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Cells & Organelles
We start this exercise by looking at some structural features of cells that can be seen in the light microscope (LM). Before beginning, be sure you have gone through the Atlas Demo and understand the navigation features of the atlas.
Every time you look at a highlighted object, you should make it a routine to click on the highlighting (or the arrow) to bring up the description window. Although some of this information may be repeated in the text, "repetition is the mother of learning" (a Finnish proverb).
Cell MembraneBlood smear, human
Follow links [1,9]. Since the cell membrane is so thin, it cannot be seen directly in the light microscope. Evidence of its existence comes from this view of a blood smear where the cell boundaries are easily seen. Pay attention to the lymphocyte, the neutrophil, and the surrounding red blood cells.w63 ovary, monkey
Follow links [1,1,1]. Identify the cuboidal epithelium. You can readily see where the cell ends at the surface of the epithelium, even if the membrane itself cannot be resolved in the LM. Where the cells abut laterally, evidence of a cell membrane cannot be found. Notice the presence of membrane specializations on the apical surface of the cells, the microvilli.
Sometimes even when cells abut you can get a glimpse of their individuality. A couple of examples follow.w51a bronchus, dog
Follow links [3,3,1,1]. This epithelium contains cells whose structure and function differ. Where two different cell types abut, it is easy to see the cell border. Identify a goblet cell and a ciliated cell, and satisfy yourself that this is the case. Note also the cilia, another surface specialization.w85 thin skin, human
Follow links [3,1,2,1]. During fixation the stratum spinosum (identify) cells of the skin that have desmosomal junctions shrink, allowing the cell border to be seen.
Follow links [2,1,1] and identify the ganglion cell nucleus. The double-layered nuclear membrane cannot be seen in the LM either. Since the staining of the nucleus and cytoplasm in this cell are so different, however, one can identify the border of the nucleus.
Neurons typically have a large, pale-staining euchromatic nucleus. Neurons are busy cells and need their DNA in the uncoiled state for active transcription to occur. It is the (acidic) phosphate groups of DNA that stain with basic stains. In the active state the DNA doesn't stain, probably because of a difference in the exposure of their phosphate groups to the stain. Inactive DNA stains intensely. This form is referred to as heterochromatin.
Identify the Schwann cell nuclei. Note that most of them are heterochromatic, but some are less so. Presumably the darker-staining nuclei are those of cells that are not transcriptionally active.
Identify the ganglion cell nucleolus. Nucleoli are especially prominent in cells active in protein synthesis. They represent the site of transcription of ribosomal RNA (rRNA) from chromosomal DNA. Nucleoli also stain basophilically.
Follow links [1,9]. Identify the lymphocyte and the neutrophil. Because this is a smear, we are looking at the whole cell, not a section through it. Therefore the lymphocyte nucleus appears dark-staining (heterochromatic).
Now pay attention to the neutrophil. Neutrophils are the end stage of a differentiated cell line. Their nuclei are lobulated, a sign of maturity in these cells, and heterochromatic.
Follow links [3,3,1,1] and identify the multilobular neutrophil. Note that even in a thin section like this the nucleus is heterochromatic. Identify the lymphocyte. Note that in contrast to thicker paraffin sections, in this much thinner plastic section parts of the lymphocyte nucleus no longer appear totally heterochromatic. The thinness of the section allows one to "see through" areas where the chromatin is not as fully condensed. Identify the erythrocytes, and notice that they lack a nucleus altogether. Because an erythrocyte is a biconcave disc, it appears, in a thin section, to be a doughnut with a hole in the middle. To see an example of a totally heterochromatic nucleus, go to the next slide:
Follow links [2,2] and identify the spermatozoan head. The DNA in the head is not active in transcription, but is packaged tightly with protamines. This DNA will remain inactive unless the spermatozoan fertilizes an oocyte.
Follow links [2,2,1] and identify the mitotic figures. Then click on one of the highlighted figures and make sure to read the description window. Then, go to the thumbnail and follow [6,4,1]. Identify the mitotic figures in metaphase and telophase. During mitosis the chromosomes condense and become visible in the LM.
Follow links [1,1,3,2] and and identify the hepatocyte nucleus. Like the neuron, a hepatocyte is a busy cell carrying out many functions. (The vast majority of metabolic processes known in animals can be carried out in the hepatocyte.) Unlike the neuron, however, there still is some heterochromacity in the hepatocyte nucleus, particularly at the periphery, i.e., not all the DNA is transcribed all the time. In many cells, such as this one, the peripheral heterochromatin indicates the location of the nuclear membrane. Note the prominent nucleolus.
Follow links [2,2,2,1,1] and identify the plasma cells. Note the abundance of heterochromatin in these nuclei. Even though these cells actively secrete protein (antibody), they each produce only a single kind of antibody. Thus most of their DNA is in inactive form.
Other intracellular organelles
Follow links [1,1,1,1] and identify the mitochondria. Also read the information in the description window. In the secretory ducts of glands, and in some kidney tubules, the mitochondria are located in the folds of the basal cell membrane and thus can be more readily seen in the LM.
Follow links [1,1,1,1] and identify the mitochondria. Cardiac muscle relies on aerobic metabolism (oxidation of fatty acids) as its main energy source and so therefore has abundant mitochondria. This special stain (Weigert) shows what is probably a group of mitochondria.
Follow links [3,1,1,1] and identify the mitochondria. In skeletal muscle mitochondria are less numerous than in cardiac muscle, because skeletal muscle derives energy for contraction anaerobically. Mitochondria tend to accumulate underneath the plasma membrane near the peripheral nuclei as shown in this view.
Lysosomes and Peroxisomes
Follow links [5,1,1,1] and identify lysosomes and peroxisomes, which cannot be distinguished from one another in the LM. The kidney collecting duct has an abundance of both. For another example, go to the next slide:
Follow links [1,2,1,1] and identify lysosomes and peroxisomes. Lysosomes are organelles of intracellular digestion. Peroxisomes are organelles containing oxidative enzymes typically using free-radical mechanisms. To distinguish between lysosomes and peroxisomes, one needs to use histochemical methods.
Follow links [1,1,1,1] and identify the secretory granules. These are storage vesicles containing zymogens for digestive enzymes. They appear as granules in the LM. To have another view of secretory vesicles, go to the following slide:
Follow links [3,3,1,1] and re-identify the goblet cell. It is filled with mucus-containing storage granules. Also look at the mast cells in this view. They are also filled with granules, smaller than those filled with mucus. Read the description window for both goblet cells and mast cells.
Rough Endoplasmic Reticulum (RER)
Follow links [1,3,1,1] and identify basophilic RER. The rough endoplasmic reticulum consists of endoplasmic reticulum with ribosomes attached. The RER is active in synthesizing proteins destined for export or bound for another intracellular organelle.
Follow links [2,1,1] and identify the Nissl substance (RNA). Click on the highlighted area and read the text in the description window. In sensory neurons like this one the RNA appears dispersed. Verify this for yourself by looking at the large neighboring neuron.
The Golgi complex is visible in the LM only by use of a special stain or histochemical methods. However, in some of our specimens one can locate it just because it doesn't stain.
Follow links [2,2,2,1,1] and identify the plasma cells. Then, make sure you undo the highlighting. Note the pink-staining area next to the nucleus. It represents the Golgi. Notice that otherwise the cytoplasm is basophilic because plasma cells have abundant RER. They produce large amounts of protein (but each cell produces only one kind of antibody).
Follow links [1,1,2,1] and identify lipid droplets. You are not seeing a lipid droplet per se, but instead the space remaining where the lipid was dissolved away in preparation. These droplets represent an intracellular storage form, in this case, for precursors necessary for the synthesis of steroid hormones. For another view of lipid droplets go to:
Follow links [2,2,1,1] and identify lipid droplets. The liver is very active in lipid metabolism and ordinarily contains numerous small lipid droplets. This liver has some abnormally large lipid droplets, perhaps an early sign of future cirrhosis.
Transmission Electron Micrographs
So far we viewed only LM images. Now you should look at the same organelles in TEMs.
Identify the cell membrane and read the description window text. In this low-power view, the cell membrane appears as one single line as a border between the cytoplasm and the extracellular matrix.
While looking at this picture, identify also the Golgi complex and read its description.
Though not labeled, the dark-staining heterochromatin inside the undulating nuclear membrane is clearly visible.
Click link . The trilaminar nature of the cell membrane is apparent in some regions. All intracellular membranes look the same if viewed at sufficiently high magnification.
Identify the euchromatin. The dark-staining material inside the nucleus represents heterochromatin. This is from a liver cell, which is known to be very metabolically active. Therefore much of the DNA is present as euchromatin. Also identify the glycogen and read the description window.
Follow link  and view the mitochondria and the description window. Although the glycogen granules on the left and the RER on the right are not labeled, identify them anyway.
Identify the euchromatic nucleus and the double nuclear membrane. Also read their descriptions. Identify the Golgi complex. Similar to liver cells, there are several Golgi complexes in neurons, another sign that they are busy cells.
Identify the nuclear pores and read the description. Do likewise for the cytolysosomes.
Identify the nucleolus, the site of rRNA synthesis. Typically nucleoli have a dense granular appearance in the TEM. Also identify the nuclear pores, one of which is labeled.
Identify the mitochondria and read the description.. Then click link  for a higher-power view. Identify the cristae which are folds of the inner membrane. The intermembranous space (identify) contains some enzymes and a major component of the electron-transport system, cytochrome c. The major permeability barrier of the mitochondrion is the inner membrane. This membrane must be intact for ATP synthesis to occur.
Identify the secretory granules and read the description. This is from the exocrine pancreas, an organ active in the synthesis and export of zymogens for digestive enzymes.
For a higher magnification view of secretory vesicles, click link . The membrane surrounding the contents is clearly visible here.
Zoom out once and identify the RER lumen and the ribosomes. Read the respective descriptions.
Identify the endocrine cell that is embedded in the exocrine pancreatic cells. Identify also the exocrine secretory vesicles and notice how much larger they are than the vesicles of the endocrine cell. Click link  for a higher-power view of the endocrine secretory vesicles. This endocrine cell secretes polypeptide hormone(s) as opposed to steroid hormones since it stores its secretory product in vesicles. Identify the lysosomes and read the description. Notice that they are much larger in size than the endocrine secretory vesicles and contain very dense material in this instance. To identify lysosomes with complete confidence histochemical methods must be used.
Identify the Golgi complex and read its description. Click link . The Golgi complex is made out of stacks of smooth-surfaced membranes and vesicles. Identify both.
Although the centriole is not identified in this view, it can be found just below the Golgi. Click link  and identify the centriole. It, together with the surrounding satellite material (not clearly seen here), organizes the microtubule system and the mitotic apparatus. The most obvious structural features of the centriole are the nine triplet microtubules (identify).
Identify the cilia and their basal bodies. Click link  and view all the identified structures. The most prominent feature of cilia are the microtubules. They, together with dynein and other motor proteins, are the engines for movement.
Identify the cilia and the mitochondria. Follow link  for a higher-power cross-sectional view of the cilia. Although not well resolved in this section, you can get strong hints of the characteristic "9+2" arrangement of microtubules.
Identify the microvilli. These are oblique sections of small microvilli lining the lumen of the pancreatic acinus.
Identify the microvilli and read the description. The actin core of the microvilli is not clearly visible in this picture.
Identify the microvilli. In cells specialized for absorption like these intestinal epithelial cells, microvilli are abundant and form a so-called brush border. The core of microvilli is formed by actin filaments (identify) that are anchored in the cytoplasm. Follow link  to see a picture, albeit fuzzy, of the actin filament anchors.
Click link  and identify cross-sectional views of microvilli, actin filaments, and the enveloping cell membrane. Read the associated descriptions for each.
In striated muscle the thin actin filaments and the thick myosin filaments are organized into sarcomeres, the functional unit of muscle. Identify the Z lines. The lighter-staining area on either side of the Z lines represents actin (thin) filaments. Identify the sarcomere. The darker-staining area in the middle represents the overlapping thin filaments together with thick filaments. Note that the mitochondria in skeletal muscle are small and located on both sides of the Z line. By comparison, cardiac muscle has more, and larger, mitochondria all over. Even though it is not visible here, skeletal muscle has mitochondria that accumulate beneath the cell membrane in the vicinty of the nuclei.
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