CELL BIOLOGY: AN INTRODUCTION
the cell theory (1839)
Cell Theory: A History
• Robert Hooke
o Built a microscope and examined
thin slices of cork
o Saw box-like compartments and
called it cells (Latin: cellula— little
room)
o Observed cell walls of dead plant
tissue not cells
o Observations were limited by
magnification power (only 30x)
• Antonie van Leeuwenhoek
o Produced small lenses with 300x
magnification
o First to observe livings cells
▪ Blood cells, sperm cells,
bacteria, algae, and protozoa
• Factors restriction understanding of the cell
o Microscopes back then had limited
resolution (resolving power)— ability
to see fine deatails of structure
o Descriptive nature of 17th century
biology
▪ Age of observation
▪ Little thought in explaining
architectural details of
biological materials
• 1830s
o Compound microscope
▪ One lens (eyepiece)
magnifies the image created
by a second lens (objective)
▪ Higher magnification and
better resolution
o Structures at 1 micrometer (µm)
could be seen
• Robert Brown
o Looked into plant cells
o Noticed that all contain a rounded
structure he termed as nucleus
(Latin for kernel)
• Matthias Schelieden (1938)
o All plant tissues are composed of
cells
o An embryonic plant always arises
from a single cell
• Theodore Schwann
o Similar conclusions as Schelieden
concerning animal tissue
o Discredited earlier notion that plants
and animals do not resemble each
other structurally
o Developed a single unified theory of
cellular organization
o Postulated the first two principles of
• Rudolf Virchow (1859)
o Added that cells arose only by the
division of other preexisting cells
• The Cell Theory
o All organisms consist of one or more
cells [Schwann]
o The cell is the basic unit of structure
for all organisms [Schwann]
o All cells arise only from preexisting
cells (omnis cellula e cellula)
[Virchow]
• The cell is not only the basic unit of
structure for all organisms but also the basic
unit of reproduction
• Cell’s shape and structure gives clues of its
function
o Spiral thickening she of xylem tissue
give strength to water-conducting
vessels in wood
o Highly branched cells of human
neuron allow numerous interactions
with other neurons
Modern Cell Biology
• Results from weaving together different
branches— cytology, biochemistry, and
genetics
• Cytology
o Concerned primarily with cellular
structure
o Greek prefix: -cyto or Greek suffix:
-cyte — hollow vessel
• Biochemistry
o Understanding of cellular structure
and function
• Genetics
o Discovers of DNA (deoxyribonucleic
acid) as the bearer of genetic
information
o Encodes proteins and RNA
(ribonucleic acid) molecules
responsible for functional and
structural features of the cell
o Recent studies resulted in the
sequencing of the entire genome (all
of DNA) of humans and other
species
o Also allowed cloning (producition of
genetically identical organisms) to
be possible
• Ref pg. 28 (The Cell Biology Timeline)

Cytological Strand of Cell Biology
• Cytology primarily dealt with cellular
structure through the use of optical
techniques
• Microscopy has been invaluable with
helping biologists deal with the size problem
of cells
Cellular Dimensions
• Challenge: cells and organelles to small to
be seen by the naked eye
• Micrometer (µm)
o Most useful unit for expressing size
of cells and organelles
o One millionth of a meter (10-6 m)
• Nanometer (nm)
o Unit of choice for molecules and sub
cellular structures that are too small
to be seen using a light microscope
o One-billionth of a meter (10-9 m)
o 1000 nm = 1 µm
Light Microscope
• Earliest tool of cytologists
• Allowed the identification of membrane-
bounded structures
o Nuclei, mitochondria, and
chloroplasts
• Organelles (“little organs)— prominent
features of most plant and animal (but not
bacterial cells)
• Microtome (mid-1800s)
o Instrument for preparation of very
thin (several µm) tissue slices of
biological sample
• Dyes
o For staining and identifying
subcellular structures
o Latter half of 19th century
o Used coal tar derivatives
• Limit of resolution
o How far apart adjacent objects must
be to appear as separate entities
o E.g. limit of resolution = 400 nm,
objects must be at least 400 nm
apart to be recognizable separate
entities
• Resolving power
o Ability to see fine details of structure
• The smaller the limit of resolution, the
greater the resolving power
• Theoretically limit of resolution of the light
microscope is half the size of the
wavelength of light used for illumination
o Visible light = 400-700 nm , limit of
resolution 200-350 nm
• Brightfield microscopy
o Using light microscope
o White light passed directly through a
specimen (stained/unstained) and
the background (field) is illuminated
o Limitation: specimens chemically
fixed, dehydrated, embedded in
paraffin or plastic and stained to
highlight features
▪ No longer alive
▪ Features observed could be
distorted and not typical of a
living cell
Specialized Light Microscopes
• Includes:
o Phase-contrast microscopy
o Differential interference contrast
microscopy
o Fluorescence microscopy
o Confocal microscopy
• Phase-contrast & differential interference
contrast microscopy
o Make it possible to see living cells
clearly
o Enhance and amplify slight changes
in the phase of transmitted light as it
passes through a structure having a
different density than the
surrounding medium
• Fluorescence microscopy
o Enable researches to detect specific
proteins, DNA sequences, and other
molecules
o Made fluorescent by:
▪ Coupling to a fluorescent dye
▪ Binding to a fluorescently
labeled antibody
o Antibody
▪ Protein molecule produced
by the immune system that
binds on particular target
molecule, the antigen
o Simultaneous use of two or more
dyes/antigens (emitting different
colors of light) distributions of
different kinds of molecules in the
same cell can be followed
o Green fluorescent protein (GFP)
▪ From bioluminescent jellyfish
Aequorea victoria
▪ Used for studying temporal
band spatial distribution of
proteins in a cell
 ▪ When protein is fused with
GFP, synthesis and
movement can be followed
o Limitation: viewer can only focuse on
a single plane of specimen at a time
yet fluorescent light is emitted
throughout the specimen blurring the
image
• Confocal microscopy
o Overcomes the limitation of
fluorescence microscopy
o Uses a laser beam to illuminate just
one plane of the specimen at a time
• Digital video microscopy
o Uses video cameras to collect digital
images for computer storage
o Done by attaching a light-sensitive
video camera to a light microscopes
o Allow researchers to observe cells
for extended periods of time using
very low levels of light
o Image intensification useful to
visualize fluorescent molecules
present at low levels in living cells
and even to see and identify
individual macromolecules such as
DNA and protein molecules
• Light microscopy is inevitably subjected to
the limit of resolution imposed by the
wavelength of light
Electron Microscope
• Developed in Germany by Max Knoll and
Ernst Ruska (1931)
• Uses a beam of electrons that is deflected
and focused by an electromagnetic field
• Practical limit of resolution 100x better than
a light microscope
• Magnification at 100,000x
• Revealed cellular structures that are too
small to be seen with a light microscope
o Ribosomes, cell membranes,
microtubules and microfilaments
• Can also reveal some macromolecules such
as DNA and protein molecules
• Transmission electron microscope (TEM)
o Forms an image from electrons that
are transmitted through the
specimen
• Scanning electron microscope (SEM)
o Scans the surface of the specimen
and forums an image by detecting
electrons that are deflected from its
outer surface
• Similar to each other in that each employs a
beam of electrons
Biochemical Strand of Cell Biology
• Other scientists were making observations
that began to explain and clarify cellular
function
• Used techniques from classical chemistry
to understand structure and function of
biological molecules
Biochemical Reactions and Pathways
• Friedrich Wöhler (1928)
o Demonstrated that urea, an organic
compound, can be synthesized in a
lab using ammonium cyanate
(inorganic)
o Dispelled the notion that biochemical
processes were exempt from the
laws of chemistry and physics
• Louis Pastuer (1958)
o Living yeast cells were responsible
for the fermentation of sugar into
alcohol
• Eduard and Hans Buchner (1897)
o Fermentation of sugar could take
place with isolated extracts from
yeast cells
▪ Intact cells themselves were
not required
• Enzymes
o Specific biological catalysts
o Greek: zyme— yeast
• Gustavo Embden, Otto Meyerhoff, Otto
Warburg, and Hans Krebs
o Described the enzymatic steps for
the Embden-Meyerhof pathway for
glycolysis for glucose breakdown
and the Krebs cycle for energy
production
o Pathways have a role in the process
by which cells extract energy from
glucose and other foodstuffs
• Fritz Lipmann
o Showed that the high-energy
compound adenosine triphosphate
(ATP) is the principal energy storag
compound in most cells
• Melvin Calvin (and colleagues in University
of California, Berkeley)
o Traced the fate of C-labeled CO2 in
illuminated algal cells that were
actively photosynthesizing
o Led to the elucidation of the Calvin
cycle
▪ Most common pathway for
photosynthetic carbon
metabolism
 ▪ First metabolic pathway to be
elucidated using a
radioisotope
Biochemistry Methods
• Centrifugation
o Means of separating and isolating
subcellular structures and
macromolecules based on their
size, shape, and/or density
▪ A process call subcellular
fractionation
o Helps study specific parts of the cell
(e.g. nucleus or specific proteins)
• Ultracentrifuge
o Useful for resolving small
organelles and macromolecules
o Developed by Theodor Svedberg
(late 1920s)
o More than 100,000 rev/min
o 500,000x the force of gravity
• Chromatography
o A variety of techniques by which a
mixture of molecules in solution is
separated into individual
components
o Separate molecules based on size,
charge, or affinity for specific
molecules or functional groups
• Electrophoresis
o Techniques that use an electrical
field to separate macromolecules
based on their mobility through a
semisolid gel
o Different molecules move at
different rate depending on their
size and charge
o Used to isolate and characterize
DNA, RNA, and protein molecules
• Mass spectrometry
o Commonly used to determine the
size and composition of individual
proteins
o Usually done after electrophoresis
o Determines the identity and
characteristics of individual proteins
Genetic Strand of Cell Biology
• Genetics— the study of inheritance of
characteristics from generation to
generation
Classical Genetics
• Gregor Mendel
o Studies with pea plants laid out the
principles of segregation and
independent assortment of the
“hereditary factors” known as genes
• Walther Flemming
o Identified chromosomes— threadlike
bodies seen in dividing cells
o Called the division process mitosis
(Greek for thread)
o Chromosome number became a
distinctive characteristic of a species
and remains constant from
generation to generation
• Wilhelm Roux (1883)
o Suggested that chromosomes
contain genetic information
o Formally expressed by August
Weissman
• Carl Correns (Germany), Ernst von
Tschermak (Austria), Hugo de Vries
(Holland)
o Cited Mendel’s works leading to its
rediscovery
o Formulation of chromosome theory
of heredity following the work of
Walter Sutton and Theodor Boveri
• Chromosome theory of heredity
o Proposed that hereditary factors
responsible for Mendelian
inheritance are located on the
chromosomes within the nucleus
• Thomas Hunt Morgan, Calvin Bridges, and
Alfred Stutervant (Columbia University)
o Used Drosophila melanogaster,
common fruit fly, as model organism
o Identified a variety of morphological
mutants of Drosophila and were able
to link specific traits to specific
chromosomes
• Johann Friedrich Miescher (1869)
o Discovered the DNA
o Used salmon sperm and human pus
o Isolated and described what he
called a “nuclein”
• Robert Feulgen
o Staining technique implicated DNA
as an important component of
chromosomes
• DNA considered as unlikely bearer of
genetic information due to its monotonous
structure
• 1930
o DNA known to only be composed of
4 nucleotides
o Proteins wee much more diverse (20
amino acids)
 o Until middle of 20th century proteins
were thought to have carried genetic
material due to its diversity
• Oswald Avery, Colin MacLeod, and Maclyn
McCarty (1944)
o Showed that DNA could “transform”
a non pathogenic strain of bacteria
into a pathogenic one causing
heritable genetic change
• Alfred Hershey and Martha Chase (1952)
o Showed that DNA, not protein,
enters the bacterial cell when it is
infected and genetically altered by a
bacterial virus
• George Beadle and Edward Tatum (1940s)
o Worked with breade mold
Neurospora crassa
o Formulated the “one gene-one
enzyme” concept
o Asserted that each gene controls the
production of a single specific
protein
Molecular Genetics
• James Watson, Francis Crick, and Rosalind
Franklin (1953)
o Proposed double helix model for
DNA structure
o Suggested hoe replication during
cell I vision could occur by base
pairing between complementary
strands
• 1960s
o Discovery of polymerase enzymes
that synthesize DNA and RNA
o “Cracking” of the genetic code,
specifying the relationship between
the order of nucleotides in a DNA or
RNA molecule
o Order of amino acids in a protein
• Jacques Monod and Francois Jacob
o Deduced the mechanism
responsible for regulating bacterial
gene expression
• Francis Crick (1953)
o Articulated a molecularly based
model of genit information flow
o Central dogma of molecular biology
• The central dogma
o Replication
▪ Production of two identical
copies of DNA
o Transcription
▪ RNA synthesis using DNA
template
▪ Transfer of information from
one nucleic acid to another
▪ Basic “”language” remains
the same
o Translation
▪ Protein synthesis using RNA
▪ Involves a language
change— from the nucleotide
sequence of RNA to amino
acid sequence of polypeptide
chain
• Messenger RNA (mRNA)
o RNA that is translated into protein
o Carries a genetic message from
DNA to the ribosomes
(macromolecular complexes)
• Ribosomal RNA (rRNA)
o Molecules that are integral
components of the ribosome
• Transfer RNA (tRNA)
o Molecules tha serve as
intermediaries that recognize the
coded base sequence of an mRNA
and bring the appropriate amino
acids to the ribosome for protein
synthesis
• Exceptions to the central dogma
o RNA viruse synthesize mRNA
molecules using RNA as a template
o Other RNA viruse (e.g. HIV) carry
out reverse transcription
▪ Viral RNA used as template
for DNA synthesis
▪ “Backward” flow of genetic
information
• Recombinant DNA technology (1970s)
o Made possible by discovery of
restriction enzymes
 o Enzymes with the ability to cleanse
DNA molecules at specific
sequences
o Allowed creation of recombinant
DNA molecules containing DNA
sequences from two different
sources
o DNA cloning
▪ Generation of many copies of
specific DNA sequences for
study and manipulation
o DNA transformation
▪ Process of introducing DNA
into cells
• DNA sequencing
o Devised for rapidly determining the
base sequences of DNA molecules
o Human Genome Project (1990-
2003)
▪ Sequencing of the entire
human genome
▪ 3.2 billion basses
Bioinformatics and “-Omics)
• Bioinformatics
o Merges computer science and
biology as a means of making sens
of sequence data
o Led to recognition that human
genome has approx, 20,000
protein-coding genes
• Genomics
o Study of all the genes of an
organism
• Proteomics
o Proteome— total protein content of
a cell
o Understand the structure and
properties of every protein
produced by the genome
o Learn how proteins interact with
each other in biological networks to
regulate cellular functions
• Bioinformatics tools
o PubMed (NCBI)— searchable
archive of 22 million citations from
life science journals
o GenBank (NCBI)— database of all
publicly available DNA sequences
(more than 165 million since mid-
2013)
o Protein Knowledgenase
[UniProtKB] (NCBI)— database of
more that 500,000 protein
sequences
o Basic Logical Alignment Search
Tool (BLAST)— tool to compare the
sequence of newly discovered gene
to all known gene sequences
o Online Mendelian Inheritance in
Man (OMIM)— encyclopedic
collection of information regarding
human genetic disorders and
mutations involving more than
14,000 genes
• Transcriptomics
o Determining the complete set of
genes transcribed in a cell
• Metabolomics
o Analysis of all metabolic reactions
happening at a given time in a cell
• Lipidomics
o Study of all the lipids in a cell
• Ionomics
o Global study of all ions in a cell
The Scientific Method
Biological “Facts”
• Cell biology is rich in “facts” once
considered true that have been altered or
discarded over the course of history
• Biological “facts” are simply provisional
pieces of information
• “Facts” are dynamic and subject to change
• A “fact” is simply an attempt to state our
best current understanding of the natural
world around us based on observations
and experiments
Experiments Test Specific Hypotheses
• First conduct a search of scientific literature
to determine what is known in the area of
interest
o Use of peer-reviewed journal articles
• Formulation of hypothesis
o A tentative explanation that can be
tested experimentally or via further
observation
o A model that appears to provide a
reasonable explanation of the
phenomenon in question
• Design of controlled experiment
o Used to test the hypothesis by
varying specific conditions while
keeping other variables constant
• Data collection, results interpretation, and
acception/rejection of hypothesis
• Better to prove the null hypothesis (opposite
of current hypothesis)
 o Sufficiently large number of attempts Escherichia coli
is indirect evidence that the
hypothesis is correct
• Certainty of its correctness increases with
the number of experimental samples and
the number of times the results are
replicated
• In vitro (“in glass”) experiments
o Conducted in a lab using purified
chemicals and cellular components
• In vivo (“in life”) experiments
o Use of live cells and organisms
o Uses a variety of model organisms
• In silico (“in silicon”) experiments
o Use of computers to test hypothesis

Model Organisms in Cell Biology • Credited for information known about basic
cellular processes (DNA replication,
Cell and Tissue Cultures membrane function, protein synthesis)
• HeLa cells • Easy to grow, generation time at 20-30 min
o First human cells grown in defined • First bacterium to have complete genome
culture conditions sequenced
o Taken from cervical cancer tissue of Saccharomyces cerevisiae
Henrietta Lacks (19510
o Descendants of here cells are still
grown today for cancer and virus
research
• Egg cells from frog Xenopus to study
channel proteins
• Chines hamster ovary cells for cell signaling
studies and commercial protein production
• Mous 3T3 fibroblast cells to assess
carcinogenicity of new compounds
• Undifferentiated embryonic stem cells to
study cellular differentiation
• Cell cultures also used for studying and
growing viruses

Model Organisms • Used to study processes unique to

• Species that is widely studied, well
characterized, and easy to manipulate, and
has particularly advantages making it useful
for experimental studies
eukaryotic cells (e.g. cell division, organelle
development, cell signalling)
• Also easy to mutagenize
• Used to isolate and characterize genetic
mutants following mutagenesis by
chemicals or radiation
• By studying mutat strains, normal cellular
function of genes and proteins can be
determined
• Yeast two-hybird system
o Used to determine whether and how
specific proteins interact within a
living cell
Drosophila melanogaster Mus musculus

• Used to study communication between

cells, differentiation of cells, and embryonic
development
• Two-week generation time, produce many
progeny, easily observable characteristics
Caenorhabditis elegans
• Used for studying cellular and physiological
processes specific to mammals
Chlamydomonas reinhardtii

• Used to study plant processes (e.g.

photosynthesis and light perception)
• Unicellular green alga
• Also used to study mating type, cellular
motility, and DNA methylation

Arabidopsis thaliana

• Also used to study communication between

cells, differentiation of cells, and embryonic
development
• Ease of manipulation, short life cycle, and
small genome
• Posses a nervous system, development
from fertilized egg predictable
• Origin and fate of approx 1000 cells
mapped out
• Hundreds of connections among 200 nerve
cells

• Smallest genome in plants, six-week life

cycle
Well-designed Experiments
• It is best to vary or perturb only one
condition (independent variable) and hold
other constant
• Dependent variable— outcome of change
that is measured (dependent on
independence variable)
• The fact that there should only be one
independent variable in an experiment is a
key reason to why genetic mutants are
valuable in studying gene function
• By changing only one component/variable
at a time, specific function of a component
and the effect of that variable can be
determined