Chapter 6: A Tour of the Cell

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Chapter 6: A Tour of the Cell• All organisms are

made of cells

• The cell is the simplest collection of matter that can live

• Cell structure is correlated to cellular function

10 µm


Microscopy• Light microscopes (LMs)

– Pass visible light through a specimen and magnify cellular structures with lenses

• Cells were discovered by ________in 1665 but their ultrastructure was largely unknown until the development of the ____________ in the 1950s.

• Electron microscopes (EMs)

– Focus a beam of electrons through a specimen (TEM) or onto its surface (SEM)

http://www.tedpella.com/mscope_html/DMBA200full.jpg


• Different types of microscopes can be used to visualize different sized cellular structures

Una

ided

eye

1 m

0.1 nm

10 m

0.1 m

1 cm

1 mm

100 µm

10 µ m

1 µ m

100 nm

10 nm

1 nm

Length of somenerve and muscle cells

Chicken egg

Frog egg

Most plant and Animal cells

Smallest bacteria

Viruses

Ribosomes

Proteins

Lipids

Small molecules

Atoms

NucleusMost bacteriaMitochondrion

Ligh

t mic

rosc

ope

Ele

ctro

n m

icro

scop

e

Ele

ctro

n m

icro

scop

e

Figure 6.2

Human height

Measurements1 centimeter (cm) = 102 meter (m) = 0.4 inch1 millimeter (mm) = 10–3 m1 micrometer (µm) = 10–3 mm = 10–6 m1 nanometer (nm) = 10–3 mm = 10–9 m

Ligh

t mic

rosc

ope

Nak

ed E

ye


– Use different methods for enhancing visualization of cellular structures

TECHNIQUE RESULT

Brightfield (unstained specimen). Passes light directly through specimen. Unless cell is naturally pigmented or artificially stained, image has little contrast. [Parts (a)–(d) show a human cheek epithelial cell.]

(a)

Brightfield (stained specimen). Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved).

(b)

Phase-contrast. Enhances contrast in unstained cells by amplifying variations in density within specimen; especially useful for examining living, unpigmented cells.

(c)

50 µm

Figure 6.3


Differential-interference-contrast (Nomarski). Like phase-contrast microscopy, it uses optical modifications to exaggerate differences indensity, making the image appear almost 3D.

Fluorescence. Shows the locations of specific molecules in the cell by tagging the molecules with fluorescent dyes or antibodies. These fluorescent substances absorb ultraviolet radiation and emit visible light, as shown here in a cell from an artery.

Confocal. Uses lasers and special optics for “optical sectioning” of fluorescently-stained specimens. Only a single plane of focus is illuminated; out-of-focus fluorescence above and below the plane is subtracted by a computer. A sharp image results, as seen in stained nervous tissue (top), where nerve cells are green, support cells are red, and regions of overlap are yellow. A standard fluorescence micrograph (bottom) of this relatively thick tissue is blurry.

50 µm

50 µm

(d)

(e)

(f)


• The scanning electron microscope (SEM)

– Provides for detailed study of the surface of a specimen

TECHNIQUE RESULTS

Scanning electron micro-scopy (SEM). Micrographs takenwith a scanning electron micro-scope show a 3D image of the surface of a specimen. This SEM shows the surface of a cell from a rabbit trachea (windpipe) covered with motile organelles called cilia. Beating of the cilia helps moveinhaled debris upward toward the throat.

(a)Cilia

1 µm

Figure 6.4 (a)


• The transmission electron microscope (TEM)

– Provides for detailed study of the internal ultrastructure of cells

Transmission electron micro-scopy (TEM). A transmission electron microscope profiles a thin section of a specimen. Here we see a section through a tracheal cell, revealing its ultrastructure. In preparing the TEM, some cilia were cut along their lengths, creating longitudinal sections, while other cilia were cut straight across, creating cross sections.

(b)

Longitudinalsection ofcilium

Cross sectionof cilium 1 µm

Figure 6.4 (b)


Interactive Questiona. Define cytology

b. What do cell biologists use a TEM to study?

c. What does and SEM show best?

d. What advantages does light microscopy have over TEM and SEM?

a. The study of cell structure

b. The internal ultrastructure of cells

c. The 3-d surface topography of a specimen

d. Light microscopy enables study of living cells and may introduce fewer artifacts than do TEM and SEM


Isolating Organelles by Cell Fractionation• Cell fractionation

– Takes cells apart and separates the major organelles from one another

• The centrifuge

– Is used to fractionate cells into their component parts


Tissuecells

Homogenization

Homogenate1000 g(1000 times theforce of gravity)

10 min Differential centrifugationSupernatant pouredinto next tube

20,000 g20 min

Pellet rich innuclei andcellular debris

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

Pellet rich in“microsomes”(pieces of plasma mem-branes andcells’ internalmembranes)

Pellet rich inribosomes

150,000 g3 hr

80,000 g60 min

APPLICATION Cell fractionation is used to isolate (fractionate) cell components, based on size and density.

TECHNIQUE First, cells are homogenized in a blender to break them up. The resulting mixture (cell homogenate) is then centrifuged at various speeds and durations to fractionate the cell components, forming a series of pellets.

RESULTS In the original experiments, the researchers used microscopy to identify the organelles in each pellet, establishing a baseline for further experiments. In the next series of experiments, researchers used biochemical methods to determine the metabolic functions associated with each type of organelle. Researchers currently use cell fractionation to isolate particular organelles in order to study further details of their function.

• The process of cell fractionation

Figure 6.5


What do all cells have in common?

1. _____, 2. _____, 3. _____, 4. _____

• Prokaryotic cells do not contain a _______ and have their DNA located in a region called the _________

• Eukaryotic cells

– Contain a true nucleus, bounded by a membranous nuclear envelope

– Are generally quite a bit ______(in size) when compared to prokaryotic cells


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

Pili: attachment structures onthe surface of some prokaryotes

Nucleoid: region where thecell’s DNA is located (notenclosed by a membrane)

Ribosomes: organelles thatsynthesize proteins

Plasma membrane: membraneenclosing the cytoplasm

Cell wall: rigid structure outsidethe plasma membrane

Capsule: jelly-like outer coatingof many prokaryotes

Flagella: locomotionorganelles ofsome bacteria

(a) A typical rod-shaped bacterium

0.5 µmBacterial

chromosome

Figure 6.6 A, B


The logistics of carrying out cellular metabolism sets limits on the size of cells

• A smaller cell

– Has a higher surface to volume ratio, which facilitates the exchange of materials into and out of the cell Surface area increases while

total volume remains constant

5

11

Total surface area (height width number of sides number of boxes)

Total volume (height width length number of boxes)

Surface-to-volume ratio (surface area volume)

6

1

6

150

125

12

750

125

6

Figure 6.7


• The plasma membrane

– Functions as a selective barrier

– Allows sufficient passage of nutrients and waste

Carbohydrate side chain

Figure 6.8 A, B

Outside of cell

Inside of cell

Hydrophilicregion

Hydrophobicregion

Hydrophilicregion

(b) Structure of the plasma membrane

Phospholipid Proteins

TEM of a plasmamembrane. Theplasma membrane,here in a red bloodcell, appears as apair of dark bandsseparated by alight band.

(a)

0.1 µm


A panoramic view: a eukaryotic cell• A animal cell

Rough ER Smooth ER

Centrosome

CYTOSKELETON

Microfilaments

Microtubules

Microvilli

Peroxisome

Lysosome

Golgi apparatus

Ribosomes

In animal cells but not plant cells:LysosomesCentriolesFlagella (in some plant sperm)

Nucleolus

Chromatin

NUCLEUS

Flagelium

Intermediate filaments

ENDOPLASMIC RETICULUM (ER)

Mitochondrion

Nuclear envelope

Plasma membrane

Figure 6.9


A panoramic view: a eukaryotic cell II• A plant cell

In plant cells but not animal cells:ChloroplastsCentral vacuole and tonoplastCell wallPlasmodesmata

CYTOSKELETON

Ribosomes (small brwon dots)

Central vacuole

MicrofilamentsIntermediate filaments

Microtubules

Rough endoplasmic reticulum Smooth

endoplasmic reticulum

ChromatinNUCLEUS

Nuclear envelope

Nucleolus

Chloroplast

PlasmodesmataWall of adjacent cell

Cell wall

Golgi apparatus

Peroxisome

Tonoplast

Centrosome

Plasma membrane

Mitochondrion

Figure 6.9


The Nucleus: Genetic Library of the Cell• The nucleus

contains most of the genes in the eukaryotic cell

• The nuclear envelope encloses the nucleus, separating its contents from the cytoplasm

Nucleus

NucleusNucleolus

Chromatin

Nuclear envelope:Inner membraneOuter membrane

Nuclear pore

Rough ER

Porecomplex

Surface of nuclear envelope.

Pore complexes (TEM). Nuclear lamina (TEM).

Close-up of nuclearenvelope

Ribosome

1 µm

1 µm0.25 µm

Figure 6.10


Ribosomes: Protein Factories in the Cell• Ribosomes are particles made of ribosomal RNA

and protein, and they carry out protein synthesis

Ribosomes Cytosol

Free ribosomes

Bound ribosomes

Largesubunit

Smallsubunit

TEM showing ER and ribosomes Diagram of a ribosome

0.5 µm


Interactive Question• How does the nucleus control protein synthesis

in cytoplasm?

The genetic instructions for specific proteins are transcribed from DNA into messenger RNA (mRNA), which then passes into the cytoplasm to complex with ribosomes where it is translated into the primary structure of proteins.


The ER membrane• Accounts for more than

half the total membrane in many eukaryotic cells

• Is continuous with the nuclear envelope

• 2 kinds of ER• Smooth: lacks ribosomes

• Rough: contains ribosomes

Smooth ER

Rough ER

ER lumenCisternae

RibosomesTransport vesicle

Smooth ER

Transitional ER

Rough ER 200 µm

Nuclearenvelope

Figure 6.12


Functions of Smooth ER• The smooth ER

– Synthesizes lipids

– Metabolizes carbohydrates

– Stores calcium

– Detoxifies poison


Functions of Rough ER• The rough ER

– Has bound ribosomes

– Produces proteins and membranes, which are distributed by transport vesicles


• The Golgi apparatus

– Receives many of the transport vesicles produced in the rough ER

– Consists of flattened membranous sacs called cisternae

• Functions of the Golgi apparatus include

– Modification of the products of the rough ER

– Manufacture of certain macromolecules

The Golgi Apparatus: Shipping and Receiving Center


Golgiapparatus

TEM of Golgi apparatus

cis face(“receiving” side ofGolgi apparatus)

Vesicles movefrom ER to Golgi Vesicles also

transport certainproteins back to ER

Vesicles coalesce toform new cis Golgi cisternae

Cisternalmaturation:Golgi cisternaemove in a cis-to-transdirection

Vesicles form andleave Golgi, carryingspecific proteins toother locations or tothe plasma mem-brane for secretion

Vesicles transport specificproteins backward to newerGolgi cisternae

Cisternae

trans face(“shipping” side ofGolgi apparatus)

0.1 0 µm16

5

2

3

4

• Functions of the Golgi apparatus

Figure 6.13


Lysosomes: Digestive Compartments• A lysosome

– Is a membranous sac of hydrolytic enzymes

– Can digest all kinds of macromolecules


• Lysosomes carry out intracellular digestion by

– Phagocytosis

Figure 6.14 A(a) Phagocytosis: lysosome digesting food

1 µm

Lysosome containsactive hydrolyticenzymes

Food vacuole fuses with lysosome

Hydrolyticenzymes digestfood particles

Digestion

Food vacuole

Plasma membraneLysosome

Digestiveenzymes

Lysosome

Nucleus


• Autophagy

Figure 6.14 B

(b) Autophagy: lysosome breaking down damaged organelle

Lysosome containingtwo damaged organelles 1 µ m

Mitochondrionfragment

Peroxisomefragment

Lysosome fuses withvesicle containingdamaged organelle

Hydrolytic enzymesdigest organellecomponents

Vesicle containingdamaged mitochondrion

Digestion

Lysosome


Vacuoles: Diverse Maintenance Compartments• A plant or fungal cell

– May have one or several vacuoles

• Food vacuoles

– Are formed by phagocytosis

• Contractile vacuoles

– Pump excess water out of protist cells


• Central vacuoles

– Are found in plant cells

– Hold reserves of important organic compounds and water

Central vacuole

Cytosol

Tonoplast

Centralvacuole

Nucleus

Cell wall

Chloroplast

5 µm

Figure 6.15


Plasma membrane expandsby fusion of vesicles; proteinsare secreted from cell

Transport vesicle carriesproteins to plasma membrane for secretion

Lysosome availablefor fusion with anothervesicle for digestion

4 5 6

Nuclear envelope isconnected to rough ER, which is also continuous

with smooth ER

Nucleus

Rough ER

Smooth ERcis Golgi

trans Golgi

Membranes and proteinsproduced by the ER flow in

the form of transport vesiclesto the Golgi Nuclear envelop

Golgi pinches off transport Vesicles and other vesicles

that give rise to lysosomes and Vacuoles

1

3

2

Plasmamembrane

• Relationships among organelles of the endomembrane system

Figure 6.16


• Concept 6.5: Mitochondria and chloroplasts change energy from one form to another

• Mitochondria

– Are the sites of cellular respiration

• Chloroplasts

– Found only in plants, are the sites of photosynthesis


• Mitochondria are enclosed by two membranes

– Are found in nearly all eukaryotic cells and have smooth outer membrane

– An inner membrane folded into cristae

Mitochondrion

Intermembrane spaceOuter

membrane

Freeribosomesin the mitochondrialmatrix

MitochondrialDNA

Innermembrane

Cristae

Matrix

100 µmFigure 6.17


Chloroplasts: Capture of Light Energy• The chloroplast contains chlorophyll

• Is a specialized member of a family of closely related plant organelles called plastids; this is where photosythesis takes place

• Are found in leaves and other green organs of plants and in algae

Chloroplast

ChloroplastDNA

RibosomesStromaInner and outermembranes

Thylakoid1 µm

Granum


• Chloroplast structure includes

– Thylakoids, membranous sacs

– Stroma, the internal fluid


Peroxisomes: Oxidation• Peroxisomes

– Convert hydrogen peroxide to water (because H2O2 is a toxic by-product

ChloroplastPeroxisome

Mitochondrion

1 µm

Figure 6.19


• The cytoskeleton

– Is a network of fibers extending throughout the cytoplasm and gives mechanical support to the cell

Figure 6.20

Microtubule

0.25 µm MicrofilamentsFigure 6.20


– Is involved in cell motility, which utilizes motor proteins

VesicleATPReceptor formotor protein

Motor protein(ATP powered)

Microtubuleof cytoskeleton

(a) Motor proteins that attach to receptors on organelles can “walk”the organelles along microtubules or, in some cases, microfilaments.

Microtubule Vesicles 0.25 µm

(b) Vesicles containing neurotransmitters migrate to the tips of nerve cell axons via the mechanism in (a). In this SEM of a squid giant axon, two vesicles can be seen moving along a microtubule. (A separate part of the experiment provided the evidence that they were in fact moving.)Figure 6.21 A, B


• There are three main types of fibers that make up the cytoskeleton

Table 6.1


Microtubules• Microtubules

– Shape the cell

– Guide movement of organelles

– Help separate the chromosome copies in dividing cells


• The centrosome

– Is considered to be a “microtubule-organizing center” and contains a pair of centrioles

Centrosome

Microtubule

Centrioles0.25 µm

Longitudinal sectionof one centriole

Microtubules Cross sectionof the other centrioleFigure 6.22


Cilia and Flagella• Cilia and flagella

– Contain specialized arrangements of microtubules

– Are locomotor appendages of some cells


• Flagella beating pattern

(a) Motion of flagella. A flagellum usually undulates, its snakelike motion driving a cell in the same direction as the axis of the flagellum. Propulsion of a human sperm cell is an example of flagellatelocomotion (LM).

1 µm

Direction of swimming

Figure 6.23 A


• Ciliary motion

(b) Motion of cilia. Cilia have a back- and-forth motion that moves the cell in a direction perpendicular to the axis of the cilium. A dense nap of cilia, beating at a rate of about 40 to 60 strokes a second, covers this Colpidium, a freshwater protozoan (SEM).

Figure 6.23 B

15 µm


• Cilia and flagella share a common ultrastructure

(a)

(c)

(b)

Outer microtubuledoubletDynein arms

CentralmicrotubuleOuter doublets cross-linkingproteins inside

Radialspoke

Plasmamembrane

Microtubules

Plasmamembrane

Basal body

0.5 µm

0.1 µm

0.1 µm

Cross section of basal body

Triplet

Figure 6.24 A-C


• The protein dynein

– Is responsible for the bending movement of cilia and flagella

Microtubuledoublets ATP

Dynein arm

Powered by ATP, the dynein arms of one microtubule doublet grip the adjacent doublet, push it up, release, and then grip again. If the two microtubule doublets were not attached, they would slide relative to each other.

(a)

Figure 6.25 A


Outer doubletscross-linkingproteins

Anchoragein cell

ATP

In a cilium or flagellum, two adjacent doublets cannot slide far because they are physically restrained by proteins, so they bend. (Only two ofthe nine outer doublets in Figure 6.24b are shown here.)

(b)

Figure 6.25 B


Localized, synchronized activation of many dynein arms probably causes a bend to begin at the base of the Cilium or flagellum and move outward toward the tip. Many successive bends, such as the ones shown here to the left and right, result in a wavelike motion. In this diagram, the two central microtubules and the cross-linking proteins are not shown.

(c)

1 3

2

Figure 6.25 C


Microfilaments (Actin Filaments)• Microfilaments

– Are built from molecules of the protein actin and are found in microvilli

0.25 µm

Microvillus

Plasma membrane

Microfilaments (actinfilaments)

Intermediate filaments

Figure 6.26


• Microfilaments that function in cellular motility

– Contain the protein myosin in addition to actin

Actin filament

Myosin filament

Myosin motors in muscle cell contraction. (a)

Muscle cell

Myosin arm

Figure 6.27 A


• Amoeboid movement

– Involves the contraction of actin and myosin filaments

Cortex (outer cytoplasm):gel with actin network

Inner cytoplasm: sol with actin subunits

Extendingpseudopodium

(b) Amoeboid movementFigure 6.27 B


• Cytoplasmic streaming

– Is another form of locomotion created by microfilaments

Nonmovingcytoplasm (gel)

ChloroplastStreamingcytoplasm(sol)

Parallel actinfilaments Cell wall

(b) Cytoplasmic streaming in plant cellsFigure 6.27 C


Intermediate Filaments• Intermediate filaments

– Support cell shape

– Fix organelles in place


Cell Walls of Plants– The cell wall is an extracellular structure of plant cells

that distinguishes them from animal cells

– Are made of cellulose fibers embedded in other polysaccharides and protein

– May have multiple layersCentral vacuoleof cell

PlasmamembraneSecondarycell wallPrimarycell wall

Middlelamella

1 µm

Centralvacuoleof cell

Central vacuole CytosolPlasma membrane

Plant cell walls

PlasmodesmataFigure 6.28


Interactive Question• If you sketched two adjacent plant cells, could

you show the location of the primary and secondary cell walls and the middle lamella?


The Extracellular Matrix (ECM) of Animal Cells• Animal cells lack cell walls and are covered by an

elaborate matrix, the ECM, which is made up of glycoproteins and other macromolecules

Collagen

Fibronectin

Plasmamembrane

EXTRACELLULAR FLUID

Micro-filaments

CYTOPLASM

Integrins

Polysaccharidemolecule

Carbo-hydrates

Proteoglycanmolecule

Coreprotein

Integrin

Figure 6.29

A proteoglycan complex


• Functions of the ECM include

– Support

– Adhesion

– Movement

– Regulation


Plants: Plasmodesmata• Plasmodesmata

– Are channels that perforate plant cell walls

Interiorof cell

Interiorof cell

0.5 µm Plasmodesmata Plasma membranes

Cell walls

Figure 6.30


Animals: Tight Junctions, Desmosomes, and Gap Junctions

• In animals, there are three types of intercellular junctions

– Tight junctions

– Desmosomes

– Gap junctions


• Types of intercellular junctions in animals

Tight junctions prevent fluid from moving across a layer of cells

Tight junction

0.5 µm

1 µm

Spacebetweencells

Plasma membranesof adjacent cells

Extracellularmatrix

Gap junction

Tight junctions

0.1 µm

Intermediatefilaments

Desmosome

Gapjunctions

At tight junctions, the membranes ofneighboring cells are very tightly pressedagainst each other, bound together byspecific proteins (purple). Forming continu-ous seals around the cells, tight junctionsprevent leakage of extracellular fluid acrossA layer of epithelial cells.

Desmosomes (also called anchoringjunctions) function like rivets, fastening cellsTogether into strong sheets. IntermediateFilaments made of sturdy keratin proteinsAnchor desmosomes in the cytoplasm.

Gap junctions (also called communicatingjunctions) provide cytoplasmic channels fromone cell to an adjacent cell. Gap junctions consist of special membrane proteins that surround a pore through which ions, sugars,amino acids, and other small molecules maypass. Gap junctions are necessary for commu-nication between cells in many types of tissues,including heart muscle and animal embryos.

TIGHT JUNCTIONS

DESMOSOMES

GAP JUNCTIONS

Figure 6.31


The Cell: A Living Unit Greater Than the Sum of Its Parts

• Cells rely on the integration of structures and organelles in order to function

5 µm

Figure 6.32

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Chapter 6: A Tour of the Cell

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