Biomolecules and cell theory

What are 4 major bio molecules make up cells and their roles?

• Nucleic acids (DNA/RNA): store & transmit hereditary info.

• Proteins: structure, enzymes, transport, signaling.

• Carbohydrates: energy (glucose, starch), structure (cellulose, chitin).

• Lipids: membranes (phospholipids), energy storage (fats), signaling (steroids

Cell theory

• All living organisms are made of one or more cells.

• Cells are the basic structural & functional unit of life.

• All cells arise from preexisting cells.

• Cells pass hereditary material to offspring during division.

Universal cell components?

Plasma membrane, cytoplasm/cytosol, DNA (chromosomes), ribosomes.

Distinguish prokaryotes from eukaryotes.

Prokaryotes (Bacteria & Archaea) lack membrane-bound organelles and a nucleus; DNA is in a nucleoid.

Key external prokaryotic structures & functions?

• Capsule: sticky layer for adhesion/protection.

• Cell wall: shape & osmotic protection (peptidoglycan in bacteria).

• Plasma membrane: selective barrier.

• Pili: attachment & DNA exchange (conjugation).

• Flagella: propeller-like motility.

Internal prokaryotic structures?

• Ribosomes: protein synthesis.

• Plasmids: small circular DNA with extra genes (e.g., antibiotic resistance).

• Nucleoid: main circular DNA.

Advantages of internal membranes in eukaryotes?

Compartmentalize functions, create specialized environments (pH, enzymes), and increase surface area for reactions.

Plant vs animal cell unique structures

• Plant: cell wall (cellulose), chloroplasts, large central vacuole, plasmodesmata.

• Animal: centrioles, lysosomes, tight & gap junctions, cilia, microvilli.

Pathway of protein secretion?

Nucleus (transcription) → Ribosome (translation) → Rough ER (folding) → Smooth ER (packaging/lipid synthesis) → Golgi (modification/sorting) → Secretory vesicles → Plasma membrane (exocytosis).

Rough vs. Smooth ER roles?

• Rough ER: protein synthesis (bound ribosomes).

• Smooth ER: lipid synthesis, detoxification, Ca²⁺ storage.

Golgi apparatus function?

Modifies proteins (e.g., add phosphate/sugar groups), sorts, packages into vesicles for secretion or lysosome formation.

Vesicle types & functions?

• Secretory vesicles: deliver membrane/secretory proteins via exocytosis.

• Vacuoles: storage (plants: large central vacuole maintains turgor pressure).

• Contractile vacuole: expels excess water (protists).

• Lysosomes: hydrolytic enzymes for digestion (animal cells only).

• Peroxisomes: break down fatty acids, detoxify hydrogen peroxide (in liver/seeds).

secretory vesicles

deliver membrane/secretory proteins via exocytosis.

vacuoles

storage (plants: large central vacuole maintains turgor pressure).

Contractile vacuole

expels excess water (protists).

Lysosomes:

hydrolytic enzymes for digestion (animal cells only).

Peroxisomes

break down fatty acids, detoxify hydrogen peroxide (in liver/seeds).

Structure & function of mitochondria?

ATP production by aerobic respiration. Inner membrane forms cristae to increase surface area; matrix contains enzymes, ribosomes, and mitochondrial DNA (maternal inheritance).

Structure & function of chloroplasts?

Photosynthesis. Thylakoids (light reactions, chlorophyll) stacked into grana for high SA; stroma contains enzymes, ribosomes, and chloroplast DNA (Calvin cycle).

What is the endosymbiotic theory and evidence?

Mitochondria and chloroplasts originated as engulfed prokaryotes. Evidence: double membranes, own DNA and ribosomes, replicate by binary fission.

Roles of the cytoskeleton?

Maintains shape, organizes organelles, enables movement (cilia/flagella), intracellular transport (motor proteins along microtubules), mitotic spindle formation.

Microtubules vs. microfilaments vs. intermediate filaments?

• Microtubules: tubulin, cell shape, chromosome movement.

• Microfilaments: actin, cell motility, cytokinesis.

• Intermediate filaments: structural support.

Plant vs. fungal vs. bacterial cell wall composition?

Cellulose (plants), chitin (fungi), peptidoglycan (bacteria).

Extracellular matrix (ECM) role in animals?

Structural support, cell adhesion, signaling (collagen networks)

Types of intercellular junctions?

• Plasmodesmata: plant cytoplasmic connections.

• Gap junctions: animal cytoplasmic channels.

• Tight junctions: prevent leakage.

• Desmosomes: strong adhesion.

Why is surface area-to-volume ratio critical?

Efficient exchange of nutrients/waste. As cell size ↑, volume grows faster than SA → lower SA:V → less efficient transport.

Adaptations to maintain high SA:V?

Small cell size, flattened or elongated shapes, internal membranes (ER, mitochondria cristae, chloroplast grana), microvilli.

Describe the fluid mosaic model.

Phospholipid bilayer (amphipathic) with embedded proteins, cholesterol, and carbohydrates; lipids/proteins move laterally for fluidity.

How does cholesterol regulate membrane fluidity?

• High temp: restrains movement → less fluid.

• Low temp: prevents packing → more fluid.

Membrane protein functions?

Transport, enzymatic activity, signal transduction, cell recognition, intercellular joining, attachment to cytoskeleton/ECM.

Role of glycoproteins/glycolipids?

Cell-cell recognition (immune system, organ transplant compatibility).

Define passive vs. active transport.

• Passive: movement down concentration gradient, no ATP (simple diffusion, osmosis, facilitated diffusion).

• Active: movement against gradient, requires ATP (protein pumps, endocytosis, exocytosis).

Factors affecting diffusion rate

Molecule size (smaller faster), temperature (higher faster), gradient steepness, charge, pressure.

Key active transport examples?

Na⁺/K⁺ pump maintains membrane potential in neurons; proton pumps create electrochemical gradients for ATP synthesis/photosynthesis.

Types of bulk transport?

• Endocytosis: uptake of large particles (phagocytosis = solids, pinocytosis = liquids).

• Exocytosis: secretion of materials.

Define osmosis.

Diffusion of water across a semipermeable membrane from high water potential (low solute) to low water potential (high solute).

Water potential equation and direction of movement?

Water moves from high ψ (less negative) to low ψ (more negative); high pressure → low pressure; low solute → high solute.

Tonicity effects on animal cells?

• Isotonic: normal.

• Hypotonic: water enters → lysis.

• Hypertonic: water leaves → crenation.

Tonicity effects on plant cells?

• Hypotonic: turgid (normal).

• Isotonic: flaccid (wilting).

• Hypertonic: plasmolysis (membrane pulls away from wall).

How does SA:V ratio limit cell size?

Cells too large cannot transport materials efficiently; explains why multicellular organisms rely on many small cells.

Why do mitochondria and chloroplasts have their own DNA?

Evidence of ancient symbiosis; allows independent replication and production of some proteins.

How does membrane fluidity affect diffusion rates?

More fluid → easier lateral movement of molecules and proteins → faster transport and signaling.

What is passive transport

Movement of molecules down their concentration or electrochemical gradient without energy (ATP).

Main types of passive transport

• Simple diffusion – small nonpolar molecules (O₂, CO₂) move directly through lipid bilayer.

• Facilitated diffusion – polar/charged molecules move through a channel or carrier protein.

• Osmosis – diffusion of water across a selectively permeable membrane (often via aquaporins).

Channel vs carrier proteins (facilitated diffusion

• Channel proteins: Hydrophilic tunnels; allow rapid movement of ions or water.

• Carrier proteins: Bind substrate, change shape to move molecule; slower but very specific.

What is active transport?

Movement of molecules against their concentration gradient (low → high) that requires energy, usually ATP.

Primary vs secondary active transport

• Primary: Direct use of ATP (e.g., Na⁺/K⁺ pump, proton pump).

• Secondary (co-transport): Uses energy stored in an ion gradient created by primary transport (e.g., H⁺/sucrose symporter).

Electrochemical gradient

Combined effect of concentration difference and membrane charge that drives ion movement.

Bulk transport (vesicular transport)

Requires energy (ATP).

• Endocytosis: Cell brings material in (phagocytosis, pinocytosis, receptor-mediated).

• Exocytosis: Vesicles fuse with plasma membrane to export materials.

Key difference between passive and active transport

• Passive: High → Low, no energy, may need transport proteins.

• Active: Low → High, requires energy (ATP or gradient), often uses pumps or vesicles.

What is the endomembrane system?

A network of membranes inside the eukaryotic cell that synthesizes, modifies, packages, and transports proteins and lipids.
Key members: nuclear envelope, rough ER, smooth ER, Golgi apparatus, vesicles, lysosomes, vacuoles, plasma membrane.

Main functions of the endomembrane system

• Protein synthesis & processing (Rough ER, Golgi)

• Lipid synthesis (Smooth ER)

• Detoxification (Smooth ER)

• Transport of molecules via vesicles

• Digestion & recycling (lysosomes)

• Export of secretory products by exocytosis.

Pathway of a secreted protein through the endomembrane system

Rough ER → Transport vesicle → Golgi apparatus → Secretory vesicle → Plasma membrane (exocytosis).

Nuclear envelope role

Double membrane surrounding the nucleus; continuous with the rough ER to allow mRNA and ribosomal subunits to exit for protein synthesis.

Rough Endoplasmic Reticulum (Rough ER)

Studded with ribosomes; synthesizes proteins for secretion, membranes, or lysosomes; proteins enter the ER lumen for folding and modification (e.g., glycosylation).

Smooth Endoplasmic Reticulum (Smooth ER)

Lacks ribosomes; functions include lipid synthesis, detoxification of drugs/toxins, and calcium storage in muscle cells (sarcoplasmic reticulum).

Golgi apparatus

Series of flattened sacs (cisternae) that modifies, sorts, and packages proteins and lipids.

• Cis face: receives vesicles from ER.

• Trans face: ships vesicles to destinations.

Transport vesicles

Small membrane-bound sacs that shuttle proteins/lipids between organelles or to the plasma membrane.

Lysosome

Vesicles containing hydrolytic enzymes; digest macromolecules, recycle cell parts (autophagy), and perform apoptosis (programmed cell death).

Vacuoles

Large vesicles for storage and structural support.

• Plant central vacuole: stores water/ions, maintains turgor pressure.

• Contractile vacuole (protists): expels excess water.

Plasma membrane in endomembrane system

Final boundary; vesicles fuse to secrete products or add new membrane components (exocytosis).

Key relationship to the endosymbiotic theory

The endomembrane system likely formed from infoldings of the plasma membrane in early eukaryotes (not from engulfed prokaryotes), unlike mitochondria/chloroplasts which came from endosymbiosis.

: Example FRQ connection

A mutation that disrupts Golgi function could lead to misfolded or unmodified proteins, causing defective secretion (e.g., hormones, enzymes).

Nice Routes Take Good Shipments

(Nucleus → Rough ER → Transport vesicle → Golgi → Secretory vesicle → Plasma membrane)

What is water potential (Ψ)?

A measure of the potential energy of water per unit volume relative to pure water.

• Pure water at standard conditions = 0 MPa.

• Water moves from higher (less negative) Ψ → lower (more negative) Ψ.

What two components determine total water potential (Ψ)?

Ψ = Ψp + Ψs

• Ψp (pressure potential): Physical pressure on the solution (can be positive or negative).

• Ψs (solute potential/osmotic potential): Always negative when solute is added because solutes bind water and lower free energy.

How does solute concentration affect water potential?

• More solute → lower (more negative) Ψs → lower total Ψ.

• Water moves toward the higher solute concentration (because it has lower Ψ).

Does water move toward higher or lower water potential?

Water always moves from higher water potential (less negative) → lower water potential (more negative).

Key relationship between solute and water potential?

• High solute = Low Ψ (more negative)

• Low solute = High Ψ (less negative)

What is the formula for solute potential (Ψs)

Ψs = –iCRT

• i = ionization constant (1 for sucrose, 2 for NaCl, etc.)

• C = molar concentration (M)

• R = pressure constant (0.0831 L·bar/mol·K)

• T = temperature in Kelvin (°C + 273)

What happens if a plant cell is placed in a hypertonic solution?

• External Ψ is lower (more negative).

• Water moves out of the cell.

• Cell becomes plasmolyzed.

What happens if a plant cell is placed in a hypotonic solution?

• External Ψ is higher (less negative).

• Water moves into the cell.

• Cell becomes turgid (pressure potential increases)

Phospholipid Bilayer Structure

• Hydrophilic heads (phosphate) face water inside/outside cell.

• Hydrophobic fatty-acid tails face each other, forming nonpolar core.

• Creates a barrier to polar/charged substances.

Cholesterol

• Inserted between phospholipids.

• Stabilizes membrane fluidity:

  • Prevents tight packing in cold temps.

  • Limits excessive fluidity in warm temps.

Membrane Proteins – Two Main Types

• Integral (transmembrane): span the bilayer; often channels, carriers, or receptors.

• Peripheral: attached to surface; roles in signaling, cytoskeleton attachment, enzyme activity.

Functions of Membrane Proteins

• Transport: channels or carriers move molecules across.

• Enzymatic activity: catalyze reactions.

• Signal reception: receptors bind ligands (hormones, neurotransmitters).

• Cell recognition: glycoproteins identify cells.

• Intercellular joining: junction proteins connect adjacent cells.

• Attachment: link to cytoskeleton or extracellular matrix.

Carbohydrates on the Membrane

• Present as glycoproteins (carb + protein) or glycolipids (carb + lipid).

• Form the glycocalyx—important for cell recognition, immune response, and adhesion.

Molecules That Pass Easily

• Small nonpolar (O₂, CO₂, N₂) diffuse directly.

• Small uncharged polar molecules (H₂O) pass slowly or through aquaporins.

Molecules That Require Transport Proteins

• Large polar molecules (glucose).

• Ions (Na⁺, K⁺, Cl⁻).

• Move via facilitated diffusion or active transport.

Temperature Effects

• High temp → membrane more fluid; cholesterol restrains movement.

• Low temp → membrane can solidify; cholesterol prevents tight packing.