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

microscope.

Internal Structure of the Cell

Membrane

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.

Cytoskeleton

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.

Vacuole

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 Tissue paper Alcohol lamp Inoculating loop Compound microscope