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Introduction of this Cell Biology course
1. Goals: convey the excitement and challenges of research in contemporary cell
biology
A cell is the basic unit of life. Understanding how cells grow, divide and
respond to environment is the major purpose of biology.
The number of applications of cell biology continues to grow in medicine,
agriculture, biotechnology, and biomedical engineering.
2. Organization of the textbook:
Part I: Introduction
Part II: The flow of genetic information
Part III: Cell structure and function
Part IV: Cell regulation
3. Companion website: www.sinauer.com/cooper5e/
Various information (animation and video clips), Homework
Have to register yourself to solve Online Quizzes (homework)
Online Quizzes Create a new account [email protected]
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Introduction of this Cell Biology course
4. Lecture materials: klms.kaist.ac.kr
5. Your performance and grading
Midterm exam (40%), Final exam (40%),
Other activities (participation/homework/attendance: 20%)
Participation: 6
Homework: 10
Attendance: 4
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Chapter 1. An Overview of Cells and Cell Research
The origin and evolution of cells
Cells and organisms as experimental models
Some of the properties of cells and organisms that make them valuable
experimental model
Tools of cell biology
Progress in cell biology depends on the availability of experimental tools.
Some of important experimental tools are discussed.
Chapter sections
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The Origin and Evolution of Cells
Two types of cells: Prokaryotic cells lack a nuclear envelope. Eukaryotic cells have a nucleus that separates genetic material from
cytoplasm.
The first cell (premordal ancestor) emerged at least 3.8 billion years ago.
Spontaneous synthesis of organic molecules probably provided the basic
materials from which the first living cells arose (Fig. 1.1).
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Macromolecules may have formed by spontaneous polymerization of
monomeric building blocks under plausible prebiotic conditions.
The critical characteristic of the macromolecule from which life evolved must
have been the ability to replicate itself.
Nucleic acids are capable of directing self-replication (Fig.1.2).
Sid Altman and Tom Cech first discovered that RNA is capable of catalyzing
chemical reactions, including the polymerization of nucleotides.
RNA can serve as a template for its own replication, and it is also able to
catalyze its own replication (= self-replicating RNA).
Consequently, RNA is generally believed to have been the initial genetic
system in evolution.
This period is known as the RNA world.
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The first cell probably arose by the enclosure of self-replicating RNA in a
membrane composed ofphospholipids.
Phospholipids are the basic components of all present-day biological
membranes.
Properties of phospholipids Amphipathic When placed in water, they spontaneously aggregate into a bilayer.
Forms a physical barrier against free influx of molecules from outside.
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Cells needed to evolve mechanisms for generating energy and synthesizing
molecules.
The principal pathways of energy generation are highly conserved in
present-day cells; and all cells use ATP as their source of metabolic energy.
The mechanisms of generation of ATP are thought to have evolved in three
stages, corresponding to the evolution of glycolysis, photosynthesis, and
oxidative metabolism (Fig. 1.4).
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Glycolysis evolved when the Earths atmosphere was anaerobic. No involvement of oxygen Breakdown of glucose to lactic acid All present-day cells carry out glycolysis.
Photosynthesis evolved more than 3 billion years ago. It allowed some cells to harness energy from sunlight; and they no longer required
preformed organic molecules. The first photosynthetic bacteria probably used H2S to convert CO2 to organic
molecules: a pathway of photosynthesis still used by some bacteria.
(Analysis of sedimentary rocks: completely anoxic, filamentous microbial tangles) The use of H2O evolved later (~1.5 billion years ago, as H2S diminished); it
changed Earths atmosphere by making free O2 available.
O2 in the atmosphere may have allowed the evolution of oxidative metabolism. It is much more efficient than glycolysis; the complete oxidative breakdown of glucose
yields 36 to 38 ATP molecules.
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Present-day prokaryotes
Archaebacteria: many live in extreme environments (e.g., hot sulfur spring).
Eubacteria: a large group that live in a wide range of environments.
Most bacterial cells are small.
Cyanobacteria, the group in which photosynthesis evolved, are the largest
and most complex prokaryotes (i.e., large number of genes)
Escherichia coli (E. coli) is a typical prokaryotic cell. It has a rigid cell wall composed of polysaccharides and
peptides (=peptidoglycan).
Beneath the cell wall is the plasma membrane, a
phospholipid bilayer with associated proteins.
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They are much larger and more complex, with a nucleus, other organelles,
and cystoskeleton.
*Organelles= subcellular organelles or compartment
The nucleus is the largest organelle; it contains the linear DNA molecules.
Mitochondria:site of oxidative metabolism.
Chloroplasts: site of photosynthesis.
Lysosomes and peroxisomes: specialized metabolic compartments for the
digestion of macromolecules and for various oxidative reactions.
Present-day eukaryotes
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Vacuoles: in plant cells; perform a variety of functions, including digestion
of macromolecules and storage of waste products and nutrients.
The endoplasmic reticulum is a network of intracellular membranes,
extending from the nuclear membrane throughout the cytoplasm.It functions in the processing and transport of proteins and the synthesis of
lipids.
In the Golgi apparatus, proteins are further processed and sorted for
transport to their final destinations.
It also serves as a site of lipid synthesis, and (in plant cells) the site ofsynthesis of some polysaccharides that compose the cell wall.
The cytoskeleton is a network of protein filaments extending throughout
the cytoplasm.
It provides structural framework, determines cell shape and organization,
and is involved in movement of whole cells, organelles, and chromosomesduring cell division.
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Acquisition of membrane-bound subcellular organelles was a critical step.
These are thought to have arisen by endosymbiosis: prokaryotic cells
living inside the ancestors of eukaryotes. Evidence is especially strong for mitochondria and chloroplasts.
Mitochondria and chloroplasts are similar to bacteria in size Like bacteria, they reproduce by dividing in two. Both contain their own DNA, which encodes some of their components.
The DNA is replicated when the organelle divides; the genes are transcribedwithin the organelle and translated on organelle ribosomes. The ribosomes and ribosomal RNAs are more closely related to those of bacteria
than to those encoded by the nuclear genomes of eukaryotes.
The origin of eukaryotes
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The first eukaryote is thought to derived from the fusion of aerobic
eubacterium with an archaebacterium rather than from one of the two. What
is a supporting evidences? the mosaic nature of eukaryotic genomes consisting of some genes derived
from eubacteria (mostly related to metabolism, e.g., glycolysis) and others from
archebacteria (mostly related to informational processes, e.g., DNA replication).
The DNA sequences of eubacteria
and archaebacteria are as differentas they are from those of present-day eukaryotes.
Mitochondria is contained in bothanimal and plant cells.
But, chloroplast is contained only inplant cells.
Therefore, a scenario would be that anarchaebacterium fused with anaerobic eubacterium first, and laterthe resulting cell fused withphotosynthetic bacterium.
Evolution of cells
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Many eukaryotes are unicellular organisms.
The simplest eukaryotes are the yeasts.
The development of multicelluar organisms
Other unicellular eukaryotes are more complex.
Amoeba proteus:its volume is more than 100,000 times that ofE. coli, and
it can exceed 1 mm in length.
Amoebas use cytoplasmic extensions, called pseudopodia, to move and
to engulf other organisms.
pseudopodia
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Some unicellular eukaryotes form aggregates (=muticellular colonies) that
may represent an evolutionary transition from single cells to multicellular
organisms.
Volvox (a green algae):
Thousands of cells are embedded
in a gelatinous matrix.
Individual cells are connected by
tiny cytoplasmic bridges.
Some division of labor; a small
number of cells are specialized in
reproduction.
Increasing cell specialization might have led to the transition from
aggregates to truly multicellular organisms.
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Cells of plants:
Organized into 3 main systems:
1. Ground tissue
(A) Parenchyma cells: site of metabolic reactions, including
photosynthesis.
(B) Collenchyma and sclerenchyma have thick cell walls and provide
structural support.
2. Dermal tissue covers the surface of the plant (=C); forms a protective coatand allows absorption of nutrients.
3. Vascular tissue (xylem and phloem) (=D):
xylem tissue- transport water mainly
phloem tissue- transport sucrose mainly
The both contains elongated cells.
Stomata
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Cells of animals:
Much more diverse than those of plants; e.g., 200 different kinds of cells in human
body. Components of 5 main types of tissues:
1. Epithelial tissue forms sheets that cover the surface of the body and lineinternal organs.
Functions: protection, nutrient absorption, secretion of molecules.
2. Connective tissueserve a connecting function- binds and support other
tissues. They includes bone, cartilage, and adipose tissue.
Loose connective tissue between organs and tissues is formed by fibroblasts.
4. Nervous tissue is composed of supporting cells and nerve cells, orneurons,
and various types of sensory cells; e.g., olfactory cells
5. Muscle tissue is responsible for the production of force and movement.
*All these complex array of cells differentiate from a single fertilized egg.
3. Blood tissues contains several different types of cells: Red blood cells (erythrocytes) function in oxygen transport. White blood cells (granulocytes, monocytes, macrophages,and
lymphocytes) function in inflammatory reactions and the immune
response.
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Representative animal cells
Epithelial cells
Fibroblasts
Blood cells
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Cells as Experimental Models
Because the fundamental properties of all cells have been conserved during
evolution, the basic principles learned from experiments on one type of cell
are generally applicable to other cells.
Several kinds of cells and organisms are used as experimental models.
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E. co li
The most thoroughly studied species of bacteria.
Our understanding of DNA replication, the genetic code, gene expression,
and protein synthesis derive from studies of this bacterium. E. coliis particularly useful because of its simplicity and ease of culture in
the laboratory.
The genome consists of approximately 4.6 million base pairs and contains
about 4300 genes. (human: 3 billion bps)
The small size of the genome is an advantage in genetic analysis. E. colidivide every 20 minutes. A clonal population can be readily isolated
as a colony grown on agar medium.
Bacterial colonies containing as many as 108
cells can develop overnight.
Selecting genetic variants of an E. colistrain is easy and rapid.
E. colican carry out biosynthetic reactions in simple defined media; thismade them extremely useful in elucidating biochemical pathways.
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Yeasts Yeasts are the simplest eukaryotes, and have been a model for
fundamental studies of eukaryote biology; e.g., RNA processing, protein
sorting and cell division.
The genome ofSaccharomyces cerevisiae consists of 12 million base pairsof DNA and contains about 6000 genes on 16 linear chromosomes.
Contains a nucleus, cytoskeleton, subcellular organelles.
Yeasts can easily be grown in the laboratory as colonies from a single cell.
Yeasts can be used for genetic manipulations similar to those performed
using bacteria.
The unity of molecular cell biology is made clear by the fact that general
principles of cell structure and function revealed by studies of yeasts apply
to all eukaryotic cells.
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Understanding the development of multicellular organisms requires
the experimental analysis of plants and animals.
The nematode C. elegansis one of the most widely used models.
Caenorhabdit is elegans
The genome ofC. elegans contains approximately 19,000 genes: nearly the
same number of genes as in humans.
C. elegans is relatively simple: adult worms consist of only 959 somatic cells.
The embryonic origin and lineage of all the cells has been traced.
Genetic studies have also identified many mutations responsible for
developmental abnormalities.
This led to isolation and characterization of genes that control development
and differentiation.
found that homologous genes in complex animals have similar functions
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The fruit fly Drosophila melanogasterhas been a crucial model
organism in developmental biology.
Drosophila is easy to grow in the laboratory, and the short
reproductive cycle (2 weeks) makes it very useful for genetic
experiments.
Many fundamental genetic concepts were derived from studies
ofDrosophila early in the 20th century.
Drosophi la melanogaster
Studies ofDrosophila have led to advances in understanding the molecular
mechanisms that govern animal development, particularly with respect to
formation of the body plan of complex multicellular organisms.
found that homologous genes and similar mechanisms exist in
vertebrates
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A model for plant molecular biology and development is the small
mouse-ear cress,Arabidopsis thaliana.
It has a small genome and is easily grown in the lab. Studies ofArabidopsis have led to the identification of genes
involved in aspects of plant development, such as the
development of flowers.
Arabido psis thal iana
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Vertebrates are the most complex animals, and the most difficult to study
due to the huge genome size and long reproductive cycle.
One approach is to use isolated cells in culture. These studies haveelucidated the mechanisms of DNA replication, gene expression, protein
synthesis, and cell division.
Vertebrates
The ability to culture cells in chemically defined media has allowed studies
of signaling mechanisms that normally control cell growth and differentiation
within the intact organism.
Highly differentiated cells are important models for studying particular
aspects of cell biology.
e.g.,
Muscle cells: a model for studying cell movement at the molecular level.
Giant neurons in squid: a model studying ion transport across the plasma
membrane and the transport of subcellular organelles
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The frogXenopus laevisis an important model for
studies of early vertebrate development.
Xenopus produces large eggs in large numbers,
facilitating laboratory study and biochemical analysis.
Zebrafish are small and reproduce rapidly.
Embryos develop outside of the mother and are transparent; early stages of
development can be easily observed. Zebrafish bridge the gap between humans and simpler invertebrate systems,
like C. elegans and Drosophila.
embryo
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The mouse is the most common mammal model.
Many mutations affecting mouse development or behavior have been
identified.
Genetically engineered mice with specific mutant genes are now used to study
the functions of these genes in the context of the whole animal.
The mouse and human genes are very similar with each other.
Not surprising that mutations in homologous genes result in similar
developmental defects in both species.
f C
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Research in cell biology depends on available laboratory methods and
experimental tools.
Many important advances have directly followed the development of new
methods that have opened novel avenues of investigation.
Tools of Cell Biology
The discovery of cells arose from the development of the light
microscope. Robert Hooke coined the term cell following his observations
of a piece of cork in 1665.
In the 1670s Antony van Leeuwenhoek was able to observe a
variety of cells, including sperm, red blood cells, and bacteria.
The cell theory proposed by Matthias Schleiden and Theodor Schwann in
1838 resulted from their studies of plant and animal cells using microscopes.
It was soon recognized that cells are not formed de novo but arise only from
division of pre-existing cells.
Light Microscopy
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Contemporary light microscopes can magnify objects up to about 1000x.
Most cells are between 1100 m, so they can be observed by light
microscopy, as can some organelles.
Resolution: the ability to distinguish objects separated by small distances;
is even more important than magnification.
The limit of resolution of the light microscope is approximately 0.2 m.
Objects separated by less than that distance appear as one object.
This limit is determined by the wavelength of visible light (), and the
numerical aperture (NA): the light-gathering power of the lens.
is fixed at approximately 0.5 mm.
NA can be envisioned as the size of the cone of light that enters the lens.
NA
0.61Resolution
sinNA
= refractive index of the medium between the objective lens and specimen.
=
vin a vacuum
vin a medium
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Numerical aperture ( sin):
= ~1.0 for air, but can be increased to a maximum of 1.4 by using an oil-
immersion lens.
Maximum foris 90, at which sin = 1, so maximum possible for NA = 1.4.
The theoretical limit of resolution is thus:
m22.04.1
5.061.0Re m
solution
Larger or :
Object lens is more closer to specimen
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Light passes directly through the cell.
Cells are often preserved with fixatives (e.g., formaldehyde) and stained withdyes to enhance the contrast.
This technique cant be used to study living cells.
Types of light microscopy
(a) formaldehye-Asn adduct
(b) cross-linking of Lys and Asn by formaldehyde Fixed and stained kidney tumor
Bright-field microscopy:
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Both convert variations in density or thickness to differences in contrast that
can be seen in the final image.
(by modification of optics, e.g., different angles of incident light)
(A) Bright-field (B) Phase-contrast (C) differential interference-contrast
Modification of optics + computer-assisted image analysis and processing. It
allows visualization of protein filaments with a diameter of only 0.025 m.
Single microtuble can be observed
Phase-contrast microscopy and differential interference-contrast microscopy:
Video-enhanced differential interference-contrast microscopy:
Shadow at this side
Fl i
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Used for molecular analysis (e.g., location of a protein).
A fluorescent dye is used to label the molecule of interest (called staining) in
fixed or living cells.
The fluorescent dye molecules absorb light at one wavelength and emit lightat a different wavelength.
This fluorescence is detected by illuminating the specimen with a
wavelength of light that excites the fluorescent dye, then using filters to
detect the specific wavelength of light that the dye emits.
Fluorescence microscopy:
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The green fluorescent protein (GFP) of jellyfish: widely used to visualize
proteins in living cells, by fusing it to a protein of interest. (no need for staining)
Fluorescence recovery after photobleaching (FRAP):
This is used to study rate of protein movement in living cells.
Methods using GFP:
Fluorescence resonance energy transfer (FRET):
This is used to study interactions between proteins in a cell.
The light emitted by one GFP variant excites the second.
High-intensity light
destroying the
chromophore
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Increases contrast and detail by analyzing fluorescence from a single point.
A small point of light from a laser is focused on the specimen at a particular
depth. The emitted fluorescent light is collected by detector such as a videocamera.
Confocal microscopy:
The emitted light must pass through a pin-
hole aperture (confocal aperture). Thus
only light emitted from the plane of focus is
able to reach the detector. Scanning across the specimen generates
a two-dimensional image of the plane of
focus.
A series of images can be used to
reconstruct a three-dimensional image.
*In fluorescence microscopy, out-of-focus
emitted lights give a blurred image.
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Excitation of a fluorescent dye is achieved by 2 or more photons.
Therefore, excitation occurs only at the point in the specimen where the
laser beams are focused.
No need for passing the emitted light through a pinhole aperture. The localization of excitation minimizes damage to the specimen, allowing
three-dimensional imaging of living cells.
Multi-photon excitation microscopy:
Fluorophore can absorb multiple low-
energy photons simultaneously and be
excited. The total energy equals its one-
photon excitation energy.
El t i
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Transmission electron microscopy Specimens are fixed and stained with salts of heavy metals, which provide contrast
by scattering electrons. A beam of electrons is passed through the specimen and forms an image on a
fluorescent screen.
Electron beams deflected by heavy metal
ions do not contribute to the final image,so that the stained area appears dark.
Specimens can be prepared by either
positive or negative staining.
Electron microscopy can achieve much greater resolution (0.2 nm) than
light microscopy because of the short wavelength of electrons (0.004 nm;
105
times shorter than the visible light).
The aperture angle of the electromagnetic lens is ~0.5
o
. The max. resolutionis about 0.2 nm (~0.61x0.004/1xsin0.5).
Resolution for biological samples is about 1 to 2 nm because of their
inherent lack of contrast. But, it is still 100x better resolution than light
microscopy.
Electron microscopy:
Negative staining of actin filament
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Electron tomography generates three-dimensional images by computer analysis
of multiple two-dimensional images obtained over a range of viewing directions.
Metal shadowing is another technique used to visualize the surface of
subcellular structures or macromolecules.
The specimen is sprayed with evaporated metal, such as platinum.
Surfaces facing the evaporated metal are coated more heavily than other
surfaces, which results in a shadowing effect.
Actin/myosine filaments
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Freeze fracturing:specimens are frozen in liquid nitrogen and then
fractured with a knife blade. This often splits the lipid bilayer, revealing the interior faces of a cell membrane. The specimen is then shadowed with platinum.
Membranes of two
adjacent cells; membrane
proteins are observed as
particles
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Scanning electron microscopy provides a three-dimensional image of cells. The surface of the cell is coated with a heavy metal, and a beam of electrons is used to scan
across the specimen.
The electron beam does not pass through the specimen.
The electrons that are scattered from the sample surface are collected to generate a3D image.
The resolution of scanning is ~10 nm, it is restricted to studying whole cell
rather than subcellular organelles or macromolecules.
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In order to determine the function of organelles, they were isolated from the
cell.
Differential centrifugation was developed in the 1940s and 1950s to
separate cell components on the basis of size and density.
Subcellular fractionation
ER at 200,000g
ribosomes at > 200,000gBreaks the plasma membranes and ER
into small fragments without breaking
up other cell compartments
Larger and more dense
ones at lower speed
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Greater purification can be achieved by density-gradient, in which organelles
are separated by sedimentation through a gradient of a dense substance,
such as sucrose. In velocity centrifugation in density-gradient, the starting material is layered on top
of the sucrose gradient. Particles of different sizes sediment through the gradient atdifferent rates.
Sample at the top
Sedimentation velocity
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Equilibrium centrifugation in density gradient is used to separate
subcellular components on the basis of their buoyant density. Sample is mixed together with sucrose or cesium chloride in a centrifuge tube;
centrifugation forms a concentration gradient of the solutes.
The sample particles are centrifuged until they reach an equilibrium position atwhich their buoyant density is equal to that of the surrounding sucrose or cesium
chloride solution. Example: separation of
14N or
15N labeled DNA molecules
Centrifugal force
G th f i l ll i lt
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In vitro culture systems of plant and animal cells enable scientists to study
cell growth and differentiation, and perform genetic manipulations.
Most animal cell types attach and grow on the plastic surface of dishes used
for cell culture.
Growth of animal cells in culture
The culture media for animal cells are complex and must include salts and
glucose, and various amino acids and vitamins that cells cant make for
themselves.
Serum provides polypeptide growth factors. The identification of individualgrowth factors makes it possible to culture cells in serum-free media.
Harry Eagle was the first researcher to describe a defined medium for
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Harry Eagle was the first researcher to describe a defined medium for
animal cells, in 1955.
This has enabled scientists to grow a wide variety of cells under defined
experimental conditions, which is critical to studies of animal cell growth and
differentiation.
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An initial cell culture from tissue is a primary
culture.
They can be replated at a lower density to form
secondary cultures many times.
Most normal cells such as fibroblasts cannot bereplated and grown indefinitely. They stop
growing and die.
Embryonic stem cells and tumor cells can proliferate
indefinitely in culture and are referred to as permanent orimmortal cell lines.
Permanent cell lines have been particularly useful for many
types of experiments because they provide a continuous and
uniform source of cells.
*Doubling time of most actively growing animal cells is ~20 hrs. That of E. coli
is 20 min.
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Plant cells can also be cultured.
In contrast to polypeptide growth factors of
animal cells, the growth factors of plant cells are
small molecules. Given appropriate growth factors, plant cells
produce a mass of undifferentiated cells called a
callus.
Many plant cells are capable of differentiation into
many different cell types. (Pluripotency)
Sometimes an entire plant can be propagated from a single cell.
This makes it easy to introduce genetic alterations, opening possibilities for
agricultural genetic engineering.
Plant cells:
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Viruses reproduce by infecting host cells and usurping the cellular machinery
to produce more virus particles.
Viruses consist of DNA or RNA surrounded by a protein coat.
Viruses:
Viruses provide simple systems that can be used to investigate the functions
of cells.
Bacterial viruses (bacteriophages) have simplified the study of bacterial
genetics.
Bacteriophage T4 infects E. coli.
In a culture of bacteria on agar, the replication of T4
leads to the formation of clear areas of lysed cells
(plaques).
Viral mutants (e.g. that will grow in one strain ofE. coli
but not another) are easy to isolate. Thus, T4 is
manipulated even more readily than E. colifor studies
of molecular genetics.
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The genome of T4 is 23 times smaller than that ofE. coli, further facilitating
genetic analysis.
Bacterial viruses have provided extremely useful experimental systems for
molecular genetics and have led to understanding many fundamental
principles.
Viruses are also important in studies of animal cells.
There are many diverse animal viruses.
The retroviruses have RNA genomes but synthesize a DNA copy of their
genome in infected cells. These viruses first demonstrated the synthesis ofDNA from RNA templates.
Some animal viruses convert normal cells to cancer cells.
This was first described by Peyton Rous in 1911.
Studies of these viruses have contributed to our current understanding ofcancer, and many of the molecular mechanisms that control animal cell
growth and differentiation.