We are going to concentrate on the study of eukaryotic cells. Prokaryotic cells also exist and are found in bacteria and cyanobacteria. All other life forms are eukaryotes. There are a number of differences between eukaryotic and prokaryotic cells, one of which is that eukaryotic cells have membrane bound nuclei.

Before we begin discussing subcellular structure and function, it is useful to suggest a few patterns to be aware of when looking at the cell structure. First, often the form cells and their internal structures take is dictated by the need to control surface area. To appreciate the relative amount of surface area involved we have to compare surface area-to-volume ratios. Two rules apply:

1) If geometric shape is held constant, smaller structures have higher surface area-to-volume ratios than larger structures. (Fig 6.8)

2) If volume is held constant, a sphere has the lowest surface area-to-volume ratio of any structure.

Another thing to look for is the compartmentalization patterns within cells.

A final thing to look for is that there is a tendency for cells that are specialized to perform certain functions that require particular subcellular structures to have an abundance of these structures.

As we develop the internal structure of eukaryotic cells, you should appreciate the differences between plant and animal cells. (Fig 6.9)

The fluid like material inside the cell but outside of the nucleus is cytosol. Cellular components are suspended in the cytosol and the combined material is called cytoplasm. Within the nucleus the analogous material is called nucleoplasm. There are openings in the nuclear envelope that allow the movement of some large molecules and subcellular structures between the nucleoplasm and the cytoplasm. These nuclear pores are like the diaphragms of cameras that can open wider than their resting diameter when necessary and each opening is surrounded with a complex of about 100 proteins that allow selective movement through the pores. (Fig 6.10)

The nuclear envelope is supported internally by a mesh-like structure made of proteins. It is called the nuclear lamina.

Ribosomes are the organelles where polypeptides are assembled. (Fig 6.11) Normally ribosomes exist in the cytoplasm as two separate subunits. Under certain situations the subunits come together about an RNA molecule and translate the nucleic acid message into the primary structure of the polypeptide. This always begins in the cytosol, but if the first several amino acids contain a signal sequence the developing polypeptide and its associated ribosome move toward membranous canals called endoplasmic reticulum. The growing polypeptide enters the canal via a pore. Often the RNA message that is being translated has a number of ribosomes attached to it simultaneously (each at a slightly different point of the translational process) forming a polysome. This process makes it appear that ribosomes are attached to the membranes. Hence this is referred to as rough endoplasmic reticulum. Ribosomes not producing polypeptides with the appropriate signals remain free in the cytosol. Any ribosome can function in either situation. Rough endoplasmic reticulum generally functions to produce proteins that are to be secreted from a cell. When the polypeptide becomes enclosed in the canal an oligosaccharide is covalently attached to it forming a glycoprotein. The sugar regions often later act as signals. (Fig 6.12)

Smooth endoplasmic reticulum does not have ribosomes associated with it. (Fig 6.12) It functions as the site where lipids are synthesized, carbohydrates are metabolized, and where drugs and poisons are detoxified. Hydroxyl groups are attached to drugs and poisons thereby making them soluble in water.

Glycoproteins synthesized in rough endoplasmic reticulum are packaged into transport vesicles in transitionary regions of the endoplasmic reticulum and these transport vesicles merge with the cis face of the Golgi Apparatus. (Fig 6.13) The golgi apparatus consists of a stack of flattened vesicles (dictyosomes). The membranes of the transport vesicles coalesce with the cis oriented dictysome and thus become part of the dictysome membrane. Each dictyosome has a specialized set of enzymes that uniquely modify the glycoproteins and movement from one dictyosome to another is via vesicles. After leaving the trans oriented dictyosome a vesicle may dock to a particular location based on signal molecules imbedded in the vesicle. If it binds to the cell membrane,the vesicle's contents are secreted from the cell. Note that these contents were always isolated from the cytosol. Sometimes glycoproteins are imbedded in the cell membrane in the rough endoplasmic reticulum (these are always directed toward the lumen of the endoplasmic reticulum). These glycoproteins become oriented toward the outside of the cell when the vesicles coalesce with the cell membrane. The golgi apparatus also produce some of its own products such as hyaluronic acid which acts to stick animal cells together.

Vesicles released from the golgi apparatus that contain digestive enzymes and don't coalesce with the cell membrane but instead float in the cytosol are lysosomes. (Fig 6.14) Lysosomes are vesicles that have an internal pH = 5 which is maintained via the pumping of H⁺ ions from the cytosol. The enzymes within the lysosomes are only efficient in acidic environments. Lysosomes provide the enzymes necessary to digest defective cellular components and invading pathogens engulfed into food vacuoles via phagocytosis.

Besides food vacuoles contractile vacuoles (which pump excess water together with waste products from cells) may exist in some freshwater protests and central vacuoles (which serve of reservoirs for water and other cellular products) exist in plants. (Fig 6.15)

The mitochondrion (mitochondria) is an organelle where ATPs are generated as the result of breaking down large organic molecules to CO₂. A mitochondrion has two double unit membranes. The inner one has inwardly directed finger like projections of its membrane (christae) that are adaptations for increased surface area. The inner membrane surrounds a fluid-like material called matrix. The matrix is separated from the cytosol by two membranes and the intermembrane region. The mitochondria are the sites of aerobic respiration. Both plant and animal cells have mitochondria. (Fig 6.17)

Chloroplasts also have two unit membranes. The inner membrane extends into the fluid-like material that it encloses (stroma) and forms stacks of flattened membrane bound vesicles called thylakoids. A stack of thylakoids is called a granum and several stacks are grana. Chlorophyll is imbedded in the thylakoid membranes. Chloroplasts function in photosynthesis and are only found in plants. (Fig 6.18)

Mitochondria and chloroplasts are thought to have originated from food vacuoles that resulted from phagocytosis of bacteria and cyanobacteria by primitive cells. These vacuoles developed a symbionic relationship with the cells. Both mitochondria and chloroplasts contain DNA of their own.

Peroxisomes are membrane bound organelles that transfer hydrogen to oxygen creating H₂O₂ (hydrogen peroxide). Hydrogen peroxide is toxic and is further converted in peroxisomes to water. Peroxisomes use oxygen to break down fatty acids. (Fig 6.19)

The cell contains a variety of structural elements that are collectively referred to as the cytoskeleton. (Fig 6.20, Table 6.1)These elements are long and thin and categorized based on their thickness. The thickest are the microtubules; these are hollow cylinders made up of protein called tubulin. There are two types of tubulin molecules alpha and beta tubulin and the tubulin is added to and removed from microtubules primarily at one end of the microtubule (the + end). Tubulin molecules are added as heterodimers (an alpha bound to a beta monomer) with the beta end oriented toward the + end. They constitute a system of tracks within the cell, along which vesicles, organelles, and other cellular components can be moved. Motor proteins bind to these cellular components and move along the microtubules in specific directions either + to -, or - to +. Motor proteins that move in a positive direction are called kinesins, and those that move in a negative direction are dyneins. (Fig 6.21, 6.25 )Microtubules also form the mitotic spindle that allows chromosomes to equally move to each daughter cell during cell division. They also form a 9+2 arrangement within eukaryotic cilia and flagella. This arrangement is crucial to the movement cilia and flagella display. (Fig 6.23)

Intermediate filaments have a variety of functions. These cytoskeleton elements are thinner than microtubules but thicker than microfilaments. They consist of proteins that have a rod-like region consisting of between two globular ends. A number of such proteins twist about each other in the rod-like region forming a rope-like structure. The rod-like regions are alpha helices and are the same for all of the filaments. It is the globular ends that differ from one intermediate filament to another. It is these globular regions that interact with other cellular components. Intermediate filaments provide strength to the cell and prevent the cell from breaking when under physical stress (e.g., epithelial cells of our skin). Another type of intermediate filaments (lamins) form a mesh-like lining that provides a skeleton upon which the nuclear envelope rests. Microfilaments are the thinnest component of the cytoskeleton. They are polymers made up of two strands of actin molecules twisted around each other. These play a significant role in muscular contraction, act in conjunction with motor proteins to direct movement of subcellular components, provide support for fine structures in cells (e.g., microvilli) and generate the contractile forces that form the cleavage furrow in animal cells during cell division. (Fig 6.26)

Cilia and flagella are thin hair-like extensions of the cell membrane that function in cell movement or creation of flows past the cell. Both have a characteristics 9+2 arrangement of microtubules internally.

Plant cells are surrounded by a cell wall. The cell wall is divided into a primary wall that is laid down first and a secondary wall that is laid down later. The primary wall can be stretched, but the secondary wall is firm. The primary wall surrounds the secondary wall. Outside of the secondary wall is middle lamella, a sticky material, that glues multiple cells together. The cell wall structurally protects the plant cell. The plant cell wall is secreted by the cell and is not, nor ever was, alive. (Fig 6.28)

Animal cells do not have cell walls, but have an Extracellular Matrix (ECM) consisting of glycoproteins secreted from the cell. One of these glycoproteins is collagen which makes up about 50% of all human proteins. Physical contact with the ECM can be transmitted via fibronectins to integrins to microfilaments contained within the cytoplasm. Cells are able to respond to such stimuli. (Fig 6.30, 6.31, 6.32)

Cells of multicellular organisms are integrated via various junctions. Plant cells have plasmodesmata which are intercellular channels lined with cell membranes. These canals are very narrow, but make the cytoplasm of adjacent cells continuous. Water and small solutes can move between cells.

Animal cells have gap junctions (analogs of plasmodesmata), desmosomes which are rivet-like junctions that make strong connections between cells (they have extracellular molecules that bind the cells together and are anchored internally to intermediate filaments) and tight junctions (which hold adjacent cells so close together that extracellular movement is prevented).