EUKARYOTIC CELLS - reformat from althea's notes (4 print purposes)

●​ CELL THEORY
-​ Fundamental scientific principle asserting that cells are the basic units of structure and function in all
living organisms
-​ First proposed in 1838 by German scientists:
-​ Theodor Schwann and Matthias Jakob Schleiden: All plants and animals are composed of cells
-​ Marked a major advancement in biological understanding
●​ Robert Hooke (1665)
-​ Published Micrographia, a detailed book featuring drawings and observations
made using an early microscope.
-​ Observed cork under the microscope and described box-like structures, which he
named “cells” because they resembled the small rooms in monasteries
○​ Microscope: Enabled the discovery of cells and spurred the development of
classical cell theory
●​ CLASSICAL CELL THEORY
○​ Proposed by Theodor Schwann, based on work with Matthias Schleiden (1838)
1.​ All organisms are composed of cells
2.​ Cells are the basic units of life
3.​ Cells come from preexisting cells (Rudolf Virchow 1858: “omnis cellulae
cellula - all cells come from cells)
●​ MODERN CELL THEORY
○​ Builds on the classical theory with advancements from improved technology
1.​ DNA is transferred from between cells during cell division
2.​ Cells of organisms within a species share similar structures and chemical composition
3.​ Energy flow (metabolism) occurs within cells

Eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes

●​ THE NUCLEUS: INFORMATION CENTRAL

○​ Main Role: Contains most of the genes in a eukaryotic cell (some located in mitochondria and chloroplasts).
○​ Size & Appearance: Most conspicuous organelle, ~5 μm in diameter.
 ●​ NUCLEAR ENVELOPE
○​ Double membrane; each membrane is a lipid bilayer with proteins.
○​ Space between membranes: 20–40 nm.
○​ Perforated by pores (~100 nm diameter), where the inner and outer membranes are continuous.
●​ PORE COMPLEX
○​ Protein structure lining each pore
○​ Regulates entry/exit of proteins, RNAs, and macromolecules
●​ NUCLEAR LAMINA
○​ Protein filament layer on the inner envelope surface
○​ Provides mechanical support and maintains nuclear shape
●​ NUCLEAR MATRIX
○​ Protein framework throughout the nucleus.
○​ Helps organize genetic material for efficient functioning.
●​ CHROMOSOMES
○​ Discrete DNA units carrying genetic information
○​ Made of long DNA molecules and proteins
○​ Proteins help coil DNA for compactness
●​ CHROMATIN
○​ Complex DNA and proteins making up chromosomes
○​ Appears diffuse when the cell is not dividing
○​ Chromosomes condense before division for visibility
●​ CHROMOSOME NUMBERS
○​ Human somatic cells: 46 chromosomes
○​ Human sex cells: 23 chromosomes
○​ Fruit fly somatic cells: 8 chromosomes; sex cells: 4 chromosomes
●​ NUCLEOLUS
○​ Dense mass of granules and fibers within the nucleus.
○​ Synthesizes ribosomal RNA (rRNA) using DNA instructions.
○​ Assembles rRNA and imported cytoplasmic proteins into ribosomal subunits.
○​ Ribosomal subunits exit through nuclear pores to form ribosomes in the cytoplasm.

Number of nucleoli varies by species and cell cycle stage.

●​ PROTEIN SYNTHESIS
○​ mRNA Synthesis
■​ Nucleus synthesizes mRNA based on DNA instructions
■​ mRNA exits the nucleus through nuclear pores to the cytoplasm
■​ Ribosomes in the cytoplasm translate mRNA into polypeptides
●​ RIBOSOMES: PROTEIN FACTORIES
○​ Complexes of ribosomal RNAs (rRNAs) and proteins.
○​ Carry out protein synthesis.
○​ Not membrane-bound; not considered organelles.
●​ Cells with high protein synthesis have:
○​ Large numbers of ribosomes
○​ Prominent nucleoli (site of ribosome assembly)
●​ EXAMPLE - Human pancreas cell
○​ Produce many digestive enzymes
○​ Contains a few million ribosomes
●​ ENDOMEMBRANE SYSTEM
○​ Regulates protein traffic and performs metabolic functions
○​ Nuclear envelope, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vesicles, vacuoles, and plasma
membrane
○​ Synthesis of proteins
○​ Transport of proteins into membranes, organelles, or out of the cell
○​ Metabolism and movement of lipids
○​ Detoxification of poisons
○​ Connected by physical continuity or the transfer of membrane segments via vesicles
○​ Membranes differ in structure and function
○​ Thickness, molecular composition, and chemical reactions in membranes can be modified multiple times
throughout their life cycle

●​ THE ENDOPLASMIC RETICULUM: BIOSYNTHETIC FACTORY

○​ Extensive network of membranes, comprising over half the total membrane in many eukaryotic cells
○​ Made up of tubules and sacs called cisternae
○​ Internal compartment: ER lumen (cavity)cisternal space
○​ ER membrane is continuous with the nuclear envelope, connecting their internal spaces
●​ SMOOTH ER
○​ Synthesizes lipids
○​ Detoxifies drugs and poisons
○​ Metabolizes carbohydrates
○​ Stores calcium ions
○​ In muscle cells, pump calcium ions from cytosol
into the ER lumen.
○​ Nerve impulses trigger calcium release, enabling
muscle contraction.
○​ In other cells, calcium release initiates processes
like vesicle secretion.
●​ ROUGH ER
1.​ Protein Synthesis and Processing:
-​ Ribosomes on rough ER produce
secretory proteins, such as insulin in
pancreatic cells
-​ Polypeptide chains are threaded into the
ER lumen, folded into functional shapes
-​ Most secretory proteins are
glycoproteins (carbohydrates added by
ER enzymes)
-​ Secretory proteins are packaged into
transport vesicles at the transitional ER
2.​ Membrane Production:
-​ Produces membrane proteins and phospholipids
-​ Inserts growing membrane proteins into its membrane
-​ Assembles phospholipids from cytosolic precursors
-​ Transfers membrane portions to other parts of the endomembrane system via vesicle
●​ GOLGI APPARATUS: SHIPPING AND RECEIVING CENTER
○​ Acts as a warehouse for receiving, sorting, shipping, and some manufacturing
○​ Modifies, stores, and sends ER products to their destinations
○​ Prominent in cells specialized for secretion
○​ Stacked, flattened membranous sacs called cisternae
○​ Each cisterna separates its internal space from the cytosol.
○​ Surrounded by vesicles transferring materials between the Golgi and other structures.
○​ Cells may have many stacks, sometimes hundreds
●​ GOLGI DIRECTIONALITY
○​ Cis Face (Receiving side):
-​ Faces the ER and receives materials via vesicles
-​ Vesicles fuse with the cis face to add membrane and contents
○​ Trans Face (Shipping side):
-​ Produces vesicles that pinch off and transport materials to other parts of the cell or plasma
membrane.
●​ FUNCTIONS AND PROCESSES
1.​ Modification of ER Products
○​ Modifies glycoproteins by altering carbohydrate structures.
○​ Alters membrane phospholipids.
2.​ Macromolecule Synthesis
○​ Synthesizes polysaccharides like pectins and non cellulose components in plant cells.
○​ Combine these polysaccharides with cellulose for cell wall formation
3.​ Sorting and Transport
○​ Sorts and packs products into transport vesicles at the trans face
○​ Uses molecular tags (e.g., phosphate groups) for targeted delivery
○​ Vesicles recognize and dock at specific organelles or membranes
●​ DYNAMIC GOLGI MODEL
○​ Cisternal Maturation
-​ Cisternae progress from cis to trans face, carrying and modifying cargo
-​ Products are sorted and dispatched via vesicles
○​ Molecular Sorting Tags
-​ Adds tags like phosphate groups for accurate targeting
-​ Vesicle membranes have docking molecules for specific delivery sites
-​ External molecules in vesicles ensure accurate docking at target sites.
●​ LYSOSOMES: DIGESTIVE COMPARTMENTS
○​ Membranous sacs of hydrolytic enzymes for digesting macromolecules.
○​ Function best in acidic environments of lysosomes.
○​ Enzymes become inactive in the neutral pH of the cytosol.
○​ Hydrolytic enzymes and lysosomal membranes are synthesized in the rough ER.
○​ Processed in the Golgi apparatus; lysosomes likely bud from the trans face.
○​ Inner membrane proteins and enzymes are protected from digestion by their 3D shapes
●​ FUNCTIONS
1.​ Intracellular Digestion (Phagocytosis):
-​ Engulf smaller organisms/particles to form food vacuoles.
-​ Vacuoles fuse with lysosomes, and enzymes digest food.
-​ Digestion products (e.g., sugars, amino acids) pass into the cytosol as nutrients.
-​ EXAMPLES: Amoebas and other eukaryotes; Human macrophages (white blood cells) engulf and
destroy invaders.
2.​ Autophagy:
-​ Recycles damaged organelles or cytosol by enclosing them in a double membrane.
-​ Lysosome fuses with the membrane, digests materials, and releases organic compounds for reuse.
-​ EXAMPLE: Human liver cells recycle ~50% of macromolecules weekly
●​ LYSOSOMAL STORAGE DISEASES
○​ Caused by a lack of functioning hydrolytic enzymes
○​ Lysosomes accumulate indigestible material, interfering with cellular activity
○​ TAY-SACHS DISEASE:
■​ Lipid-digesting enzymes are missing, leading to lipid accumulation in brain cells.
■​ Results in brain impairment. Lysosomal storage diseases are rare.
●​ VACUOLES: DIVERSE MAINTENANCE COMPARTMENTS
○​ Vacuolar membrane is selective, resulting in unique internal composition
○​ Large vesicles derived from the ER and Golgi apparatus. Part of the endomembrane system
●​ TYPES AND FUNCTIONS
1.​ Food Vacuoles:
-​ Formed by phagocytosis for intracellular digestion
2.​ Contractile Vacuoles:
-​ Found in freshwater unicellular eukaryotes
-​ Pump excess water out to maintain ion/molecule balance
3.​ Hydrolytic Vacuoles:
-​ Perform enzymatic hydrolysis in plants and fungi (similar to lysosomes)
4.​ Storage Vacuoles:
-​ Store organic compounds like seed proteins
-​ Contain toxic or unpalatable compounds for herbivore defense
5.​ Pigment Vacuoles:
-​ Store pigments (e.g. red/blue in petals) to attract pollinators
●​ CENTRAL VACUOLE (Plant Cells)
○​ Contains “cell sap” - Repository/storage of inorganic ions like potassium and chloride
○​ Major role in plant cell growth by absorbing water
○​ Enables cell enlargement with minimal cytoplasmic investment
○​ Maintains a sufficient plasma membrane-to-cytosol volume ratio
●​ THE EVOLUTIONARY ORIGINS OF MITOCHONDRIA AND CHLOROPLASTS
○​ Organelles that convert energy to forms that cells can use for work
○​ Similarities with bacteria that led to the endosymbiont theory
●​ MITOCHONDRIA:
○​ Site of cellular respiration
○​ Uses oxygen to generate ATP by extracting energy from sugars, fats, and other fuels
●​ CHLOROPLASTS:
○​ Site of photosynthesis in plants and algae
○​ Converts solar energy into chemical energy by synthesizing organic compounds (e.g. sugars) from carbon
dioxide and water
●​ ENDOSYMBIONT THEORY
○​ An ancestral eukaryotic cell engulfed an oxygen-using prokaryote, which became an endosymbiont (a cell
living within another). Over time, they evolved into a single organism: a eukaryotic cell with mitochondria.
Later, some of these cells engulfed photosynthetic prokaryotes, leading to the evolution of eukaryotic cells
with chloroplasts.
●​ EVIDENCE SUPPORTING THIS THEORY
1.​ Double Membranes:
-​ Both mitochondria and
chloroplasts are surrounded
by two membranes, unlike
other organelles in the
endomembrane system
-​ Derived from the ancestral
engulfed prokaryote's outer
membranes.
2.​ Prokaryotic Traits:
-​ Contain ribosomes and
circular DNA, similar to
bacterial chromosomes
-​ DNA programs the synthesis
of some proteins using their
own ribosomes.
3.​ Autonomy:
-​ Mitochondria and
chloroplasts grow and
reproduce independently
within the cells
●​ MITOCHONDRIA: CHEMICAL ENERGY
CONVERSION
○​ Found in nearly all eukaryotic cells
(plants, animals, fungi, unicellular
eukaryotes).
○​ Number correlates with metabolic
activity; active cells have more
mitochondria.
○​ Enclosed by two membranes (phospholipid bilayers with unique proteins).
■​ Outer membrane: Smooth.
■​ Inner membrane: Convoluted with folds called cristae.
○​ Intermembrane Space: Narrow region between inner and outer membranes.
○​ Mitochondrial Matrix: Contains enzymes, mitochondrial DNA, and ribosomes.
○​ Enzymes in the matrix catalyze cellular respiration steps.
○​ Inner membrane proteins (e.g., ATP synthase) facilitate ATP production.
○​ Cristae provides a large surface area, enhancing cellular respiration efficiency.
○​ Typically 1–10 μm long.
○​ Dynamic, moving, changing shape, fusing, and dividing.
○​ Form a branched tubular network in living cells, unlike static electron micrograph views.
●​ CHLOROPLASTS: CAPTURE OF LIGHT ENERGY
○​ Contains chlorophyll (green pigment), enzymes, and molecules for photosynthesis
○​ Lens-shaped, ~3–6 μm in length.
○​ Found in green parts of plants and algae
○​ Double Membrane Envelope: Two membranes with a narrow intermembrane space.
○​ Thylakoids: Flattened, interconnected sacs; stacks of thylakoids are called grana (singular: granum).
○​ Stroma: Fluid outside thylakoids, containing chloroplast DNA, ribosomes, and enzymes.
○​ Divided into intermembrane space, stroma, and thylakoid space.
○​ Compartmentalization aids in converting light energy to chemical energy during photosynthesis.
○​ Shape changes, growth, and self-replication by division.
○​ Mobile within the cell, moving along cytoskeletal tracks.
●​ PLASTID FAMILY
○​ Chloroplasts are specialized plastids
○​ Amyloplasts: Colorless plastids that store starch in roots and tubers
○​ Chromoplasts: Contain pigments for orange and yellow hues in fruits and flowers
●​ PEROXISOME: OXIDATION
○​ Specialized metabolic compartment bounded by a single membrane
○​ Enzymes remove hydrogen atoms from substrates and transfer them to oxygen (O₂), producing hydrogen
peroxide (H₂O₂) as a by-product.
○​ Breakdown of fatty acids into smaller molecules, which are then used by mitochondria for cellular
respiration.
○​ Glyoxysomes: Specialized peroxisomes in plant seeds that convert fatty acids to sugar for energy until
photosynthesis begins.
○​ Grow by incorporating proteins from the cytosol and ER, and lipids from the ER and within peroxisomes.
○​ Can increase in number by splitting when they reach a certain size, suggesting a possible endosymbiotic
origin (still debated)

●​ CYTOSKELETON
○​ Network of fibers that organizes structures and activities in the cell
○​ Organelles were thought to float freely in the cytosol
○​ Improved microscopy revealed a network of fibers throughout the cytoplasm
○​ Found in eukaryotic cells (focus of this section).
○​ Bacterial cells also have a simpler cytoskeleton made of similar proteins.
○​ 3 main molecular structures:
1.​ Microtubules
2.​ Microfilaments
3.​ Intermediate filaments
●​ ROLES: SUPPORT AND MOTILITY
■​ Mechanical Support:Provides structural support and maintains cell shape, especially in animal cells
(no cell walls).
■​ Strength and resilience come from its balanced, tent-like architecture.
■​ Anchors organelles and cytosolic enzymes.
○​ Dynamic Nature:
■​ Can be quickly dismantled and reassembled to change cell shape.
○​ Cell Motility:
■​ Facilitates movement of the cell or its parts.
■​ Requires interaction with motor proteins.
○​ Examples of Cytoskeleton Roles:
■​ Works with motor proteins and plasma membrane molecules for whole-cell movement.
■​ Provides tracks for vesicle and organelle transport (e.g., neurotransmitter vesicles along axons).
■​ Manipulates the plasma membrane for processes like food vacuole formation and phagocytosis.
■​
●​ COMPONENTS
1.​ MICROTUBULES
○​ Structure:
■​ Hollow rods made of tubulin dimers (α-tubulin and β-tubulin).
■​ Can grow and shrink dynamically, with a "plus end" having
●​ higher rates of tubulin addition/removal.
○​ Functions:
■​ Shape and support the cell
■​ Serve as tracks for motor-protein-driven organelle/vesicle movement.
■​ Guide vesicle transport (e.g., ER to Golgi to plasma membrane).
■​ Separate chromosomes during cell division.
○​ CENTROSOMES AND CENTRIOLES:
■​ Microtubules in animal cells grow from centrosomes near the nucleus.
■​ Centrosomes contain centrioles (9 triplet microtubules arranged in a ring)
○​ CILIA AND FLAGELLA:
■​ Motile structures with a "9+2" arrangement of microtubules.
■​ Anchored by a basal body ("9+0" structure)
■​ Powered by dynein motor proteins for bending movement.
■​ Functions: locomotion, fluid movement (e.g., in the trachea and reproductive tract), and signal
reception (primary cilium)
2.​ MICROFILAMENTS (ACTIN FILAMENTS)
○​ Structure:
■​ Thin solid rods of actin arranged in twisted double chains
■​ Can form branched networks for structural support
○​ Functions:
■​ Bear tension and maintain cell shape (e.g., in the cortex)
■​ Support microvilli in intestinal cells
■​ Enable cell motility (e.g., muscle contraction, amoeboid movement via pseudopodia) | Myosin:
Protein making thousands of actin filaments and thicker filaments made
■​ Drive cytoplasmic streaming in plant cells, aiding intracellular material distribution
 3.​ INTERMEDIATE FILAMENTS
○​ Structure:
■​ Diameter between microfilaments and microtubules.
■​ Composed of diverse proteins, such as keratins.
■​ More permanent and sturdy than other cytoskeletal
components
○​ Functions:
■​ Reinforce cell shape and fix organelle positions (e.g., nucleus
in a filament cage).
■​ Form the nuclear lamina supporting the nuclear envelope.
■​ Provide structural integrity to dead skin cells (keratin
networks).
■​ Serve as a durable framework for cell-specific functions.

EXTRACELLULAR COMPONENTS AND CONNECTIONS

●​ CELL WALL OF PLANTS

○​ Found in plants, prokaryotes, fungi, and some unicellular eukaryotes
○​ Made of cellulose microfibrils embedded in a matrix of
polysaccharides and proteins
○​ Protects the cell, maintains shape, prevents water uptake, and provides
structural support against gravity
○​ Layers:
■​ Primary Cell Wall: Thin and flexible; secreted by young
cells
■​ Middle Lamella: Rich in pectin; glues adjacent cells
together
■​ Secondary Cell Wall: Adds strength and durability; present
in mature cells (e.g., in wood).
●​ EXTRACELLULAR MATRIX (ECM) OF ANIMAL CELLS
○​ Components:
■​ Collagen: Major structural protein (40% of total
body protein).
■​ Proteoglycans: Core proteins with carbohydrate
chains; form large complexes.
■​ Fibronectin: Glycoprotein connecting ECM to
integrins.
■​ Integrins: Membrane proteins that connect ECM
to the cytoskeleton, transmitting signals
○​ Functions:
■​ Supports tissue structure.
■​ Influences cell behavior and gene activity through
mechanical and chemical signaling.
■​ Guides cell migration in embryos.
●​ CELL JUNCTIONS
1.​ Plasmodesmata (Plants):
■​ Connect cells via cytoplasmic channels
■​ Allow water, solutes, and some macromolecules to
move between cells
2.​ Animal Cell Junctions:
■​ Tight Junctions:
-​ Membranes of adjacent cells tightly
pressed and sealed together.
-​ Prevent leakage of extracellular fluid (e.g., in intestinal lining).
■​ Desmosomes:
-​ Function like rivets, anchoring cells together into strong sheets
-​ Anchored by intermediate filaments (e.g., in skin tissue)
 ■​ Gap Junctions:
-​ Cytoplasmic channels between adjacent cells, similar to plasmodesmata
-​ Allow ions and small molecules to pass (e.g., in heart muscle and embryos)

“A Cell is Greater Than the Sum of Its Parts”

●​ The cell functions as an integrated system, with its components interacting dynamically
●​ Extracellular components like the ECM and cell junctions play crucial roles in coordination and communication among
cells, enabling multicellular life
SUMMARY