Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings I-1- 1 EXPLORING LIFE & A...

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings I-1- 1

EXPLORING LIFE & A TOUR OF THE CELL


Exploring Life• Biology

– Is the scientific study of life

• We recognize life

– By what living things do

Figure 1.1


Some properties of life

(c) Response to the environment

(a) Order

(d) Regulation

(g) Reproduction (f) Growth and development

(b) Evolutionary adaptation

(e) Energy processing


From the biosphere to organisms

1 The biosphere


From cells to molecules

Cell

8 Cells

6 Organs and organ systems

7 Tissues

10 Molecules

9 Organelles

50 µm

10 µm

1 µm

Atoms

Figure 1.3


A Closer Look at Ecosystems

• Each organism

– Interacts with its environment

• Both organism and environment

– Are affected by the interactions between them


A Closer Look at Cells

• The cell

– Is the lowest level of organization that can perform all activities required for life

25 µmFigure 1.5


The Cell’s Heritable Information

• Cells contain chromosomes made partly of DNA, the substance of genes

– Which program the cells’ production of proteins and transmit information from parents to offspring

Egg cell

Sperm cell

NucleicontainingDNA

Fertilized eggwith DNA fromboth parents

Embyro’s cells with copies of inherited DNA Offspring with traits

inherited fromboth parentsFigure 1.6


The molecular structure of DNA

• Accounts for it information-rich nature

DNA

Cell

Nucleotide

ACTA

T

A

CC

G

G

TA

TA

(b) Single strand of DNA. These geometric shapes and letters are simple symbols for the nucleotides in a small section of one chain of a DNA molecule. Genetic information is encoded in specific sequences

of the four types of nucleotides (their names are abbreviated here as A, T, C, and G).

(a) DNA double helix. This model shows

each atom in a segment of DNA.Made up of two long chains of building blocks called nucleotides, a DNA molecule takes the three-dimensional form of a double helix.

Figure 1.7

Nucleus


Two Main Forms of Cells

• All cells share certain characteristics

– They are all enclosed by a membrane

– They all use DNA as genetic information

• There are two main forms of cells

– Eukaryotic

– Prokaryotic


• Eukaryotic cells

– Are subdivided by internal membranes into various membrane-enclosed organelles

• Prokaryotic cells

– Lack the kinds of membrane-enclosed organelles found in eukaryotic cells


EUKARYOTIC CELL

Membrane

Cytoplasm

Organelles

Nucleus (contains DNA) 1 µm

PROKARYOTIC CELL

DNA

(no nucleus)Membrane

Figure 1.8


Biologists explore life across its great diversity of species

• Diversity is a hallmark of life

Figure 1.13


Grouping Species: The Basic Idea

• Taxonomy

– Is the branch of biology that names and classifies species according to a system of broader and broader groups


Classifying life

Species Genus Family Order Class Phylum Kingdom Domain

Mammalia

Ursusameri-canus(Americanblack bear)

Ursus

Ursidae

Carnivora

Chordata

Animalia

EukaryaFigure 1.14


The Three Domains of Life

• At the highest level, life is classified into three domains

– Bacteria

– Archaea

– Eukarya

• Domain Bacteria and domain Archaea

– Consist of prokaryotes

• Domain Eukarya, the eukaryotes

– Includes the various protist kingdoms and the kingdoms Plantae, Fungi, and Animalia


Life’s three domains

Figure 1.15

100 µm

0.5 µm

4 µmBacteria are the most diverse and widespread prokaryotes and are now divided among multiple kingdoms. Each of the rod-shapedstructures in this photo is a bacterial cell.

Protists (multiple kingdoms)are unicellular eukaryotes and their relatively simple multicellular relatives.Pictured here is an assortment of protists inhabiting pond water. Scientists are currently debating how to split the protistsinto several kingdoms that better represent evolution and diversity.

Kingdom Plantae consists of multicellula eukaryotes that carry out photosynthesis, the conversion of light energy to food.

Many of the prokaryotes known as archaea live in Earth‘s extreme environments, such as salty lakes and boiling hot springs. Domain Archaea includes multiple kingdoms. The photoshows a colony composed of many cells.

Kindom Fungi is defined in part by thenutritional mode of its members, suchas this mushroom, which absorb nutrientsafter decomposing organic material.

Kindom Animalia consists of multicellular eukaryotes thatingest other organisms.

DOMAIN ARCHAEA


Unity in the Diversity of Life

• As diverse as life is

– There is also evidence of remarkable unity

Cilia of Paramecium.The cilia of Parameciumpropel the cell throughpond water.

Cross section of cilium, as viewedwith an electron microscope

15 µm

1.0 µm

5 µm

Cilia of windpipe cells. The cells that line the human windpipe are equipped with cilia that help keep the lungs clean by moving a film of debris-trapping mucus upward.


A Tour of the CellOverview: The Importance of Cells

• 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


To study cells, biologists use microscopes and the tools of biochemistry

• Different types of microscopes

– Can be used to visualize different sized cellular structures

Una

ide

d e

ye

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

Lig

ht m

icro

sco

pe

Ele

ctro

n m

icro

sco

pe

Ele

ctro

n m

icro

sco

pe

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


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


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)


Electron microscopes (EMs)

• 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)

Cilia1 µm


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


Isolating Organelles by Cell Fractionation

Tissuecells

Homogenization

Homogenate1000 g(1000 times theforce of gravity)

10 min Differential centrifugation

Supernatant 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


Comparing Prokaryotic and Eukaryotic Cells

• All cells have several basic features in common

– They are bounded by a plasma membrane

– They contain a semifluid substance called the cytosol

– They contain chromosomes

– They all have ribosomes


Prokaryotic cells: Do not contain a nucleus; Have their DNA located in a region called the nucleoid.

(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


Eukaryotic cells: Contain a true nucleus, bounded by a membranous nuclear envelope; Are generally quite a bit bigger than prokaryotic cells

• The plasma membrane:

Functions as a selective barrier

Allows sufficient passage

of nutrients and waste

Carbohydrate side chain

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 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


A plant cell

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

CYTOSKELETON

Ribosomes (small brwon dots)

Central vacuole

Microfilaments


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


Concept : The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes

• 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 membrane

Outer membrane

Nuclear pore

Rough ER

Porecomplex

Surface of nuclear envelope.

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

Close-up of nuclearenvelope

Ribosome

1 µm

1 µm

0.25 µm


Ribosomes: Protein Factories in the Cell

– Are particles made of ribosomal RNA and protein; Carry out protein synthesis

ER

Endoplasmic reticulum (ER)

Ribosomes Cytosol

Free ribosomes

Bound ribosomes

Largesubunit

Smallsubunit

TEM showing ER and ribosomes Diagram of a ribosome

0.5 µm


Concept : The endomembrane system regulates protein traffic and performs metabolic functions in the cell

• The endomembrane system

– Includes many different structures


The Endoplasmic Reticulum: Biosynthetic Factory

Accounts for more than half the total membrane in many eukaryotic cells

• The ER membrane

Is continuous with the

nuclear envelope

Smooth ER

Rough ER

ER lumenCisternae

RibosomesTransport vesicle

Smooth ER

Transitional ER

Rough ER 200 µm

Nuclearenvelope


There are two distinct regions of ER

– Smooth ER, which lacks ribosomes

– Rough ER, which contains ribosomes

• The smooth ER: Synthesizes lipids; Metabolizes carbohydrates; Stores calcium; Detoxifies poison

• 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


Lysosomes: Digestive Compartments

Membranous sac of hydrolytic enzymes; Can digest all kinds of macromolecules

• 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


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


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

The Endomembrane System: A Review

• Relationships among organelles of the endomembrane system


Concept: 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: Chemical Energy Conversion

• Are found in nearly all eukaryotic cells

• Mitochondria are enclosed by two membranes

– A smooth outer membrane; An inner membrane folded into cristae

Mitochondrion

Intermembrane space

Outermembrane

Freeribosomesin the mitochondrialmatrix

MitochondrialDNA

Innermembrane

Cristae

Matrix

100 µm


Chloroplasts: Capture of Light Energy

• The chloroplast is a specialized member of a family of closely related plant organelles called plastids

– Contains chlorophyll; Are found in leaves and other green organs of plants and in algae

Chloroplast

ChloroplastDNA

RibosomesStroma

Inner and outermembranes

Thylakoid

1 µm

Granum


Peroxisomes: Oxidation

– Produce hydrogen peroxide and convert it to water

ChloroplastPeroxisome

Mitochondrion

1 µm


Concept: The cytoskeleton is a network of fibers that organizes structures and activities in the cell

• Cytoskeleton is a network of fibers extending throughout the cytoplasm

Microtubule

0.25 µm Microfilaments


Roles of the Cytoskeleton: Support, Motility, and Regulation

– Is involved in cell motility, which utilizes motor proteins

VesicleATP

Receptor 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.)


Components of the Cytoskeleton

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


Microtubules

– Shape the cell

– Guide movement of organelles

– Help separate the chromosome copies in dividing cells


Centrosomes and Centrioles

• The centrosome is considered to be a “microtubule-organizing center”; Contains a pair of centrioles

Centrosome

Microtubule

Centrioles

0.25 µm

Longitudinal sectionof one centriole

Microtubules Cross sectionof the other centrioleFigure 6.22


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


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).

15 µm


Cilia and flagella share a common ultrastructure

(a)

(c)

(b)

Outer microtubuledoublet

Dynein arms

Centralmicrotubule

Outer 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


Microfilaments (Actin Filaments)

– Are built from molecules of the protein actin

– Are found in microvilli

0.25 µm

Microvillus

Plasma membrane

Microfilaments (actinfilaments)



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


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 movement


Cell Walls of Plants

– 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 layers

Central vacuoleof cell

Plasmamembrane

Secondarycell wall

Primarycell wall

Middlelamella

1 µm

Centralvacuoleof cell

Central vacuole Cytosol

Plasma membrane

Plant cell walls

Plasmodesmata


The Extracellular Matrix (ECM) of Animal Cells

• Animal cells lack cell walls and covered by an elaborate matrix, the ECM.

– Is made up of glycoproteins and other macromolecules

Collagen

Fibronectin

Plasmamembrane

EXTRACELLULAR FLUID

Micro-filaments

CYTOPLASM

Integrins

Polysaccharidemolecule

Carbo-hydrates

Proteoglycanmolecule

Coreprotein

Integrin

A proteoglycan complex


Functions of the ECM include

– Support

– Adhesion

– Movement

– Regulation


Intercellular Junctions

– Plants: Plasmodesmata

– Are channels that perforate plant cell walls

Interiorof cell

Interiorof cell

0.5 µm Plasmodesmata Plasma membranes

Cell walls


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


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 µ

m

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