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A Tour of the Cell Chapter 6

You should be able to:

1. Distinguish between the following pairs of

terms: magnification and resolution;

prokaryotic and eukaryotic cell; free and bound

ribosomes; smooth and rough ER

2. Describe the structure and function of the

components of the endomembrane system

3. Briefly explain the role of mitochondria,

chloroplasts, and peroxisomes

4. Describe the functions of the cytoskeleton

5. Compare the structure and functions of

microtubules, microfilaments, and intermediate

filaments

6. Explain how the ultrastructure of cilia and

flagella relate to their functions

7. Describe the structure of a plant cell wall

8. Describe the structure and roles of the

extracellular matrix in animal cells

9. Describe four different intercellular junctions

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BioFlix Animal Cell Movie

Overview: The Fundamental Units

of Life

o All organisms are made of cells

o The cell is the simplest collection of matter

that can be alive

o Cell structure is correlated to cellular function

o Though usually too small to be seen by the

unaided eye, cells are complex

Microscopy

o Scientists use microscopes

to visualize cells too small

to see with the naked eye

o In a light microscope

(LM), visible light passes

through a specimen and

then through glass lenses,

which magnify the image

o Lenses refract (bend) the

light, so that the image is

magnified

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o The quality of an image depends on

oMagnification, the ratio of an objects image size to its real size

oResolution, the measure of the clarity of the image, or the minimum distance of two distinguishable points

oContrast, visible differences in parts of the sample

Brightfield Phase Contrast Hoffman mod-

ulation contrast

o LMs can magnify effectively to about 1,000 times the size of the actual specimen

o Various techniques enhance contrast and enable cell components to be stained or labeled

o Most subcellular structures, including organelles (membrane-enclosed

compartments), are too small to be resolved by an LM

10 m

1 m

0.1 m

1 cm

1 mm

100 m

10 m

1 m

100 nm

10 nm

1 nm

0.1 nm Atoms

Small molecules

Lipids

Proteins

Ribosomes

Viruses

Smallest bacteria

Mitochondrion

Nucleus

Most bacteria

Most plant and animal cells

Frog egg

Chicken egg

Length of some nerve and muscle cells

Human height

Un

aid

ed

eye

Lig

ht

mic

ros

co

pe

Ele

ctr

on

mic

ros

co

pe

(unstained specimen)

50

m

Brightfield

Brightfield

(stained specimen)

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(unstained specimen)

50

m

Brightfield

Phase-contrast

(unstained specimen)

50

m

Brightfield

Differential-interference-

contrast (Nomarski)

Super-resolution

Fluorescence

Confocal

Deconvolution

Cilia

Scanning electron

microscopy (SEM)

Longitudinal section

of cilium

Cross section

of cilium

Transmission electron

microscopy (TEM)

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o Two basic types of electron

microscopes (EMs) are used to

study subcellular structures

o Scanning electron microscopes

(SEMs) focus a beam of electrons

onto the surface of a specimen,

providing images that look 3-D

o Transmission electron

microscopes (TEMs) focus a

beam of electrons through a

specimen

o TEMs are used mainly to study the

internal structure of cells

Cilia

o Recent advances in light microscopy o Confocal microscopy and deconvolution

microscopy provide sharper images of three-

dimensional tissues and cells

o New techniques for labeling cells improve

resolution

Deconvolution

Confocal

Cell Fractionation

o Cell fractionation takes cells apart and

separates the major organelles from one

another

o Centrifuges fractionate cells into their

component parts

o Cell fractionation enables scientists to determine

the functions of organelles

o Biochemistry and cytology help correlate cell

function with structure

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Figure 6.4 TECHNIQUE

Homogenization

Tissue

cells

Homogenate

Centrifugation

Differential

centrifugation

Centrifuged at

1,000 g

(1,000 times the

force of gravity)

for 10 min Supernatant

poured into

next tube

20,000 g

20 min

80,000 g

60 min Pellet rich in

nuclei and

cellular debris

150,000 g

3 hr

Pellet rich in

mitochondria

(and chloro-

plasts if cells

are from a plant)

Pellet rich in

microsomes

(pieces of plasma

membranes and

cells internal

membranes) Pellet rich in

ribosomes

Prokaryotic and Eukaryotic Cells

o Basic features of ALL cells (EUK and PROK)

1. Plasma membrane (the outer border, a phospholipid bilayer)

2. Semifluid substance called cytosol inside

3. DNA/Chromosomes (carry genes)

4. Ribosomes (make proteins)

o The basic cell(s) of every organism is either

prokaryotic or eukaryotic

o Only organisms of the domains Bacteria and Archaea

consist of prokaryotic cells

o Protists, fungi, animals, and plants all consist of

eukaryotic cells

o Prokaryotic cells are characterized by

having:

oNo nucleus

oDNA in an unbound region called the nucleoid

oNo membrane-bound organelles (none surrounded by a phospholipid membrane)

oCytoplasm bound by the plasma membrane

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Fimbriae

Bacterial

chromosome

A typical rod-shaped bacterium

(a)

Nucleoid

Ribosomes

Plasma

membrane

Cell wall

Capsule

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

(b)

0.5 m

Figure 6.5

o Eukaryotic cells have internal membranes that compartmentalize their functions

oOrganelles

o Eukaryotic cells are characterized by having

oDNA in a nucleus that is bounded by a membranous nuclear envelope

oMembrane-bound organelles

oCytoplasm in the region between the plasma membrane and nucleus

o Eukaryotic cells are generally much larger than prokaryotic cells

Eukaryotic Cell

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o The plasma membrane is a selective

barrier that allows sufficient passage of

oxygen, nutrients, and waste to service the

volume of every cell

o The general structure of a biological

membrane is a double layer of

phospholipids

Figure 6.6

Outside of cell

Inside of cell 0.1 m

(a) TEM of a plasma membrane

Hydrophilic region

Hydrophobic region

Hydrophilic region

Carbohydrate side chains

Proteins Phospholipid

(b) Structure of the plasma membrane

o Metabolic requirements set upper limits on

the size of cells

o The surface area to volume ratio of a cell is

critical

o As the surface area increases by a factor of

n2, the volume increases by a factor of n3

o Small cells have a greater surface area

relative to volume

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Surface area increases while

total volume remains constant

Total surface area [sum of the surface areas (height width) of all box sides number of boxes]

Total volume [height width length number of boxes]

Surface-to-volume (S-to-V) ratio [surface area volume]

1

5

6 150 750

1

125 125 1

1.2 6 6

Figure 6.7

A Panoramic View of the

Eukaryotic Cell

o A eukaryotic cell has internal membranes that

partition the cell into organelles

o Plant and animal cells have most of the same

organelles

BioFlix: Tour of an Animal Cell

BioFlix: Tour of a Plant Cell

Figure 6.8a

ENDOPLASMIC RETICULUM (ER)

Rough ER

Smooth ER

Nuclear envelope

Nucleolus

Chromatin

Plasma membrane

Ribosomes

Golgi apparatus

Lysosome Mitochondrion

Peroxisome

Microvilli

Microtubules

Intermediate filaments

Microfilaments

Centrosome

CYTOSKELETON:

Flagellum NUCLEUS

Animal Cell

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NUCLEUS

Nuclear envelope

Nucleolus

Chromatin

Golgi apparatus

Mitochondrion

Peroxisome

Plasma membrane

Cell wall

Wall of adjacent cell

Plasmodesmata

Chloroplast

Microtubules

Intermediate filaments

Microfilaments

CYTOSKELETON

Central vacuole

Ribosomes

Smooth endoplasmic reticulum

Rough endoplasmic

reticulum

Figure 6.8c

Plant Cell

The eukaryotic cells genetic instructions are housed in the nucleus

and carried out by the ribosomes

o The nucleus contains most of the DNA in a

eukaryotic cell

o Ribosomes use the information from the

DNA to make proteins

o The nucleus contains most of the cells genes and is usually the most conspicuous organelle

o The nuclear envelope encloses the nucleus,

separating it from the cytoplasm

o The nuclear membrane is a double membrane;

each membrane consists of a lipid bilayer

The Nucleus: Information Central

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Nucleus

Rough ER

Nucleolus

Chromatin

Nuclear envelope:

Inner membrane

Outer membrane

Nuclear pore

Ribosome

Pore complex

Close-up of nuclear envelope

Surface of nuclear envelope

Pore complexes (TEM)

0.2

5

m

1

m

Nuclear lamina (TEM)

Chromatin

1 m

Figure 6.9

o Pores regulate the entry and exit of

molecules from the nucleus

o The shape of the nucleus is maintained by

the nuclear lamina, which is composed of

protein

oNetwork of strong fibers (intermediate fibers)

o In the nucleus, DNA is organized into discrete units

called chromosomes

o Each chromosome is composed of a single DNA

molecule associated with proteins

o The DNA and proteins of chromosomes are together

called chromatin

o Chromatin condenses to form discrete chromosomes

as a cell prepares to divide

o The nucleolus is located within the nucleus and is the

site of ribosomal RNA (rRNA) synthesis

Chromosomes

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Ribosomes: Protein Factories

o Ribosomes are particles made of ribosomal

RNA and protein

o Ribosomes carry out protein synthesis in two

locations:

o In the cytosol (free ribosomes)

omake proteins that stay within the cell

oOn the outside of the endoplasmic reticulum or the

nuclear envelop (bound ribosomes)

omake proteins that will incorporate into the plasma

membrane or proteins that are secreted from the cell

Fig. 6-11

Cytosol

Endoplasmic reticulum (ER)

Free ribosomes

Bound ribosomes

Large subunit

Small subunit

Diagram of a ribosome TEM showing ER and ribosomes

0.5 m

The endomembrane system regulates

protein traffic & performs metabolic

functions in the cell

o Components of the endomembrane system:

oNuclear envelope

o Endoplasmic reticulum

oGolgi apparatus

o Lysosomes

o Vacuoles

o Plasma membrane

o These components are either continuous with

each other OR connected via transfer by vesicles

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o The endoplasmic reticulum (ER) accounts for

more than half of the total membrane in many

eukaryotic cells

o The ER membrane is continuous with the nuclear

envelope

o There are 2 distinct regions: of ER:

o Smooth ER, which lacks ribosomes

o Rough ER, surface is studded with

ribsosomes

The Endoplasmic Reticulum: Biosynthetic Factory

Figure 6.11 Smooth ER

Rough ER

ER lumen

Cisternae Ribosomes

Smooth ER

Transport vesicle

Transitional ER

Rough ER 200 nm

Nuclear

envelope

Functions of ER o The smooth ER

o Synthesizes lipids

o Metabolizes carbohydrates

o Detoxifies poison

o Stores calcium

o The rough ER

o Has bound ribosomes, which secrete glycoproteins

(proteins covalently bonded to carbohydrates)

o Distributes transport vesicles, proteins surrounded

by membranes

o Is a membrane factory for the cell

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o The Golgi apparatus consists of flattened

membranous sacs called cisternae

o Functions:

oModifies products of the ER

oManufactures certain macromolecules

o Sorts and packages materials into transport vesicles

The Golgi Apparatus: Shipping and Receiving Center

Lysosomes:

Digestive Compartments

o A lysosome is a membranous sac of

hydrolytic enzymes that can digest

macromolecules

o Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids

o Lysosomal enzymes work best in the acidic environment inside the lysosome

o Some types of cell can engulf another cell by phagocytosis; this forms a food vacuole

o A lysosome fuses with the food vacuole and digests the molecules

o Lysosomes also use enzymes to recycle the cells own organelles and macromolecules, a process called autophagy

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Figure 6.13

Nucleus

Lysosome

1 m

Digestive

enzymes

Digestion

Food vacuole

Lysosome

Plasma membrane

(a) Phagocytosis

Vesicle containing

two damaged

organelles 1 m

Mitochondrion

fragment

Peroxisome

fragment

(b) Autophagy

Peroxisome

Vesicle Mitochondrion

Lysosome

Digestion

o A plant cell or fungal cell may have one or several vacuoles, derived from the ER or Golgi apparatus

o Food vacuoles are formed by phagocytosis

o Contractile vacuoles, found in many

freshwater protists, pump excess water out of

cells

o Central vacuoles, found in many mature plant

cells, hold organic compounds and water

Vacuoles: Diverse Maintenance Compartments

Figure 6.14

Central vacuole

Cytosol

Nucleus

Cell wall

Chloroplast

Central

vacuole

5 m

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The Endomembrane System: A

Review o The endomembrane system is a complex and

dynamic player in the cells compartmental organization

Figure 6.15-1

Smooth ER

Nucleus

Rough ER

Plasma

membrane

Figure 6.15-2

Smooth ER

Nucleus

Rough ER

Plasma

membrane

cis Golgi

trans Golgi

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Figure 6.15-3

Smooth ER

Nucleus

Rough ER

Plasma

membrane

cis Golgi

trans Golgi

Mitochondria and Chloroplasts change

energy from one form to another

o Mitochondria are the sites of cellular

respiration, a metabolic process that

generates ATP

o Chloroplasts, found in plants and algae,

are the sites of photosynthesis

o Peroxisomes are oxidative organelles

o Mitochondria and chloroplasts have

similarities with bacteria:

o (Are not part of the endomembrane system)

oHave a double membrane (2 membranes with a

space between)

oContain free ribosomes and circular DNA

molecules

oGrow and reproduce somewhat independently

in cells

The Evolutionary Origins of

Mitochondria and Chloroplasts

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o The Endosymbiont theory

o An early ancestor of eukaryotic cells engulfed

a nonphotosynthetic prokaryotic cell, which

formed an endosymbiont relationship with its

host

o The host cell and endosymbiont merged into

a single organism, a eukaryotic cell with a

mitochondrion

o At least one of these cells may have taken up

a photosynthetic prokaryote, becoming the

ancestor of cells that contain chloroplasts

Nucleus Endoplasmic

reticulum

Nuclear

envelope

Ancestor of

eukaryotic cells

(host cell)

Engulfing of oxygen-

using nonphotosynthetic

prokaryote, which

becomes a mitochondrion

Mitochondrion

Nonphotosynthetic

eukaryote

Mitochondrion

At least

one cell

Photosynthetic eukaryote

Engulfing of

photosynthetic

prokaryote

Chloroplast

Figure 6.16

Mitochondria: Chemical Energy Conversion

o Mitochondria are in nearly all eukaryotic cells

o They have a smooth outer membrane and an

inner membrane folded into cristae

o The inner membrane creates two compartments:

intermembrane space and mitochondrial matrix

o Some metabolic steps of cellular respiration are

catalyzed in the mitochondrial matrix

o Cristae present a large surface area for enzymes

that synthesize ATP

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Figure 6.17

Intermembrane space

Outer

membrane

DNA

Inner

membrane

Cristae

Matrix

Free

ribosomes

in the

mitochondrial

matrix

(a) Diagram and TEM of mitochondrion (b) Network of mitochondria in a protist

cell (LM)

0.1 m

Mitochondrial

DNA

Nuclear DNA

Mitochondria

10 m

Chloroplasts: Capture of Light Energy

o Chloroplasts are found in leaves and other green organs of plants and in algae

o The chloroplast is a member of a family of organelles called plastids

o Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis

o Produce Sugars

o Typically used by Mitochondria

oChloroplast structure includes:

oThylakoids, membranous sacs, stacked to form a granum

oStroma, the internal fluid

Ribosomes

Stroma

Inner and outer

membranes

Granum

1 m Intermembrane space Thylakoid

(a) Diagram and TEM of chloroplast (b) Chloroplasts in an algal cell

Chloroplasts

(red)

50 m

DNA

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Peroxisomes: Oxidation

o Peroxisomes are specialized metabolic compartments bounded by a single membrane

o Peroxisomes a) produce hydrogen peroxide (H2O2) and b) convert it to water (H2O)

o Used to metabolize other foods (like fatty acids) & toxins

o How peroxisomes are related to other organelles is still unknown

The Cytoskeleton is a network of fibers that

organizes structures and activities in the cell

o The cytoskeleton is a network of fibers

extending throughout the cytoplasm

o It organizes the cells structures and activities, anchoring many organelles

o It is composed of three types of molecular

structures: oMicrotubules

oMicrofilaments

o Intermediate filaments

Microtubule

Microfilaments

Roles of the Cytoskeleton:

Support, Motility, and Regulation

o The cytoskeleton helps to support the cell

and maintain its shape

o It interacts with motor proteins to produce

motility

o Inside the cell, vesicles can travel along

monorails provided by the cytoskeleton

o Recent evidence suggests that the

cytoskeleton may help regulate biochemical

activities

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Components of the

Cytoskeleton

o Three main types of fibers make up the

cytoskeleton:

oMicrotubules are the thickest of the three

components of the cytoskeleton

oMicrofilaments, also called actin filaments, are

the thinnest components

o Intermediate filaments are fibers with diameters

in a middle range

Column of tubulin dimers

Tubulin dimer

25 nm

Actin subunit

7 nm

Keratin proteins

812 nm

Fibrous subunit (keratins

coiled together)

10 m 10 m 5 m

Table 6.1

Microtubules

o Microtubules are hollow rods about 25

nm in diameter and about 200 nm to 25

microns long

o Functions of microtubules:

o Shaping the cell

oGuiding movement of organelles

o Separating chromosomes during cell division

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Tubulin dimer

25 nm

Column of tubulin dimers

10 m

Table 6.1a

Centrosomes and Centrioles

o In many cells, microtubules grow out from a

centrosome near the nucleus

o The centrosome is a microtubule-organizing center

o In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring

Cilia and Flagella

o Microtubules control the beating of cilia and flagella, locomotor appendages of some cells

o Cilia and flagella differ in their beating patterns (& length)

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Fig. 6-23

5 m

Direction of swimming

(a) Motion of flagella

Direction of organisms movement

Power stroke Recovery stroke

(b) Motion of cilia 15 m

Cilia and flagella share common

ultrastructure:

o A core of microtubules sheathed by the plasma

membrane

o A basal body that anchors the cilium or

flagellum

o A motor protein called dynein, which drives the

bending movements of a cilium or flagellum

Fig. 6-24

0.1 m

Triplet

(c) Cross section of basal body

(a) Longitudinal section of cilium

0.5 m

Plasma membrane

Basal body

Microtubules

(b) Cross section of cilium

Plasma membrane

Outer microtubule doublet

Dynein proteins

Central microtubule

Radial spoke

Protein cross-linking outer doublets

0.1 m

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o How dynein walking moves flagella and cilia:

oDynein arms alternately grab, move, and release the outer microtubules

o Protein cross-links limit sliding

o Forces exerted by dynein arms cause doublets to curve, bending the cilium or flagellum

Animation: Cilia and Flagella

Microtubule doublets

Dynein protein

ATP

ATP

(a) Effect of unrestrained dynein movement

Cross-linking proteins inside outer doublets

Anchorage in cell

(b) Effect of cross-linking proteins

1 3

2

(c) Wavelike motion

Microfilaments (Actin Filaments)

o Microfilaments are solid rods about 7 nm in

diameter, built as a twisted double chain of

actin subunits

o The structural role of microfilaments is to bear tension, resisting pulling forces within the cell

o They form a 3-D network called the cortex just inside the plasma membrane to help support the cells shape

o Bundles of microfilaments make up the core of microvilli of intestinal cells

o Microfilaments that function in cellular

motility contain the protein myosin in

addition to actin

o In muscle cells, thousands of actin filaments

are arranged parallel to one another

o Thicker filaments composed of myosin

interdigitate with the thinner actin fibers

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o Localized contraction brought about by actin and

myosin also drives amoeboid movement

o Pseudopodia (cellular extensions) extend and

contract through the reversible assembly and

contraction of actin subunits into microfilaments

o Cytoplasmic streaming is a circular flow of

cytoplasm within cells

o This streaming speeds distribution of

materials within the cell

o In plant cells, actin-myosin interactions and

sol-gel transformations drive cytoplasmic

streaming

Video: Cytoplasmic Streaming

10 m

Actin subunit

7 nm

Table 6.1b

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Intermediate Filaments

o Intermediate filaments range in diameter

from 812 nanometers, larger than microfilaments but smaller than

microtubules

o They support cell shape and fix organelles

in place

o Intermediate filaments are more permanent

cytoskeleton fixtures than the other two

classes

5 m

Keratin proteins

Fibrous subunit (keratins

coiled together)

812 nm

Table 6.1c

Extracellular components and

connections between cells help

coordinate cellular activities

o Most cells synthesize and secrete materials

that are external to the plasma membrane

o These extracellular structures include:

oCell walls of plants

o The extracellular matrix (ECM) of animal cells

o Intercellular junctions

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Cell Walls of Plants

o The cell wall is an extracellular structure that distinguishes plant cells from animal cells

o Prokaryotes, fungi, and some protists also have cell walls

o The cell wall:

o protects the plant cell

omaintains its shape

o prevents excessive uptake of water

o Plant cell walls are made of cellulose fibers embedded in other polysaccharides and protein

o Plant cell walls may have multiple layers:

o Primary cell wall: relatively thin and flexible

oMiddle lamella: thin layer between primary

walls of adjacent cells

o Secondary cell wall (in some cells): added

between the plasma membrane and the primary

cell wall

o Plasmodesmata are channels between adjacent

plant cells

The Extracellular Matrix (ECM) of

Animal Cells

o Animal cells lack cell walls, but are covered by an

elaborate extracellular matrix (ECM)

o The ECM is made up of glycoproteins such as

collagen, proteoglycans, and fibronectin

o ECM proteins bind to receptor proteins in the

plasma membrane called integrins

o Functions of the ECM: o Support o Adhesion o Movement o Regulation

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Fig. 6-30

EXTRACELLULAR FLUID Collagen

Fibronectin

Plasma membrane

Micro- filaments

CYTOPLASM

Integrins

Proteoglycan complex

Polysaccharide

molecule

Carbo- hydrates

Core protein

Proteoglycan molecule

Proteoglycan complex

Intercellular Junctions

o Neighboring cells in tissues, organs, or organ

systems often adhere, interact, and

communicate through direct physical contact

o Intercellular junctions facilitate this contact

o There are several types of intercellular

junctions

o Plasmodesmata

o Tight junctions

oDesmosomes

oGap junctions

Plasmodesmata in Plant Cells

Interior of cell

Interior of cell

0.5 m Plasmodesmata Plasma membranes

Cell walls

o 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

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Tight Junctions, Desmosomes, and

Gap Junctions in Animal Cells

o At tight junctions, membranes of neighboring

cells are pressed together, preventing leakage

of extracellular fluid

o Desmosomes (anchoring junctions) fasten

cells together into strong sheets

o Gap junctions (communicating junctions)

provide cytoplasmic channels between

adjacent cells

o Ions can flow

Fig. 6-32

Tight junction

0.5 m

1 m Desmosome

Gap junction

Extracellular matrix

0.1 m

Plasma membranes of adjacent cells

Space between cells

Gap

junctions

Desmosome

Intermediate filaments

Tight junction

Tight junctions prevent fluid from moving across a layer of cells

The Cell: A Living Unit Greater

Than the Sum of Its Parts

o Cells rely on the integration of structures

and organelles in order to function

o For example, a macrophages ability to destroy bacteria involves the whole cell,

coordinating components such as the

cytoskeleton, lysosomes, and plasma

membrane

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Figure 6.UN01

Nucleus

(ER)

(Nuclear

envelope)

Figure 6.UN01a

Nucleus

(ER)

Figure 6.UN01b

(Nuclear

envelope)

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Figure 6.UN01c