Ch 4 A Tour of the Cell

Concept 4.1 Biologists use Microscopes & The tools of biochemistry to study cells
Cell Fractionation
•	Cell fractionation breaks up cells and separates the components, using centrifugation
•	Cell components separate based on their
relative size
•	Cell fractionation enables scientists to determine the functions of organelles

Concept 4.2: Eukaryotic cells have internal membranes that compartmentalize their functions
•	The basic structural and functional unit of every organism is one of two types of cells: prokaryotic or eukaryotic
Comparing Prokaryotic and Eukaryotic Cells
•	Basic features of all cells 
•	Plasma membrane
•	Semifluid substance called cytosol
•	Chromosomes (carry genes)
•	Ribosomes (make proteins)
Comparing Prokaryotic and Eukaryotic Cells
Eukaryotic Cells: Plant vs. Animal

The Plasma Membrane
•	Figure 4.5
•	The plasma membrane is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell
•	The general structure of a biological membrane is a double layer of phospholipids

Surface Area:Volume Ratio
Figure 4.6: Surface Area:Volume Ratio 
Metabolic requirements set upper limits on the size of cells 
The ratio of surface area to volume of a cell is critical
Higher S:V ratio allows more diffusion
To successfully support the metabolic requirements a cell needs to be SMALL 

A Panoramic View of the Eukaryotic Cell
•	A eukaryotic cell has internal membranes that divide the cell into compartments—organelles
•	The plasma membrane and organelle membranes participate directly in the cell’s metabolism

Concept 4.3: The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes
•	The nucleus contains most of the DNA in a eukaryotic cell
•	Ribosomes use the information from the DNA to make proteins
•	Figure 4.8
•	Figure 4.9

Concept 4.4: The endomembrane system regulates protein traffic and performs metabolic functions in the cell
•	Components of the endomembrane system
•	Nuclear envelope
•	Endoplasmic reticulum
•	Golgi apparatus
•	Lysosomes
•	Vacuoles
•	Plasma membrane
•	These components are either continuous or connected through transfer by vesicles

The Endoplasmic Reticulum: Biosynthetic Factory
•	The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells
•	The ER consists of a network of sacs and tubules 
•	ER lumen is the internal compartment of the ER 
•	Cisternae fluid filled membranous sacs and tubules 
•	There are two distinct regions of ER
•	Smooth ER: lacks ribosomes
•	Synthesizes lipids & steroids (ie: steroid hormones lots in ovaries & testies)
•	Metabolizes carbohydrates
•	Detoxifies drugs and poisons 
•	Stores calcium ions 
•	Rough ER: surface is studded with ribosomes
•	Polypeptide (proteins) made in bound ribosomes, thread into inside of the rough ER
•	These dpolypeptides get folded into their 3D shape (2nd-ary & Tertiary structure
•	Has bound ribosomes, which secrete glycoproteins 
•	Distributes transport vesicles, proteins surrounded by membranes
•	Is a membrane factory for the cell
•	Figure 4.10

The Golgi Apparatus: Shipping & Receiving Center
•	The Golgi apparatus consists of flattened membranous sacs called cisternae
•	Cis- vs Trans face
•	Functions of the Golgi apparatus
•	Modifies (attaches ID tags that act like “zip codes” on  mailing labels) on to products of the ER
•	Manufactures certain macromolecules
•	Sorts and packages materials into transport vesicles
•	Not just a wharehouse for receiving, sorting and shipping but also dynamic modification of cargo (cisternal maturation model)
•	Figure 4.11

Lysosome Formation
•	The hydrolytic enzemes and lysosome membranes are made by the rough ER and Golgi apparatus
•	A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules for food or recycling old organelles
•	Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids
•	Lysosomal enzymes work best in the acidic environment inside the lysosome
•	Figure 4.12
•	Some types of cell (macrophage – type of WBC) (amoebas) can engulf another cell by phagocytosis; this forms a food vacuole
•	A lysosome fuses with the food vacuole and digests the molecules
•	Figure 4.13 pg 80
•	Lysosomes also use enzymes to recycle the cell’s own organelles and macromolecules, a process called autophagy
•	This helps cell to renew themselves (ie: Liver cells)

Vacuoles: Diverse Maintenance Compartments
•	Vacuoles are large vesicles derived from the endoplasmic reticulum and Golgi apparatus
•	Membrane bound storage organelle
•	There are several types:
•	Food vacuoles are formed by phagocytosis
•	Contractile vacuoles, found in many freshwater protists, pump excess water out of cells
•	Central vacuoles, found in many mature plant cells, hold organic compounds (waste products, pigments & chemical compounds that could be poisonous) and water
•	Certain vacuoles in plants and fungi carry out enzymatic hydrolysis like lysosomes
•	Figure 4.14 pg 80

The Endomembrane System: A Review
•	The endomembrane system is a complex and dynamic player in the cell’s compartmental organization
•	Figure 4.15

The Evolutionary Origins of Mitochondria and Chloroplasts
•	Mitochondria and chloroplasts have similarities with bacteria 
•	Enveloped by a double membrane
•	Contain free ribosomes and circular DNA molecules
•	Grow and reproduce somewhat independently in cells
•	The endosymbiont theory 
•	An early ancestor of eukaryotic cells engulfed a non-photosynthetic prokaryotic cell, which formed an endosymbiont relationship with its host
•	The host cell and endosymbiont merged into a single organism, a eukaryotic cell with a mitochondrion
•	At least one of these cells may have taken up a photosynthetic prokaryote, becoming the ancestor of cells that contain chloroplasts
•	Figure 4.16 pg 82

Mitochondria: Chemical Energy Conversion
•	Mitochondria are in nearly all eukaryotic cells & are the energy producers
•	They have a smooth outer membrane and an inner membrane folded into cristae 
•	Cristae allow for grater surface area for cell respiration
•	The inner membrane creates two compartments: 
•	intermembrane space and 
•	mitochondrial matrix = liquidy inside inner membrane
•	Mito has own DNA & ribosomes
•	Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix
•	Break down sugars to produce energy in the form of ATP (Adenasine TriPhophate)
•	Cristae present a large surface area for enzymes that synthesize ATP
•	In cells with a lot of metabolic activity there are a lot (1000s) of mitochondria
•	Figure 4.17

Chloroplasts: Capture of Light Energy
•	Chloroplasts are energy producers
•	Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis
•	Chloroplast structure includes
•	2 membranes (inner & outer)	
•	Thylakoids, membranous sacs, stacked to form 
a granum (grana=plural)
•	Stroma, the internal fluid
•	The chloroplast is one of a group of plant organelles called plastids
•	Plastids store starch, have pigments to give flowers colors
•	Chloroplastss have own DNA and
•	Figure 4.18a

Peroxisomes: Oxidation
•	Peroxisomes are specialized metabolic compartments bounded by a single membrane
•	Peroxisomes contain enzymes that remove hydrogen from certain molecules and transfer them to Oxygen producing hydrogen peroxide (as a byproduct) which is toxic but they can break down H2O2 & convert it to water
•	Peroxisomes perform reactions with many different functions
•	Ie: Liver peroxisomes detoxify alcohol by transferring the Hydrogen from the alcohol and other harmful compounds to oxygen
•	Figure 4.19 pg, 84

Concept 4.6: The Cytoskeleton is a network of fibers that organizes structures & activities in the cell
•	The cytoskeleton is a network of fibers extending throughout the cytoplasm
•	It organizes the cell’s structures and activities, anchoring many organelles
•	Figure 4.20 pg. 84
•	Three main types of fibers make up the cytoskeleton
•	Microtubules are the thickest of the three components of the cytoskeleton
•	Microfilaments, also called actin filaments, are the thinnest components
•	Intermediate filaments are fibers with diameters in a middle range
•	Table 4.1 pg 86

Centrosomes and Centrioles
•	In animal cells, microtubules grow out from a centrosome near the nucleus
•	The centrosome is a “microtubule-organizing center”
•	The centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring
•	Figure 4.22

Cilia and Flagella
•	Microtubules control the beating of cilia and flagella, microtubule-containing extensions projecting from some cells
•	Flagella are limited to one or a few per cell, while cilia occur in large numbers on cell surfaces
•	Cilia and flagella also differ in their b eating patterns
•	Cilia like row boat oars stroking back & forth
•	Flagella undulate or “S-wave” pattern
•	Cilia and flagella share a common structure
•	A core of microtubules sheathed by the plasma membrane (cytoskeleton) w/9+2 pattern
•	With 9 + 2 pattern: 9 pairs(doublets) around central pair
•	A basal body that anchors the cilium or flagellum
•	A motor protein called dynein, which drives the bending movements of a cilium or flagellum, uses ATP

Cell Walls of Plants
•	The cell wall is an extracellular structure that distinguishes plant cells from animal cells
•	The cell wall protects the plant cell, maintains its shape, and prevents excessive uptake of water
•	Plant cell walls are made of cellulose fibers embedded in other polysaccharides and protein
•	Figure 4.25

The Extracellular Matrix (ECM) of Animal Cells
•	Animal cells lack cell walls but are covered by an elaborate extracellular matrix (ECM)
•	ECM helps:
•	 support,
•	 move, 
•	regulate cell behavior &
•	Adhere cells to other cells
•	Figure 4.26 pg 89
•	The ECM is made up of glycoproteins such as collagen, proteoglycans, and fibronectin
•	ECM proteins bind to receptor proteins in the plasma membrane called integrins

Cell Junctions
•	Neighboring cells in an animal or plant often adhere, interact, and communicate through direct physical contact
•	There are several types of intercellular junctions that facilitate this
•	Plasmodesmata
•	Tight junctions
•	Desmosomes
•	Gap junctions
•	Plasmodesmata are channels that perforate plant cell walls
o	Through plasmodesmata, water and small solutes (and sometimes proteins and RNA) can pass from cell to cell
•	Animal cells have three main types of cell junctions:
•	Tight junctions 
o	Membranes of adjacent cells are fused, forming continuous belts around cells; 
o	Prevent fluids from leaking in/out 
o	Ie: TJs between skin cells make us water tight by preventing leakage btwn cells in our sweat glands
•	Desmosomes
o	Anchoring junctions like “Rivets”
o	Fasten cells together into strong sheets
o	Ie: Desmosomes attach muscle cells 
•	Gap junctions
o	Communicating junctions
o	Allows cystoplasm, ions, sugars, amino acids, & other small molecules to move between adjacent animal cells
o	Ie: heart muscle, brain cells
•	All are especially common in epithelial tissue
•	Figure 4.27 pg 90