Preview of Cell

BIO 321 Cell Biology ▪ Hartz
A Preview of Cell Biology
Beginnings of Cell Biology
Discovery of cells was based on the remarkable ability of curved glass surfaces to bend light and form images
 Mid 1600’s Robert Hook
 Examined cork (from bark which is dead plant cells)  saw lots of tiny compartments he called cells
 His observations were limited by the low magnification power (30X enlargement) of his microscope
 A few years later  Antonie van Leewenhoek
 He produced an improved lens which enabled him to be the first to observe living cells (single-celled
organisms in pond water that he called “animalcules”; bacteria from teeth scrapings); increased magnification
to 300X
 Although not inventor of microscope, he advanced it so that by 1673, Leeuwenhoek was discovering things
that no human eye had ever seen! (many believed his lens magnified 500x verses R.Hooke’s which was 30x)
 He started bacteriology and protozoology, he advanced parasitology, and he accurately described many human
cells, including RBCs, WBCs, sperm, and other human tissues (e.g. skeletal muscle).
 Leeuwenhoek was not ashamed to give glory to God in all his discoveries as evident in his letters to the
Royal Society of England1.
 Leeuwenhoek’s faith and convictions:
 “Leeuwenhoek thought that microscopic organisms were greater marvels than macroscopic ones. His
works are full of his admiration for the Wise Creator and His creation, a theme frequently found in his
writings of this period. In becoming better acquainted with creation, men wanted to be near the Creator,..”2
 His apologetic against spontaneous generation and for biogenesis (life comes from life) laid groundwork
for Pasteur in 1800’s. He worked diligently to demonstrate the Genesis principle: that all living things
reproduce faithfully and continually after their kind3.
 “He always referred to God [i.e., Christ, the Creator] as the Maker of the Great All. He not only believed
in God but he admired him immensely—“What a Being, Who would know how to fashion a bee’s wings
so prettily. … His good sense told him that life comes from life. His simple belief was that God had
invented all life in six days.”4
Two factors restricted progress in early cell biology
• Microscopes had limited resolution (ability to see fine detail)
• The descriptive nature of cell biology; the focus was on observation, with little emphasis on explanation
By the 1830s, compound microscopes were used (two lenses)
 Increased magnification and resolution
 Structures only 1 micrometer in size could be seen
 Using a compound microscope, Robert Brown identified the nucleus, a structure inside plant cells
1839 observations of Matthias Schleiden on plant cells and Theodor Schwann on animal cells led to the development
of the Cell Theory in 1839
 Tenet 1: All organisms consist of one or more cells
 Tenet 2: The cell is the basic structural unit for all organisms and thus is the structural unit of life
1855 addition of a new tenet to the Cell Theory by Rudolf Virchow
 Tenet 3: All cells arise only from preexisting cells
Dobell, C. 1932. Anthony van Leeuwenhoek and His “Little Animals.” London: Staples Press.
Schierbeek, A. 1959, p.200. Measuring the Invisible World: The Life and Works of Antoni van Leeuwenhoek. London: AbelardSchuman Publishing.
Dobell, C. 1932. Anthony van Leeuwenhoek and His “Little Animals.” London: Staples Press.
DeKruif, P. 1954 (reprint of 1926), p.12. Microbe Hunters. New York: Harcourt, Brace & World, Inc.
There is a huge diversity of cell types (Fig 1.1)
Emergence of Modern Cell Biology
Involves the weaving together of 3 distinctly different strands into a single cord (most intertwining has occurred within
only the last 75 years) (Fig 1.2: don’t need to memorize all the details in this figure, but understand the bigger idea).
(1) Cytology  understanding cell structure
(2) Biochemistry  understanding the chemistry of biological structure and function
(3) Genetics  information flow; DNA is bearer of genetic info and responsible for protein which is used for
structure and function in cells
CYTOLOGY = Study of cells and their structure
Light microscope: used to understand cell structure; allows the identification of cells and some organelles
(membrane-bound structures; “little organs”) such as mitochondria, chloroplast and nuclei
Light Pathway of a Compound Microscope
Microtome (1870’s) and stains/dyes
 Microtomes are used to make thin sections of samples (eg. tissues containing cells). Cells are
dehydrated (killed; “fixed”) and embedded in paraffin/plastic before being sectioned by the
microtome. Stains/dyes are added which can penetrate throughout the thin section giving
contrast, aiding in the identification of subcellular structures.
Units of measurement in cell biology
1,000 millimeters (mm) = 1 meter
1,000, 000 micrometers (um) = 1 meter
1,000,000,000 nanometers (nm) = 1 meter
10,000,000,000 angstroms = 1 meter
1,000 um = 1mm
1,000 nm = 1um
10 angstroms = 1 nm
Micrometer (um) = this unit of widely used to express cell sizes and larger organelles. In general, if
you can see it with a light microscope, you can use micrometer (Fig 1.3a)
Nanometer (nm) = this unit is good to describe molecules and subcellular structures that are hard to
see with a light microscope (Fig 1.3b)
Angstrom = this unit is used to describe at the level of molecules and even chemical bonds
KEY POINT: um and nm are both necessary measurements for the cell biologists
 Optical Principles of Microscopy (also can see Appendix A1-A11 for more background)
When viewing a specimen, two elements are needed to form an image. These elements differ
depending on the use of a light microscope or an electron microscope (Fig A-1).
Two elements needed to form image
Light Microscopy
Source of illumination
Visible light
Electron beam
(λ = 400-700nm)
electrons; λ ~
System of lenses that focuses the illumination on
specimen and forms the image
An object can only be detected by its effect on a wave (either light wave- photons, or electron waves)
(Fig A-2 in appendix)
When a specimen is placed in the path of light or electron beams, the physical characteristics of
the beam is changed in a way that creates an image that can be interpreted by human eyes or film
or video
Resolution: The ability to distinguish adjacent objects as separate from one another. It provides
ability to see fine details in structure. It is governed by 3 factors:
 Wavelength: the smaller the wavelength, the greater the chances of detecting smaller objects
because of their ability to interfere with the wave
 Angular aperature (Fig A-4 in appendix)
 ½ angle of the cone of light entering objective lens (α)
 The larger the angle, the more illumination leaves the specimen and passes through the
objective lens, the sharper and clearer the image
Refractive index (n)
 Light bends (refracts) as it moves from gases to air. Refraction can prevent light rays from
entering high power objective lens.
 Refractive index is a measure of change in velocity of light as it passes from one medium to
another (ex: from air to oil). In air n is approximately equal to 1; in oil n is approximately
1.5. Oil bridges gap between specimen on glass and objective lens and reduces refractions.
Oil has nearly the same refractive index as glass, therefore light rays aren’t bent and this
gives an improved resolution (see below).
o The NA found on the side of all microscope objectives refers to the numerical aperature
 NA = n (refractive index) x angular aperature
 NA ranges from 1-1.4. The greater the NA, the more expensive the objective and better image
quality obtained
o Resolution (“r” values) are theoretical in actual practice. Such limits are rarely reached because of
technical flaws in lenses.
o The 3 factors affecting resolution are described by the Abbe’s equation. You don’t need to memorize
this but understand the basic principle: the larger the numerical aperature (N.A.) (the denominator)
and smaller the wavelength of light (numerator), the greater the resolution.
R (resolution) = 0.61 λ
Can you now see why there is better resolution viewing specimens in oil verses water? Or using EM
verses light microscopy?
Note: Smaller the resolution, the larger the magnification; Resolution is inversely proportional to magnification
Magnification Approximate Resolution
Light Microscopy using a glass lens (Air)
Light Microscopy using a glass lens (Oil)
Electron Microscope
► New advanced light microscopes can now see with a resolution of 100nm!
o Bright field microscopy:
 White light passed directly through specimen
 Unless cell is naturally pigmented, image has little contrast (cells are ~70% water)
– Even though there may be different refractive indexes, the optics are missing to enhance
these differences, so it is best to use a stain for visualization. Problem: Most staining
procedures require that cells be fixed (killed, usually with formaldehyde), so features
observed could be artifacts due to fixation process.
To overcome this disadvantage, a variety of special optical techniques have been developed to make it
possible to observe living cells.
– To allow observation of living cells: Phase contrast and Differential interference contrast
– To allow observation of either living or dead cells: Fluorescence microscopy and Confocal
Phase Contrast and Differential Interference Contrast
 Cells don’t need staining, so can view live cells!
 Special optics enhance and amplify slight changes in the phase of transmitted light as it passes
through a structure that has a different refractive index than the surrounding medium  causes
the light waves to be out of phase resulting in a dim image. Special optics give contrast to the
image without having to kill cells and stain them
Summary: Two ways to obtain contrast in Light Microscopy: both ways have varying refractive
indexes and out of phase wavelengths, but each case gets its’ contrast by a different method.
(A) Contrast obtained by use of stains. Cell usually killed. Certain wavelengths of light are absorbed by
stain, resulting in a decrease in the amplitude of light. Stains can bind with different affinities to
different types of molecules. Since cells and tissues are composed of different types of molecules,
different areas of the specimen absorb different amounts of stain, which is how contrast is obtained. So
contrast isn’t due so much to altering amplitude of light from out of phase wavelengths (though this
occurs), but contrast is due to differential binding of dye molecules resulting in different amounts of dye
molecules in different places of the cell.
(B) Contrast obtained by use of special optics. Living cell. In this case, contrast is due to altering the
amplitude of light from out of phase wavelengths, such that the amplitude is not changed because the
optics can enhance the phase difference.
Fluorescence Microscopy (Figs A-11-A13)
 Commonly used to find the location of a specific protein within a cell or tissue. It uses antibodies
which have been labeled with a fluorochrome.
 Antibodies are proteins which contain highly specific regions that can recognize a specific
three-dimensional structure of another molecule, called an antigen. Antigens can be a
protein, DNA, lipid, or some other molecule. [Antibodies function in an animal’s immune
system. They recognize foreign (non-self) molecules, called antigens, binding them to help
rid the body of them.]
 Fluorochromes are molecules that can emit visible light when UV light of a specific
wavelength is absorbed by it. Typical fluorochromes are rhodamine (red) and fluorescein
Since the fluorochrome is conjugated to the antibody which in turn is recognizing a specific
protein, you can actually visualize the cellular localization of that protein within a cell!
Primary/Direct Immunoflourescent microcospy: In this example, a fluorochrome-labeled
primary antibody is used to detect a protein located on the surface of a cell. However, this same
principle can also be used to detect proteins inside cells. (Fig 1A-2)
Secondary/Indirect Immunofluorecent Microcopy: Instead of attaching a fluorochrome to
the primary antibody (which recognizes the antigen directly), attach the fluorochrome to a
secondary antibody. The secondary antibody specifically recognizes several locations on a
single primary antibody (forming a “sandwich-like” interaction). The benefit of this approach
is to amplify the signal if the antigen is in very small amounts in a cell. (Fig 1A-3)
More recently quantum dots (instead of fluorochromes) have been conjugated to antibodies. These dots are tiny,
light-emitting crystals that are more stable and tuned to a very specific wavelength of UV light.
Labeling Cells Using Two Different
Colors. Antibodies that recognize any
one of thousands of specific antigens are
commercially available. By using
different combinations of antibodies and
dyes, more than one molecule in a cell
can be labeled at the same time.
Different dyes can be imaged using
different combinations of fluorescent
filters, and the different images can be
combined to generate striking pictures
of cellular processes (Fig 1A-4). In
some cases, instead of a fluorescent dye,
antibodies can be linked to an enzyme
performing chemical reaction, resulting
in a colored precipitation product that
can be seen using a standard
Limitation of fluorescent microscopy is that there is emitted light above and below the focal plane
of the image which can cause the image to look blurred; this in turn can make it hard to be certain
of a protein’s true intracellular location.
Green Fluorescent Protein (GFP) (Fig A-14)
 GFP is a naturally fluorescent protein made by jellyfish
 Using recombinant DNA techniques, scientists can fuse DNA encoded GFP to a gene coding
for a particular cellular protein of which you are wanting to study inside a cell. The resulting
recombinant DNA can then be introduced into cells, where it is expressed to produce a
fluorescently-tagged version of the normal cellular protein (a hybrid protein)  allowing
researchers to follow a particular protein in living cells (one can find the location and
subsequent path a newly made protein takes to its final destination).
Confocal Microscopy (Fig A-17)
 The confocal makes up for the limitations with conventional fluorescent microscopy.
 It uses a laser beam to scan only a single focal plane at a time, eliminating emitted light above
and below the image. In other words, it takes optical “sections” through the image without using
a knife. Images captured in multiple focal planes can be recombined into a 3D image of the cell!
 Several human diseases, such as Tay-Sachs disease, are due to a mistargeting of a protein, such as
an enzyme, to its proper intracellular compartment. In the case of Tay-Sachs a critical enzyme
never reaches the lysosomes so it can digest certain lipids in nerve cells. The accumulation of
these lipids in the brain usually results in death of the child by age 3. The power of confocal
microscopy is that it can be used to look at a protein’s true intracellular location. Procedurally,
this can be done by performing a double fluorescent labeling where the intracellular compartment
of interest (like lysosomes) can be labeled with one colored-fluorochrome (such as green) and the
protein of interest (like the enzyme that degrades lipids) can be tagged with an antibody labeled
with a different colored-fluorochrome (such as red). The question of whether the protein arrives
in a particular cellular compartment can then be addressed. If the protein is located in the correct
cellular compartment true colocalization will be visualized in a new color that forms when the
two fluorescent colors overlap in a thin optical section taken through a cell with a confocal
microscope. For example, the color produced by an overlap of red and green fluorochromes is
yellow. The limitation of fluorescent microscopy is that it is possible to get yellow when the
protein’s location is not in that actual cellular compartment, that is, it can give a false
colocalization for reasons mentioned above.
Comparison of confocal microscopy and traditional fluorescent microscopy (A-15)
Digital Video Microscopy
 Uses a video camera and computer storage
 Can observe living cells for extended periods of time
o TEM (tramsmission electron microscopy) [Some representative pictures below]
Root tip cell
(TEM Fig 1.5)
Useful for viewing internal cellular and organelle structures
Electrons can be transmitted through specimen in TEM (but not in SEM)
General procedure: Specimen is fixed and penetrated with a resin so that it is a solid block of
plastic. Then, an ultramicrotome (diamond knife) is used to prepare ultrathin sections (1/200th of a
single cell!). Since cells are organic they are rich in carbon atoms, which have lower atomic
density than other atoms. Atomic density needs to be added to the specimen so that contrast can
be seen. This is done by by shadowing (soaking) the specimen in a heavy metal solution.
Shadowing may (or may not) be added to the specimen at an angle (addition of heavy metal to the
specimen at an angle can add depth to the image). Contrast is due to differential binding of the
heavy metal atoms to the specimen. In other words, different areas of the cell bind metal
differently. Then when subjected to EM, at less dense areas, electrons go through specimen, hit
detector, and are seen as light areas on an image. At more dense areas (where have greater
binding of metal), electrons are lost due to being scattered from the detector, and thus appear as
dark areas in an EM image.
SEM (scanning EM) (Fig 1.5)
SEM is similar to TEM, but cheaper, has additional magnet, and a little less resolution.
Commonly used to study whole cells and tissues rather than subcellular organelles.
General procedure: Cells are killed but not usually sectioned with an ultramicrotome. Entire
surface shadowed with a thin film of metal. In this case, shadowing is not done at an angle. Then
the electron microscope scans surface of specimen to form an image by detecting electrons
deflected from outer surface. The sense of depth and 3D look has to do with the angle of the
specimen’s surface relative to the electron beam.
Other specialized approaches in electron microscopy (which we won’t discuss) allow for 3D
visualization of specimens, and one approach even allows visualization of individual atoms!
Beginnings  Friedrich Wohler, 1828
1860’s Louis Pasteur
Showed that fermentation of sugar was carried out by living yeast cells  he linked the activity of living
organisms to specific biochemical processes. Living cells can undergo biochemical reactions. “Biochemical” refers to the idea that a chemical could be made by a living organism.
1897 Eduard and Hans Buchner
Showed that the laws of Chemistry and Physics not only apply to the nonliving world, but also to the
living world. He demonstrated that biological, organic compound urea could be synthesized in lab from
inorganic starting materials.
Demonstrated that fermentation could take place in yeast cell extract (outside intact living cells). It
eventually became clear that the active ingredient in the yeast extract were enzymes.
1920’s and 1930’s  elucidation of biochemical pathways (ex: fermentation and related cellular pathways)
Gustav Embden and Otto Meyerhof  Embden-Meyerhof pathway; glycolysis pathway
Hans Krebs; Krebs cycle, also known as TCA (tricarboxylic acid) cyle
Fritz Lipmann  showed that ATP is the principled energy storage in cells
Use of radioactive isotopes
Melvin Calvin’s work in 1950’s elucidated the Calvin cycle in photosynthesis using C14 isotope
Centrifugation: usefulness in separating and isolating organelles and macromolecules on the basis of size,
shape, and/or density, called subcellular fractionation. (see page 327-329): Types: Differential, Density
gradient, Equilibrium density centrifugations
Equipment = ultracentrifuge: Speeds up to 100,000 rpm with forces of 500,000 xg (force of gravity); armor
plating chamber under vacuum
Differential centrifugation
Separates based on size and/or density. Dense particles sediment rapidly vs. smaller, less dense ones
(Fig 4B-1)
The Svedberg unit (S) is a unit for sedimentation rate. The sedimentation rate for a particle of a given
size and shape measures how fast the particle 'settles', or sediments in a tube subjected to high g-force.
The Svedberg unit (S) offers a measure of particle (such as an organelle or macromolecule) size based
on its rate of travel using Svedberg units = S (after Swedish scientist who developed ultracentrifuge
~1920-1940). The Svedberg coefficient is a nonlinear function. A particle’s mass, density, and shape
will determine its S value. Typically bigger particles sediment faster and have higher S values. “S”
units are not additive since they represent rate of sedimentation, not weight. (Fig 12A.2, 8th Edition)
Basic procedure (Fig 4B-2):
 Homogenize (ice cold isotonic media) tissue
 Subject homogenate to successively higher centrifugal forces and for longer times to isolate
subcellular fractions. The supernatant from one step is poured off and added to a new tube
that is centrifuged at a higher speed, ect..
 The material from each pellet can be analyzed by EM or biochemical studies (eg. look for
particular enzyme activities).
Density gradient centrifugation (Fig 4B-3)
 Place sample as a thin layer on top of a concentration gradient of solute  centrifuge
 Particles of different size or density move down as discrete zones (bands) that migrate at different
rates since the gradient is less dense than the organelles to be separated. If centrifugation occurs over
a long time, all bands will pile up at bottom. However, if stop centrifugation as discrete point, one can
collect each separate band for analysis by poking a hole in bottom of tube and collecting fractions.
Each fraction can be tested biochemically or by EM to determine which organelles it is enriched in.
Equilibrium density centrifugation
 Similar to above, except the solute used to make the concentration gradient is more concentrated at
some point along the tube than the organelles to be separated. In other words, the gradient spans the
range of densities of organelles [the solute used to separate organelles is typically sucrose; whereas the
solute used to separate nucleic acids is cesium chloride].
 Organelles migrate through the tube until they reach their buoyant density at which point they remain
there indefinitely, even if spin for long periods of time. Following centrifugation, the bottom of the
tube can be poked and fraction collected as mentioned above for analysis.
EM and ultracentrifuge were developed at around the same time and both are critical to biochemical
understanding of cells
Chromatography  also important for isolation and purification of subcellular components
o A mixture of molecules in solution is progressively fractionated as this solution (called the “mobile
phase”) flows over the column (called the “nonmobile phase”).
o There are different types of nonmobile phases that can be used. Each type is used to separate by a
different chemical property, such as size, charge, or the affinity of specific molecules.
Comparing centrifugation and chromatography:
 Both can separate according to size.
 Centrifugation typically separates organelles and macromolecules based only on size/shape/density;
whereas, chromatography is usually used to separate macromolecules and smaller cellular components
(instead of organelles) not only based on size but also based on charge and chemical affinity (ex:
ability to bind to specific antibodies covalently attached to the immobile phase)
o Related to the above procedure but uses an electric field to separate proteins or nucleic acids based on
charge and/or size.
o SDS-PAGE (sodium dodecylsulfate polyacrylamide gel electrophoresis) is used for separating proteins;
whereas agarose is used for separating nucleic acids.
SDS-PAGE for protein separation
(A dalton = mass of one hydrogen atom, or 1.66 x 10-24grams)
Mass spectrometry
o After proteins have been separated by electrophoresis, they can be digested into smaller peptides
o Mass spectrometry can be used to identify these peptides based on differences in mass and charge. This
data can then be compared to predicted masses of peptides that would be produced by DNA sequences
present in genomic databases. This comparison permits the proteins produced by newly discovered genes
to be identified. Mass spectrometry has led to significant advances in the emerging field of proteomics
where researchers are attempting to determine the structure and properties of all the proteins produced by a
GENETICS: Flow of genetic information.
Genetic information flow in a Cell (Fig 1.7)
1866 Gregor Mendel: Used pea plants to lay out principles of segregation and independent assortment of
hereditary factors (which we now know as genes)
1869 Friedrich Miescher: Discovered DNA using human pus from bandages
1880 Walter Flemming: Saw chromosomes in dividing cells; calls the division process “mitosis”
o Chromosome number became known as a distinctive characteristic for a species and shown to remain constant
from generation to generation
1903 Walter Sutton: Formulates the “Chromosome Theory of Heredity”: he was the first the link the
chromosome threads described by Flemming with the hereditary factors mentioned by Mendel; Thus, he suggested
that Mendel’s hereditary factors were located on chromosomes in the nucleus
o Thomas Morgan provided strong evidence for the Chromosome Theory by demonstrating that specific
morphological traits in the fruit fly were found on specific chromosomes (sex-linkage)
1914 Robert Feulgen: His staining technique showed that DNA was a component of chromosomes
Initially thought DNA was not the genetic material, but 1944 Avery, MacLeod, McCarty demonstrated this was the
case. Scientific community remained unconvinced until 1952 when Hershey/Chase showed that bacterial DNA,
not protein, enters bacterial cells when infected with virus.
1940’s Beadle and Tatum: Formulated the “One Gene-One Enzyme” hypothesis, which states that the function
of a gene is to control the production of a single protein
1953 Watson and Crick: Proposed the double-helix model for DNA structure
Establish that DNA specifies amino acid order and the property of a protein; several kinds of RNAs serve as
intermediates in protein synthesis
o Discovery of enzymes that synthesize DNA (Kornberg) and RNA
o Cracking the genetic code (relationship between order of nucleotides and order of amino acids)
o Monod and Jacob deduced mechanism for regulation of bacterial gene expression (lac operon)
Important Techniques Developed in Genetics:
 Gel electrophoresis and ultracentrifugation to separate RNA and DNA molecules
 Nucleic acid hybridization
o Two nucleic acids with complementary sequences can form double-stranded hybrid DNA/DNA, or
DNA/RNA, or RNA/RNA hybrids  this is used in the identification and isolation of specific DNA or RNA
 1970’s Recombinant DNA technology (the greatest contribution to the area of biotechnology)
o Restriction enzymes: Like “molecular scissors” = cut double-stranded DNA at specific sequence sites
producing DNA fragments which can be joined in various ways to form recombinant DNA molecules,
which lead to the process of DNA cloning
o Cloning (Berg, Boyer, Cohen): Generation of many copies of specific DNA sequences
 DNA sequence technology
o We now have the ability to sequence entire genomes (total DNA of a cell) Ex: bacteria, yeast, roundworm,
plants, animals, human (3.2 billion bases were determined to make up the human genome in a internationally
cooperative project that began in 1990 and was completed in 2003; called the Human Genome Project)
 Use of computer science and biology to analyze vast amounts of DNA sequence data  led to a new discipline
o Bioinformatics: merges computer science with biology to organize and interpret enormous amounts of
sequencing and other data
 This field has shown that there are ~20,000 protein-coding genes in the human genome; half of these
were not known to exist prior to sequencing the genome
 With the DNA sequences for these genes now known, scientists are beginning to look beyond the genome
to study the proteome, the total protein content of a cell. Proteomic studies aim to understand the set of
expressed proteins in a given type of cell or an organism at a given time under defined conditions. An
organism’s proteome is considerably more complex than its genome. For example, the 20,000 genes in
human cells produce 100,000’s of different proteins! The mechanism responsible for this is discussed
more in Genetics class, but involves in part alternative splicing and subsequent biochemical
modifications. This allows cells to produce many protein from a smaller number of genes.
 Yeast two-hybrid system allows determination of how proteins interact within a cell
 Nanotechnology: development of tiny tools – nanometer-sized machines, tools, and biosensors, and computeraided analysis of experimental results (used in medicine as well as other areas).
o Nanotechnology is projected to play a critical role in patient-specific therapy. This will depend heavily upon
the development of a systems biology approach to clinical medicine based upon "-omic" technology analysis:
the ability to simultaneously analyze 1000’s of different types of molecules globally throughout the cell.
 Transcriptomics: the study of all transcribed genes in a particular cell (use of DNA/RNA microarrays)
 The expression levels of hundreds or even thousands of genes can be monitored simultaneously,
making it possible to study all the genes in the genome at the same time.
A DNA microarray assay: Each colored spot on
microchip contains DNA of one specific gene in a
cell. Color indicates levels of transcriptional activity
in response to a stimulus. Green represents genes
whose activity has increased, red activity decreased,
and yellow no change in transcriptional activity.
 Proteomics: the study of all the proteins in a cell
 Metabolomics: the analysis of all metabolic reactions happening at a given time in a cell
 Lipidomics: the study of all the lipids in a cell
Since many diseases have overlapping symptoms, “omic” technology may provide useful biomarkers in
medicine for diagnosing and treating certain diseases.
CRISPR Technology is a recently developed (in 2012) tool for editing genomes. It allows researchers to easily
alter DNA sequences and modify gene function. In popular usage, "CRISPR" (pronounced "crisper") is shorthand
for "CRISPR-Cas9." CRISPRs are specialized stretches of DNA. The protein Cas9 (or "CRISPR-associated") is an
enzyme that acts like a pair of molecular scissors, capable of cutting strands of DNA.Its many potential
applications include correcting genetic defects, treating and preventing the spread of diseases and improving crops.
In spite of its boasted promise, several ethical challenges arise from using this system which involve the use of
fertilized eggs. These include adapting this technology to create “savior babies”, genetic enhancements/designer
babies, eugenics, and editing entire populations of a particular species.
Model Organisms which Play a Key Roll in Cell Research:
Use of Cell Tissue Culture as a Model Organism
• Cell cultures are commonly used as model systems to study cancer, viruses, proteins, and cellular
• Some of what is learned from cultured cells may not reflect what happens within an intact organism
Use of the Scientific Method to Study Cells
 In a typical experiment, one condition is varied, called the independent variable
 All other variables are kept constant
 The outcome is called the dependent variable
 In vivo experiments involve living organisms
 In vitro experiments are done outside the living organisms, for example, in a test tube
End of the Chapter Problems: pgs19-20; #1-1 - 1-5 [Note: There is an error in the solution manual. For 1-3(b) the
answer should be 3x108th (not 5x108th). A clarification needs to be made with the answer given in problem 1.5f: both
chromatography and electrophoresis can be used to separate based on charge, but electrophoresis can be used to
determine a relatively accurate molecular weight for a protein or DNA molecule whereas chromoatography isn’t as
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