Chapter 6: A Tour of the Cell

1. Studying Cells2. Intracellular Structures3. The Cytoskeleton4. Extracellular Structures

1. Studying Cells

10 m

1 m

0.1 m

1 cm

1 mm

100 µm

10 µm

1 µm

100 nm

10 nm

1 nm

0.1 nm Atoms

Small molecules

Lipids

Proteins

Ribosomes

VirusesSmallest bacteria

Mitochondrion

NucleusMost bacteria

Most plant and animal cells

Frog egg

Chicken egg

Length of some nerve and muscle cells

Human height

Una

ided

eye

Ligh

t mic

rosc

ope

Elec

tron

mic

rosc

ope

Concepts of Microscopy

MAGNIFICATION• factor by which the image produced is larger than the actual object (e.g. “100X”)

RESOLUTION• minimum distance acrosswhich 2 points can be resolved or seen distinctly(limited by wavelength)

CONTRAST• degree to which objects differ

from background

Limits of Resolution

Light Microscopy

a typical compound microscope such as used in your lab

(a) Brightfield(unstained specimen)

(b) Brightfield(stained specimen)

TECHNIQUE RESULTS

50 µm

Bright Field Microscopy

Standard form of Light Microscopy, poor contrast

Staining increases contrast,though the staining processusually kills the specimen

(c) Phase-contrast

(d) Differential-interference-contrast (Nomarski)

TECHNIQUE RESULTS

Phase Contrast Microscopy

Enhances misalignment of light waves to create contrast

A variation of phase-contrast microscopy involving a more complex

combination of filters and prisms.

Reveals internal detailwithout staining, useful

for viewing live specimens

(e) Fluorescence

TECHNIQUE RESULTS

50 µm

Fluorescence Microscopy

Fluorescent dyes or antibodies with a

fluorescent tag stick to specific targets which then fluoresce under UV light.

Only the objects or structures that fluoresce are visible.• objects that bind the fluorescent stain or antibody• objects that are naturally fluorescent

Confocal Fluorescence Microscopy

Only light from a given depth or plane is transmitted, “out of focus” light is excluded

(a) Scanning electronmicroscopy (SEM)

TECHNIQUE RESULTS

(b) Transmission electronmicroscopy (TEM)

Cilia

Longitudinalsection ofcilium

Cross sectionof cilium

1 µm

1 µmElectron

Microscopy

specimen cut in thin sections, higher

resolution

view of whole specimen, reveals surface features

Electromagnetic lenses focus electron beam onto heavy metal-stained specimen.

• electron beams have very short wavelengths

• allows far greater resolution than with light microscopy

Homogenization

TECHNIQUE

HomogenateTissuecells

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

10 min Differential centrifugationSupernatant 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

Fractionation by Centrifugation

In addition to microscopic examination, cells and their structures are also studied biochemically:

• in order to study a cellularcompartment biochemically,it must be separated from the rest of the cell

• this is accomplished through successive centrifugation steps at increasing speeds

Surface area increases whiletotal volume remains constant

5

11

6 150 750

125 1251

6 61.2

Total surface area[Sum of the surface areas(height ´ width) of all boxessides ´ number of boxes]

Total volume[height ´ width ´ length ´number of boxes]

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

Why are cells the size they are?

Why aren’t cells bigger?1) Cell size is limited by the rate of diffusion:• if cells get too large, it takes too much time for

nutrients, wastes, etc, to disperse in the cell

2) And also by the surface to volume ratio (S/V):surface area of sphere = 4pr2

volume of sphere = (4/3)pr3

*Surface Area increases by square of radius*Volume increases by cube of radius

***The larger the cell, the smaller the S/V ratio***

2. Intracellular Structures

Cells come in 2 basic types:1. Prokaryotic cells

(“before” nucleus)

• lack a nucleus & otherorganelles

• small, unicellular

• organisms in thefollowing domains:

Bacteria

diameter ~1-10 µm

Archaea

2. Eukaryotic cells (“true” nucleus)• have a nucleus, subcellular organelles• unicellular or multicellular

• Eukarya: Protists, Fungi , Plants & Animals• “large” (diameter ~10 µm – 1 mm)

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

Prokaryotic Cells

Have intracellular organization despite no organelles.

ENDOPLASMIC RETICULUM (ER)

Smooth ERRough ERFlagellum

Centrosome

CYTOSKELETON:Microfilaments

Intermediatefilaments

Microtubules

Microvilli

Peroxisome

MitochondrionLysosome

Golgiapparatus

Ribosomes

Plasma membrane

Nuclearenvelope

Nucleolus

Chromatin

NUCLEUS

Animal Cell

*not in plant cells

*

*

*

*

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)

The NucleusWhere genetic material (DNA) is stored, gene expression begins.

Nucleolus

where ribosomalsubunits areassembledfrom rRNA& proteins

Chromatincomplexof DNA &histoneproteins

Cytosol

Endoplasmic reticulum (ER)

Free ribosomes

Bound ribosomes

Large subunit

Small subunit

Diagram of a ribosomeTEM showing ER and ribosomes

0.5 µm

RibosomesCarry out protein synthesis by the process of translation.

Smooth ER

Rough ER Nuclear envelope

Transitional ER

Rough ERSmooth ERTransport vesicle

RibosomesCisternaeER lumen

200 nm

Endoplasmic Reticulum

Rough ER (RER)• ribosomes on cytoplasmicface of ER membrane synthesize proteins across ER membrane into lumen of ER

Smooth ER (SER)• has membrane-associated enzymes that catalyze new lipid synthesis(also found in RER),neutralizing toxins

• beginning of the secretorypathway

• storage of calcium ions

cis face(“receiving” side of Golgi

apparatus)Cisternae

trans face(“shipping” side of Golgi

apparatus)TEM of Golgi apparatus

0.1 µm

The Golgi apparatus

• proteins destined to leave ER are transported to the Golgi where they are modified, sorted and sent to various destinations. • polysaccharides are produced in the Golgi apparatus as well

Nucleus 1 µm

Lysosome

Digestiveenzymes

Lysosome

Plasmamembrane

Food vacuole

(a) Phagocytosis

Digestion

(b) Autophagy

Peroxisome

Vesicle

Lysosome

Mitochondrion

Peroxisomefragment

Mitochondrionfragment

Vesicle containingtwo damaged organelles

1 µm

Digestion

Lysosomes

• acidic compartments full of enzymes for the breakdown or digestion of foreign or waste material

Smooth ER

Nucleus

Rough ER

Plasma membrane

cis Golgi

trans Golgi

The Endomembrane System

aka the “Secretory

Pathway”

Free ribosomesin the mitochondrial matrix

Intermembrane spaceOuter membrane

Inner membraneCristae

Matrix

0.1 µm

Mitochondria

ATP production via cellular respiration• convert energy from glucose, fatty acids, etc, to energy in ATP

Have ribosomes

that resemble those of

prokaryotes

NUCLEUSNuclear envelopeNucleolusChromatin

Rough endoplasmic reticulum

Smooth endoplasmic reticulum

Ribosomes

Central vacuole

MicrofilamentsIntermediate filamentsMicrotubules

CYTO-SKELETON

Chloroplast

PlasmodesmataWall of adjacent cell

Cell wall

Plasma membrane

Peroxisome

Mitochondrion

Golgiapparatus

Plant Cell*

*

*

*

*not in animal cells

Central vacuole

Cytosol

Central vacuole

Nucleus

Cell wall

Chloroplast

5 µm

Central VacuolePlant organelle that stores water and various ions

Source of “turgorpressure” that maintains rigidity of plant cells

• swells when water is plentiful due to osmosis

• cell wall provides support, prevents lysis

Chloroplast

Stroma

Inner and outermembranes

Granum

Intermembranespace

ChloroplastsSite of photosynthesis in plant cells.

• production of glucose from CO2 and H2O using sunlight • the basis of essentially all ecosystems

Like mitochondria, have ribosomes and other components that resemble those of prokaryotes

1 µm

ChloroplastPeroxisome

Mitochondrion

PeroxisomesContain enzymes that oxidize (i.e., remove H) various organic molecules thus forming H2O2from O2

• H2O2 is then converted to O2 and H2O

Involved in the detoxification oftoxic substances, breakdown of fatty acids

3. The Cytoskeleton

Microtubule

Microfilaments0.25 µm

The CytoskeletonA complex, highly dynamic intracellular network of protein filaments largely responsible for:

• cell shape, rigidity • cell movement, motility

• localization of organelles

• movement of vesicles (and organelles)

• dynamics of cell division

3 Basic Cytoskeletal FilamentsActin filaments/microfilaments (MF) intermediate filaments (IF) microtubules (MT)

IF

MT

MF

Actin subunit

10 µm

7 nm

Microfilaments

5 µm

Keratin proteins

Fibrous subunit (keratinscoiled together)

8–12 nm

Intermediate Filaments

10 µm

Column of tubulin dimers

Tubulin dimera b

25 nm

Microtubules

VesicleATP

Receptor for motor protein

Microtubuleof cytoskeleton

Motor protein (ATP powered)

(a)

Microtubule Vesicles

(b)

0.25 µm

VesicleTransport

• a variety of motor proteins are involved in binding and transporting vesicles along cytoskeletalfibers to their destination

Centrosome

Microtubule

Centrioles0.25 µm

Longitudinal section of one centriole

Microtubules Cross sectionof the other centriole

Centrosomes• centrosomes contain a pair of centrioles(animal cells only)

• these structures are involved in the formation of the mitotic spindle or “spindle fibers” that play such an important role in cell division

5 µm

Direction of swimming

(a) Motion of flagella

Direction of organism’s movement

Power stroke

Recovery stroke

(b) Motion of cilia15 µm

Flagella & CiliaFLAGELLAare involved in cell motility, are very long, and cells have relatively few (1 or several)

CILIAare involved in motility, moving material across the cell surface, and are present on the cell surface in high numbers

4. Extracellular Structures

Secondary cell wall

Primary cell wall

Middle lamella

Central vacuoleCytosol

Plasma membrane

Plant cell walls

Plasmodesmata

1 µm

Plant Cell Walls

Interior of cell

Interior of cell

0.5 µm Plasmodesmata Plasma membranes

Cell walls

Plant cell walls contain fibers of cellulose and other polysaccharides as well as proteins

• one or more layers of secondary cell wall may be produced in some plant cells

Tight junction

0.5 µm

1 µmDesmosome

Gap junctionExtracellularmatrix

0.1 µm

Plasma membranesof adjacent cells

Spacebetweencells

Gapjunctions

Desmosome

Intermediatefilaments

Tight junction

Tight junctions preventfluid from movingacross a layer of cells

IntercellularJunctions

TIGHT JUNCTIONSare impenetrable seals connecting adjacent cells that prevent fluid and other materials from passing between the cells

DESMOSOMESare strong connections between cells that create a very strong sheet of cells

GAP JUNCTIONS (animal) & PLASMODESMATA (plant)provide channels through which ions & other small molecules can pass from cell to cell

Polysaccharide molecule

Carbohydrates

Core protein

Proteoglycanmolecule

Proteoglycan complex

Collagen

Fibronectin

Plasma membrane

Proteoglycan complex

Integrins

CYTOPLASMMicro-filaments

EXTRACELLULAR FLUID

The Extracellular MatrixA meshwork of protein fibers and polysaccharides that retain fluid and produce gel-like matrix that holds cells together in tissues.

Key Terms for Chapter 6

• Golgi apparatus, lysosome, peroxisome, vesicle

• mitochondria, chloroplasts

• endomembrane system, central vacuole

• prokaryotic vs eukaryotic

• nucleus, nucleolus, endoplasmic reticulum, ribosome

• cell wall, capsule, flagella, nucleoid, cytoplasm

• magnification, resolution, contrast

• bright field, phase contrast, fluorescent, confocal, transmission & scanning electron microscopy

• cytoskeleton, cilia, flagella, centrosome, centriole

• microtubules, microfilaments, intermediate filaments

• motor proteins

• tight junctions, gap junctions, desmosomes,plasmodesmata

• extracellular matrix, proteoglycan

Relevant Chapter Questions

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