Cells are small and complex. It is hard to see their structure, hard to discover their
molecular composition, and harder still to find out how their various components function.
What we can learn about cells depends on the tools at our disposal. Principal methods in
microscopy used to study cells. Understanding the structural organization of cells is an essential
prerequisite for understanding how cells function. Optical microscopy will be our starting point.
An important advantage of optical microscopy is that light is relatively nondestructive
Light microscopy is limited in the fineness of detail that it can reveal.
A typical animal cell is 10-20 μm in diameter, which is about one-fifth the size of the smallest
particle visible to the naked eye. It was not until good light microscopes became available in
the early part of the nineteenth century that all plant and animal tissues were discovered to
be aggregates of individual cells.
Animal cells are not only tiny, they are also colorless and translucent. Consequently, the
discovery of their main internal features depended on the development, in the latter part of
the nineteenth century, of a variety of stains that provided sufficient contrast to make those
features visible. Similarly, the introduction of the far more powerful electron microscope in the
early 1940s required the development of new techniques for preserving and staining cells before
the full complexities of their internal fine structure could begin to emerge. To this day,
microscopy depends as much on techniques for preparing the specimen as on the performance of
the microscope itself.
To make a permanent preparation that can be stained and viewed at leisure in the
microscope, one first must treat cells with a fixative so as to immobilize, kill, and preserve them.
In chemical terms, fixation makes cells permeable to staining reagents and cross-links their
macromolecules so that they are stabilized and locked in position. Some of the earliest fixation
procedures involved immersion in acids or in organic solvents, such as alcohol.
There is little in the contents of most cells (which are 70% water by weight) to impede the
passage of light rays. Thus, most cells in their natural state, even if fixed and sectioned, are
almost invisible in an ordinary light microscope. One way to make them visible is to stain
them with dyes.
In the early nineteenth century, the demand for dyes to stain textiles led to a fertile period for
organic chemistry. Some of the dyes were found to stain biological tissues and, unexpectedly,
often showed a preference for particular parts of the cell the nucleus or mitochondria, for
example making these internal structures clearly visible. Today a rich variety of organic
dyes is available, with such colorful names as Malachite green, Sudan black, and Coomassie
blue, each of which has some specific affinity for particular subcellular components. The
dye hematoxylin, for example, has an affinity for negatively charged molecules and
therefore reveals the distribution of DNA, RNA, and acidic proteins in a cell. The chemical
basis for the specificity of many dyes, however, is not known.
Figure 9-7. Two ways to obtain contrast in light microscopy. (A) The stained portions of the
cell reduce the amplitude of light waves of particular wavelengths passing through them. A
colored image of the cell is therebyobtained that is visible in the ordinary way. (B) Light passing
through the unstained, living cell undergoes very little change in amplitude, and the structural
details cannot be seen even if the image is highly magnified. The phase of the light, however, is
altered by its passage through the cell, and small phase differences can be made visible by
exploiting interference effects using a phase-contrast or a differential-interference-contrast
Internal Structure of the Cell
Membrane protein. Special proteins inserted in cellular membranes create pores that permit the
passage of molecules across them
These have a polar head group and two hydrophobic hydrocarbon tails. The tails are usually
fatty acids, and they can differ in length (they normally contain between 14 and 24 carbon
atoms). One tail usually has one or more cis-double bonds (i.e., it is unsaturated), while the other
tail does not (i.e., it is saturated)
Intracellular compartment and Protein sorting
Unlike a bacterium, which generally consists of a single intracellular compartment
surrounded by a plasma membrane, a eucaryotic cell is elaborately subdivided into
functionally distinct, membrane-enclosed compartments.
Nucleus - contains the main genome and is the principal site of DNA and RNA synthesis. The
surrounding cytoplasm consists of the cytosol and the cytoplasmic organelles suspended in it.
The ER has many ribosomes bound to its cytosolic surface; these are engaged in the synthesis of
both soluble and integral membrane proteins, most of which are destined
either for secretion to the cell exterior or for other organelles. We shall see that whereas proteins
are translocated into other organelles only after their synthesis is complete, they are translocated
into the ER as they are synthesized
Golgi apparatus consists of organized stacks of disclike compartments called Golgi cisternae; it
receives lipids and proteins from the ER and dispatches them to a variety of destinations, usually
covalently modifying them en route.
Mitochondria and (in plants) chloroplasts generate most of the ATP used by
cells to drive reactions that require an input of free energy; chloroplasts are a
specialized version of plastids, which can also have other functions in plant
cells, such as the storage of food or pigment molecules
Lysosomes contain digestive enzymes that degrade defunct intracellular organelles, as well as
macromolecules and particles taken in from outside the cell by endocytosis.
On their way to lysosomes, endocytosed material must first pass through a series of organelles
called endosomes. Peroxisomes are small vesicular compartments that contain enzymes utilized
in a variety of oxidative reactions.
Cells have to organize themselves in space and interact mechanically with their environment.
They have to be correctly shaped, physically robust, and properly structured internally. Many of
them also have to be able to change their shape and move from place to place. All of them have
to be able to rearrange their internal components as they grow, divide, and adapt to changing
circumstances. All these spatial and mechanical functions are developed to a very high degree in
eucaryotic cells, where they depend on a remarkable system of filaments called the cytoskeleton.
The cytoskeleton pulls the chromosomes apart at mitosis and then splits the dividing cell into
two. It drives and guides the intracellular traffic of organelles, ferrying materials from one part of
the cell to another. It supports the fragile plasma membrane and provides the mechanical
linkages that let the cell bear stresses and strains without being ripped apart as the environment
shifts and changes. It enables some cells, such as sperm, to swim, and others, such as fibroblasts
and white blood cells, to crawl across surfaces. It provides the machinery in the muscle cell for
contraction and in the neuron to extend an axon and dendrites. It guides the growth of the plant
cell wall and controls then amazing diversity of eucaryotic cell shapes.
membrane-bound sac with liquid + dissolved salts, ions, pigments, and waste products
maintains cell shape (turgid)
temporary storage area
A vacuole may occupy 90% of the cell when the plant cell is mature
the membrane of the vacuole is tonoplast like how a plasma membrane works
turgid cell is swollen or firm because of water uptake
Onion bulb for plant cell
Cheek cell for animal cell
Root nodules of Makahiya plant(Mimosa pudica) or yakult for live bacterial cells
Bread molds for fungi
Methylene blue and iodine solution
Glass slides and cover slips
Knife or cutter