11/7/2016

1

Chapter 6:

A Tour of the Cell

1. Studying Cells

2. Intracellular Structures

3. The Cytoskeleton

4. 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

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

Concepts of

Microscopy MAGNIFICATION

• factor by which the image

produced is larger than the

actual object (e.g. “100X”)

RESOLUTION

• minimum distance across

which 2 points can be resolved

or seen distinctly

(limited by wavelength)

CONTRAST

• degree to which objects differ

from background

Limits of Resolution

11/7/2016

2

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 process

usually 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 detail

without staining, useful

for viewing live specimens

11/7/2016

3

(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 electron

microscopy (SEM)

TECHNIQUE RESULTS

(b) Transmission electron

microscopy (TEM)

Cilia

Longitudinal

section of

cilium

Cross section

of cilium 1 µm

1 µm Electron

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

11/7/2016

4

Homogenization

TECHNIQUE

Homogenate Tissue cells

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

10 min Differential centrifugation

Supernatant poured into next tube

20,000 g

20 min

80,000 g

60 min Pellet rich in nuclei and cellular debris

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)

150,000 g

3 hr

Pellet rich in ribosomes

Fractionation by

Centrifugation

In addition to microscopic

examination, cells and their

structures are also studied

biochemically:

• in order to study a cellular

compartment biochemically,

it must be separated from

the rest of the cell

• this is accomplished through

successive centrifugation

steps at increasing speeds

Surface area increases while

total volume remains constant

5

1

1

6 150 750

125 125 1

6 6 1.2

Total surface area

[Sum of the surface areas

(height width) of all boxes

sides 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***

11/7/2016

5

2. Intracellular Structures

Cells come in 2 basic types:

1. Prokaryotic cells

(“before” nucleus)

• lack a nucleus & other

organelles

• small, unicellular

• organisms in the

following domains:

Bacteria

diameter ~1-10 mm

Archaea

2. Eukaryotic cells (“true” nucleus)

• have a nucleus, subcellular organelles

• unicellular or multicellular

• Eukarya: Protists, Fungi , Plants & Animals

• “large” (diameter ~10 mm – 1 mm)

11/7/2016

6

Fimbriae

Nucleoid

Ribosomes

Plasma membrane

Cell wall

Capsule

Flagella

Bacterial chromosome

(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 ER Rough ER Flagellum

Centrosome

CYTOSKELETON:

Microfilaments

Intermediate filaments

Microtubules

Microvilli

Peroxisome

Mitochondrion Lysosome

Golgi apparatus

Ribosomes

Plasma membrane

Nuclear envelope

Nucleolus

Chromatin

NUCLEUS

Animal Cell

* not in plant cells

*

*

*

*

Nucleolus

Nucleus

Rough ER

Nuclear lamina (TEM)

Close-up of nuclear envelope

1 µm

1 µm

0.25 µm

Ribosome

Pore complex

Nuclear pore

Outer membrane Inner membrane

Nuclear envelope:

Chromatin

Surface of nuclear envelope

Pore complexes (TEM)

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

Nucleolus

where

ribosomal

subunits are

assembled

from rRNA

& proteins

Chromatin

complex

of DNA &

histone

proteins

11/7/2016

7

Cytosol

Endoplasmic reticulum (ER)

Free ribosomes

Bound ribosomes

Large subunit

Small subunit

Diagram of a ribosome TEM showing ER and ribosomes

0.5 µm

Ribosomes Carry out protein synthesis by the process of translation.

Smooth ER

Rough ER Nuclear envelope

Transitional ER

Rough ER Smooth ER

Transport vesicle

Ribosomes Cisternae

ER lumen

200 nm

Endoplasmic

Reticulum

Rough ER (RER)

• ribosomes on cytoplasmic

face 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 secretory

pathway

• 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

11/7/2016

8

Nucleus 1 µm

Lysosome

Digestive

enzymes Lysosome

Plasma

membrane

Food vacuole

(a) Phagocytosis

Digestion

(b) Autophagy

Peroxisome

Vesicle

Lysosome

Mitochondrion

Peroxisome

fragment

Mitochondrion

fragment

Vesicle containing

two 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 ribosomes in the mitochondrial matrix

Intermembrane space

Outer membrane

Inner membrane

Cristae

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

11/7/2016

9

NUCLEUS

Nuclear envelope

Nucleolus

Chromatin

Rough endoplasmic reticulum

Smooth endoplasmic reticulum

Ribosomes

Central vacuole

Microfilaments

Intermediate filaments

Microtubules

CYTO- SKELETON

Chloroplast

Plasmodesmata

Wall of adjacent cell

Cell wall

Plasma membrane

Peroxisome

Mitochondrion

Golgi apparatus

Plant Cell *

*

*

*

* not in animal cells

Central vacuole

Cytosol

Central vacuole

Nucleus

Cell wall

Chloroplast

5 µm

Central Vacuole

Plant organelle

that stores water

and various ions

Source of “turgor

pressure” that

maintains rigidity

of plant cells

• swells when water

is plentiful due to

osmosis

• cell wall provides

support, prevents

lysis

Chloroplast

Stroma

Inner and outer membranes

Granum

Intermembrane space

Chloroplasts

Site 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

11/7/2016

10

1 µm

Chloroplast

Peroxisome

Mitochondrion

Peroxisomes Contain enzymes

that oxidize

(i.e., remove H)

various organic

molecules thus

forming H2O2

from O2

• H2O2 is then

converted to O2

and H2O

Involved in the

detoxification of

toxic substances,

breakdown of

fatty acids

3. The Cytoskeleton

Microtubule

Microfilaments 0.25 µm

The Cytoskeleton

A 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

11/7/2016

11

3 Basic Cytoskeletal Filaments Actin filaments/microfilaments (MF)

intermediate filaments (IF)

microtubules (MT)

IF

MT

MF

Actin subunit

10 µm

7 nm

Microfilaments

5 µm

Keratin proteins

Fibrous subunit (keratins coiled together)

8–12 nm

Intermediate Filaments

11/7/2016

12

10 µm

Column of tubulin dimers

Tubulin dimer

25 nm

Microtubules

Vesicle ATP

Receptor for

motor protein

Microtubule

of cytoskeleton

Motor protein

(ATP powered)

(a)

Microtubule Vesicles

(b)

0.25 µm

Vesicle

Transport

• a variety of

motor proteins

are involved in

binding and

transporting

vesicles along

cytoskeletal

fibers to their

destination

Centrosome

Microtubule

Centrioles

0.25 µm

Longitudinal section of one centriole

Microtubules Cross section of 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

11/7/2016

13

5 µm

Direction of swimming

(a) Motion of flagella

Direction of organism’s movement

Power stroke

Recovery stroke

(b) Motion of cilia 15 µm

Flagella & Cilia FLAGELLA

are involved in

cell motility, are

very long, and

cells have

relatively few

(1 or several)

CILIA

are 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 vacuole

Cytosol

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

11/7/2016

14

Tight junction

0.5 µm

1 µm Desmosome

Gap junction

Extracellular matrix

0.1 µm

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

Intercellular

Junctions TIGHT JUNCTIONS

are impenetrable seals

connecting adjacent cells

that prevent fluid and other

materials from passing

between the cells

DESMOSOMES

are 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

Proteoglycan molecule

Proteoglycan complex

Collagen

Fibronectin

Plasma membrane

Proteoglycan complex

Integrins

CYTOPLASM Micro-filaments

EXTRACELLULAR FLUID

The Extracellular Matrix A 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

11/7/2016

15

• cytoskeleton, cilia, flagella, centrosome, centriole

• microtubules, microfilaments, intermediate filaments

• motor proteins

• tight junctions, gap junctions, desmosomes,

plasmodesmata

• extracellular matrix, proteoglycan

Relevant Chapter

Questions 1-9