The plasma membrane encloses the cell, defines its boundaries, and maintains the essential difference between the cytosol and the extracellular environment. The cell membrane is an organized sea of lipid in a fluid state, a nonaqueous dynamic compartment of cells.

The cell membranes are assembled from four major components: a lipid bilayer, membrane proteins, sugar residues, and a network of supporting fibers.

The basic structure of a cell membrane is a lipid bilayer of phospholipid molecules. The fatty acid portions of the molecules are hydrophobic and occupy the center of the membrane, while the hydrophilic phosphate portions form the two surfaces in contact with intra- and extracellular fluid (Fig. 2.2). This lipid bilayer of 7–10 nm thickness is a major barrier, impermeable to water-soluble molecules such as ions, glucose, and urea. The three major classes of membrane lipid molecules are phospholipids (phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, sphingomyelin,), cholesterol, and glycolipids. The lipid composition of different biological membranes varies depending upon the specific function of the cell or cell membrane, as summarized in Table 2.2.

The proteins of the membrane are responsible for most membrane functions such as transport, cell identity, and cell adhesion and constitute transport channels, transporters, specific receptors, and enzymes. The membrane proteins can be associated with the lipid bilayer in various ways depending on the function of the protein. The polypeptide chain may extend across the lipid bilayer (transmembrane proteins) or may simply be attached to one or the other side of the membrane.

The cell surface often has a loose carbohydrate coat called glycocalyx. The sugar residues generally occur in combination with proteins (glycoproteins, proteoglycans) or lipids (glycolipids). The oligosaccharide side chains are generally negatively charged and provide the cell with an overall negative surface charge. While some carbohydrates act as receptors for binding hormones such as insulin, others may be involved in immune reactions and cell–cell adhesion events.

The main function of the cell membrane is to protect the cytoplasm and the component of the cell from the external media. It also helps the exchange of different substance to the cell. It can help the identification of the cell and its communication with other cells.

The water-soluble molecules, such as ions, glucose, and urea, only cross the membrane through transmembrane channels, carriers, and pumps, which regulate the supply of the cell with nutrients, control internal ion concentrations, and establish a transmembrane electrical potential. Transmembrane receptors bind extracellular signaling molecules, such as hormones and growth factors, and transduce their presence into chemical or electrical signals that influence the activities of the cell. Genetic defects in signaling proteins can lead to signals for growth in the absence of appropriate extracellular stimuli and cause some human cancers.

Adhesive glycoproteins of the plasma membrane allow cells to bind specifically to each other or to the extracellular matrix. These selective interactions allow cells to form multicellular structures, like epithelia. Similar interactions allow white blood cells to bind bacteria, so that they can be ingested and digested in lysosomes.

Although lipid bilayers provide a barrier to diffusion of ions and polar molecules larger than about 150 D, protein pores provide selective passages for these larger molecules across membranes. These proteins allow cells to control solute traffic across membranes, an essential feature of many physiological processes. Integral proteins that control membrane permeability fall into three broad classes: pumps, carriers, and channels each with distinct properties.

The following are examples of membrane types:

The cytoplasm contains an interconnecting network of tubular and flat membranous vesicular structures called the endoplasmic reticulum (ER). Like the cell membrane, the walls of the ER are composed of a lipid bilayer containing many proteins and enzymes. The regions of ER rich in ribosomes are termed rough or granular ER, while the regions of ER with relatively few ribosomes are called smooth or agranular ER. Ribosomes are large molecular aggregates of protein and ribonucleic acid (RNA) that are involved in the manufacture of various proteins by translating the messenger RNA (mRNA) copies of genes. Subsequently, the newly synthesized proteins (hormones and enzymes) are incorporated into other organelles (Golgi complex, lysosomes) or transported or exported to other target areas outside the cell. Enzymes anchored within the smooth ER catalyze the synthesis of a variety of lipids and carbohydrates. Many of these enzyme systems are involved in the biosynthesis of steroid hormones and in detoxification of a variety of substances.

The Golgi complex or apparatus is a network of flattened smooth membranes and vesicles. It is the delivery system of the cell. It collects, packages, modifies, and distributes molecules within the cell or secretes the molecules to the external environment. Within the Golgi bodies, the proteins and lipids synthesized by the ER are converted to glycoproteins and glycolipids and collected in membranous folds or vesicles called cisternae, which subsequently move to various locations within the cell. In a highly secretory cell, the vesicles diffuse to the cell membrane and then fuse with it and empty their contents to the exterior by a mechanism called exocytosis. The Golgi apparatus is also involved in the formation of intracellular organelles such as lysosomes and peroxisomes.

Lysosomes are small vesicles (0.2–0.5 μm) formed by the Golgi complex and have a single limiting membrane. Lysosomes maintain an acidic matrix (pH 5 and below) and contain a group of glycoprotein digestive enzymes (hydrolases) that catalyze the rapid breakdown of proteins, nucleic acids, lipids, and carbohydrates into small basic building molecules. The enzyme content within lysosomes varies and depends on the specific needs of an individual tissue. Through a process of endocytosis, a number of cells remove either extracellular particles (phagocytosis) such as microorganisms or engulf extracellular fluid with the unwanted substances (pinocytosis). Subsequently, the lysosomes fuse with the endocytotic vesicles and form secondary lysosomes or digestive vacuoles. Products of lysosomal digestion are either reutilized by the cell or removed from the cell by exocytosis. Throughout the life of a cell, lysosomes break down the organelles and recycle their component proteins and other molecules at a fairly constant rate. However, in metabolically inactive cells, the hydrolases digest the lysosomal membrane and release the enzymes, resulting in the digestion of the entire cell. By contrast, metabolically inactive bacteria do not die, since they do not possess lysosomes. Programmed cell death (apoptosis) or selective cell death is one of the principal mechanisms involved in the removal of unwanted cells and tissues in the body. In this process, however, lysosomes release the hydrolytic enzymes into the cytoplasm to digest the entire cell.

Peroxisomes are small membrane-bound vesicles or microbodies (0.2–0.5 μm), derived from the ER or Golgi apparatus. Many of the enzymes within the peroxisomes are oxidative enzymes that generate or utilize hydrogen peroxide (H₂O₂). Some enzymes produce hydrogen peroxide by oxidizing D-amino acids, uric acid, and various 2-hydroxy acids using molecular oxygen, while certain enzymes such as catalase convert hydrogen peroxide to water and oxygen. Peroxisomes are also involved in the oxidative metabolism of long-chain fatty acids, and different tissues contain different complements of enzymes depending on cellular conditions.

Mitochondria are tubular or sausage-shaped organelles (1–3 μm). They are composed mainly of two lipid bilayer–protein membranes. The outer membrane is smooth and derived from the ER. The inner membrane contains many infoldings or shelves called cristae which partition the mitochondrion into an inner matrix called mitosol and an outer compartment. The outer membrane is relatively permeable, but the inner membrane is highly selective and contains different transporters. The inner membrane contains various proteins and enzymes necessary for oxidative metabolism, while the matrix contains dissolved enzymes necessary to extract energy from nutrients. Mitochondria contain a specific DNA. However, the genes that encode the enzymes for oxidative phosphorylation and mitochondrial division have been transferred to the chromosomes in the nucleus. The cell does not produce brand new mitochondria each time the cell divides; instead, mitochondria are self-replicative: the mitochondrion divides into two and these are partitioned between the new cells. The mitochondrial reproduction, however, is not autonomous but is controlled by the cellular genome. The total number of mitochondria per cell depends on the specific energy requirements of the cell and may vary from less than a hundred to up to several thousands. Mitochondria are called the “powerhouses” of the cell. The cell derives energy from glucose, amino acids, and fatty acids. In a process called glycolysis, glucose is converted to pyruvic acid, which subsequently enters mitochondria where it begins a sequence of chemical reactions called the citric acid or Krebs cycle. Various enzymes present in the inner membrane oxidize the pyruvic acid to carbon dioxide and water. The oxidative metabolism of the glucose molecule generates 36 molecules of ATP. The amino acids and fatty acids are converted to acetyl coenzyme A (in the cytoplasm) which also enters the citric acid cycle and gets oxidized with the generation of ATP molecules.

Ribosomes are large complexes of RNA and protein molecules and are normally attached to the outer surfaces of the ER. The major function of ribosomes is to synthesize proteins. Each ribosome is composed of one large and one small subunit with a mass of several million daltons.

DNA was first discovered in 1869 by a chemist, Friedrich Miescher, who extracted a white substance from the cell nuclei of human pus and called it “nuclein.” Since nuclein was slightly acidic, it was known as nucleic acid. In the 1920s, a biochemist, P.A. Levine, identified two sorts of nucleic acid: DNA and RNA. Levine also concluded that the DNA molecule is a polynucleotide (Fig. 2.3a), formed by the polymerization of nucleotides. Each nucleotide subunit of DNA molecule is composed of three basic elements: a phosphate group, a five-carbon sugar (deoxyribose), and one of the four types of nitrogen-containing organic bases. Two of the bases, thymine and cytosine, are called pyrimidines, while the other two, adenine and guanine, are called purines. Their first letters commonly represent the four bases: T, C and A, G.

The presence of 5′-phosphate and the 3′-hydroxyl groups in the deoxyribose molecule allows DNA to form a long chain of polynucleotides via the joining of nucleotides by phosphodiester bonds. Any linear strand of DNA will always have a free 5′-phosphate group at one end and a free 3′-hydroxyl group at the other. Therefore, the DNA molecule has an intrinsic directionality (5′–3′ direction). Although some forms of cellular DNA exist as single-stranded structures, the most widespread DNA structure, discovered by Watson and Crick in 1953, represents DNA as a double helix containing two polynucleotide strands that are complementary mirror images of each other. The “backbone” of the DNA molecule is composed of the deoxyribose sugars joined by phosphodiester bonds to a phosphate group, while the bases are linked in the middle of the molecule by hydrogen bonds. The relationship between the bases in a double helix is described as complementarity, since adenine always bonds with thymine and guanine always bonds with cytosine. As a consequence, the double-stranded DNA contains equal amounts of purines and pyrimidines. An important structural characteristic of double-stranded DNA is that its strands are antiparallel, meaning that they are aligned in opposite directions.

In order to serve as the basic genetic material, all the chromosomes in the nucleus duplicate their DNA prior to every cell division. When a DNA molecule replicates, the double-stranded DNA separates or unzips at one end, forming a replication fork (Fig. 2.3b). The principle of complementary base pairing dictates that the process of replication proceeds by a mechanism in which a new DNA strand is synthesized that matches each of the original strands serving as a template. If the sequence of the template is ATTGCAT, the sequence of a new strand in the duplex must be TAACGTA. Replication is semiconservative, in the sense that at the end of each round of replication, one of the parental strands is maintained intact, and it combines with one newly synthesized complementary strand.

DNA replication requires the cooperation of many proteins and enzymes. While DNA helicases and single-stranded binding proteins help unzip the double helix and hold the strands apart, a self-correcting DNA polymerase moves along in a 5′→3′ direction on a single strand (leading strand) and catalyzes nucleotide polymerization or base pairing. Since the two strands are antiparallel, this 5′→3′ DNA synthesis can take place continuously on the leading strand only, while the base pairing on the lagging strand is discontinuous and involves synthesis of a series of short DNA molecules that are subsequently sealed together by the enzyme DNA ligase. In mammals, DNA replication occurs at a polymerization rate of about 50 nucleotides per second. At the end of replication, a repair process known as DNA proofreading is catalyzed by DNA ligase and DNA polymerase enzymes, which cut out the inappropriate or mismatched nucleotides from the new strand and replace these with the appropriate complementary nucleotides. The replication process almost never makes a mistake and the DNA sequences are maintained with very high fidelity. For example, a mammalian germline cell with a genome of 3 × 10⁹ base pairs is subjected on average to only about 10–20 base pair changes per year. Genetic change, however, has great implications for evolution and human health; it is the product of mutation and recombination.

A mutation is any inherited change in the genetic material involving irreversible alterations in the sequence of DNA nucleotides. These mutations may be phenotypically silent (hidden) or expressed (visible). Mutations may be classified into two categories: base substitutions and frameshift mutations. Point mutations are base substitutions involving one or a few nucleotides in the coding sequence and may include replacement of a purine–pyrimidine base pair by another base pair (transitions) or a pyrimidine–purine base pair (transversions). Point mutations cause changes in the hereditary message of an organism and may result from physical or chemical damage to the DNA or from spontaneous errors during replication. Frameshift mutation involves spontaneous mispairing and may result from insertion or deletion of a base pair. Mutational damage to DNA is generally caused by one of three events: (a) ionizing radiation causes double-stranded breaks in DNA due to the action of free radicals on phosphodiester bonds, (b) ultraviolet radiation creates DNA cross-links due to the absorption of UV energy by pyrimidines, and (c) chemical mutagens modify DNA bases and alter base-pairing behavior. Mutations in germline tissue are of enormous biological significance, while somatic mutations may cause cancer.

DNA can undergo important and elegant exchange events through recombination, which refers to a number of distinct processes of genetic material rearrangement. Recombination is defined as the creation of new gene combinations and may include exchange of an entire chromosome or rearranging the position of a gene or a segment of a gene on a chromosome. Homologous or general recombination produces an exchange between a pair of distinct DNA molecules, usually located on two copies of the same chromosome. Sections of DNA may be moved back and forth between chromosomes, but the arrangement of genes on a chromosome is not altered. An important example is the exchange of sections of homologous chromosomes in the course of meiosis that is characteristic of gametes. As a result, homologous recombination generates new combinations of genes that can lead to genetic diversity. Site-specific recombination does not require DNA homology and involves alteration of the relative positions of short and specific nucleotide sequences in either one or both of the two participating DNA molecules. Transpositional recombination involves insertion of viruses, plasmids, and transposable elements, or transposons into chromosomal DNA. Gene transfer in general represents the unidirectional transfer of genes from one chromosome to another. The acquisition of an AIDS-bearing virus by a human chromosome is an example of gene transfer.

Proteins are the tools of heredity. The essence of heredity is the ability of the cell to use the information in its DNA to control and direct the synthesis of all proteins in the body. The production of RNA is called transcription and is the first stage of gene expression. The result is the formation of messenger RNA (mRNA) from the base sequence specified by the DNA template. All types of RNA molecules are transcribed from the DNA. An enzyme called RNA polymerase first binds to a promoter site (beginning of a gene), then unwinds the two strands of DNA double helix, moves along the DNA strand, and synthesizes the RNA molecule by binding complementary RNA nucleotides with the DNA strand. Upon reaching the termination sequence, the enzyme breaks away from the DNA strand, and at the same time, the RNA molecule is released into the nucleoplasm. It is important to recognize that only one strand (the sense strand) of the DNA helix contains the appropriate sequence of bases to be copied into an RNA sense strand. This is accomplished by maintaining the 5′–3′ direction in producing the RNA molecule. As a result, the RNA chain is complementary to the DNA strand and is called the primary RNA transcript of the gene. This primary RNA transcript consists of long stretches of noncoding nucleotide sequences called introns that intervene between the protein-coding nucleotide sequences called exons. In order to generate mRNA molecules, all the introns are cut out and the exons are spliced together. Further modifications to stabilize the transcript include 5-methylguanine capping at the 5′ end and polyadenylation at the 3′ end. The spliced, stabilized mRNA molecules are finally transported to the ER in the cytoplasm, where proteins are synthesized.

Both transcription and translation are mediated by the RNA molecule, an unbranched linear polymer of ribonucleoside 5′-monophophates. RNA is chemically similar to DNA, the main difference being that the RNA molecule contains ribose sugar and another pyrimidine, uracil, in place of thymine. RNAs are classified according to the different roles they play in the course of protein synthesis. The length of the molecules varies from approximately 65–200,000 nucleotides, depending upon the role they play. There are many types of RNA molecules within a cell, and some RNAs contain modified nucleotides which provide greater metabolic stability. mRNA molecules carry the genetic code to the ribosomes, where they serve as templates for the synthesis of proteins. The transfer RNA (tRNA) molecule, also generated in the nucleus, transfers specific amino acids from the soluble amino acid pool to the ribosomes and ensures the alignment of these amino acids in a proper sequence. Ribosomal RNA (rRNA) forms the structural framework of ribosomes, where most proteins are synthesized. All RNA molecules are synthesized in the nucleus. While the enzyme RNA polymerize II is mainly responsible for the synthesis of mRNA, RNA polymerases I and III mediate the synthesis of rRNA and tRNA, respectively.