chapter 6:

Chapter 6:A Tour of the Cell

Key Concepts6.1 To study cells, biologists use microscopes and the tools of

biochemistry.6.2 Eukaryotic cells have internal membranes that

compartmentalize their functions, and membrane bound organelles.

6.3 The Eukaryotic cell’s genetic instructions are found in the nucleus and carried out by the ribosomes.

6.4 The endomembrane system (ER) regulates protein traffic and performs metabolic function of the cell.

6.5 Mitochondria and chloroplasts change energy from one form to another.

6.6 The cytoskeleton is a network of fibers that organizes structures and activities inside the cell.

6.7 Extracellular components (outside the cell) and connections between cells (desmosomes, gap junctions, tight junctions, and plasmodesmata) help coordinate cellular activities.

Microscopy• The study of cells progressed with the invention

of the microscope in 1590, and their improvement in the 17th century.

• Light Microscope- earliest form, uses beam of light passed thru specimen and then thru glass lenses.

• Electron Microscope- (1950’s) focuses a beam of electrons thru a specimen, or onto its surface. Highest magnification and resolution.

• Transmission EM- (TEM) used to study the internal structures of a cell.

• Scanning EM- (SEM) used to study the surface of a specimen.

Light Microscope

TEM

SEM

Fig. 6-4

(a) Scanning electron microscopy (SEM)

TECHNIQUE RESULTS

(b) Transmission electron microscopy (TEM)

Cilia

Longitudinalsection ofcilium

Cross sectionof cilium

1 µm

1 µm

Parameters in Microscopy

• Magnification- the ratio of an objects image size to its real size

• Resolution- a measure of the clarity of an object

Staining Technique• The addition of certain chemical

pigments allows for increased contrast between cell structures.

• Makes structures easier to distinguish and study.

• Examples- bromthymol blue, methylene blue, crystal violet, safranin, malachite green, eosin

Fig. 6-3ab

(a) Brightfield (unstained specimen)

(b) Brightfield (stained specimen)

TECHNIQUE RESULTS

50 µm

Cell Fractionation•The goal of cell fractionation is to take cells apart and separate major organelles from one another.

•The instrument used is a Centrifuge.

•The centrifuge spins test tubes holding mixtures of disrupted cells at high speeds.

•Uses centrifugal force.

•Enable scientists to prepare specific components of cells in bulk quantities to study their composition and structure.

Fig. 6-5

Homogenization

TECHNIQUE

HomogenateTissuecells

1,000 g(1,000 times theforce of gravity)

10 min Differential centrifugation

Supernatant pouredinto next tube

20,000 g20 min

80,000 g60 minPellet rich in

nuclei andcellular debris

Pellet rich inmitochondria(and chloro-plasts if cellsare from a plant)

Pellet rich in“microsomes”(pieces of plasmamembranes andcells’ internalmembranes)

150,000 g3 hr

Pellet rich inribosomes

Fig. 6-5b

1,000 g(1,000 times the force of gravity)

10 min

Supernatant poured into next tube

20,000 g20 min

80,000 g60 min

150,000 g3 hr

Pellet rich in nuclei and cellular debris

Pellet rich in mitochondria (and chloro-plasts if cellsare from a plant)

Pellet rich in “microsomes” (pieces of plasmamembranes and cells’ internal membranes) Pellet rich in

ribosomes

TECHNIQUE (cont.)

Cells of Living Things

ProkaryoticUsually single celled.

Can form colonies.No nucleus or

membrane-bound organelles.

Genetic material localized (nucleoid)

Ex. Bacteria

Eukaryotic

Kingdoms: Protista, Fungi, Plants, Animals.

Nuclear membrane encloses DNA.

Organelles that have membrane.

• Surface to Volume Ratio limits size of cells. Large cells require more raw materials.

• V = cm3 S.A. = cm2 Restrictions on size and shape

• Cells compartmentalize to increase SA/Vol, specialize rxn within, localize reactions where needed.

Cell Size and Shape

Basic Aspects of Cell Structure and Function

• Plasma membrane• Lipid bilayer

• Proteins

– Channels, transport, pumps, receptors

• DNA-containing region

• Cytoplasm

Prokaryotic Cells•Highly disorganized

•No membrane bound organelles

•Have a nucleoid (like a nucleus)

•Nucleoid contains genetic material (DNA)

•Have a plasma membrane

•Have cytosol inside the cell in which the organelles are found

•Have ribosomes

•Smaller than Eukaryotic cells

•Examples- Bacteria, Archae

Typical Prokaryote (Bacterial) Cell

Fig. 6-6

Fimbriae

Nucleoid

Ribosomes

Plasma membrane

Cell wall

Capsule

Flagella

Bacterialchromosome

(a) A typical rod-shaped bacterium

(b) A thin section through the bacterium Bacillus coagulans (TEM)

0.5 µm

Eukaryotic Cells• Have membrane bound organelles

• Are very organized

• Have a nucleus (DNA)

• Surrounded by either a cell wall or a plasma membrane

• Examples- plants, animals, fungi, protists (amoeba, paramecium,euglena)

Defining Structures of Eukaryotic Cells

A Plant Cell An Animal Cell

Plant vs. Animal Cell

Fig. 6-9a

ENDOPLASMIC RETICULUM (ER)

Smooth ERRough ERFlagellum

Centrosome

CYTOSKELETON:

Microfilaments

Intermediatefilaments

Microtubules

Microvilli

Peroxisome

MitochondrionLysosome

Golgiapparatus

Ribosomes

Plasma membrane

Nuclearenvelope

Nucleolus

Chromatin

NUCLEUS

Fig. 6-9b

NUCLEUS

Nuclear envelopeNucleolus

Chromatin

Rough endoplasmic reticulum

Smooth endoplasmic reticulum

Ribosomes

Central vacuole

Microfilaments

Intermediate filaments

Microtubules

CYTO-SKELETON

Chloroplast

PlasmodesmataWall of adjacent cell

Cell wall

Plasma membrane

Peroxisome

Mitochondrion

Golgiapparatus

Structures in the Cell• The tiny organs found inside the cell are

called organelles.

• Each of these structures performs a specific function that allows the cell to survive.

Major Cellular Components • Nucleus

• Ribosomes

• Endoplasmic reticulum– Smooth and Rough

• Golgi body

• Various vesicles

• Mitochondria

• Cytoskeleton

Structures found in both Plant and Animal Cells

1. Plasma membrane2. Nucleus3. Chromatin4. Nucleolus5. Ribosomes6. Endoplasmic Reticulum7. Golgi Apparatus8. Mitochondria9. Peroxisomes10. Cytoskeleton11. Centrosomes

Structures Associated with Animal Cells

1. Lysosomes

2. Centrioles

3. Flagella

4. Extracellular matrix

5. Tight Junctions

6. Desmosomes

7. Gap Junctions

Structures Associated with Plant Cells

1. Central Vacuoles

2. Chloroplasts

3. Cell Wall

4. Plasmodesmata

Components of the Nucleus

• Nuclear envelope - Surrounds nucleus

• Chromosome - One DNA molecule and associated

proteins. Organized DNA.

• Chromatin - DNA molecules and histone proteins.

Condenses to form DNA.

• Nucleolus - RNA and proteins that will be assembled

into ribosomal subunits. Cells may have more than

one.

The Nuclear Envelope• Double - membrane system

– Two lipid bilayers. 20-40 nm thick.

– Surrounds chromatin/nucleoplasm

• Pores allow exchange. Composed of about 100 proteins.

Ribosomes• Smallest, most numerous

organelle.• Composed of rRNA and proteins.

Synthesized by nucleolus. • Large and small subunits.• Found free and bound to E.R.

Differ only in what they are making.

• Catalyzes formation of peptide bonds.

The Endomembrane System

• Organelles in which lipids are assembled and

proteins are produced and modified

• Are in direct contact or send vesicles (membrane-

bound sacs).

• Occupy ½ of cell volume.

• Nuclear envelope, endoplasmic reticulum, golgi

apparatus, lysosomes, vacuole

The Endoplasmic Reticulum

• Network of tubes and sacs that are continuous with nuclear membrane. Most extensive mem. Sys.

• Rough (ribosome studded) and Smooth.– Rough: production of secretory proteins. Signal sequence

on polypeptide instructs ribosome to attach to ER.

– Smooth: Lipids production, CH2O metabolism, storage of

ions, detoxification of drugs/alcohol

Fig. 6-11

Cytosol

Endoplasmic reticulum (ER)

Free ribosomes

Bound ribosomes

Large subunit

Small subunit

Diagram of a ribosomeTEM showing ER and ribosomes

0.5 µm

Fig. 6-10

NucleolusNucleus

Rough ER

Nuclear lamina (TEM)

Close-up of nuclear envelope

1 µm

1 µm

0.25 µm

Ribosome

Pore complex

Nuclear pore

Outer membraneInner membraneNuclear envelope:

Chromatin

Surface ofnuclear envelope

Pore complexes (TEM)

Fig. 6-12Smooth ER

Rough ER Nuclear envelope

Transitional ER

Rough ERSmooth ERTransport vesicle

RibosomesCisternaeER lumen

200 nm

Fig. 6-16-1

Smooth ER

Nucleus

Rough ER

Plasma membrane

Fig. 6-16-2

Smooth ER

Nucleus

Rough ER

Plasma membrane

cis Golgi

trans Golgi

Fig. 6-16-3

Smooth ER

Nucleus

Rough ER

Plasma membrane

cis Golgi

trans Golgi

Golgi Bodies

• Enzymatic finishes on proteins

and lipids, and packaging in

vesicles.

• Polarity of cisternae.

• Forms glycolipids,

glycoproteins,

• Products of Golgi leave as

vessicles. From one cisternae

to another or out of cell.

Cis (forming) face

Trans (exit) face

Lysosomes

• Membrane-bound organelle that contains hydrolytic enzymes responsible for the digestion of macromolecules, autolysis, intracellular digestion.

• Dead cells no longer able to maintain H+ gradient (use H+ pump) so organelle breaks down releasing contents.

• Made by ER and Golgi.

Lysosome Function and Production

From Production to Export

Vacuoles

• Storage of water or ions, pigments, hold food, pump out water.

• Are larger than vesicles formed from golgi/E.R.

• In plants is enclosed by Tonoplast (membrane) and provides cell with hydrostatic pressure

Peroxisomes• Contain enzymes

(catalase) that break down H2O2 formed during metabolism of alcohols, F.A.’s.

• Specialized forms [glyoxysome] found in seeds and function during germination.

Mitochondria

• Production of ATP

• Double-membrane system– Two distinct compartments

• Have their own DNA. Maternal in

origin.

• Divide on their own, independent

of cell.

• Have ribosomes, produce

enzymes necessary for ATP

production.

Chloroplast

• Found in photosynthetic eukaryotes

• Two outer membranes

• Semifluid stroma; site of carbon fixation.

• Inner thylakoid membrane system; converts l.e. into c.e.

• Photosynthetic pigments found in other plastids.

Cytoskeleton

• Protein fibers that support and give shape to a cell, involved in organelle movement throughout cell, chromosome movement during cell division and large cell movements (cell motility and cytokinesis)

• 3 Groups of Fibers classified according to size:– Mircrotubules (thickest)– Intermediated filaments (middle sized)– Microfilaments (thinnest)

Components of the Cytoskeleton

• Microtubules and Tubulin subunits; form hollow tube.

– Provide framework for cell, organized by

centrosome from which they usu. originate.

– “Rail” system for organelle transport.

• Component of Centriole.

– Replicated prior to mitosis.

• Form Cilia and Flagella.

– 9 + 2 arrangement (eukaryotic characteristic)

Fig. 6-UN3

Cilia and Flagella and the Structural Basis of Cell Motility

• Surrounded by plasma membrane.

• Motor proteins (dynein) on microtubules use ATP to change shape and “ratchet” past one another.

• Movement causes bending of cilia/flagella.

Components of the Cytoskeleton

• Microfilaments (aka actin filaments)

– Solid “rope”of two actin proteins

– Thinner and more flexible than microtubules

– Principle component of muscle fibers.

– Provide mechanism to support cell shape. Found just inside the c. mem.

– Enable cell movement, phagocytosis and cytokinesis.

Components of the Cytoskeleton

• Intermediate Filaments

– Tough and durable; made of keratin.

– Mechanically strengthen/reinforce cells or cell parts that are under stresses.

• Provide structure to long cells.

• Found in desmosomes.

• Give nucleus shape (nuclear lamina)

Cell-to Cell Junctions

• Plants

– Plasmodesmata

• Perforations in cell wall that allow passage for water/solutes to adjacent

cells.

• Animals

– Tight Junctions. Prevent leakage between cells (ie. Stomach)

– Desmosomes. Mechanically attach cells to each other. Serve as

anchoring sites for inter. filaments in cell.

– Gap Junctions. Analogous to plasmodesma. Fxn as comm.

Pathway between cells. Cardiac muscle, nerves.

Intracellular Junctions

Fig. 6-32

Tight junction

0.5 µm

1 µmDesmosome

Gap junction

Extracellularmatrix

0.1 µm

Plasma membranesof adjacent cells

Spacebetweencells

Gapjunctions

Desmosome

Intermediatefilaments

Tight junction

Tight junctions preventfluid from movingacross a layer of cells

Fig. 6-32a Tight junctions prevent fluid from moving across a layer of cells

Tight junction

Intermediate filaments

Desmosome

Gap junctions

Extracellular matrixSpace

between cells

Plasma membranes of adjacent cells

Fig. 6-32b

Tight junction

0.5 µm

Fig. 6-32c

Desmosome1 µm

Fig. 6-32d

Gap junction

0.1 µm

Plant Cell Walls

• Protect plants, allow for

shape and prevent excess

H2O uptake.

• Composed of cellulose

• Plasmodesmata connect

neighboring cells.

• Secondary cell wall inside of

primary wall. Forms wood

Plant Cell Wall

• Cell secretions form pectin (polysaccharide glue) which acts as adhesive. Laid down in middle lamella to hold cells together.

Fig. 6-31

Interior of cell

Interior of cell

0.5 µm Plasmodesmata Plasma membranes

Cell walls

Plasma Membrane• Forms the boundary for a cell• Selectively permeable• Made up of phospholipids• Fluid mosaic of lipids and proteins• Integral proteins are embedded in

the membrane• Peripheral proteins are loosely bound to the

membrane’s surface• Carbohydrates on the membrane’s surface

are crucial in cell to cell recognition• Found in both plant and animal cells

Fig. 6-7TEM of a plasmamembrane

(a)

(b) Structure of the plasma membrane

Outside of cell

Inside ofcell 0.1 µm

Hydrophilicregion

Hydrophobicregion

Hydrophilicregion Phospholipid Proteins

Carbohydrate side chain

Fig. 6-30

EXTRACELLULAR FLUIDCollagen

Fibronectin

Plasmamembrane

Micro-filaments

CYTOPLASM

Integrins

Proteoglycancomplex

Polysaccharidemolecule

Carbo-hydrates

Coreprotein

Proteoglycanmolecule

Proteoglycan complex

Fig. 6-30a

Collagen

Fibronectin

Plasma membrane

Proteoglycan complex

Integrins

CYTOPLASMMicro-filaments

EXTRACELLULAR FLUID

Extracellular matrix (ECM)

• Intricate network of proteins and polysaccharides that are organized into a meshwork on the outside of cells.

• Large polysaccharides and proteoglygans form a “gel-like” material that resist compression.

• Proteins like collagen (most abundant protein in animals as part of

bone and skin) and elastin (stretch and recoil) provide structure and strength.

• Adhesive-like proteins (fibronectins and laminin) help cells attach to the appropriate part of the ECM.

Extracellular matrix (ECM)

Table 6-1

10 µm 10 µm 10 µm

Column of tubulin dimers

Tubulin dimer

Actin subunit

25 nm

7 nm

Keratin proteins

Fibrous subunit (keratins coiled together)

8–12 nm

Table 6-1a10 µm

Column of tubulin dimers

Tubulin dimer

25 nm

Table 6-1b

Actin subunit

10 µm

7 nm

Table 6-1c

5 µm

Keratin proteins

Fibrous subunit (keratinscoiled together)

8–12 nm

Fig. 6-UN1Cell Component Structure Function

Houses chromosomes, made ofchromatin (DNA, the geneticmaterial, and proteins); containsnucleoli, where ribosomalsubunits are made. Poresregulate entry and exit ofmaterials.

Nucleus

(ER)

Concept 6.3 The eukaryotic cell’s geneticinstructions are housed inthe nucleus and carried outby the ribosomes

Ribosome

Concept 6.4 Endoplasmic reticulum The endomembrane systemregulates protein traffic andperforms metabolic functionsin the cell

(Nuclearenvelope)

Concept 6.5 Mitochondria and chloro-plasts change energy fromone form to another

Golgi apparatus

Lysosome

Vacuole

Mitochondrion

Chloroplast

Peroxisome

Two subunits made of ribo-somal RNA and proteins; can befree in cytosol or bound to ER

Extensive network ofmembrane-bound tubules andsacs; membrane separateslumen from cytosol;continuous withthe nuclear envelope.

Membranous sac of hydrolyticenzymes (in animal cells)

Large membrane-boundedvesicle in plants

Bounded by doublemembrane;inner membrane hasinfoldings (cristae)

Typically two membranesaround fluid stroma, whichcontains membranous thylakoidsstacked into grana (in plants)

Specialized metaboliccompartment bounded by asingle membrane

Protein synthesis

Smooth ER: synthesis oflipids, metabolism of carbohy-drates, Ca2+ storage, detoxifica-tion of drugs and poisons

Rough ER: Aids in synthesis ofsecretory and other proteins frombound ribosomes; addscarbohydrates to glycoproteins;produces new membrane

Modification of proteins, carbo-hydrates on proteins, and phos-pholipids; synthesis of manypolysaccharides; sorting of Golgiproducts, which are then released in vesicles.

Breakdown of ingested substances,cell macromolecules, and damagedorganelles for recycling

Digestion, storage, wastedisposal, water balance, cellgrowth, and protection

Cellular respiration

Photosynthesis

Contains enzymes that transferhydrogen to water, producinghydrogen peroxide (H2O2) as aby-product, which is convertedto water by other enzymesin the peroxisome

Stacks of flattenedmembranoussacs; has polarity(cis and transfaces)

Surrounded by nuclearenvelope (double membrane)perforated by nuclear pores.The nuclear envelope iscontinuous with theendoplasmic reticulum (ER).

Fig. 6-UN1a

Cell Component Structure Function

Concept 6.3 The eukaryotic cell’s geneticinstructions are housed inthe nucleus and carried outby the ribosomes

Nucleus Surrounded by nuclearenvelope (double membrane)perforated by nuclear pores.The nuclear envelope iscontinuous with theendoplasmic reticulum (ER).

(ER)

Houses chromosomes, made ofchromatin (DNA, the geneticmaterial, and proteins); containsnucleoli, where ribosomalsubunits are made. Poresregulate entry and exit osmaterials.

Ribosome Two subunits made of ribo-somal RNA and proteins; can befree in cytosol or bound to ER

Protein synthesis

Fig. 6-UN1b

Cell Component Structure Function

Concept 6.4 The endomembrane systemregulates protein traffic andperforms metabolic functionsin the cell

Endoplasmic reticulum

(Nuclearenvelope)

Golgi apparatus

Lysosome

Vacuole Large membrane-boundedvesicle in plants

Membranous sac of hydrolyticenzymes (in animal cells)

Stacks of flattenedmembranoussacs; has polarity(cis and transfaces)

Extensive network ofmembrane-bound tubules andsacs; membrane separateslumen from cytosol;continuous withthe nuclear envelope.

Smooth ER: synthesis oflipids, metabolism of carbohy-drates, Ca2+ storage, detoxifica-tion of drugs and poisons

Rough ER: Aids in sythesis ofsecretory and other proteinsfrom bound ribosomes; addscarbohydrates to glycoproteins;produces new membrane

Modification of proteins, carbo-hydrates on proteins, and phos-pholipids; synthesis of manypolysaccharides; sorting ofGolgi products, which are thenreleased in vesicles.

Breakdown of ingested sub-stances cell macromolecules, and damaged organelles for recycling

Digestion, storage, wastedisposal, water balance, cellgrowth, and protection

Fig. 6-UN1c

Cell Component

Concept 6.5Mitochondria and chloro-plasts change energy fromone form to another

Mitochondrion

Chloroplast

Peroxisome

Structure Function

Bounded by doublemembrane;inner membrane hasinfoldings (cristae)

Typically two membranesaround fluid stroma, whichcontains membranous thylakoidsstacked into grana (in plants)

Specialized metaboliccompartment bounded by asingle membrane

Cellular respiration

Photosynthesis

Contains enzymes that transferhydrogen to water, producinghydrogen peroxide (H2O2) as aby-product, which is convertedto water by other enzymesin the peroxisome