while the stored gradient runs down. That delay is a clue in data questions.
Pick a route by asking three questions: Is it small and nonpolar? Is it moving down or against its gradient? Is it a single molecule or a large particle?

A steep gradient builds up: Na⁺ crowded outside animal cells, H⁺ crowded outside plant cells. A cotransporter can open a path for them, but only if it can bring a second substance along. Glucose is moved into the cell even when it is already more concentrated inside (symport: both in the same direction). Na⁺ flowing in can push something else out, such as Ca²⁺ in heart muscle cells. The gradient runs down and cotransport fails too, even though the cotransporter never used ATP. Those three facts decide its route: simple diffusion, facilitated diffusion, a pump, cotransport or bulk transport.

primary active transport: Active transport in which the transport protein itself spends ATP to move a substance against its gradient. The sodium-potassium pump and the proton pump are examples.
cotransport: Transport in which a protein lets one substance flow down its gradient and uses that flow to move a second substance against its gradient. The protein spends no ATP; the energy comes from a gradient a pump built earlier. Also called secondary active transport.
symport: Kinds of cotransport. In symport the two substances cross the membrane in the same direction (a symporter); in antiport they cross in opposite directions (an antiporter).
proton pump: A pump that uses ATP to move hydrogen ions (H⁺) out of the cytoplasm, building an H⁺ gradient. Plant cells use the gradient to drive cotransport, for example of sucrose.
sodium-glucose cotransporter: A symporter in intestinal and kidney cells that lets two Na⁺ flow into the cell and carries one glucose molecule in with them, even when glucose is more concentrated inside. Plant cells use a similar H⁺-sucrose symporter.
choosing a transport route: Matching a substance to the way it crosses a membrane, using its size, polarity and charge and the direction of its gradient: simple diffusion, facilitated diffusion, active transport (primary or cotransport) or bulk transport.

2.9 Cell Compartmentalization

Internal membranes divide a eukaryotic cell into compartments. Because membranes and their transport proteins control what crosses, each compartment keeps its own contents and conditions: lysosomes stay at about pH 5 inside a cytosol at about 7.2, opposing processes run apart, and reactants stay concentrated. Folded membranes such as cristae and thylakoids pack extra area for membrane proteins. Prokaryotes have no membrane-bound organelles, but their DNA is concentrated in a nucleoid and some have other specialized regions.

Compartmentalization means internal membranes divide a eukaryotic cell into organelles, each with its own contents and conditions.
Three payoffs: separate conditions (acid lysosome, neutral cytosol), separate processes that would undo each other, and concentrated reactants in small spaces.
Folded membranes (cristae, thylakoids, ER) add area. More area means more room for membrane proteins that do the work.
Prokaryotes lack membrane-bound organelles but are not unorganized: their DNA sits in a nucleoid, a region with no membrane around it.

Each organelle can hold its own mix of molecules: its own enzymes, its own concentrations, its own pH. Lysosomal enzymes work well inside the lysosome but poorly if they leak out, so the rest of the cell is protected. They do not undo each other, and the cell can run and control each one separately. Reactions run faster than they would if the same molecules were spread through the whole cell. Far more membrane area, and so more membrane proteins, fits in a small space. They still organize their insides: DNA gathers in the nucleoid, and some have internal membrane folds or protein-walled compartments.

compartmentalization: The division of a eukaryotic cell by internal membranes into separate spaces, the organelles, each holding its own set of molecules and conditions.
separate reaction conditions: Keeping different chemical conditions, such as pH, in different compartments, so reactions that need different conditions, or that would undo each other, can run in the same cell at the same time.
folded membranes: Internal membranes folded into ridges or stacks, such as the cristae of mitochondria and the thylakoids of chloroplasts. Folding packs more membrane area, and so more membrane proteins, into a small space.
nucleoid: The region of a prokaryotic cell where its DNA is concentrated. Unlike a nucleus, it has no membrane around it.
specialized regions in prokaryotes: Prokaryotes have no membrane-bound organelles, but their insides are still organized: DNA gathers in the nucleoid, and some have internal membrane folds or protein-walled compartments for particular jobs.

2.10 Origins of Cell Compartmentalization

Eukaryotic cells have membrane-bound organelles and prokaryotes generally do not. Two of those organelles have an unusual history: by the endosymbiotic theory, mitochondria and chloroplasts descend from free-living prokaryotes taken in by ancestral host cells, first an oxygen-using bacterium and later, in one line, a photosynthetic one. Evidence: double membranes, their own circular DNA, bacteria-like ribosomes, division by a fission-like process and DNA that matches living bacteria. The nucleus and endomembrane system may have formed by infolding of the plasma membrane, a less settled hypothesis.

Endosymbiosis: one organism living inside the cells of another. The endosymbiotic theory says mitochondria and chloroplasts began as free-living prokaryotes taken in by host cells.
Four pieces of evidence to know: a double membrane, their own circular DNA, ribosomes like bacterial ones, and new ones forming only by splitting, like binary fission.
Mitochondria came first (nearly all eukaryotes have them); chloroplasts came later in one branch (plants and algae).
Prokaryotes generally have no membrane-bound organelles; eukaryotes have many. The nucleus and endomembrane system may have begun as infoldings of the plasma membrane, a hypothesis that is less settled than endosymbiosis.
Evolution is change in the inherited traits of populations over generations; features shared because they were inherited from one ancestor are evidence of common ancestry.

The bacterium ended up inside the host, enclosed by its own plasma membrane plus a second membrane from the host: a double membrane. The two lived in endosymbiosis: the host gained ATP, and the bacterium gained shelter and food (mutualism). It could no longer live on its own and became an organelle, the mitochondrion, still with circular DNA, bacteria-like ribosomes and division by splitting. It became the chloroplast, which is why plants and algae have both organelles while animals and fungi have only mitochondria. Double membranes, circular DNA, bacteria-like ribosomes, fission and close DNA matches to living bacteria are the evidence for the endosymbiotic theory.

mutualism: A close relationship between two species in which both benefit. The full set of species relationships is taught with community ecology.
symbiosis: Two different species living in close, long-term contact, one often inside or on the other. Whether each partner gains or loses differs from case to case.
evolution: Change in the inherited traits of populations over many generations. The causes of that change are taught in Unit 7.
common ancestry: The idea that different groups of organisms descend from a shared ancestor. Features that groups share because they inherited them from that ancestor are evidence of common ancestry.
host cell: A cell that has another organism or cell living inside it. In endosymbiosis, the larger cell that took in a bacterium is the host cell.
endosymbiosis: One organism living inside the cells of another. In the history of eukaryotes, bacteria taken in by a host cell came to live inside it permanently and became organelles.
circular DNA: DNA whose two ends are joined in a closed loop. Bacteria, mitochondria and chloroplasts carry circular DNA; the nucleus of a eukaryotic cell holds chromosomes that are not loops.
binary fission: The way a prokaryote reproduces: it copies its DNA, grows, and splits into two cells. Mitochondria and chloroplasts multiply by a similar splitting process.
endosymbiotic theory: The well-supported explanation that mitochondria and chloroplasts descend from free-living prokaryotes taken in by ancestral host cells. Evidence: double membranes, their own circular DNA, bacteria-like ribosomes and division by fission.
membrane infolding: A hypothesis that the nuclear envelope and the endomembrane system began as folds of an ancestral cell's plasma membrane that pinched inward around the DNA and into the cytoplasm.