- Using Magnification
There are many things in the world that our eyes just
aren't built to see: things too far away, or
too small, are beyond our ability to observe without some sort of
devices to help. Just as the telescope was a critical device
for astronomers, the invention and development of the microscope was critically
important to the progress of biology.
Although magnifying spectacles (glasses, sort of) had been in
widespread use since the 1300s, the use of lenses to see very tiny
objects was a slowly-developing technology. First of all,
the tinier an object is, the less light reflects off it or passes through
seeing anything really tiny requires a decent illumination system -
you've got to get a lot of light on it.
Secondly, magnifying lenses used in early microscopes were made of glass
that was not
particularly even or clear, and tended to split light into colors like a
prism, which affected the resolution limits of the lenses.
Resolution can be thought of as how clear a focus you can get;
technically, it is the limit at which two tiny objects which are
close together stop looking separate. The resolution
of early microscopes was very limited by the glass used in the
Resolution in digital cameras.
A slideshow of particularly beautiful microscopic images.
Some important work was done with early
microscopes, although for a long time they were really more of a toy than a
scientific instrument. Like telescopes that were being
developed through that same period, many early microscopes used lenses
in sequence (making them multi-lens or compound microscopes)
to magnify an image. In 1660, Italian Marcello
Malpighi was able to use a microscope to see blood capillaries in
the tail of a fish, providing powerful supporting evidence that
blood circulates in the body (prior to this, since no one knew of
how blood runs from arteries through too-tiny-to-see capillaries to veins and back, it was
thought that the blood flow was one-way from production in the
intestines to consumption in the body tissues). In 1665,
Englishman Robert Hooke found that cork was full of tiny chambers,
which he called cells (there were no actual cells as they are now
known in the dead cork, but the term did come from his label). In the 1670s, Dutchman Antony van
Leeuwenhoek, using a special,
especially pure, non-prisming single lens (a simple microscope) placed
in a holder and held up very close to the eye, was the first
person to write extensively about a world of tiny independent
creatures, which he called animalcules, which seemed to exist all around
but were too small to be seen by eye. Imagine what an odd idea
that must have been to the people of the day!
A history of the microscope.
It wasn't until the 1800s, through a interesting
development period that included instances of thievery, plagiarism and questionable patent
ethics, that many of the distortions of the lenses were corrected.
With the technological limitations for microscopes mostly solved,
by the end of that century microscopes had begun to hit resolution
limits set by physics: to oversimplify, light beams
themselves have a physical size, and when a gap is at or below about 0.2
micrometers the light itself can no longer fit through that gap - you can't see the gap,
just a smudgy blob where the light has been blocked. Objects below that size just could not be resolved
as long as light was used in the imaging system. Light
microscopes (called that because they use light as an imaging
system) would always remain useful, but most of the objects
discussed in the next section on cell structures were invisible to
them. Although there have been some
recent techniques in improving light microscopes' abilities, they
are still limited.
Through the middle of the 1900s, a new system
was developed that could use an electron system, an
adjustable beam much smaller than visible light beams. Electron
beams can be narrowed to below the size of atoms producing incredibly good
The beam is focused with magnets and the final image converted to
light in a way similar to how television screens work.
Recent versions of electron microscopes have been
used to produce images of
microscopes are more expensive and
complicated than light
microscopes, and the beam needs to travel through a vacuum to
avoid scattering off air atoms. They are very useful in
research but not practical to use in classroom teaching labs any time soon.
Basics of light
New advances in light microscopes.
A video showing
how an electron microscope works.
Image of some interacting molecules.
A microscope for seeing atoms.
Picture of an
how microscopes are set up.
There are two basic
microscope set-ups that affect
the type of specimen that can be viewed and what the final image
looks like; both light and
electron microscopes can be set up these two ways. In a typical laboratory class
microscope, light must pass through a specimen to reach the eyes
of the viewer; this set-up is an example of a transmission
microscope. For a specimen to be useful in a
transmission 'scope, the beam needs to be able to pass
through it and reveal its internal details, so it either has to be thin
and semi-transparent, or sliced very thin into sections. Objects are embedded in a
will hold them together (commonly wax for light
microscopy, plastic for electron microscopy) and then thinly
sliced. The ability to translate the two-dimensional
information of sections into three-dimensional concepts is
important in microscopy. Specimens may
then need to be
stained, colored or darkened with special
dyes, to produce clear details. Colored dyes are used in
light microscopy (the use of microscopes is called
"microscopy"), while electron microscope stains have heavy
metals in them (the images are
black-and-white, so the stain
just needs to produce variations in electron absorption).
The other set-up involves reflecting the beam
off the surface of the specimen, which creates a much more
three-dimensional image. This is done by
microscopes, named for the necessity in the electron
version of scanning the surface with the electron beam. A
dissecting microscope is a type of scanning 'scope.
article showing stained sections of
a transplanted bit of kidney.
Basic technique for preparing specimens, mostly for pathology
A typical section of a (slightly broken) cell seen with an electron microscope.
Scanning electron micrograph of an insect head.
A penny seen through a dissecting microscope.
In 1838, two scientists whose research centered on
the microscopic inspection of living things proposed the Cell
Schleiden worked with plants
and may have come up with most of the hypothesis that Theodor
extended to animals. The Cell Theory, as it is applied
Everything alive is made up of
at least one cell.
Cells can only be made from
existing, related cells.
The smallest single thing that
can be considered alive is a cell.
Cells of all living things are
more alike than different.
More on cell
There are two basic types
of cells, prokaryotes and eukaryotes. Prokaryote
species can be found in Archaea and Monera, and are commonly called
bacteria. The rest of the Kingdoms contain eukaryotes.
Prokaryotes are always single cells; they
rarely even form colonial groups. They have cell membranes and
commonly have cell walls. Compared to eukaryotes, prokaryotes
have a simpler architecture: internal chambers are rare.
This means that prokaryotes do not have a nucleus, or most of
the cellular structures dealt with later in this chapter.
Prokaryotes have a single, loop-shaped chromosome in a
specialized zone. Many prokaryotes can make special small
loops of DNA with one to a few genes on them. These are called
plasmids, and may be shared with other cells, changing their
genetics - this is the closest that prokaryotes get to sexual
reproduction. For their "regular" reproduction, they copy the
chromosome, hook each copy to the membrane, and divide the cell
between the copies.
Eukaryotes have 2-ended chromosomes, usually in
matched or homologous pairs; they carry two copies of
every gene. Eukaryotes have many more special internal
structures than prokaryotes, which will be the topic of the rest of
Cells seem to have size limits:
bacteria seem to be close to the smallest a cell can be, and active
cells seem to have a maximum allowable size. No one knows why
for sure, but the leading hypothesis is based on math. If a
spherical cell doubles in volume, it won't have double the surface,
but much less - so all of the workings are doubled, but the way to
get materials to and from those workings don't keep up.
Non-spherical cells aren't quite so restricted, but it is still
thought that rather than get big, cells get more from groupings and
specialization of members in the group, from
More on prokaryotes.
All about prokaryotes (bacteria).
Plasmid production (OriC is a particular gene).
cartoon about plasmids and antibiotic resistance.
Picture of prokaryote cell reproduction.
A 2-ended eukaryote chromosome (2 copies still attached to each
other, preparing for cell reproduction).
An explanation of the math of size limits.
Structures - Outside
Cells of any kind have a barrier
layer around them, the cell membrane or plasma membrane,
that somewhat isolates what's going on inside from the solutions around
the cell (cells can only be fully active in a liquid environment):
this barrier is made by molecules that are lipids with a hydrophilic
phosphate group where one of the hydrophobic fatty acids would normally
be. These phospholipid molecules, in water, naturally form
a bilayer with the fatty acids turned toward each other, a
waterproof layer, and the phosphates facing out at the water, allowing
the membrane to interact with the solution around it. The membrane
is somewhat impermeable, meaning that many materials cannot just
go through the barrier. Since some things can move through, the
membrane is semipermeable.
The membrane is not just phospholipids; floating among those
molecules are many types of proteins, some of which go through both
layers, and some which float in just one side. This concept of
floating phospholipids with a pattern of proteins is called the fluid
mosaic model of membrane.
The proteins can form pores, which will let small particles
through; channels, which may be more selective;
carriers, to move specific molecules through; pumps to
move materials in directions they wouldn't naturally go; receptors,
to allow the cell to interact with its surroundings; markers,
a recognition system for other cells; and many other types of
Image of a phospholipid molecule.
The bilayer (showing how cholesterol acts as a "spacer.")
Fluid mosaic membrane.
And in video.
Some embedded proteins.
Some cells have a secreted
structure outside of the cell membrane that contributes to structure
and can provide a bit of protection. These cell walls,
found in every Kingdom but the animals, can be made of many
Plant cell, showing the cell wall.
There are a few ways that
materials can get into or out of a cell through the membrane.
If a material can pass through the membrane (the membrane is
permeable to it), it moves naturally from where it is in higher
concentration to where the concentration is lower. For
instance, as a cell uses oxygen, there is more oxygen on the outside
moving in than on the inside headed out, so there is a net movement
inside; as cells produce carbon dioxide, the movement is
outward for the same reason. This movement is called
diffusion. Water molecules also diffuse, but then it's
called osmosis. Osmotic movement can actually generate
a pressure - that's what moves water up short plants (eventually,
the weight of the water counteracts the osmotic pressure or root
pressure). When materials diffuse through, they
essentially move by themselves - this is called passive
transport. Some materials can only diffuse when special
proteins let them through: this is facilitated diffusion.
The fact that a cell can control and change what can and cannot
move through it makes them selectively permeable.
What if a material must be moved
through the membrane, going opposite to the way diffusion would move
it? This is active transport, and requires energy from
the cell and specialized structures: protein pumps to move
small particles, or a system to surround materials with membrane and
pull them in as membrane-lined chambers. Going in, this is
endocytosis; going out, as often happens with
secretions, it is exocytosis.
showing diffusion from single spot in an irregular container.
Osmotic pressure raises a water column.
Endocytosis, showing proteins involved.
Cells may have structures
which project outward, including:
Pseudopods are an extension of the cell that has an inside
similar to the cell's insides. These structures can be used
many ways. Pseudopods can be used as slow, directional,
crawling structures, as seen in an ameba or a white blood cell (or a
cancer cell when it turns malignant). They may also function
as a thin extension to aid in floating, or to be used as a kind of
Microvilli are many very thin extensions
whose main purpose is to give the cell more surface area.
They are commonly found in cells that need to move a lot of material
in or out, such as intestinal lining cells (absorbing nutrients) or
in waste-removal systems like our kidneys.
Flagella and cilia are both thin
projections with a core of mobile structures called microtubules.
They are used for swimming, or for moving materials past a
stationary cell. Although homologous, they have several
Rarely any more than 12 on a cell.
Always many on a cell.
May have add-on structures.
not have add-on structures, although they may form
structures by fusing together.
Prokaryotes may have flagella, but they are not
built like eukaryote flagella.
Pseudopod movement video.
Crawling ameba video.
Some pseudopod variations.
Internal structure of flagella and cilia.
Flagella and cilia in action (video).
Cilia on respiratory surfaces (video).
Prokaryote vs eukaryote
Inside a eukaryote cell is a wide variety of chambers, channels,
and clusters of cooperative molecules, doing for the cell jobs that
in our bodies would be done by our organs. These structures
are called organelles. Organelles float in a
water-based fluid with many atoms, molecules, and even larger
particles floating in it - this is called cytoplasm.
The cell is given physical structure by an assortment of proteins
organized into a cytoskeleton.
Cytoskeleton is made up mostly of microfilaments, which hold
things in place and are used to move things like pseudopods and
microvilli, and microtubules, used for structure but also as
conveyors of particles, movers of chromosomes during cell
reproduction, and as the driving force in cilia and flagella.
A fairly famous animation video of cell activity.
A set of animation videos of the cell
and cell structures.
Much more on cytoskeleton.
silly little game good for learning the cell parts (But not how cells
really get them).
Organelles that are made up of
cooperative clusters of molecules are generally found in prokaryotes
as well. Chromosomes, a cluster of DNA and proteins
that keep it tightly packaged except when needed or being copied,
are such a structure. Another such structure are the
ribosomes, a collection of RNA and protein molecules that act to
take a gene code and translate it into a protein sequence. A
nucleolus, a molecular cluster inside the nucleus, is a
storage place and processor of RNA. These are just three
examples of molecule cluster organelles.
How molecules interact in a chromosome.
Nucleolus in a nucleus.
Many organelles have an
internal membrane component. Some are chambers with
specialized, isolated chemistry in them, and some form channels and
ways to subdivide parts of the cell. Here is a list of a few
types of membrane-based organelles:
Cell with organelles labeled.
Many membrane-based organelles
fall into the category of just being simple membrane chambers where
certain functions are performed. Small chambers are
vesicles, and include lysosomes, which contain digestive
enzymes, and peroxisomes, where a lot of recycling of
materials happens. Larger chambers are called vacuoles,
and include food vacuoles, pinched off from the outer
membrane to get materials inside that couldn't otherwise enter,
central vacuoles, which help reinforce support in multicelled
plant systems, and contractile vacuoles, which pump out water
when cells are exposed to dilute surroundings.
Lysosomes sometimes participate when a cell purposely
kills itself, a process called apoptosis. This is a
very important process in multicelled systems: failure to do
this properly is a common underlying cause of cells becoming
Many types of
Electron micrograph of a cell, with "fv" as food vacuoles.
Apoptosis as a response to virus damage.
Golgi bodies (also called Golgi apparatus and Golgi
complexes) are a collection of chambers, often roughly pyramidal in
shape, where materials are processed to be secreted from the
cell. The top of Golgi bodies break off as vesicles, which
carry the secretions to the membrane, fuse with the membrane, and
dump the secretions out of the cell.
More on Golgi Apparatus.
Endoplasmic reticulum is a
network of channels that is used to move materials from place to
place with a bit more control than just letting them diffuse.
Smooth endoplasmic reticulum (SER) are just membrane
channels; rough endoplasmic reticulum (RER) has
ribosomes stuck in the membranes, so newly-made proteins are
released into the proper channel to go where they need to in the
ER often connects to the nucleus.
nucleus actually has a double membrane, called the
nuclear envelope, to isolate it from the rest of the cell.
This is a chamber where DNA is stored and processed, so it's where
the chromosomes (when somewhat unwound, they are in the form called
chromatin) and nucleoli are.
There are at least two organelles that seem to have a weird
history. Although they are found inside eukaryote cells, these
chambers have chemistry, structure, and genetics like certain
prokaryote cells. The endosymbiont theory proposes that
in the distant past, a large cells took in prokaryotes whose
abilities made them more useful alive than digested, and the
prokaryotes were protected by being in the larger cells. Cells
that were able to get "guests" into every offspring cell continued
to have an advantage over competitors; eventually, the guests
became more of an organelle than independent agents. Today,
these organelles have small prokaryote-type chromosomes, but not
enough genes to make more of themselves - they need to use genes
from the nucleus for that.
History and evidence for the endosymbiont theory.
still happening - amebas with methane-processing bacteria inside
Almost every eukaryote cell contains an organelle called a
mitochondrion. Inside, the process of aerobic
respiration allows a very efficient mobilization of the energy
in glucose, using oxygen in the process and producing carbon
dioxide and water. The energy that was holding the carbons
together in the glucose is largely moved to many ATP, the basic
energy-supplying molecule of cells.
Mitochondrion and chloroplast.
Mitochondrial diseases: modifying human embryos,
producing 3-parent babies.
Eukaryote cells that perform photosynthesis do the process in
organelles called chloroplasts. These absorb light into
chlorophyll molecules, freeing electrons that energize the reaction
that captures carbon dioxide and water (freeing oxygen) and bonds
the carbons together into the sugar glucose.
More on chloroplasts.
library of cell structure images.