Fluid Mosaic Model

Glycerol linked with three fatty acids creates a triglyceride, two fatty acids a diglyceride, and a single fatty acid a monoglyceride. Only a few naturally occurring triglycerides have the same fatty acid in all three ester positions. Most are mixed acylglycerols. Phospholipids demonstrated by the general formula shown in Figure 2.3, also contain a phosphoric acid residue. The alcohol moiety in many phospholipids is also glycerol but for others, for example, the sphingophospholipids the alcohol is sphingosine. Phospholipids are often drawn in the form of a ball to represent the polar head of the molecule and two trailing tails to represent the nonpolar hydrocarbon chains of the fatty acids. Along with associated proteins and some other lipids, the capacity of the phospholipids to spontaneously form bilayers is essential to understand the formation of all the cellular membranes. The now classic organization of the plasma membrane is described as a fluid mosaic model. This consists of a mosaic of globular proteins suspended in a sea of phospholipids. Membranes are organized with the polar heads of two layers of phospholipids oriented either toward the aqueous environment of the interstitial fluid or toward the aqueous environment of the cytoplasm. The hydrophilic hydrocarbon chains of the fatty acids interact so that the membrane has a trilaminar appearance, with phospholipid heads on either side with fatty acid tails in the center. This organization is apparent in well‐preserved tissues, embedded in plastic resins thinly sectioned (~900 nm) and prepared for examination in an electron microscope. This organization is often likened to a peanut butter sandwich with the peanut butter as the tails and the two slices of bread as the phospholipid heads. This fundamental structure is true for all cellular membranes but there are differences in the specific composition, for example, the Golgi membranes versus the plasma membrane. Proteins associated with the membranes are oriented within either the outer or inner membrane leaflets. Other proteins completely span the membrane. Whatever their specific arrangement these proteins are called integral membrane proteins. Those that span the membrane occur so that less polar amino acids reside within the central hydrocarbon tails of the fatty acid chains with polar amino acids located with the polar heads or aqueous surfaces of the membrane. Examples of complex plasma membrane proteins include receptors for hormones or growth factors (GFs) and those required for the transport of metabolites and nutrients.

Cellular membranes are fluid, dynamic, and active structures. Membrane components are also interchangeable between many cellular components. For example, in the mammary gland of a lactating mammal, milk components are packaged into secretory vesicles within the Golgi apparatus. These product‐containing packets progressively make their way to the apical surface of the cell for expulsion or secretion from the cell via exocytosis. The membrane surrounding the secretory vesicles becomes part of the plasma membrane. Furthermore, lipid droplets synthesized in the cells progressively enlarge and migrate to the apical surface of the cells for secretion. However, in this case, the droplets literally begin to protrude pushing a part of the plasma membrane away from the cell surface. This continues until the droplets pinch off with the former plasma membrane now encapsulating the droplet. In this state, the membrane is referred to as milk fat globule membrane, but its origin was the plasma membrane of the epithelial cell. Figure 2.4 illustrates the organelles and secretion activity of such a mammary epithelial cell. Similar events would occur in many other secretory cells, for example, the pancreas, liver, salivary gland, and pituitary gland.

Microscopy Techniques

Beginning with the invention of the light microscope in the 1600s and progressive improvements in cell preservation, techniques to embed tissue in materials for sectioning, and staining to identify specific cellular components, much has been learned regarding cell structure and function. However, even simple smears of dislodged isolated cells can be very useful in physiological or clinical situations. The Pap smear is routinely used in women’s health to monitor the cells of the cervix. The morphology of the cells is classified to determine if any of the cells appear to have precancerous attributes, for example, altered nuclear morphology or staining characteristics. Another example is the blood smear, that is, a small sample of blood is spread and dried on a microscope slide and then stained. Such smears are cover‐slipped, and a differential count is performed. In this procedure, the slide is scanned in a standard pattern and the first 100 white blood cells encountered are identified (lymphocyte, neutrophil, etc.) and tabulated. This information is used to produce a distribution profile of the types of leucocytes in the sample. For example, the horse averages about 55% neutrophils, 35% lymphocytes, 5% monocytes, 3% eosinophils, and 1% or fewer basophils. Changes in these proportions can reflect various diseases. What would be your prediction about a classmate with mononucleosis or a cat with leukemia?

In dairy animals, mastitis status (mastitis is inflammation of the mammary gland) is routinely evaluated by the presence and number of leukocytes in the milk. The technology used is based on a well‐characterized relationship between cell number and the amount of a specific dye that binds to DNA. As the cell number increases in the milk sample, the amount of dye binding increases proportionally. Although these assays are now automated, the milk smear is used to calibrate these machines. Table 2.2 illustrates the relationship between milk somatic cell count and milk production.

In some experimental situations, it is useful to know the stage of the estrus cycle. For many laboratory animals, it is problematic to collect enough repetitive blood samples to measure reproductive hormones (estrogen, progesterone, follicle‐stimulating hormone, luteinizing hormone) for this purpose. However, the use of daily vaginal smears allows for monitoring the stages of the estrus cycle. The number of cornified epithelial cells and leukocytes varies according to the stage of the estrus cycle so that changes in these cellular profiles indicate the stage of the estrus cycle.

Although information obtained from smears of various cells is useful, the technique is limited because most cells are part of tissues. More importantly, the organization and differentiation of the various cell types and their products are fundamental to understanding the physiology of a tissue or organ. For this evaluation, it is necessary to infiltrate the tissue and cells with a medium that is sufficiently solid to allow sections thin enough for light to penetrate to be prepared. The most common embedding medium is paraffin wax. Because tissues and cells are largely water‐based, fresh tissues are first preserved or fixed in an aqueous solution containing chemicals that cross‐link major cell structures and macromolecules. These include formalin, formaldehyde, glutaraldehyde, and others. After a period of fixation, the tissues are dehydrated by transferring the tissue through a series of increasing concentrations of ethanol, then into xylene, a mixture of xylene and paraffin, and finally pure paraffin. This gradual process allows the water to first be replaced by ethanol, then the ethanol by xylene, and the xylene by paraffin. The tissue blocks are submerged in additional paraffin in a mold and allowed to harden. Imagine the string in the center of a candle is the processed tissue. If the candle is carefully sliced in cross section a piece of string would be in the center of each slice, representing the fixed embedded tissue. The slicing of the tissue blocks needs to be precise and uniform. Embedded blocks of tissue are sliced in a machine called a microtome. The machine uses a thin steel blade, much like a razor blade, and the sections usually are cut off in a ribbon. Cut sections float on a water bath and are transferred to a microscope slide. Once the sections are dried, the slides are typically dipped in xylene and processed back into an aqueous environment to allow the staining of the sections. The staining allows visualization of structures in a standard bright field microscope. H&E or hematoxylin and eosin are very common stains. This technique makes the cell nuclei dark blue, the cytoplasm various shades of blue to pink, and extracellular components pink to red. Most histological slides used in physiological classes are H&E stained. Many other stains developed for specific uses and examples are illustrated in various sections of the text. One especially exciting recent innovation in tissue staining is the use of specific antibodies to localize proteins within cells or even within cellular organelles. Figure 2.5 shows tissue blocks, molds, and processed sections for tissue embedded in paraffin.

Despite the widespread use of paraffin‐embedded tissue sections and the rich experimental and pathological history of this technique, there are serious limitations. One of these is that tissue sections thinner than about 5 microns (μm) cannot be easily prepared. A reasonable approximation of an epithelial cell is about 10 × 10 × 10 μm. This means that for the study of intracellular organelles, the sections are too thick so, making it difficult to distinguish these structures. These limitations led to the development of plastic resins designed for embedding cells and tissues. With the subsequent development of specialized microtones designed to use pieces of fractured glass or even diamond knives, it became possible to section fixed tissues embedded in plastic very thin indeed. In fact, for light microscopic study sections of 0.5–1 μm in thickness can be easily prepared. To distinguish sections from the paraffin blocks from those in plastic they are often called semi‐thin sections.

Perhaps more importantly, these breakthroughs allowed even thinner sections to be examined by using the electron microscope. While a detailed consideration of the electron microscope is beyond the scope of our text, some analogy with the readily understood light microscope is useful. The standard compound microscope is essentially a two‐part magnifying system in which the specimen is first magnified by the lens in the objective barrel and secondly by the lens of the eyepiece or ocular. Total magnification is the product of the magnification of the objective lens used and that of the eyepiece. For example, using a 20X objective lens with a typical 10X eyepiece produces an image that is 200‐fold greater than the original. The specimen is placed on a stage below the objective lens. Light is then directed from a light source, through an aperture, then a sub‐stage condenser, and then through the specimen. Light rays from the specimen pass through the objective lens and are focused for view through the eyepieces. This is accomplished mechanically by raising or lowering the position of the objective lens relative to the specimen. Resolution is the degree of separation that can be seen between adjacent points in a specimen, in other words, the degree of detail. The smaller the distance that can be distinguished between two points, the greater the detail in the image. With the unaided eye, points appear as independent structures only if 0.2 mm or 200 μm separates them but with a good microscope points as close as 0.25 μm can be distinguished. Ultimately resolution of the bright field microscope is limited by the wavelength of light and sample preparation. The maximum useful magnification of the light microscope is about 1400‐fold. Images can be reproduced to larger sizes in the printing process, but this does not increase true resolution.

In the electron microscope, a beam of electrons replaces the bean of light. The sample (now only about 900 nanometers (nm) in thickness) is positioned on a copper grid and the grid is inserted into a sealed chamber and placed under vacuum. A bean of electrons passes through the sample. To increase the electron density of the sample, the tissue is treated with heavy metals (usually lead citrate or uranyl acetate), which bind with macromolecules in the sample and improve sample resolution. The electron bean penetrates the tissue located in the open spaces of the grid and the image produced is brought into focus by altering the voltage applied to a series of electromagnets located on either side of the column, which houses the electron beam. The image is viewed first on a phosphorescent screen and the image is saved by positioning and exposing film. The film is developed, and images of the specimen are prepared by making photographic prints from the film. The process as described is called transmission electron microscopy. A similar process called scanning electron microscopy relies on images produced by coating surfaces often with a thin layer of gold. Detailed images of intracellular structure became possible only with electron microscopy; several examples are included along with descriptions of cell organelles. Figure 2.6 shows a block of tissue prepared for study in an electron microscopy, one of the small copper grids, and an example of an exposed, developed photographic plate.

Organelles of the Cytoplasm

While many complete texts are devoted to aspects of cell and molecular biology, a basic appreciation of cell structure is important in understanding cellular physiology and ultimately tissue, organ, and systems‐level physiology. It is imperative to appreciate that essentially all organelles occur in all cells. However, the total number and arrangement of these organelles vary markedly from cell type to cell type. Numbers can also change dramatically within a given cell type depending on the activity of the cell. These differences reflect the degree of differentiation of the cell. For example, mammary alveolar epithelial cells taken from a non‐lactating pregnant animal have a very different complement of cellular organelles than cells collected during lactation. This reflects differences in activity between these stages of development.

Certainly, biochemical differentiation of the secretory cells is required for the onset of milk secretion. However, the cells must also acquire the structural machinery needed to synthesize, package, and secrete milk constituents. When alveolar cells first appear during mid‐gestation, they exhibit few of the organelles needed for copious milk biosynthesis or secretion. The cells are characterized by a sparse cytoplasm with few polyribosomes, some clusters of free ribosomes, limited rough endoplasmic reticulum (RER), and rudimentary Golgi usually in close apposition to the nucleus, some isolated mitochondria and widely dispersed vesicles. Individual cells often contain large lipid droplets (especially during later stages of gestation) that along with irregularly shaped nuclei account for much of the cellular area. Electron microscopic studies solidified the dramatic structural changes in the alveolar secretory cells at the onset of lactation. These differences are illustrated in Figure 2.7 and Figure 2.8. Also, it is important to appreciate that similar changes in cell differentiation occur in many epithelial cells, that is, various glands, intestine, pancreas, etc. The mammary gland is a convenient and dramatic example.

Mitochondria

Called the powerhouses of the cell, mitochondria provide most of the ATP necessary for energy‐requiring reactions. Two membranes enclose the generally elongated thin hot dog‐shaped mitochondria. The outer membrane smoothly encapsulates the organelle, but the inner membrane occurs as multiple folds that form partitions called cristae. The surfaces of the cristae are studded with embedded enzymes that interact with the internal gel‐like matrix of the mitochondria. Briefly, as energy‐yielding nutrients are metabolized, intermediate products from the digestive process, for example, glucose, amino acids, and fatty acids are converted into compounds that enter the mitochondria. These compounds are catabolized to carbon dioxide and water by the action of the mitochondrial enzymes, a portion of the bond energy is captured and used to attach phosphate groups to ADP to generate ATP. This is called aerobic respiration because it requires oxygen. Essentially the need for oxygen is explained by the fact that it is required for the production of adequate amounts of ATP.

Mitochondria are very complex organelles. They have their own DNA (derived incidentally from the mother) and RNA. As energy demand increases, mitochondria increase the density of cristae or undergo fission to create new mitochondria. Active cells such as those in muscle, pancreas, or the lactating mammary gland may have hundreds of mitochondria but inactive cells (nonlactating mammary gland) or quiescent lymphocytes, for example, have only a few. In living cells, the mitochondria can also change shape. Regardless of its morphology, the emergence of mitochondria was a major evolutionary event. Figure 2.9 illustrates typical mitochondria. It is widely believed that mitochondria arose from bacteria that invaded the ancestors of plant and animal cells.

Ribosomes

These small dark‐staining organelles are composed of proteins and a class of RNA called ribosomal RNA (rRNA). Each of the ribosomes has two subunits identified based on size as 18 and 28s RNA. Ribosomes can appear singly as free structures in the cytoplasm or sometimes arranged along coiled loops of mRNA called polyribosomes. Alternatively, especially in cells that are synthesizing abundant amounts of protein for secretion, ribosomes are attached to membranes to create RER. As subsequently discussed, the ribosomes are the sites of protein synthesis. Because of the relationship between the endoplasmic reticulum and the Golgi apparatus, ribosomes of the RER allow newly manufactured proteins to be packaged in secretory vesicles for secretion from the cell. Free ribosomes in the cytoplasm function to synthesize proteins destined to act within the cell (Fig. 2.10).

Endoplasmic Reticulum and Golgi Apparatus

The endoplasmic reticulum or ER is an interconnected network within the cytoplasm of the cell. This system of interconnecting membrane tubes or sheets encloses fluid‐filled spaces that appear in two variations, smooth or rough ER. It is also continuous with the nuclear membrane. Protein synthesis depends on three forms of RNA. These are (1) transfer RNA (tRNA), (2) rRNA, and (3) messenger RNA (mRNA). When the mature mRNA reaches the cytoplasm, it binds to a small ribosomal subunit by base pairing to rRNA. The tRNA transfers amino acids to the ribosome. There are approximately 20 different types of tRNA, each capable of binding a specific amino acid. The linkage process depends on a synthetase enzyme linked to the cleavage of ATP to form the peptide bonds between amino acids in the growing peptide chain. Once its amino acid is loaded, the tRNA migrates to the ribosome, where it moves the amino acid into position, based on the codons of the mRNA strand. The amino acid is bound to one end of the tRNA (the tail), but the other end of the molecule (the head) has a three‐nucleotide base sequence (anticodon), which is complementary to the codon of the mRNA. For a given strand of mRNA, multiple ribosomes can become attached and as the ribosomes move along the molecule, many chains of new protein can be made simultaneously. In fact, it is not uncommon to find polyribosomes in the cytoplasm. These are represented in transmission electron microscopic views of active cells by chains or coils of ribosomes seemingly organized in the cytoplasm.

However, proteins destined for secretion from the cell are synthesized by ribosomes attached to the endoplasmic reticulum. The mRNA for these proteins’ codes an initial short peptide sequence (signal peptide), which directs the growing peptide chains into the cisternal space of the endoplasmic reticulum. Because this space is continuous with the Golgi apparatus, proteins destined for secretion transfer into Golgi for packaging into secretory vesicles and secretion from the cell by exocytosis. After synthesis in the RER, modifications to secretory proteins may also occur in the Golgi apparatus. These posttranslational modifications can markedly affect the structure of the protein and its functional properties. Common modifications include the addition of sugar or phosphate groups. Other components can also be added to developing secretory vesicles in the Golgi. For example, in the mammary gland, the milk sugar lactose is synthesized within the Golgi apparatus by the action of galactosyl‐transferase and α‐lactalbumin.

As discussed in more detail in subsequent chapters, there are many small single‐stranded RNA molecules (21–23 nucleotides long) referred to as microRNAs (miRNAs) that are synthesized in plants and animals. These molecules do not code for proteins, but they play a very important but still evolving role in silencing some genes and in posttranslational modifications of proteins. They represent an important additional layer of control in gene expression. Indeed, Drs. Victor Ambros and Dr. Gary Ruvkun were awarded the 2024 Nobel Prize in Physiology or Medicine for their discovery of these unique molecules and their actions in control of gene regulation. As you might expect this discovery has caught the eye of many researchers and pharmaceutical companies seeking new and novel methods to silence or otherwise control genes involved in the progression of disease.

As discussed in subsequent chapters, small vesicles called endosomes, apparently produced virtually by all cells are known to contain miRNAs (and other substances) that can impact other tissues and cells. An especially intriguing example is exosomes, which are secreted into colostrum and into milk. These exosomes are believed to have major impacts on the protection of the GI tract of newborns via interactions with immune elements housed in the mucosal lining of the intestine. These possibilities are outlined in the chapters on digestion, immunity, and lactation.

Lysosomes and Peroxisomes

Peroxisomes are intracellular vesicles containing a mixture of enzymes, namely oxidases and catalases. Oxidases depend on the presence of oxygen to detoxify various noxious substances, for example, alcohols and aldehydes. They also convert toxic free radicals into hydrogen peroxide for neutralization by catalase. Free radicals are hyperreactive substances known to alter the structure and function of a variety of regulatory molecules. Thus, the peroxisomes are essential to limit free radical accumulation. Peroxisomes are abundant in liver and kidney cells, two organs recognized for their capacity to detoxify harmful substances.

Lysosomes also contain hydrolytic enzymes that can digest many cellular proteins. Known as suicide bags or sacs, inappropriate release of the contents of these organelles could destroy the cell. In fact, the rupture of activated lysosomes is involved in some aspects of programmed cell death or apoptosis. Lysosomes are present in all cell types, but they are especially plentiful in neutrophils, macrophages, and other leucocytes. The acid hydrolases within the lysosomes function best in an acidic environment. Consequently, the lysosomal membrane contains hydrogen transport proteins that sequester hydrogen ions from the cytoplasm to maintain a low pH. Many cells are capable of capturing materials from near the cell surface by endocytosis. Vesicles produced in this manner can then fuse with lysosomes. Captured molecules can be digested by the acid hydrolyses and released into the cytoplasm for use by the cell or for excretion. This digestion process is especially important in macrophages and neutrophils because these cells actively engulf potentially harmful bacteria and other toxins. Destruction of these agents by the lysosomes is protective and in the case of processed foreign proteins, fragments of the digested proteins are presented to other cells of the immune system to allow the development of specific immunity. Lysosomes are also critical in the recycling of worn‐out or nonfunctional organelles as well as a variety of metabolic actions, for example, the release of thyroid hormones from storage.

Microfilaments, Microtubules, and Intermediate Filaments

It was originally assumed that the cytoplasm of the cell was essentially a water‐filled space with multiple dissolved substances. However, appropriate fixation and embedment techniques for electron microscope led to the realization that the cytoplasm contains an elaborate array of structures that make up the cytoskeleton of the cell. This does not mean that cells are rigid but microtubules, microfilaments, and intermediate filaments of the cytoskeleton provide an unexpected structure and organization to the cell cytoplasm. Some of these organelles are for communication between the cell surface and interior, for transport of vesicles for secretion, for cell division, or for cell adhesion.

Microtubules are the largest of these organelles and as the name suggests are hollow tubes composed of α and β subunits of the globular protein tubulin. They are slender with an outside diameter of 25 nm. When cut in cross section they appear as small circles with 13 subunits of tubulin around the circumference. Its cylindrical structure develops as heterodimers of tubulin packed around a central core, which appears as a space in electron micrographs. At 37°C, purified tubulin polymerizes into microtubules in vitro in the presence of Mg and GTP. Several antimitotic cancer drugs (colchicine and its relatives) act by interfering with tubulin polymerization. Another antimitotic drug, Taxol, stabilizes microtubules and arrests cells in mitosis. These effects demonstrate the critical role of microtubules in cell division. Polymerization of tubulin to form microtubules occurs initially in a region near the nucleus called the centrosome. This is seen most clearly in cultured cells first treated with colchicine to disrupt the microtubules. After various periods groups of cells were fixed and the microtubules were stained by using fluorescent‐tagged antibodies against tubulin. When the drug is removed, new microtubules can be seen growing out from the centrosome to create a star‐like structure called an aster. The microtubules then elongate toward the outer regions of the cell to reestablish the microtubule network.

It is also known that disruption of microtubules dramatically impairs cellular secretion. For example, intramammary infusion of colchicine into the lactating mammary gland virtually stops milk secretion but once the treatment ends milk secretion rapidly returns to normal. This demonstrates the requirement for microtubules for trafficking and exocytosis of secretory vesicles. An increase in the relative abundance of microtubules in mammary epithelial cells corresponds with increased milk secretion following parturition or increased secretory activity in other epithelial cells. Two families of microtubule‐dependent motor proteins, kinesins, and dyneins are involved in organelle transport in the cytoplasm, in mitosis, and movement of vesicles of neurotransmitter from sites of synthesis in the cell body to sites of release at the ends of axon terminals. Table 2.3 provides an example of changes in microtubule number and orientation related to cell function and Figure 2.11 shows the appearance of microtubules in the mammary cells of a lactating cow.

The protein actin is the primary component of microfilaments and in many cell types actin accounts for 5% or more of the total cellular protein. Actin can exist as a monomer or like the tubulin of microtubules can polymerize to form thin thread‐like structures (~7 nm in thickness) called filamentous actin. In most cells, about half of the available actin is present in the monomeric conformation because it is bound to a regulatory protein, thymosin. Rapid changes in rates of polymerization–depolymerization induce changes in the cell surface that produce lamellipodia (essentially cell projections) and ultimately cell movement and migration. Specific arrangements of microfilaments within the cytoplasm can be driven by the activation of cell surface receptors. This is especially important for the action of highly mobile phagocytic cells of the immune system. Bundles of microfilaments are also found near cell surfaces and are highly ordered within the microvilli of absorptive epithelial cell layers. In this way, bundles of actin filaments provide structural integrity for the microvilli. This is functionally significant because the adaptation of having the microvilli on the surface of an intestinal epithelial cell, for example, markedly increases the surface area available for absorption. A single intestinal enterocyte has several thousand microvilli. Actin filaments do not act independently, rather a variety of actin‐binding proteins control rates of filament formation and creation of the specific filament groupings. For example, cross‐linked microfilaments can form loose gels, or rigid bundles to anchor plasma membranes.

Intermediate filaments are less labile than microfilaments or microtubules and are more elemental members of the cytoskeleton. The protein structure of these filaments can vary between cell types, but the proteins are bound together something like a braided, woven rope. These filaments are called neurofilaments in nerve cells and keratin filaments in many epithelial cells. Regardless, they provide additional support for the cell. They are especially important in the creation of desmosomes. Desmosomes are a type of anchoring junction that serves to hold adjacent epithelial cells together. In these regions, the plasma membranes of the neighboring cells do not touch but linker proteins (cadherins) extend outward from the desmosomal plaque of each cell. On the cytoplasmic side of the plaque in each cell, intermediate fibers extend into the cytoplasm of the cell to interact with other cytoskeletal elements and provide additional support. Other chapters describe types of cell junctions and their properties.

	Nonlactating	Lactating
Location
Apical	4.6 ± 0.9	17.4 ± 2.1
Basal	0.9 ± 0.2	3.7 ± 0.8
Orientation
Apical‐basal	4.2 ± 0.8 (50.3%)	18.9 ± 2.1 (65.6%)
Lateral‐lateral	4.1 ± 0.6 (49.7%)	9.9 ± 1.5 (34.4%)

The average number of microtubules in the apical or basal cytoplasm observed in an apical to basal or lateral to lateral orientation with respect to the plasma membrane in mammary epithelial cells of nonlactating and lactating cows.

Centrioles

These structures are composed of a short cylindrical arrangement of microtubules. They occur as a pair near the center of the centrosome. The centrosome acts as an organizing center for building microtubules and serves as the spindle pole during mitosis. The pair of centrioles are oriented at right angles to each other in an L‐shaped pattern. The centrosome duplicates and divides into two equal parts during the interphase period of cell division, so that each half contains a duplicated centriole pair. The daughter centrosomes migrate to either side of the nucleus at the start of mitosis forming the two poles of the mitotic spindle. The granular appearance of the cytoplasm in the region surrounding the centrioles results from a complex of proteins and fibers involved in the movement and duplication of the centrioles. Each centriole resembles a pinwheel made of each of nine triplets of microtubules arranged to form a hollow tube. They also form the basal structures of cilia and flagella. Whereas the centriole has a pattern of nine microtubule triplets, the basal bodies have an arrangement of nine pairs of microtubules oriented around a central pair of microtubules. Although each of the central microtubules is complete, the outer doublets fuse so that the pair shares a common layer. This 9 + 2 organization is characteristic of most if not all types of cilia and flagella. The bending of the central core of the structure, the axoneme, produces the movement of the cilia or flagella.

Figure 2.12 illustrates a cross section through the tail of a bovine sperm cell. The arrangement of doublets of microtubules around a central pair of microtubules is apparent. The diagram shows that the microtubules are linked with molecules of the protein nexin to form the circular array. The doublets are decorated with inner and outer arms composed of the protein dynein and anchorage proteins that position the outer doublets around the central core. In sperm cells, the asymmetric arrangement of filaments around the outside of the axoneme allows the movement of the tail to follow a figure eight pattern of motion characteristic of bovine sperm cell motility.

Nuclear Structure

Apart from mitochondrial DNA, most of the DNA in eukaryotic cells is nuclear. Comparable to the double membrane of the mitochondria, the nucleus is delimited by a double membrane called the nuclear envelope. Unlike mitochondria, these membranes are interspersed with nuclear pores. A complex of proteins populates these areas and acts to control the passage of molecules into and out of the nucleus. This is important because DNA, or genes must be transcribed to generate molecules of messenger RNA. Newly synthesized mRNA molecules are processed and transferred to the cytoplasm for translation by the ribosomes to create the many proteins needed by the cell. The presence of the nucleus in eukaryotic cells allows processing related to DNA synthesis and gene activation localized away from other activities in the cytoplasm. This likely serves to minimize possible disruption of these critical gene‐related activities. In short, the eukaryotic cells have evolved with the creation of numerous membrane‐bound organelles that allow for segregation of specific, divergent, biochemical reactions. This increases the metabolic and biochemical efficiency of eukaryotic compared to prokaryotic cells.

The nucleus houses all the chromosomes and therefore the genes. Fortunately for most cells, only a fraction of the total DNA is actively utilized at any given moment. For example, although all cells would contain the gene copies for making the milk proteins or for synthesizing lactose, these genes would only be activated in the epithelial cells of the lactating mammary gland. Many other genes are activated only at a particular developmental period or in response to very specific stimuli. Consequently, much of the DNA is tightly compacted in the nucleus.

Most cells have a single nucleus but there are exceptions. Skeletal muscle cells, bone osteoclasts, cardiac cells, and some liver cells are multinucleated. This is usually associated with cells that have a larger‐than‐normal cytoplasmic volume. Except for mature red blood cells of mammals, all cells are nucleated and even these cells have a nucleus until late in their developmental sequence. Of course, without the nucleus and the genes necessary for protein synthesis, these cells cannot replace proteins that are progressively degraded by normal functioning. Although it is expected that the appearance of the nucleus would change dramatically during cell division, even in nondividing cells (so‐called interphase or G₀ phase of the cell cycle) there are distinct differences between cell types. These differences can be useful to identify some cell types. For example, plasma cells have a distinct pattern of condensed chromatin around the periphery of the nucleus resembling a clock face. Neutrophils have elongated, lobed nuclei that make the appearance of these cells unique.

Figure 2.13 shows an electron microscopy section through the nucleus of an epithelial cell. During most of the life of the cells, the DNA is in a complex with strongly basic proteins called histones, some nonhistone proteins, and a small amount of RNA. This combination of proteins and DNA is called chromatin. While the double helix structure of DNA is widely familiar, the degree of order or compaction of the DNA within the chromatin matrix varies. Compaction is extreme in cells that are preparing for the final stages of mitosis as chromatin appears as distinct pairs of chromosomes. However, even in cells in G₀ degrees of chromatic condensation vary. Dark staining areas indicate regions containing condensed, presumably inactive, chromatin. Lighter areas contain more active, extended chromatin. Clumps of condensed chromatin often appear around the periphery of the nucleus (peripheral chromatin) along with scattered islands of condensed chromatin throughout the nucleus. The interphase nucleus also has a protein network called the nuclear matrix. Much of this material appears as a thin, interwoven layer (the nuclear lamina) that adheres to the internal surface of the nuclear envelope. This provides support and anchorage for the nuclear pores. An extension of the nuclear lamina radiates into the interior of the nucleus. This layer also interacts with a similar lamina that surrounds the nucleolus. Together they regulate nuclear shape, reinforce the inner membrane of the nuclear envelope, secure the location of nuclear pores, and anchor condensed chromatin to the nuclear envelope. This organization remains except during mitosis. Maintenance of the nuclear matrix is essential for routine gene transcription.

Proteins

In the absence of disease or trauma, most cellular proteins are synthesized from free amino acids or peptides absorbed from the blood stream. The cell membrane (and associated carrier proteins) regulates the uptake of these molecules from the interstitial fluids. Understanding amino acid transporters is an area of active research but many features are common between tissues. Some of these transporters depend on ions (e.g., Na⁺, Cl^−, and K⁺) or use an H⁺‐gradient to drive transport. The Na⁺‐ dependent system – A regulates the accumulation of neutral amino acids regulate the accumulation of neutral amino acids within the cells when compared with plasma concentrations. There is much interest in the regulation of amino acid uptake to understand factors limiting milk and meat protein synthesis. From an animal production viewpoint, much of the value of animal products resides in their protein content, for example, meat, milk, and eggs.

While the significance of proteins as important building blocks in anabolism is evident, the enzymes that are vital for cell function are also proteins. Like most biologically critical macromolecules, linking together subunit monomers—the amino acids—in this case allows the creation of a large variety of proteins. Individual amino acids share the common structure illustrated below. The R (or residual group) is attached to the α carbon and is unique for each amino acid. For the simplest, the amino acid glycine, the R is a hydrogen atom. Individual amino acids bind together by a dehydration synthesis reaction (named because of the release of water in the reaction). Newly created covalent bonds between amino acids are called peptide bonds (Fig. 2.18).

There are 20 common amino acids. The essential amino acids are so named because they are needed in the diet. Others are created by intermediary metabolism. However, specific amino acids considered essential vary between species, especially in ruminants compared with non‐ruminant species. This is because the bacteria and protozoa of the ruminant can generate amino acids not initially available in the diet fed to the animals. As illustrated in Figure 2.18, all amino acids have two functional groups (or reactive groups), an amine (—NH₂) and a carboxylic acid residue (—CHOOH). Differences in the number and arrangement of atoms in the R group give each of the amino acids its unique chemical attributes. For example, if the side group is a simple string of hydrocarbons (leucine, e.g.), this region of the amino acid will be very hydrophobic, much like the fatty acid tails of a phospholipid. Other side groups, for example, the inclusion of an additional amine group (lysine, e.g.), would make the amino acid very hydrophilic and more basic. Thus, the properties of the R groups give each amino acid its unique properties. These are acidic, basic, uncharged polar or nonpolar attributes. In addition to the common names, the amino acids are also denoted by simple abbreviations or a single‐letter code. Other important amino acids or their derivatives such as ornithine, 5‐hydroxytrytophan, L‐dopa, and thyroxine occur but these molecules do not typically appear in proteins. Interconversions between some of the amino acids, as well as between amino acids and intermediates of carbohydrate metabolism associated with Krebs cycle reactions are also common, as part of normal cellular activity. Transamination reactions allow the conversion of selected amino acids into their corresponding keto acid and the simultaneous conversion of another keto acid into an amino acid. Oxidative deamination of amino acids occurs primarily in the liver. This initially leads to the generation of ammonia, which is highly toxic to cells. Fortunately, most ammonia is rapidly converted into water‐soluble urea, which can then be excreted. Table 2.6 provides a listing of some of the properties of the amino acids. These properties explain much of the physical‐chemical properties of proteins.

Proteins are long chains of amino acids linked by peptide bonds. Two amino acids create a dipeptide, three a tripeptide, and so forth. Ten or more linked amino acids create polypeptides and those with greater than about 50 amino acids are simply called proteins. Because each of the amino acids has unique properties because of variation in the R groups, the sequence of amino acids produces polypeptide and protein chains with correspondingly varied and complex properties. With the availability of 20 different amino acids, the variation of possible structures and therefore functional properties is very large. This is analogous to the huge number of words possible with the 26 letters of the alphabet.

Four levels of structure illustrate the organization of proteins. The linear sequence of amino acids in a protein is its primary structure. Analogous to the beads on a string, with each bead an amino acid. However, proteins in solution do not simply exist as a long strand. Instead, variations in the properties of the R groups allow interactions between the protein and other molecules in the local environment as well as interactions between other amino acids of the same protein chain. This twisting and bending produces a more complex secondary structure. One of the more common results is the formation of coils. Imagine a coiled telephone cord, if you can recall seeing old home telephone landlines. Perhaps at your grandparents’ home? Parts of proteins organized in this way create what are called α helix segments or regions. The α helix configuration is stabilized by hydrogen bonds that occur between NH and CO groups of amino acids of the primary chain that are spaced about four amino acids apart along the series. To reinforce the significance of the primary sequence, this interaction can only occur if the side groups of the amino acids allow hydrogen bonds to form. The α helix formation only occurs within a single protein chain. In contrast, the formation of β pleated secondary structure can occur via interactions with amino acids within the same protein or by interactions between independent proteins. In this secondary structure arrangement, the amino acids are oriented side by side to produce a layer somewhat like a pleated ribbon. A given protein can exhibit both α helix and β pleated sheet structure in different regions of the protein. A further or tertiary structure occurs when α‐helical or β‐pleated regions of a protein twist or fold upon on another to create globular‐like structures. To maintain this complex array, both hydrogen bonds and covalent bonds are required. When two or more independent protein chains interact to produce larger aggregates, the protein(s) are said to have a quaternary structure. Examples include the 4 chains that create functional hemoglobin or the 12 proteins that create the enzyme fatty acid synthetase.

As the discussion suggests, the three‐dimensional structure of a protein is critically important in allowing the protein to carry out its function. Because much of the secondary, tertiary, or quaternary structure depends on interactions between amino acids and the creation of hydrogen and or ionic bonds, it is easy to see that changes in the local environment of the protein can markedly affect function. For example, changes in pH or aqueous conditions can alter interactions that depend on ionic or hydrogen bonds. These changes in protein structure are called denaturation. Depending on the degree of insult and the protein involved, when conditions return to normal the protein can return to its appropriate, functional state. As an example of irreversible denaturation, consider what happens to the jelly‐like albumin of the egg white when it is heated, or it is mixed with a bit of vinegar to make a sauce. There is no going back to the original protein structure.

Fibrous or globular are additional classifications of proteins. Fibrous proteins are usually elongated and relatively insoluble. Examples include structural proteins found in the connective tissues of blood vessels; in subcutaneous regions, surrounding muscles, or other glandular structures; and in tendons and ligaments. The most abundant of these is collagen, made by fibroblasts located throughout the body. Collagen begins with the synthesis of a monomeric form, helical tropocollagen. Other types of collagens occur in the basement membrane just underneath epithelial cells. In fact, collagens are the most abundant proteins in the body. Other examples of fibrous proteins include other connective tissue proteins, such as elastin and keratin, and the contractile proteins of muscle cells, such as actin and myosin.

Globular proteins, by contrast, are generally very soluble, compact, and spherical. These proteins are reactive and therefore more fragile than fibrous proteins. Because their functionality depends on their three‐dimensional shapes and a high degree of structural organization, disruption or denaturation effectively destroys function. Enzymes, antibodies, and protein hormones are examples of globular proteins. Adequate functioning of globular proteins depends on the maintenance of active site(s) of the protein. Figure 2.19 illustrates the denaturation of a globular protein.

The 2024 Nobel Prize in chemistry was awarded to three scientists, Dr. David Baker, Dr. Demis Hassabis, and Dr. John Jumper for their work using a powerful computational tool and AI to accurately predict how proteins twist and fold to create complex three‐dimensional structures. Previously, such attempts depended on tedious, laborious crystallography and X‐ray diffraction methods. It has been known for many years that proteins are strands of amino acids but using that information to predict shape and function had largely been a pipe dream. That is until the creation of the AI tool, called AlphaFold2, which was shown to be able to predict three‐dimensional structures of proteins. The Nobel committee concluded, “This is one of the really first big scientific breakthroughs of AI.” As noted by the director of the National Institute of General Medical Sciences (a division of NIH), “Structure determines function, it’s as easy as that. If we can design proteins to look a certain way, then they might have a certain function that could be useful.” The possibilities are indeed staggering. Imagine custom proteins with unique shapes and functions. Perhaps new enzymes that degrade toxins or plastics or blockers for actions of pathogens. Regardless, our central theme of structure and function being linked to physiological function shines yet again.

Classic autoradiographic studies, which traced the movement of radiolabeled amino acids through the secretory cells, established that the site of protein synthesis was the RER. For example, when lactating rats were injected with [³H]‐leucine or tissue explants were incubated with radiolabeled leucine, the percentage of labels in the RER subsequently fell following peak labeling of the Golgi region of the secretory cells. Within 30 minutes of exposure, labels began to decrease in the Golgi but increased in the alveolar lumen. These simple but convincing studies demonstrated that after synthesis in the RER, proteins were rapidly transported to the Golgi for packaging into secretory vesicles and subsequent exocytosis.

Steps for protein synthesis are essentially the same for all cells, although the final packaging and fate of newly synthesized proteins varies between cells and tissue types. Aside from directing its own replication, DNA also directs protein synthesis by its capacity to generate mRNA. Each gene is composed of a segment of DNA, which carries the chemical instructions for the synthesis of one polypeptide chain in its arrangement of nucleotide bases (Adenine, Thymine, Cytosine, and Guanine). Each sequence of three bases—the triplet code—directs the joining of a specific amino acid in the mature mRNA molecule. Although one‐half of the double‐stranded DNA serves as a template for synthesis of the mRNA (transcription), not all the nucleotides in the gene appear in the final mRNA blueprint. The genes of higher organisms contain exons, the amino acid specifying sequences, separated by introns. These noncoding introns range from 60 to 100,000 nucleotides in length. Transcription of a particular gene depends on the binding of a transcription factor to a site on the DNA adjacent to the start sequence for the gene. This region is the promoter. The transcription factor mediates the binding of the enzyme RNA polymerase. This enzyme acts to open the DNA helix and the DNA segment coding for the protein is uncoiled. Only one strand of the DNA, the sense strand, serves as the template for the creation of a complementary mRNA. However, before the mRNA can direct protein synthesis, the noncoding introns are enzymatically removed before the newly made mRNA exits the nucleus for translation. Single‐stranded RNA also differs from double‐stranded DNA in having the sugar ribose instead of deoxyribose and the base uracil instead of thymine. This feature provides a prepared means to assess the ability of cells for proliferation or synthesizing of proteins by measuring the incorporation of radiolabeled thymidine or uracil, respectively.

While it is beyond the scope of this book, elegant molecular studies have confirmed that the specific proteins for secretion are synthesized by membrane‐associated ribosomes and that the newly made proteins have short sequences of amino acids, which serve as signals to allow binding and vectoring of the nascent protein into the cisternal spaces of the RER. The signal peptide is cleaved as the protein progresses to the Golgi apparatus for possible posttranslational modification, that is, enzymatic addition of sugar residues or phosphate groups. The proteins are then released from the Golgi as secretory vesicles. Subsequently, they migrate to the apical membrane of the cell where they are released by exocytosis (see Fig. 2.4). Thus, mechanisms of protein synthesis are essentially the same in all cell types. However, total protein synthesis and the degree to which proteins are manufactured for secretion varies markedly from cell type to cell type.

Carbohydrates

As with proteins, carbohydrates are utilized as both structural components in cells and as precursor molecules for energy production. The primary dietary carbohydrates are polysaccharides, disaccharides, and monosaccharides. Carbohydrates are classified according to size and relative solubility. For example, monosaccharides are more soluble than larger polysaccharides. Polymeric forms of carbohydrates are stored as relatively insoluble granules, that is, starch in plants and glycogen in animal cells. Common monosaccharides include those with 3, 4, 5, 6, or 7 carbons these are trioses, tetroses, pentoses, hexoses, and heptoses, respectively. Derivatives of trioses are generated when the enzymes of the glycolysis biochemical pathway break down the common hexose sugar glucose. These molecules are used by the cells for various catabolic and anabolic activities. For example, trioses are used to produce glycerol needed to synthesize the backbone for the attachment of fatty acids in triglycerides (see Fig. 2.2). Understanding this biochemical pathway is critical to gaining an appreciation of cellular energy production. Pentose sugars (ribose and deoxyribose) are key components of nucleotides, nucleic acids, and several coenzymes. The hexose monosaccharide, glucose plays an especially critical role in intermediary metabolism, particularly as an energy source. The hexose sugars, glucose, galactose, and fructose are especially important. These monosaccharides serve as the monomers of building blocks for the generation of more complex carbohydrates needed by the cells. Many glycoproteins (proteins with attached sugar residues) appear on cell surfaces. Other complex polysaccharides appear in connective tissues, for example, glycosaminoglycans where they serve important roles in the maintenance of tissue structure and hydration.

Carbohydrates contain carbon, hydrogen, and oxygen with the hydrogen and oxygen occurring in a 2 : 1 ratio as in water. This explains the word carbohydrate, that is, hydrated carbon. Structurally, these simple sugars can be represented as chains, but more often, a cyclic ring structure is preferred. Figure 2.20 illustrates the formulae and structures of some of these common simple sugars. Compounds that have the same structural formulae but have a different spatial arrangement of their atoms are called stereoisomers. The presence of carbon atoms attached to four different atoms or groups, known an asymmetric carbon, allows for the formation of isomers. The number of possibilities depends on the total number of asymmetric carbons in the molecule (n) and is determined by the following expression 2ⁿ. Glucose with its 4 asymmetric carbons has 16 possible spatial isomers. Furthermore, the orientation of the H and OH groups around the carbon adjacent to the terminal primary alcohol residue (OH group) determines whether the sugar is a D or L isomer. Nearly all monosaccharides in mammals are D isomers.

Whether they are created via dehydration synthesis or because of digestion from larger polysaccharides, disaccharides are physiologically important. One of the most common is lactose or milk sugar. Lactose is made of glucose plus galactose. For most mammals, lactose supplies much of the energy needed by the suckling neonate as well as the monomeric building blocks needed for rapid tissue development. Maltose, which derives from two glucose molecules, is a common cleavage product generated by the hydrolysis of starch. Table sugar, sucrose, is a combination of glucose and fructose. As the name suggests, six‐carbon fructose is a common fruit sugar. It also is a component in reproductive tract secretions. Figure 2.21 illustrates the structures of some of these common disaccharides.

Whether plant starch or glycogen, both are polymers of glucose and are the essential sources of glucose used throughout the body in monogastric species. Glucose is also essential for ruminants. However, fed starches are fermented before any glucose reaches the small intestine for absorption. For these animals, the primary fermentation products: acetate, butyrate, and propionate supply the precursors for fatty acid synthesis and energy production. To supply needed glucose, portal blood supplied to the liver contains the propionate produced by rumen fermentation. The liver converts propionate into glucose for use by the cells. This is gluconeogenesis. It is important in all animals at times but is especially critical in ruminants because so little dietary glucose is available for absorption across the small intestine.

Dietary starches undergo some hydrolysis by α‐amylase in the saliva. However, reduced stomach pH suppresses this initial breakdown, that is, α‐amylase pH optima is near neutrality. However, hydrolysis of starches increases again as starch reaches the small intestine and additional amylases from the pancreas and small intestine appear. Glucose is stored primarily in liver and muscle cells in the form of glycogen. Mobilization of these reserves of glycogen provides glucose when needed. When ATP is plentiful, and stocks of glycogen are sufficient, additional energy reserves are produced by the conversion of glucose to acetate and ultimately fatty acids are stored as triglycerides in adipocytes. Figure 2.22 illustrates the structure of glycogen. Subsequent chapters will describe the biochemical reactions and pathways involved in the catabolism of glycogen and other carbohydrates needed to supply the energy and building blocks for the synthesis of important macromolecules.

Lipids

Although we have discussed triglycerides and phospholipids related to membrane formation, other lipids are also important. Some are messenger molecules. Details of endocrine and other aspects of cell signaling will be considered in subsequent chapters but some appreciation of these special lipids is warranted. Steroids are structurally very different from triglycerides. Cholesterol provides the core structure for the synthesis of these critical molecules. Despite its “bad press” cholesterol is nonetheless essential. In addition to serving as the parent molecule for steroid hormone production, it is also a vital element in membranes, where it acts to increase membrane fluidity. It is also essential to produce vitamin D and production of bile salts.

Unlike the hydrocarbon chain of fatty acids, cholesterol is composed of a series of interlocking rings with a side chain. Specifically, the four interlocking A, B, C, and D rings of the cholesterol core contain the cyclopentanohydrophenanthrene nucleus that occurs repeatedly in all the steroid hormones. For example, two structural types of steroid hormones are made in the cortex of the adrenal gland. Those that have a two‐carbon side chain attached at position 17 of the D ring for a total of 21 carbons the C₂₁ steroids and those that have a keto or hydroxyl group at position 17 for a total of 19 carbons the C₁₉ steroids. Most C₁₉ steroids have a keto group at position 17 referenced as 17‐ketosteroids. The C₁₉ steroid hormones have androgenic or testosterone‐like effects or actions. The C₂₁ steroids of the adrenal gland are either mineralocorticoids or glucocorticoids. The mineralocorticoids have primary effects on sodium and potassium excretion. The major hormone in this class is aldosterone. The glucocorticoids as you might guess from the name have primary effects related to glucose and carbohydrate metabolism. Examples of specific steroids in this class are cortisol and corticosterone. We discuss other sex steroids, for example, estrogen and progesterone in subsequent chapters. The primary point is to appreciate the fact that despite the seemingly small differences in structure between, for example, estrogen and testosterone, these two steroid hormones have markedly different effects. The specificity of hormone receptors expressed in various target cells explains these differences in action. For example, estrogen molecules bind very poorly to androgen receptors, and conversely, testosterone binds very poorly to the estrogen receptors.

The eicosanoids are a diverse family of lipids generated from a 20‐carbon fatty acid called arachidonic acid. Arachidonic acid is plentiful in the plasma membrane. The four major groups of eicosanoids include prostaglandins, prostacyclins, thromboxanes, and leukotrienes. A commercial preparation of prostaglandin F₂α, lutalyse (dinoprost tromethamine) is familiar to many dairy and beef producers because it is used in a management scheme to synchronize estrus in cattle. The product acts to cause early dissolution of the corpus luteum on the ovary. Various eicosanoids are important in the control of blood pressure, gastrointestinal tract motility, vasoconstriction, and blood flow.

Because the major lipids in plasma do not circulate freely in the aqueous environment of the blood, fatty acids and other important lipids associate with carrier molecules. Free fatty acids are bound to albumin (a major protein produced by the liver). Most of the cholesterol, triglycerides, and phospholipids appear in a complex with lipoproteins for transport. Variation in the ratio of protein to lipid explains the differences between the five families of lipoproteins. They can be identified based on the position they migrate to following high‐speed centrifugation. Those with greater lipid contents (less density) orient closer to the top of the centrifuge tube and those with less lipid further toward the bottom of the tube. This is somewhat like the cream rising to the top of a container of non‐homogenized milk. This explains the description of the lipoproteins as very low (VLDL), intermediate (IDL), low (LDL), or high (HDL) density lipoproteins. The other class includes the chylomicra produced in the intestinal villi. These are critical in the initial packaging and transport of digested triglycerides. Lipoproteins are topics in the popular press, because of their involvement with lipid and cholesterol transport in the blood and relationships with health. For this purpose, usually, only the major classes HDLs and LDLs are distinguished. The amounts and ratios of these in the blood are important diagnostic tools related to cardiovascular health in humans and animals. Cells can take up cholesterol and other lipids from the blood. Most of the cholesterol is associated with LDLs. When cells need cholesterol to make new membranes or for other purposes, they synthesize transmembrane receptors for the LDL proteins. These receptor proteins migrate within the membrane and localize in clathrin‐coated pits. These LDL‐rich pits undergo endocytosis. LDLs that bind to the receptors are internalized. These coated vesicles are processed by interactions with lysosomes to release the cholesterol for use by the cell. Interestingly, more than 25 different receptors are processed via this clathrin‐coated pit pathway. In the case of cholesterol, if the LDL receptor‐mediated up take of cholesterol is blocked this leads to excess accumulation of cholesterol‐laden LDL in the blood, and this excess cholesterol is believed to contribute to the production of atherosclerotic plaques and consequently cardiovascular disease. The study of families with strong genetic links to cardiovascular disease initially led to the discovery of this relationship. That is one of the mechanisms responsible for increased disease was a mutation that prevented normal expression of the LDL receptor. The structures of selected lipids are illustrated in Figure 2.23.

Nucleic Acids

Understanding DNA or RNA requires an appreciation of the molecules that compose these macromolecules. Nucleic acids are produced from combinations of nucleotides, but nucleotides are in turn a combination of three elements: (1) a phosphate group, (2) a pentose sugar (either ribose or deoxyribose), and (3) a nitrogen‐containing base (either a purine or a pyrimidine). There are three types of pyrimidines: cytosine (C), thymine (T), and uracil (U). The two types of pyrimidines are adenine (A) and guanine (G). Thymine is unique to DNA and uracil is unique to RNA.

Variation between DNA strands or in other words between different genes depends on the sequence of nitrogenous bases that occur. A combination of either deoxyribose or ribose and one of the bases creates a nucleoside. Including the phosphate group (sugar + base + phosphate) creates a nucleotide. The phosphate groups join the hydroxyl group on the C₅ carbon of the sugar residue. Moreover, as you will see related to ATP production it is common to find mono‐, di‐, or triphosphates attached to many nucleotides. To illustrate, a combination of adenine + deoxyribose + one phosphate makes adenosine monophosphate or AMP. The same base and sugar with two phosphates make ADP or adenosine diphosphate. With the addition of a third phosphate adenosine triphosphate or ATP is generated.

Single strands of DNA or stands of RNA are produced when a phosphate group from one nucleotide (attached to the C₅ carbon of the pentose sugar) links with the hydroxyl group located on the C₃ carbon of the pentose sugar of another nucleotide. Thus, the nucleic acid chain grows in a 3′ to 5′ direction. This means that along the course of a growing nucleotide chain, the nitrogenous bases do not directly link with other bases in the same chain. For DNA, this arrangement allows for complementary base pairing occurring between adjacent chains. This is the essence of double‐stranded DNA. The DNA molecule resembles a ladder. The outside is represented by the covalently linked, pentose sugars and phosphate groups of the nucleotides. Complementary bonding between bases creates the rungs of the ladder. Now if the ladder is imagined as being twisted like a spiral staircase, this gives a reasonable approximation of the DNA.

However, it is important to remember that while linkages between sugars within a chain are maintained by strong covalent bonds, the interactions between nitrogenous bases between two DNA chains depend on simple hydrogen bonding, like the interactions between adjacent water molecules (see Fig. 2.1). These hydrogen bonds, while not strong individually, are critical because of their abundance, this also allows the double‐stranded DNA to unzip as required for gene transcription. Once this occurs, the strands can then readily rejoin. Interactions between bases allow for bonding between adenine and thymine, cytosine and guanine. These linkages are called complementary bonds or A + T and C + G are called complementary bases. However, the stands are oriented so that one is oriented in a 5′ to 3′ direction and the other 3′ to 5′ (the numbering is based on the orientation of phosphate groups linking the 3 or 5 carbons of the pentose sugar). In single‐stranded RNA molecules, the bases are A, G, C, and U (replaces the T found in DNA). Ribose is the pentose sugar involved instead of deoxyribose. Examples of nucleic acid structures and components appear in Figure 2.24 and Figure 2.25.

Chemical Bonds

Cellular activity reflects both the creation of complex macromolecules dependent on combining other simpler molecules and the creation of new bonds, as well as catabolic activity to break the bonds in nutrient molecules to supply the building blocks for these new creations. Some of the energy derived from breaking chemical bonds is reserved for future use by the cells. Enzymes catalyze chemistry. As you learned in general chemistry, attractive forces maintain orientations between atoms in molecules to produce chemical bonds. Three major types of bonds are: hydrogen bonds, ionic bonds, and covalent bonds. In addition, Van der Waals forces, such as hydrogen bonds, are important in the maintenance of structure of complex biological molecules when charge differentials aid the maintenance of structural relationships. We have already discussed hydrogen bonds in our description of the behavior of water (see Fig. 2.1). Hydrogen bonds exist when a hydrogen atom is covalently bound to an electronegative atom. The most common examples are oxygen and nitrogen. When these groups occur close to other strongly electronegative atoms, this produces a kind of tug of war as the two electronegative atoms “fight” for dominion of the hydrogen atom. These reactions create attractive forces that link or bridge the molecules. Hydrogen bonds are particularly important as intramolecular forces that act to mold the three‐dimensional shape of many macromolecules. Much of the folding of proteins that define their tertiary structure depends on hydrogen bonds. Another example is the interactions between complementary strands of the DNA molecule. Despite the relative weakness of individual hydrogen bonds, they are collectively critical for normal cellular functioning.

Ionic bonds exist when the transfer of electrons from one atom to another generates attractive forces between atoms. This happens because the usual balance between + and − charges is lost, and ions are formed. The atom that accepts electrons acquires a net negative charge becoming an anion. The electron donor, now called a cation, has a net positive charge. Atoms with opposite charges attract. This is the basis of the ionic bond. A commonly used example of ionic bonds is table salt or sodium chloride. As you may recall from general chemistry, sodium has an atomic number of 11 and therefore has only one electron in its third or outer valence shell. To achieve stability the atom would have to acquire an additional seven electrons (the third orbit around the nucleus can accept eight electrons). Stabilizing this outer orbit is more likely to happen by shedding the single electron so that the second orbit gets filled and becomes the valence shell around the nucleus of the atom. Chlorine has an atomic number of 17. The outer valence shell needs only one electron to fill its valence orbit. When it accepts an electron, stability is increased but the atom acquires a net negative charge and becomes an anion. As you would suspect, ionic bonds are common between atoms with one or two valence electrons in metallic elements (e.g., sodium, calcium, and potassium) and elements with seven valence electrons (e.g., chlorine, fluorine, and iodine). Most ionic compounds exist as salts. When dry they form highly organized crystals because of their ionic bonds. In aqueous environments, salts dissociate to produce ions. Many more common ions (Ca⁺², Na⁺, K⁺, Cl⁻) are critical to normal cellular physiology because of their roles in the regulation of the activity of many enzymes and are significant in the maintenance of polarity across cell membranes. Calcium, which is the most abundant essential mineral in the body, is especially important. It not only is critical for the activation of various cytoplasmic kinases, but it is also essential for muscle function, and in a more stable form (hydroxyapatite—Ca₁₀(PO₄)₆(OH₂)) it is a fundamental part of the inorganic, extracellular structure of bone. This likely explains the reason for the lack of finding shed antlers or skeletal remains of animals in rural areas. Other animals, especially rodents use these materials to supply their mineral needs.

Maintenance of ionic gradients across the plasma membrane of cells uses about one‐third of basal energy generated from ATP hydrolysis. Na‐K ATPase protein transporters in the plasma membrane move Na⁺ and K⁺ against their concentration gradients (energy‐requiring) so that concentrations of intracellular Na⁺ are about 10‐fold lower inside than outside the cell (~15 vs. 150 mEq/L) with the opposite for K⁺ ions (~14 vs. 140 mEq/L). Because these ions passively move down their concentration gradients, the ATPase pumps must be constantly active. Somewhat like the bilge pumps of a boat that act to constantly remove water that leaks or splashes into the boat. The transporters link sodium and potassium movement so that each action of the protein ejects 3Na⁺ out of the cell and carries 2K⁺ ions into the cell. Coupled with the fact that the membrane is slightly more permeable to K⁺ than Na⁺ under basal conditions, the action of the ATPase protein maintains the ionic and electrical gradient across the cell membrane. These actions, combined with the accumulation of cellular proteins cause the production of an electrical gradient across most cells of about −40 mV (inside relative to outside). Many cells, especially nerve cells, take advantage of changes in ion concentrations or polarity for cell signaling. The activity of chemical and voltage‐regulated gates for sodium and potassium (transporter proteins) explains the abrupt changes in membrane potential that occur during nerve transmissions.

Aside from transferring electrons, the sharing of electrons between atoms stabilizes atoms as well. In these cases, the valence orbits of the two atoms are shared. This is the essence of covalent bonds. If a single pair of electrons is shared, this creates a single covalent bond. This is shown as a single line connecting two atoms. In other cases, atoms can share two or three electron pairs, this produces double or triple covalent bonds that are illustrated by double or triple lines between atoms (O—O) as in O₂ gas or (NN) in N₂ gas (see Fig. 2.18). Some atoms are considered relatively reactive and others are relatively inert. Figure 2.26 shows the atomic structure of some example atoms and explains the reason for these differences.

Carbon is an especially abundant cellular atom. It has four electrons in its outer or valence orbit, but stability is achieved when the orbit is filled (eight electrons). This means that there are numerous possibilities for sharing electrons to achieve stability. One possibility is to create a sharing of four electrons from four distinct neighbors. This would be the case in the creation of methane gas (CH₄). Because hydrogen needs either to lose an electron or gain another to complete its outer valence orbit, sharing between the single carbon atom and four hydrogen atoms satisfies both atoms. Numerous examples of covalent bonds involving carbon atoms are shown in the structures of neutral lipids (essentially hydrocarbon chains), carbohydrates, and proteins (see Figs. 2.2, 2.18, and 2.20). By convention, carbon atoms are not explicitly shown but are understood to be positioned at line intersections. A simple example of double bonds is the sharing of electrons between a carbon atom and two oxygen atoms. In carbon dioxide (CO₂ or O=C=O) sharing of electrons is equal between the atoms. Because there is no separation of charge this covalent bond is also called a nonpolar covalent bond. Nonpolar covalent bonds are common. For example, consider the fatty acid tails of the phospholipids in cellular membranes (see Fig. 2.3). Our prior discussion of water (see Fig. 2.1) illustrates an example of a polar covalent bond. In these instances, like spoiled children, one or more atoms of the bond unit have a greater capacity to attract the shared electrons. Because the electrons spend more of their time in orbit near the stronger partner, these covalent bonds produce a separation of charge. In other words, on average there is a separation of charge, one area of the new molecule has a net negative charge (shared electron(s) more often in this region) and a net positive charge (shared electrons more often playing next door). As a rule, small atoms with six or seven valence electrons (oxygen, nitrogen, and chlorine) are better able to attract electrons and thus described as being strongly electronegative. These atoms favor “hogging” shared electrons to complete their valence orbital shells. Atoms with only one or two valence electrons are more likely to relinquish control of shared electrons and are therefore described as electropositive atoms. Examples of these include hydrogen, potassium, and sodium. If you ponder the difference between polar and nonpolar covalent bonds, it should be easy to imagine why molecules with an abundance of polar covalent bonds easily dissolve (associate) with water. Conversely, molecules with few or any polar covalent bonds, lipids, for example, have little capacity to interact with the abundant polar water molecules in our cells and bodies.

Chemical Reactions

It is apparent that living processes depend on an almost bewildering array of chemical reactions. Molecules in our food or in the rations fed to our animals are destroyed (chemical bonds broken) to supply intermediate molecules for building blocks, that is, consider hydrolysis of plant starches to supply glucose for production of glycogen in liver cells. Some of the glucose is oxidized to produce ATP needed to supply cellular energy. DNA and RNA are synthesized as cells flourish and grow. How do we organize and make sense of these reactions? Fortunately, despite the number of individual molecules involved, patterns begin to evolve. For example, the breaking down of bonds between the glucose and fructose in the disaccharide sucrose or the peptide bonds between alanine and lysine in a protein molecule are both hydrolysis reactions. Chemical reactions occur when chemical bonds are created between atoms, chemical bonds between atoms are broken, or when chemical bonds are rearranged. A common illustration is to denote the reactions in simple symbolic expressions as chemical equations. For example, the combination of carbon and oxygen to create carbon dioxide could be written in the following manner.

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