AP Biology Unit 2

1. Overview: Cells are Busy, Complex Systems

• Cells have their own departments (organelles) that do a specialized job. Organelles work together to keep the cell alive and functioning smoothly

• Cells are membrane bound

• Each structure has a form that supports its function (tested a lot)

• Eukaryotic cells: cells w/ a nucleus & membrane bound organelles are compartmentalized (Having internal membrane-bound spaces that separate different processes within a cell.)

• Prokaryotic cells: cells w/o a nucleus & membrane bound organelles are not compartmentalized

2. Plasma Membrane: The Gatekeeper

Membrane controls what comes in and out of the cell & protects the internal environment

Structure: 

• Made of a phospholipid bilayer (A double layer of phospholipids with hydrophilic heads facing outward and hydrophobic tails inward)

• Proteins throughout the membrane assist w/ transport and communication

Function: 

• Selectively permeable—regulates the cell’s internal chambers

3. The Nucleus: Command Center

• Houses DNA and where gene expression begins

• Structure:

  • Surrounded by a nuclear envelope: A double membrane around the nucleus that contains pores for transport.

  • Contains the nucleolus where ribosomes are assembled

• Function:

  • Directs cell activities by controlling gene expression

  • Stores genetic information

4. Ribosomes: Protein-Making Machines

• Every living cell has ribosomes

• Structure:

  • Made of rRNA and proteins

  • Two types based on location:

    • Free ribosomes floating in cytosol: synthesize proteins used inside the cell

    • Bound ribosomes attached to the rough ER (synthesizes & folds proteins): make proteins for membranes or transport

5. Endoplasmic Reticulum (ER): Cell’s Manufacturing Department

• Rough ER: 

  • Ribosomes attatched—gives it a “rough” appearance

  • Synthesizes & folds proteins

  • Sends finished proteins to the Golgi in vesicles

    • Vesticles: Small membrane sacs that transport and store materials within the cell.

• Smooth ER: 

  • No ribosomes

  • Functions: 

    • Lipid synthesis

    • Detox (of drugs/poisons)

    • Stores calcium

6. Golgi Apparatus: Post Office of the Cell

• Golgi processes & ships proteins where they need to go

• Structure: 

  • Stacks of flattened membrane sacs

  • Has cis face (entry) and trans face (exit)

• Function:

  • Modifies and packages proteins

  • Sorts & sends proteins in vesicles

  • Helps form lysosomes

7.Mitochondria: The Power of Plants

• Generate energy for the cell and central to cellular respiration

• Structure: 

  • Double membrane

    • Outer: smooth

    • Inner: folded into cristae (inc surface area for reactions) 

  • Inside is the matrix (site of Krebs cycle)

• Function: 

  • Site of aerobic respiration => produces ATP (energy)

  • Has its own DNA => supports endosymbiotic theory (Idea that mitochondria and chloroplasts originated as free-living prokaryotes engulfed by early eukaryotes.)

8.Lysosomes: Trash and Recycling

• Digest materials the cell no longer needs

• Structure: 

  • Membrane-enclosed sacs containing hydrolytic enzymes

  • Very acidic interior

• Function: 

  • Break down macromolecules, old organelles, or pathogens

  • Involved in apoptosis (programmed cell death)

9. Vacuoles: Storage Units

• Vacuoles are the cell’s containers, with different purposes depending on the organism

• In plant cells: Eukaryotic cells that typically have chloroplasts, a large central vacuole, and a cell wall.

  • Have 1 lrg central vacuole 

  • Stores water/ions; maintains turgor pressure for structure

• In protists:

  • Contractile vacuoles pump excess water out

• In animal cells: Eukaryotic cells that lack chloroplasts and a cell wall and often have centrioles.

  • Smaller, more random, store substances

10. Chloroplasts: Solar Power Stations (Plants only)

• Only found in plant cells, powering photosynthesis

• Chloroplasts: Plant organelles that carry out photosynthesis to make sugars from sunlight.

• Structure: 

  • Double membrane

  • Thylakoids: Internal membrane stacks in chloroplasts where the light reactions occur.

  • Storms is the fluid surrounding them

• Function: 

  • Converts sunlight into glucose (chemical energy)

  • Contains green pigment chlorophyll

11. Centrioles and Microtubules: Cell Division Helpers (Animal Cells Only)

• These aren't involved in daily function but they’re crucial during mitosis/meiosis.

  • Structure: 

    • Small cylinders made of microtubules, found in animal cells.

  • Function: 

    • Help pull chromosomes apart during cell division.

Cell Types: Prokaryote vs Eukaryote vs Plant vs animal

• Prokaryotes:

  • No nucleus, no membrane bound organelles

  • Have ribosomes & plasma membrane

  • DNA is free floating

• Plant Cells: 

  • Have chloroplasts, central vacuole, and cell wall (cellulose).

  • No centrioles.

• Animal Cells: 

  • Have centrioles.

  • No chloroplasts or large central vacuole.

2.10 Compartmenalization

1. What is Cell Compartmentalization?

• Compartmentalizatoin: The division of a eukaryotic cell into distinct, membrane-separated spaces so different reactions can occur without interfering.

  • Eukaryotic Cells: Cells that have a nucleus and membrane-bound organelles; generally larger and more complex.

  • Membrane-bound organelles: Specialized structures inside eukaryotic cells that are enclosed by membranes and perform focused jobs.

• Improves efficiency by keeping processes in separate areas

2. Key Membrane-Bound Organelles & Their Functions

• Focus on how each organelle uses its membranes to support specialized tasks

• Nucleus: 

  • Double membrane (nuclear envelope) w/ pores

  • Separates DNA from cytoplasm

  • DNA => RNA (transcription) happens here, shielded from the rest of the cell

• Endoplasmic Reticulum (ER)

  • Smooth ER: A membrane network without ribosomes that makes lipids, detoxifies, and stores calcium ions.

    • No ribosomes

    • Makes lipids, detoxifies the cell, stores calcium

  • Rough ER: A membrane network studded with ribosomes where proteins are synthesized and folded.

    • Studded w/ ribosomes

    • Site of protein synthesis & folding

    • Linked closely to nucleus 4 fast RNA transfer
      

• Golgi Apparatus

  • Series of flattened membranes (cisternae)

  • Modifies proteins from ER

  • Packages products into vesticles for transport

  • Has unique internal pH to support diff enzymes

• Lysosome

  • Contains hydrolytic enzymes active in acidic conditions

  • Breaks down macromolecules, damaged organelles, & invaders

  • Membrane keeps those enzymes safely contained

• Mitochondria

  • Double membrane: outer membrane + highly folded inner membrane (cristae) 

  • Site of aerobic respiration and ATP production

  • Cristae = more surface area 4 reactions = more ATP making enzymes

  • Has own DNA & ribosomes (supports endosymbiotic theory

• Peroxisomes

  • Break down fatty acids/toxins

  • Carry out reactions that produce then degrade hydrogen peroxide 

  • Prevent damage by isolating potentially harmful substances

• Vacuoles

  • Store water, waste, or nutrients

  • In plants, helps maintain turgor pressure

  • Keeps stored materials away from the rest of the cytoplasm

3. Why Compartmenalization Matters

• Creates specialized environments

  • Organelles maintain unique internal conditions

  • These conditions allow enzymes 2 work

  • Ex: lysosomes are acidic, cytoplasm is neutral

• Increases surface area for reactions

  • Inner membranes (like in mitochondria & chloroplasts) are often folded

  • More folds = more surface area = more room for important reactions

  • Ex: cristae in mitochondria = more ATP production

• Separates Conflicting Reactions

  • Some processes wouldd cancel each other out if they happened in the same area

  • Ex: if RNA transcription & protein synthesis happened side by side, enzymes might interfere

  • Nucleus & ER help keep them quiet

• Organizes Cellular Workflow

  • Compartments keep functions efficient & orderly

  • Proteins are made in rough ER modified in Golgi shipped to where they’re nedded

  • Vesicles transport materials between compartments w/o mixing everything

4. Eukaryotes vs. Prokaryotes: The Comparison

This might show up as a simple chart, MCQ, or a “justify” question.

Eukaryotic Cells

• Have many membrane-bound organelles

• Use compartmentalization to separate reactions

• Bigger and more complex

• Can perform multiple complex tasks simultaneously

Prokaryotic Cells

• No membrane-bound organelles

• All reactions happen in one open space (cytoplasm)

• Simpler, but less efficient

• Still functional, but limited in complexity

5. Compartmentalization & Evolution

This section connects structure to the origin of complexity in cells.

🧬 Endosymbiotic Theory

• Mitochondria and chloroplasts used to be independent prokaryotes

• Got engulfed by a larger cell and formed a symbiotic relationship

• Evidence:

  • Own circular DNA

  • Double membranes

  • Can replicate independently

  • Have their own ribosomes

Evolutionary Outcomes

• Internal membranes likely originated by membrane infolding

• Led to improved specialization of tasks inside cells

• Gave eukaryotes a serious advantage: higher efficiency and complexity

2.4 Plasma Membrane

1. Structure: Phospholipid Bilayer = The Base Layer

The structure of the membrane sets the stage for everything else—understanding this foundation will help make everything else make sense.

• Phospholipid BIlayer: The basic membrane structure made of two layers of phospholipids with hydrophilic heads facing water and hydrophobic tails tucked inside.

This orientation creates a bilayer that is flexible & selectively permeable .

Selective Permeability: A property of membranes where only some substances cross easily while others are blocked or need help.

2. Fluid Mosaic Model: A Living, Moving Barrier

• This keyword model keeps coming back on the AP exam—know what it means and who’s involved.

  • Fluid = components that can move laterally across the membrane like rafts in water

  • Mosaic = made up of a mix of molecules

    • Phospholipids: form the base structure of the membrane

    • Proteins: scattered throughout; responsible for communication, transport, & reactions

    • Cholesterol (in eukaryotes): 

      • Maintains fluidity at different temperatures (prevents rigidity or too much flexibility) 

    • Glycoproteins & glycolipids

      • Involved in cell recognition, signaling, & attatchment

3. Membrane Proteins: The Workhorses

• Proteins embedded in the membrane that do a lot of jobs—memorizing their categories can help on application questions

• Protein positioning depends on the side chain properties: 

  • Hydrophobic parts stay w/ tails, hydrophilic parts face watery regions

• Functional types of membrane proteins include: 

  • Transport proteins: move molecules across 

    • Channel proteins: Membrane proteins that form hydrophilic tunnels for specific ions or polar molecules to pass by diffusion.

    • Carrier proteins: Membrane proteins that bind a specific molecule and change shape to move it across the membrane

  • Receptor proteins: Membrane proteins that bind signaling molecules (like hormones) and trigger specific cellular responses.

  • Adhesion (anchoring) proteins: intercellular connections

  • Enzymatic proteins: speed up chemical reactions at membrane surface

  • Cell surface makers: Membrane molecules, often glycoproteins, that act as identification tags to show a cell’s identity and “self” status.

4. Selective Permeability: Controlled Access

The phospholipid bilayer doesn’t let everything in. 

• What passes freely: Small, Nonpolar molecules that diffuse directly thru the bilayer

• What needs help:

  • small polar (H2O), limited diffusion, faster w/ channel proteins 

  • Large, polar, or charged molecules (glucose or ions) that req channel/carrier proteins

• This "gatekeeping" is important for:

  • Maintaining ion balance

  • Nutrient uptake

  • Waste removal

  • Regulating pH, water levels, etc.

5. Membranes and Homeostasis

• Everything we’ve talked about contributes to a cell’s ability to maintain a stable internal environment, regardless of external changes.

  • The membrane lets the cell respond to signals and adjust to external conditions.

  • It prevents harmful molecules from entering and controls what useful substances come in.

  • All of this is essential for the cell to survive and carry out processes like metabolism, communication, and reproduction.

2.5 Membrane Permeability

Topic 2.5 focuses on how the structure of cell membranes affects their ability to control the movement of substances in and out of the cell. It also covers the function of cell walls in maintaining structure and filtering external materials before they reach the membrane.

1. Structure of the Cell Membrane

The cell membrane’s structure is essential for how it controls what enters and leaves the cell — this is what makes selective permeability possible.

• Built from a phospholipid bilayer

  • Phospholipids have hydrophilic (water-loving) heads and hydrophobic (water-fearing) tails

  • This arrangement creates a barrier that repels many substances, especially charged or polar ones

• Proteins are embedded in the bilayer

  • Channel proteins and carrier proteins allow specific substances to pass

  • Cholesterol helps maintain fluidity in animal cell membranes

• The fluid mosaic model (The idea that the membrane is a fluid layer with moving lipids and proteins embedded like tiles in a mosaic.) explains this dynamic structure:

  • Membrane components (lipids, proteins) move around more like a fluid than a solid wall

  • This model helps explain why the membrane can be both protective and flexible

2. Selective Permeability: What Gets Through?

• Freely pass (no help needed):

  • Small, nonpolar molecules (ex: O₂, CO₂, N₂)

  • These are small and neutral, so they slip through the hydrophobic core easily

• Somewhat pass (slowly or w/ help)

  • Small, polar uncharged molecules (ex: H₂O)

  • Water can diffuse a little on its own, but mostly uses aquaporins (protein channels)

• Need transport proteins: Membrane proteins that move specific substances across the membrane (via channels or carriers).

  • Large, polar molecules (ex: glucose, amino acids)

  • Ions (ex: Na⁺, K⁺, Cl⁻, Ca²⁺)

  • Too big or too charged to cross hydrophobic interior alone

3. Transport Types

• Membranes use both passive and active transport depending on conditions.

• Passive transport: Movement of substances across the membrane without energy input, down their concentration gradient.

  • No ATP required

  • Molecules move down their concentration gradient: A difference in concentration between two areas. (high → low)

  • Includes:

    • simple diffusion

    • facilitated diffusion: Passive transport that uses membrane proteins to help substances cross down their gradient. (via channels or carriers)

    • osmosis: The diffusion of water across a selectively permeable membrane.

• Active transport

  • Requires ATP

  • Molecules move against their gradient (low → high)

  • Often involves ion pumps or co-transporters

4. The Role of Membranes in Cell Function

• One of the biggest points to get: why all this matters.

  • The membrane keeps the cell's internal environment stable (homeostasis)

    • Separates inside of cell from outside world

    • Controls nutrient uptake, waste removal, ion concentrations

  • By having selective permeability, cells regulate what goes in and out — vital for any metabolic process

5. Cell Walls: Extra Protection and Support

• Only some cells have cell walls, but when they do, they serve extra structural and filtering functions.

  • Key Functions: 

    • Acts as a rigid boundary around the plasma membrane

    • Provides physical strength and helps maintain shape

    • Acts as a pre-filter, protecting the membrane from large or harmful particles

  • Composition by Cell Type

    • Plants: cellulose

    • Fungi: chitin

    • Bacteria: peptidoglycan (thickness distinguishes Gram-positive & Gram-negative bacteria)

2.7 Facilitated Diffusion

Facilitated DIffusion

• A type of passive transport (no ATP required) that helps certain molecules cross the plasma membrane with the help of proteins when molecules are too big or too polar to pass directly through the lipid bilayer. 

• Concentration gradient: A difference in the amount of a substance between two areas, driving diffusion from high to low concentration. 

  • Steeper the gradient, the faster the diffusion + spontaneous & doesn’t need energy

• Passive Transport: Movement of substances across a membrane from high to low concentration without using cellular energy.

• Plasma Membrane: The cell’s boundary made of a phospholipid bilayer with embedded proteins that controls what enters and leaves the cell.

Membrane Proteins

• Facilitated diffusion relies on two main kinds of membrane proteins: 

• Channel Proteins = faster, like an open door

  • Provide a narrow water filled passageway through the membrane

  • Hydrophilic inside allows polar/charged substances through aquaporins and ion channels

• Carrier Proteins = slower, like a revolving door

  • Change their shape to move molecules across and binds to specific molecules and undergo a shape change

  • Slower than channel proteins

  • Common for glucose or amino acids

Aquaporins

• Channel proteins that speed up osmosis (water diffusion) 

• Critical in kidney cells, plant roots, & red blood cells

Ion Channels

• Allows movement of charged ions

• Often gated—meaning they open in response to signals (important in neurons & muscles)

• Movement of ions create membrane potential (difference in electrical charge)

Sodium-Potassium Pump

• Active transport pump that requires energy (ATP) to maintain electrical gradient across the membrane for nerve signaling & muscle function using transport proteins

• Secondary active transport: Coupled transport that uses the downhill movement of one molecule to drive another molecule uphill without directly using ATP.

Active transport vs. Facilitated Diffusion

• Facilitated diffusion

  • Energy Needed? No

  • Direction? High=>Low (with gradient)

  • Proteins used? Yes (channel/carrier) 

• Active Transport

  • Energy Needed? Yes (ATP)

  • Direction? Low=>High (against gradient)

  • Proteins Used? Yes (pumps like Na+/K+)

2.8 Tonicity and Osmoreregulation

Osmosis

• Passive movement of water across a semipermeable membrane from higher water potential to lower water potential.

• Water Potential: A measure of the potential energy of water; water moves from higher (less negative) to lower (more negative) water potential.

• Solute Concentration: The amount of dissolved particles in a solution; higher solute typically lowers water potential.

Osmosis equation

• Ψ = water potential

• Ψs = solute potential (always 0 or negative)

• Ψp = pressure potential (mostly 0 in open systems)

Solute Potential Equation: 

Ψs = −iCRT

• i = ionization constant (e.g., NaCl = 2, glucose/sucrose = 1)

• C = molar concentration

• R = 0.0831

• T = temperature in Kelvin = °C + 273

Tonicity

• The relative solute concentration outside a cell compared to inside, which determines net water movement.

Hypotonic

• Environment has less solute than the cell; water enters the cell.

• Animal cells swell (might burst) while plant cells become turgid (ideal)

• HYPO => HIPPO (cell inflates)

Hypertonic

• Environment has more solute than the cell; water leaves the cell.

• Animal cell shrinks and plant cell plasmolyzed

• HYPER = run outside (water leaves)

Isotonic

• External and internal solute concentrations are equal; water still moves but with no net change.

• Animal cell stable (ideal) while plant cell is flaccid (not ideal)

Turgor Pressure

• The internal pressure of the cell contents against the plant cell wall due to water in the vacuole that allows plant cells to be more resistant to water changes

Osmoregulation

• Processes that maintain proper water and solute balance inside an organism.

• Examples: 

  • Protists

    • Contractile vacuole pumps excess water out; helpful in freshwater environments

  • Plants:

    • Central vacuole holds water and pushes against cell wall (turgor pressure)

    • Plasmolysis occurs in hypertonic environments

  • Animals: 

    • Cells rely on stable isotonic conditions

    • Advanced organisms (like humans) use kidneys to help

Equation Practice & Application Tips

• When to Use:

  • Ψ = Ψs + Ψp: Calculate water potential for both cell and surrounding solution

  • Ψs = –iCRT: Find solute potential of a solution and cell to predict water movement of high to low or can compare W

  • If the cell and solution are at equilibrium then find the Ws for each solute potential then the cell’s Wp is the difference between the two solute potentials.

  Quick Strategy:

  • More solute → lower Ψ → water moves there

  • Less solute → higher Ψ → water moves out

2.9 Mechanisms of Transport

Cell Membrane

• A thin boundary of the cell made of a phospholipid bilayer with embedded proteins that controls what enters and leaves.

Simple Diffusion

• Direct movement of small, nonpolar molecules across the membrane down a gradient (like O2 and CO2)

Active Transport

• Movement of substances against their concentration (low => high) gradient that requires energy.

Primary Active Transport

• Active transport that uses ATP directly to move substances against a gradient. (Sodium-Potassium pump) 

Secondary Active Transport (Cotransport) 

• One molecule moves down its gradient, powering another to move up

• Symport: both molecules travel in same direction

• Antiport: molecules go in opposite directions

Endocytosis

• A cellular process in which substances are brought into the cell.

• Phagocytosis: A form of endocytosis where the cell engulfs large particles or whole cells.

• Pinocytosis: A form of endocytosis that non-specifically takes in extracellular fluid and dissolved solutes.

• Receptor-Mediated Endocytosis: Selective uptake where target molecules bind to membrane receptors, triggering vesicle formation.

Exocytosis

• Active transport process that exports substances from inside the cell to the outside environment for removing cellular waste

Pump Proteins

• Membrane proteins that use ATP to move substances against their gradient. (e.g., Na⁺/K⁺ pump)

Receptor Proteins

• Membrane proteins that bind signaling molecules and start cellular responses; they can trigger endocytosis.

All these transport methods work together to help the cell:

• Maintain internal balance (ion levels, pH, nutrients) 

• Communicate thru signals (NTs or Hormones)

• Detect & defend against invaders via phagocytosis

Without these processes, cells can’t exchange materials or respond to their environment—which would mean no function, no adaptation, no life.

2.10 Compartmentalization

Compartmentalization

• The division of a eukaryotic cell (cells w/ a nucleus & membrane-bound organelles) into distinct, membrane-separated spaces so different reactions can occur without interfering.

Nucleus

• Double membrane (nuclear envelope) with pores

• Separates DNA from cytoplasm

• DNA → RNA (transcription) happens here, shielded from the rest of the cell

Endoplasmic Reticulum

• Rough ER: A membrane network studded with ribosomes where proteins are synthesized and folded.

• Smooth ER: A membrane network without ribosomes that makes lipids, detoxifies, and stores calcium ions.

Golgi Apparatus

• Series of flattened membranes (cisternae)

• Modifies proteins from ER

• Packages products into vesicles for transport

• Has unique internal pH across cisternae to support different enzymes

Vesicles

• Small membrane-bound sacs that carry materials between organelles or to the cell membrane.

Lysosome

• Contains hydrolytic enzymes active in acidic conditions (pH ≈ 4.5)

• Breaks down macromolecules, damaged organelles, and invaders

• Membrane keeps those enzymes safely contained

Mitochondria

• Double membrane: outer membrane + highly folded inner membrane (cristae)

• Site of aerobic respiration and ATP production

• Cristae = more surface area = more ATP-making enzymes

• Has own DNA and ribosomes (supports endosymbiosis theory)

Peroxisomes

• Break down fatty acids and toxins

• Carry out reactions that produce and then degrade hydrogen peroxide (H₂O₂)

• Prevent damage by isolating potentially harmful substances

Vacuoles

• Store water, waste, or nutrients

• In plants, helps maintain turgor pressure

• Keeps stored materials away from rest of the cytoplasm

Why compartmentalization matters

• Creates Specialized Environments w/ unique pH 

  • Lysosomes acidic, cytoplasm neutral 

• Increases Surface Area for Reactions (more folds = more surface are = more room for important reactions)

  • Cristae in mitochondria/chloroplasts = more ATP production

• Separates Conflicting reactions via Nucleus & ER to keep transcription & protein synthesis apart

• Organized Cellular Workflow to keep functions orderly

Eukaryotes vs Prokaryotes

• Eukaryotic Cells

  • Have many membrane-bound organelles

  • Use compartmentalization to separate reactions

  • Bigger and more complex

  • Can perform multiple complex tasks simultaneously

• Prokaryotic Cells

  • No membrane-bound organelles

  • All reactions happen in one open space (cytoplasm)

  • Simpler, but less efficient

  • Still functional, but limited in complexity

• Features Present in BOTH

  • Cell membrane

  • Cytoplasm

  • DNA (not always in a nucleus)

  • Ribosomes (protein factories)

2.11 Origins of Cell Compartmentalization

Endosymbiotic Theory

• The idea that mitochondria and chloroplasts began as free-living bacteria that were engulfed and then lived inside a host cell in a mutually beneficial relationship.

  • Mitochondria: evolved from aerobic bacteria (used oxygen, made lots of ATP)

  • Chloroplasts: evolved from cyanobacteria (used light to make food)

Evidence for Endosymbiosis

Several features of mitochondria and chloroplasts point to their bacterial origins.

• Points of Evidence:

  • Their own circular DNA (like bacteria)

  • Double membranes:

    • Inner membrane from engulfed prokaryote

    • Outer membrane from host cell

  • Replicate independently via binary fission

  • Bacterial-sized ribosomes

  • Can make some of their own proteins