I.

Introduction
A. The Origin and Evolution of Cells
B. Cells as Experimental Models
C. Tools of Cell Biology

Cell biology (formerly cytology,

from the Greek kytos, "container") is
an academic discipline that studies
cells their physiological properties
their structure,
the organelles they contain
interactions with their
environment,
their life cycle, division and
death.

Cell basic unit of life structurally

and functionally.
History:
a. Robert Hooke (1665)using his microscope
discovers cells in cork
b. Schleiden ; Schwann and Virchow
Cell theory:
1. All organisms are composed of one
or more cells
2. The cell is the structural unit of life
3. Cells can arise only by division from
preexisting cells

Various cell types:

shape, size, intracellular organizations,
polarization Functions

Dynamic Nature of Cell

-it has the capacity
to grow
to reproduce
become specialized
ability to respond to stimuli
adapt to changes in its environment

Fundamental properties shared by all cells:

(conserved throughout evolution)

1. all cells employ DNA as their

genetic material
2. surrounded by plasma membrane
3. use the same basic mechanisms for
energy metabolism

A bacterium

Fig.1.2.Average_prokaryote_cell_en.svg (SVG file, nominally 494 402

pixels, file size: 135 KB)

The animal cell

A plant cell

The Main Functions of the Membrane-bounded

Compartments of a Eukaryotic Cell
Compartment

Main Function

Cytosol

contains many metabolic pathways

protein synthesis

Nucleus

contains main genome

DNA and RNA synthesis

Endoplasmic
reticulum (ER)

synthesis of most lipids

synthesis of proteins for distribution to many organelles and
plasma membrane

Golgi apparatus

modification, sorting, and packaging of proteins and lipids

for either secretion or delivery to another organelle

Lysosomes

intracellular degradation

Endosomes

sorting of endocytosed material

Mitochondria

ATP synthesis by oxidative phosphorylation

Chloroplasts (in
plant cells)

ATP synthesis and carbon fixation by photosynthesis

Peroxisomes

oxidation of toxic molecules

Organisms:
1. Unicellular (eg. bacteria, amoebas &
yeasts) capable of independent selfreplication
2. Multicellular(eg. Humans)- composed of
collection of cells w/c fxns in a
coordinated manner w/ diff cells
specialized to perform particular tasks.

Table 1: Comparison of features of prokaryotic and eukaryotic cells

Typical organisms

Prokaryotes
bacteria, archaea

Typical size

~ 1-10 m

Type of nucleus

nucleoid region; no real nucleus

DNA

circular (usually)

RNA-/protein-synthesis

coupled in cytoplasm

Ribosomes

50S+30S

Cytoplasmic structure

very few structures

Cell movement

flagella made of flagellin

Mitochondria

none

Chloroplasts

none

Eukaryotes
protists, fungi, plants, animals
~ 10-100 m (sperm cells, apart
from the tail, are smaller)
real nucleus with double
membrane
linear molecules (chromosomes)
with histone proteins
RNA-synthesis inside the nucleus
protein synthesis in cytoplasm
60S+40S
highly structured by
endomembranes and a
cytoskeleton
flagella and cilia containing
microtubules; lamellipodia and
filopodia containing actin
one to several thousand (though
some lack mitochondria)
in algae and plants

Organization

usually single cells

single cells, colonies, higher

multicellular organisms with
specialized cells

Cell division

Binary fission (simple division)

Mitosis (fission or budding)

Meiosis

1 106 to 5 106

1.5 107 to 5 109

DNA content (base pairs)

The Origin and Evolution of Cells

the First Cell:

-all present day cells (both prokaryotes &
eukaryotes) descended from a single ancestor.
-the 1st cell is thought to have arisen at least
3.8 B years ago as a result of enclosure of selfreplicating RNA in a phospholipid membrane (RNA
world hypothesis)
Present-Day Prokaryotes
-divided into two groups: the archaebacteria and
the eubacteria which
diverged early in evolution
Eukaryotic Cells
-thought to have evolved from symbiotic
associations of prokaryotes (ENDOSYMBIONT
THEORY)

ENDOSYMBIOSIS
A large anaerobic, heterotrophic prokaryote engulfs a
small aerobic prokaryote
The aerobic endosymbiont has evolved into a mitochondrion
A portion of the plasma membrane has invaginated
and evolved into a nuclear envelope and endoplasmic
reticulum
(primitive eukaryote)
Nonphotosynthetic protist, fungal,Engulfs a photosynthetic
prokaryote
animal cells
Evolve into a chloroplast

Algal & plant cells

Endosymbiont Theory

Fig.1.5. Time scale of evolution The scale indicates the approximate

times at which some of the major events in the evolution of cells are
thought to have occurred.

The Evolution of Metabolism:

Figure 1.6. Generation of metabolic energy Glycolysis is the anaerobic breakdown of glucose to lactic acid.
Photosynthesis utilizes energy from sunlight to drive the synthesis of glucose from CO2 and H2O, with the release
of O2 as a by-product. The O2 released by photosynthesis is used in oxidative metabolism, in which glucose is
broken down to CO2 and H2O, releasing much more energy than is obtained from glycolysis.

Figure 1.6. Evolution of cells Present-day cells evolved from a common prokaryotic ancestor along three
lines of descent, giving rise to archaebacteria, eubacteria, and eukaryotes. Mitochondria and chloroplasts
originated from the endosymbiotic association of aerobic bacteria and cyanobacteria, respectively, with
the ancestors of eukaryotes.

Cells as Experimental Models

E. coli

Arabidopsis thaliana

S. cerevisiae

Dictyostelium discoideum

Caenorhabditis elegans Drosophila

melanogaster

Xenopus laevis

zebrafish

House mouse

Choosing the Right Experimental Organism for

the Job

Table 1.2 DNA Content of Cells

Organism

Bacteria
Mycoplasma
E. coli
Unicellular eukaryotes
Saccharomyces cerevisiae (yeast)
Dictyostelium discoideum
Euglena
Plants
Arabidopsis thaliana
Zea mays (corn)
Animals
Caenorhabditis elegans (nematode)
Drosophila melanogaster (fruit fly)
Chicken
Zebrafish
Mouse
Human

Haploid DNA content (millions of base

pairs)

0.6
4.6

12
70
3000
130
5000
97
180
1200
1700
3000
3000

C. Tools of Cell Biology

Tools of Cell Biology

1. Light Microscopy
Bright-field microscopy
Phase-contrast microscopy
Differential interference contrast microscopy
Video-enhanced differential interference-contrast microscopy
Fluorescence microscopy
Confocal scanning microscopy

2. Electron microscopy
Transmission electron microscopy
Scanning electron microscopy

Light Microscope
-

earliest tool of cytologist

Limit of resolution is /2= 0.20-0.35 um

- To magnify an object, it uses a system of lenses to

manipulate the path a light beam travels between the
object being studied and the eye
- Produce a maximum useful magnification of about
1000 times the original size.
- Has three lenses:
1. the condenser(focuses light on the specimen
2. the objective(s)
a. Low-power objective
b. High-power objective
c. Oil-immersion objective
3. the eyepiece (ocular)

Table 2-1
Objective
Designation

Objective
Magnification

Eyepiece
Magnification

Total
Magnification

Low Power

10

10

100

High Power (high

dry)

40

10

400

Oil Immersion

100

10

1000

Table 2-2. Metric unit equivalents in expressing cell dimensions

Unit of
length

Meter (m)

Centimeter
(cm)

Millimeter
(mm)

Micrometer Nanometer
(um)
(nm)

Micrometer
(um)

0.000001
10-6

0.0001
10-4

0.001
10-3

1000
103

Nanometer
(nm)

0.000000001
10-9

0.0000001
10-7

0.000001
10-6

0.001
10-3

Angstrom
()

0.0000000001
10-10

0.00000001
10-8

0.0000001
10-7

0.0001
10-4

0.1
10-1

A. Light Microscope
Terms:
1. Limit of Resolution-refers to how far apart
adjacent objects must be in order to be distinguished as
separate entities. (eg. LOR of microscope is 400 nm)

2. Resolving Power-expressed in terms of (the

wavelength of light used to illuminate the sample)
-the smaller is the limit of resolution the
greater is the resolving power
Resolving Power of any microscope
-a measure of its ability to discriminate between two adjacent
objects.
- is a function of the wavelength of light and the numerical
aperture of the lens system
- light microscopes (using visible light) have RP of approximately
0.25 um which means that particles of a smaller size cannot be
distinguished from one another).

Fig.1-9. Resolving Power

Of the Human Eye, the
Light microscope and the
Electron Microscope

1 um = 10-6 m (one-millionth of a meter)

1 nm = 10-9 m (one-billionth of a meter)
1000 nm = 1 um
Angstrom () = 10-10 m or 0.1 nm

Type of
Microscopy

Maximum useful
magnification

Appearance of
specimen

Useful
Applications

Bright-field

1000-2000

Specimens stained
or unstained;
bacteria generally
stained and appear
color of stain

Gross
morphological
features of
bacteria, yeasts,
molds,algae and
protozoa

Dark-field

1000-2000

Generally
unstained; appears
brightorlightedin
an otherwise dark
field

Microorganisms
that exhibit some
characteristic
morphological
feature in the living
state and in fluid
suspension e.g.
spirochetes

Fluorescence

1000-2000

Bright and colored;

color of the
fluorescent dye

Diagnostic
techniques where
fluorescent dye
fixed to organism
reveals the
organismsidentity

a. Differential-interferencecontrast micrograph of a mitotic

yeast cell.

b. Fluorescence microscopy

c. Phase-contrast micrograph of fibroblasts

in culture.

Type of
Microscopy

Maximum useful
magnification

Appearance of
specimen

Useful
Applications

Phase-contrast

1000-2000

Varying degrees of
darkness

Examination of
cellular structures
in living cells of the
larger
microorganisms,
e.g yeasts, algae,
protozoa and some
bacteria

a) Flourescent microscope b) flourescent micrograph

of chromosomes and mitotic spindle

c) Dark-field photomicrograph of Mysis

d)Phase-contrast
micrograph of a cheek
cell

B. Electron Microscope
-uses a beam of electrons controlled by a system of
magnetic fields
-has high resolving power thus greater magnification
(can resolve objects separated by a distance of 0.003 um
compared to 0.25 um of light microscope).
-useful magnification is 200,000 to 400,000
-use in the examination of viruses and the ultrastucture of microbial cells.
- has two types:
a. Scanning electron microscopy (SEM)
-employed to study the surface structure
of a specimen(eg. Attachment of bacterial cells to
objects)
b. Transmission electron microscopy (TEM)
-used to view subcellular components
(even nucleic acid molecules)

Techniques and Methods

of Studying Cells

Several different techniques exist to study

cells:
1. Cell culture
2. Cell Fractionation
3. Immunostaining
4. Computational Genomics
5. DNA MICROARRAYS
6. Gene knockdown
7. In situ hybridization
8. Polymerase Chain Reaction (PCR)

Figure 1-7. A procedure used to make a transgenic plant.

Figure 8-63. Using cluster

analysis to identify sets of
genes that are coordinately
regulated.
Figure 1.8. Using DNA
microarrays to monitor the
expression of thousands of
genes simultaneously.

Basic Local Alignment Search Tool (BLAST)

Figure 8-47. Results of a BLAST search. Sequence databases can be

searched to find similar amino acid or nucleic acid sequences. Here a
search for proteins similar to the human cell-cycle regulatory protein
cdc2 (Query) locates maize cdc2 (Subject), which is 68% identical (and
82% similar) to human cdc2 in its amino acid sequence.

Cell staining
-a technique that can be used to better visualize
cells and cell components under a microscope.
-by using different stains, one can preferentially
stain certain cell components, such as a nucleus or a
cell wall, or the entire cell.
- Most stains can be used on fixed, or nonliving cells, while only some can be used on living
cells; some stains can be used on either living or
non-living cells.

Why Stain Cells?

-most basic reason that cells are stained is
to enhance visualization of the cell or certain
cellular components under a microscope.
-Cells may also be stained to highlight
metabolic processes or to differentiate
between live and dead cells in a sample.
- to determine biomass in an environment of
interest.

How Are Cells Stained and Slides Prepared?

Cell staining techniques and preparation depend on the type of stain and analysis used. One
or more of the following procedures may be required to prepare a sample:
Permeabilization - treatment of cells, generally with a mild surfactant, which dissolves cell
membranes in order to allow larger dye molecules to enter inside the cell.
Fixation - serves to "fix" or preserve cell or tissue morphology through the preparation
process. This process may involve several steps, but most fixation procedures involve adding a
chemical fixative that creates chemical bonds between proteins to increase their rigidity.
Common fixatives include formaldehyde, ethanol, methanol, and/or picric acid.
Mounting - involves attaching samples to a glass microscope slide for observation and
analysis. Cells may either be grown directly to the slide or loose cells can be applied to a slide
using a sterile technique. Thin sections (slices) of material such as tissue may also be applied
to a microscope slide for observation.

Staining - application of stain to a sample to color cells, tissues, components, or metabolic

processes. This process may involve immersing the sample (before or after fixation or
mounting) in a dye solution and then rinsing and observing the sample under a microscope.
Some dyes require the use of a mordant, which is a chemical compound that reacts with the
stain to form an insoluble, colored precipitate. The mordanted stain will remain on/in the
sample when excess dye solution is washed away.

A. Dye-cellular interactions

____________________________________
Fig. 1. Schematic representation of dye-protein interactions. At pI of protein
(center), negligible binding of charged dyes occurs. Below pI (left), protein

binds acid

(=anionic) dyes; above pI (right), protein binds basic (=cationic) dyes. At

physiologic pH, specific proteins may exhibit net (+) or net (-) charges and
are therefore characterized as acidophilic (=affinity for acid dyes) or
basophilic (=affinity for basic dyes), respectively.

Important stains and reactions

1. Cationic ("basic") Dyes: tissue components stained

with these dyes are basophilic.

a. Examples of basic dyes

i. Hematoxylins (behave as cationic dyes)
ii. Azures
iii. Methylene blue
iv. Toluidine blue
b. Examples of basophilic tissue components
i. Nuclei and nucleoli
ii. Cytoplasmic RNA (e.g . ,ergastoplasm,
Nissl)

2. Anionic ("acid") Dyes: tissue components stained

with these dyes are acidophilic.

a. Examples of acid dyes

i. Aniline blue: blue
ii. Eosin: pink-red
iii. Fast green: green
iv. Orange G: orange
v. Picric acid: yellow

components

b. Examples of acidophilic tissue

i. Most cytoplasm
ii. Hemoglobin
iii. Keratin
iv. Collagens

3. Special Stains and Reactions

a. Alcian blue (=basic dye) for polyanions
and acidic glycoproteins (alcianophilia)

b. Elastic stains (e.g., orcein, resorcin fuchsin,

Verhoeff)
c. Feulgen reaction for DNA
d. Lipid colorants/stains (e.g., Sudan black, oil
red O, osmium tetroxide)
e. Masson trichrome for differential staining of
several tissues
f. Metachromasia (e.g., toluidine blue for
polyanions)
g. PAS reaction for vic-glycols
h. Silver stains for Golgi, basement
membranes, reti- cular fibers, neurofibrils
(argyrophilia)

j. Oxidation-reduction reactions and

staining
k. Romanowsky dyes: mixtures of acid and basic dyes for
staining blood smears
i. Mechanism
Orthochromasia -cellular components
stained either pink/red due to eosin or blue
due to basic dye component
Polychromasia layered staining with both
dyes

Metachromasia -color shift of basic dye

from blue to violet-purple due to high
concentrations of polyanions
ii. Examples
Wright stain
Giemsa stain