Plasma Membrane

All living cells, both prokaryotes and eukaryotes, are surrounded by a plasma membrane, about 8 nm (nanometer) thick, creating an intracellular and extracellular environment/compartment. The intracellular and extracellular fluid compartments (ICF and ECF, respectively) are aqueous and the plasma membrane provides the barrier between them. The membrane is composed primarily of phospholipids and proteins. Phospholipids are polar molecules with a polar (hydrophilic) head and a nonpolar (hydrophobic) tail (see Chapter 2, Chemistry of Life). Because the environment on each side of the plasma membrane is aqueous, the hydrophobic tails face each other and the hydrophilic heads are exposed to water on both surfaces of the membrane. This results in the formation of a phospholipid bilayer, illustrated in Figure 3.1.

Embedded in the phospholipid bilayer are peripheral and integral (transmembrane) proteins and cholesterol. The peripheral proteins are partially embedded on one side of the membrane, whereas integral proteins extend from one side through the membrane to the other side. Although the specific lipid and protein components vary in different membranes, the basic structure and composition of the plasma membrane are the same, as are those membranes that surround cell organelles. Because the plasma membrane is not solid, its components are freely movable, presenting a constantly changing fluid-mosaic membrane structure (see Figure 3.1, A).

Whereas the phospholipids are the main lipid component of the cell membrane, cholesterol is another major cellular membrane lipid and the amount varies with the type of plasma membrane. For example, the plasma membrane of animal cells contains almost one cholesterol molecule per phospholipid molecule, plant cells contain much less, and prokaryotic cells have no cholesterol but instead contain sterol-like molecules called hopanoids. Cholesterol and hopanoids (pentacyclic sterol–like compounds) immobilize the first few hydrocarbon groups of the phospholipid molecules. This makes the lipid bilayer less elastic and decreases permeability to small water-soluble molecules.

Glycolipids, also a component of membranes, project into the extracellular space. Functionally, these may protect, insulate, and serve as receptor-binding sites. In addition, the outer membrane of gram-negative cell walls (see Chapter 6, Bacteria and Archaea) contains lipopolysaccharide bacterial endotoxins that are released on lysis of these cells.

The functions of membrane proteins differ depending on their composition and location in the plasma membrane. They can:

Glycocalyx

Many cells have a matrix formed outside the plasma membrane. This extracellular fabric is composed of polymeric material called a glycocalyx, produced by some bacteria, epithelia, and other cells. In general the glycocalyx is a network of polysaccharides that project from the cellular surface and functions in/as:

In the case of bacteria the glycocalyx is a coating of macromolecules that protects the cell and sometimes helps the bacteria to adhere to its environment. The chemical composition, thickness, and organization of the glycocalyx differ among bacteria. One specialized function of the bacterial glycocalyx is the formation of capsules (Figure 3.2). Capsules protect pathogens, such as Streptococcus pneumoniae and Bacillus anthracis, from phagocytosis by white blood cells, thus adding to their pathogenicity.

Cell Wall

A cell wall is located immediately below the glycocalyx surrounding the plasma membranes. Bacteria, archaea, fungi, plants, and algae can all have cell walls of different chemical composition. The purpose of the cell wall is to maintain the shape of a cell and to protect the cell from any physical or chemical damage.

The bacterial cell wall is a unique rigid structure that maintains the shape of bacteria and protects them from hostile environments, including protection from the immune system of a host (see Chapter 20, The Immune System). The strength of the cell wall is due to the presence of peptidoglycan (mucopeptide or murein), a mixed polymer of hexose sugars (N-acetylglucosamine and N-acetylmuramic acid) cross-linked by short peptide fragments (Figure 3.3). The amount and composition of peptidoglycan vary among the major bacterial groups and provide the basis for Gram staining (see Chapter 4, Microbiological Laboratory Techniques), dividing bacteria into so-called gram-positive and gram-negative organisms.

However, some bacteria do not have a characteristic cell wall structure and some lack a cell wall altogether (i.e., Mycobacterium; see Chapter 6, Bacteria and Archaea). Differences in cell wall composition are an important consideration in the selection of antimicrobial drugs in treatment regimens of bacterial diseases. The cell wall structure is also important in choosing specific methods to control microbial growth in a variety of environments (see Chapter 19, Physical and Chemical Methods of Control).

Characteristics of cell walls in the different microorganisms are as follows:

Gram-positive bacteria have a thick peptidoglycan layer (20–80 nm) located external to the cell membrane (Figure 3.4, A). It also contains acidic polysaccharides such as teichoic acid and lipoteichoic acid, which aid in cell wall maintenance and contribute to an acidic cell surface. The small space between the plasma membrane and the cell wall is the periplasmic space, which can be minimal in some of the gram-positive bacteria.

Gram-negative bacteria have a thin (5- to 10-nm) peptidoglycan layer that is more complex because it has an outer membrane that provides a cover that is anchored to the lipoprotein molecules of the peptidoglycan layer (Figure 3.4, B). The outer membrane is similar in structure to the plasma membrane, but it contains lipopolysaccharides extending from its surface. These lipopolysaccharides can function as receptors or as antigens. In addition, the membrane contains porin proteins, which allow penetration only of small molecules. This serves as a defense mechanism against larger molecules such as antibiotics. The periplasmic space between the plasma membrane and the outer membrane may constitute up to 40% of the total cell volume. This space houses biochemical pathways for nutrient acquisition, peptidoglycan synthesis, electron transport, and detoxification of substances otherwise harmful to the cell.

Diffusion

Diffusion, like other passive transport mechanisms, uses the concentration gradient to move molecules from an area of higher concentration to an area of lower concentration (Figure 3.22). Diffusion is an important mechanism by which cells can readily obtain diffusible materials such as oxygen and release carbon dioxide waste molecules into the external environment.

Facilitated Diffusion

Facilitated diffusion is a process necessary for molecules that cannot readily diffuse through cellular membrane barriers and require membrane transporters for movement across the membrane. As with diffusion, this type of transport does not require energy from ATP. The necessary transport molecules can either be specific membrane carriers or transmembrane channels. Carrier-mediated transport (Figure 3.23):

Protein channel–mediated membrane transport provides selective pathways for specific ions or other small water-soluble molecules. For example, sodium ions can only pass through sodium channels and potassium can only pass through potassium channels. Furthermore, these channels are gated, that is, they are either open or closed. Gated channels can be triggered to open or close by voltage, light, mechanical, or chemical stimuli, and they are named according to the stimuli activating them (i.e., sodium channels, voltage-gated channels, pressure-gated channels, etc.)

Osmosis

Osmosis is the diffusion of water across a selectively permeable membrane. The plasma membrane of cells is selectively permeable to water molecules, allowing them to diffuse but excluding substances dissolved in the water. When the concentration of water on one side of the plasma membrane is greater than that on the other side, water will follow its concentration gradient and diffuse to the area of lower water concentration (Figure 3.24). In living cells, however, isotonicity between the ICF and ECF avoids excessive movement of water either into or out of the cells (see Figure 2.11 in Chapter 2, Chemistry of Life). Although water is the solvent molecule that moves across the membrane during osmosis, the solute concentrations of the ECF and ICF dictate how much water is available for diffusion. For example, a 30% solution contains 30 parts of solute and 70 parts of water and a 3% solution contains 3 parts of solute and 97 parts of water. When these two solutions are placed on the opposite sides of a selectively permeable membrane, water will diffuse from an area of higher concentration of water molecules (the 3% solution) to an area of lower concentration of water molecules (the 30% solution).

Moreover, whereas isotonic conditions do not create stress on cells, hypotonic or hypertonic environments do. Some specific microbes adapt to different osmotic environments as illustrated by amoeba living in a freshwater pond, which is a hypotonic environment. In this case water continuously enters the cell through the plasma membrane. In order to prevent the eventual rupture of the cell, water is actively pumped out of the cell with the help of the contractile vacuole by the process of active transport.

Filtration

Filtration is the movement of molecules through a membrane along a concentration gradient from an area of high hydrostatic pressure to an area of lower hydrostatic pressure. The driving force for filtration can be gravity or, as exemplified in the human body, by the hydrostatic effects of blood pressure on blood plasma, filtering it from the blood capillaries into the ECF. Another important example is filtration from the capillaries of the kidneys into the collecting ducts during urine formation. In microbiology, filtration systems can eliminate microbes from liquid environments (see Chapter 4, Microbiological Laboratory Techniques).

Pump Transport

Active transport of ions or molecules is due primarily to a pump transport mechanism working against a gradient. This work requires energy obtained by hydrolysis of ATP. Active transport carriers are composed of transmembrane proteins. The pump transport process requires:

Active pumping systems are important for cells because they allow the cells to move needed ions and other molecules to specific areas. The calcium pump, for example, moves calcium ions to specific areas within the muscle cell during muscle contraction and relaxation. The sodium–potassium pump removes three sodium ions (Na⁺) out of a cell while it transports two potassium ions (K⁺) into the cell. Both ions are transported against their chemical concentration gradient, which maintains an electrical charge on the cell membrane, referred to as membrane potential. Most cells contain many Na⁺ /K⁺ pumps that are constantly active to maintain the membrane potential. The steep gradient of sodium and potassium ion concentration across cell membranes is essential for conduction and transmission of electrochemical impulses in nerve and muscle cells. If the active extrusion of Na⁺ is blocked or markedly impeded, the increased Na⁺ concentration in the cell promotes osmosis, a challenge to isotonic conditions that could result in cell damage, including rupture of the membrane or crenation (see Figure 2.11 in Chapter 2, Chemistry of Life).

Endocytosis

Extracellular material may be brought into the cell by endocytosis, a bulk transport mechanism that uses vesicles. Some eukaryotic cells transport large molecules, particles, liquids, or other cells across the cell membrane via this process. Typically, a cell surrounds and encloses a particle with its membrane, forming an endocytotic vesicle, and then engulfs it. Whole cells or large particles of solid matter are brought into the cell by the process of phagocytosis (“cell eating”; Figure 3.25, A) (see Chapter 20, The Immune System). Liquids, or molecules dissolved in liquids, are transported into the cell by pinocytosis (“cell drinking”; Figure 3.25, B). If it is necessary for a molecule to bind to a membrane receptor before endocytosis can occur, it is called receptor-mediated endocytosis (Figure 3.25, C).

Exocytosis

Large molecules, such as polypeptides, proteins, and others, may be excreted from the cell via the process of exocytosis (Figure 3.26). Unicellular organisms (i.e., protozoans) use exocytosis for the elimination of waste products. In multicellular organisms exocytosis has a signaling or regulatory function. Vesicles for exocytosis are produced by the Golgi apparatus, from which they are transported to the cell membrane. Here the vesicles fuse with the cell membrane and their contents are emptied into the extracellular space or into a capillary. In addition to its transport function, exocytosis also adds material to the plasma membrane.

Enzyme Specificity

The degree to which enzymes bind to specific binding sites on their substrates determines their specificity. The initial contact between the enzyme and substrate most likely occurs via attraction between electrostatic forces. How well the shape of the enzyme fits (complements) the binding site on the substrate defines specificity—like a key fitting into a lock. Some additional movement of the enzyme shape is often required, just like “jiggling” a key in a lock might be required to open it. This process between enzymes and their substrate(s) can be summed up and explained by:

Classification and Naming of Enzymes

Enzymes are classified according to the type of reaction they catalyze and all metabolic reactions are catalyzed by a specific class of enzyme. Thus, individual enzymes are typically named according to the type of reaction they catalyze, the name of the substrate they act on, and using the suffix -ase.

Exoenzymes and Endoenzymes

Enzymes may also be named according to the site in which they act. Exoenzymes are secreted by a cell into the extracellular environment, where they act to break down large molecules into smaller ones so that they can be taken up into the cell. The exoenzyme amylase produced by some microorganisms hydrolyzes starch into monosaccharides, which can then be transported across their plasma membrane. Other exoenzymes can be released into the intracellular environment for metabolic purposes within the cell. These include cellulase, caseinase, lipase, and nucleotidase. In contrast, endoenzymes work within specific biological membranes such as the enzymes used in cellular respiration.

Cofactors and Coenzymes

In many cases the enzymes require nonprotein coenzymes or cofactors, that is, other ions or molecules, in order to catalyze a reaction. The protein portion of an enzyme is the apoenzyme and the nonprotein portion is a coenzyme if it is an organic molecule (usually a derivative from water-soluble vitamins); if it is a metal ion, it is a cofactor. Holoenzymes are enzymes that may require one or more cofactors or coenzymes when combined (Figure 3.29).

Microorganisms require specific metal ions as trace elements and certain organic growth factors for survival (see Chapter 6, Bacteria and Archaea). The need for these substances occurs because of their roles as cofactors. Enzymes that require cofactors do not have an appropriate shape for the active site until they combine with the cofactor. Metals, therefore, activate enzymes by bringing the active site and the substrate closer together and then participate directly in the chemical reaction as a part of the enzyme–substrate complex. Coenzymes, on the other hand, remove a functional group from one substrate molecule and add it to another substrate. Coenzymes often function as intermediate carriers of hydrogen atoms, electrons, carbon dioxide, and amino groups. An example would be the role of nicotinamide adenine dinucleotide (NAD) in the transfer of electrons in coupled oxidation–reduction reactions (see Cellular Respiration, later in this chapter). Because coenzymes are vitamin derivatives, it might explain the importance of vitamins in our diet; a vitamin deficiency prevents the completion of the holoenzyme and the chemical reaction to be catalyzed fails to occur.

Regulation of Enzyme Activity

Rates at which enzyme reactions proceed within the metabolic pathways are influenced by temperature; pH; concentrations of substrate, enzyme, and product; and the presence or absence of cofactors and coenzymes.

In addition, a variety of other substances such as drugs can either inhibit or reduce the rate of a reaction. The effectiveness of such an inhibitory substance depends on its reversible or irreversible binding properties with the enzyme. For example, in irreversible inhibition, the inhibitor competes with the substrate for the active site of the enzyme (Figure 3.30, A). The degree of inhibition is dependent on the relative concentrations of the inhibitor and the substrate; increasing the amount of substrate may result in reversible inhibition. Competitive enzyme inhibition is the basis for treatment of some infectious diseases by selectively inhibiting a specific metabolic pathway required for the pathogen but not necessary for the human. Antimetabolites function this way, and in so doing they provide an effective weapon against infectious diseases.

Another mechanism that influences the rate of enzyme reactions is noncompetitive inhibition, in which the substance binds to an allosteric site of an enzyme, causing a conformational change of the enzyme’s active site (Figure 3.30, B). The process is irreversible and the degree of inhibition is dependent on the concentration of the inhibitor. Also, enzyme activity is often regulated at specific points of the metabolic pathways by the process of end-product inhibition—when the amount of product formed is sufficient the reaction shuts down. This is negative feedback inhibition and is an example of allosteric inhibition. In other words, in end-product inhibition, the inhibiting substance is the product formed by the initial enzyme activity. The amount of product formed then feeds back to slow down the reaction and prevent excessive accumulation of more final product (Figure 3.31).

Cellular Respiration

Cellular respiration is the process by which the chemical energy of nutrient molecules is released and captured in the form of ATP. This energy transfer involves a series of oxidation–reduction reactions. In the breakdown of glucose and other nutrient molecules, some of the electrons originally present in these molecules are transferred to intermediate carriers and then to a final electron acceptor. When the breakdown is complete, with the end product being carbon dioxide and water, and oxygen the final electron acceptor, the pathway used is aerobic cellular respiration. If oxygen is not available cellular respiration continues with other inorganic molecules acting as the final electron acceptors, and this process is known as anaerobic cellular respiration or fermentation.

Aerobic cellular respiration requires three consecutive pathways: glycolysis, the Krebs cycle (citric acid cycle), and the electron transport chain (oxidative phosphorylation). The overall reaction for aerobic cellular respiration of glucose is as follows:

C6H12O6+6O→6CO2+6H2O+energy

Glycolysis, the first pathway of the series, occurs in the cytoplasm and uses 10 enzyme reactions to break down glucose to produce a net yield of 2 molecules of pyruvic acid, 2 molecules of ATP, and 2 molecules of reduced NAD (Figure 3.32). The sequence of the principal steps of glycolysis that form ATP is as follows:

The overall equation for glycolysis is as follows:

Glucose+2NAD+2ATP+2Pi→2 pyruvic acid+2NADH+2ATP

This is followed by:

Pyruvic acid→acetyl-CoA+CO2

Glycolysis is connected to the Krebs cycle by converting pyruvic acid into acetyl-coenzyme A (acetyl-CoA) and carbon dioxide (CO₂) while transferring two hydrogen ions to NADH. The NADH formed during this reaction will be sent to the electron transport chain. Each acetyl-CoA molecule will enter the Krebs cycle.

The Krebs cycle is the second pathway in aerobic cellular respiration. It occurs in the plasma membrane of prokaryotes and within the matrix of mitochondria in eukaryotes. After acetyl-CoA enters the Krebs cycle it combines with oxaloacetic acid to form citric acid. Through a series of reactions involving the elimination of two carbons and four oxygens (two CO₂ molecules) and the removal of hydrogens, citric acid is eventually converted to oxaloacetic acid to complete this metabolic cycle (Figure 3.33).

Steps in the Krebs cycle include the following:

For each glucose molecule entering aerobic respiration, the Krebs cycle runs twice because glycolysis produced two molecules of pyruvic acid. Molecules of NAD and FAD in glycolysis and the Krebs cycle are essential to pick up hydrogens and electrons. The reduced forms of these molecules then enter the electron transport chain, where they are oxidized in a series of reduction–oxidation reactions to regenerate coenzymes while producing ATP, oxygen, and water.

The electron transport chain, the last step in aerobic cellular respiration, takes place in the cristae of the inner mitochondrial membrane. In order to regenerate NAD⁺ and FAD⁺, electrons and hydrogen ions are transferred from reduced NAD and FAD molecules to carrier molecules in the electron transport chain. These molecules include flavoproteins, coenzyme Q, iron–sulfur enzymes, and cytochromes. The last carrier transfers the electrons to oxygen, the final electron acceptor of aerobic respiration. As the hydrogen ions and electrons are transferred in a stepwise fashion from NADH to the chain of carriers, energy is released. This energy is captured by ADP to generate many ATP molecules from each glucose molecule (Figure 3.34).

The breakdown of one glucose molecule in aerobic respiration is summarized in Table 3.4:

The total of 38 ATP molecules produced is theoretical, because the actual ATP yield is less in eukaryotic cells because of the energy expended in transporting NADH across the mitochondrial membrane. However, there are some aerobic bacteria that come close to achieving this theoretical total because they lack mitochondria and do not have to use ATP to transport NADH across the mitochondrial membrane.

The phosphogluconate pathway (also called the pentose phosphate pathway or hexose monophosphate shunt) is an alternative catabolic pathway followed by some bacteria (Figure 3.35). This pathway generates NADPH and synthesizes pentose sugars in two distinct phases. The first is the oxidative phase, which generates NADPH, and the second phase synthesizes pentose sugars. This is a common pathway for heterolactic fermentative bacteria. It yields various end products including lactic acid, ethanol, and carbon dioxide. In addition, this pathway is a significant source of pentose sugars during nucleic acid synthesis.

Anaerobic cellular respiration is a metabolic pathway by which glucose is converted to lactic acid if oxygen is not available. Some bacteria utilize anaerobic respiration (anaerobes) for energy production and the final electron acceptor is an inorganic molecule and not oxygen. Actually, oxygen is toxic to anaerobic microbes and exposure to it kills most of such bacteria. On the other hand, facultatively anaerobic bacteria can use anaerobic respiration when oxygen is absent or present in limited amounts only. The final electron acceptor of anaerobic bacteria can be CO₂, the ion SO₄^2–, or NO₃^– .

If the final electron acceptor is an organic molecule, then fermentation takes place. The process starts with glycolysis but the end product varies because of the variety of organic molecules that can act as final electron acceptor. Fermentative bacteria and yeast use specific enzymes to metabolize the end product of glycolysis, namely pyruvic acid, into the final product. In this process an electron transport system is not used and reduced NAD from glycolysis is oxidized by an organic molecule accepting electrons and hydrogens. With this pathway, the cell can catabolize sugar without oxygen, but this process is far less efficient than aerobic cellular respiration for the generation of ATP.

Fermentation end products produced by microorganisms can be beneficial to human life and various industries (i.e., dairy and brewing). Examples of bacteria and their fermentation end products are as follows:

Photosynthesis

Photosynthesis is a fundamental biochemical process by which plants, most algae, cyanobacteria, and some phototrophic bacteria convert light energy into chemical energy via ATP. Chlorophyll, a pigment found in chloroplasts (Figure 3.36, A) of plants and algae, is the site of photosynthesis. Photosynthetic bacteria do not have chloroplasts and photosynthesis takes place directly within the cell. Cyanobacteria contain thylakoid membranes (Figure 3.36, B) similar to those in chloroplasts and these are the only prokaryotes that perform oxygen-generating photosynthesis. Other photosynthetic bacteria contain a variety of different pigments, called bacteriochlorophylls, but they do not produce oxygen. Photosynthesis requires water for oxidation but some bacteria oxidize hydrogen sulfide instead and produce sulfur as a waste product. The rate of photosynthesis is affected by carbon dioxide, light intensity, and temperature.

Processes in photosynthesis are divided into two categories: reactions that require light, and reactions that occur in the dark and are light-independent. A simplified general equation for photosynthesis is as follows:

6CO2+12H2O+light→C6H12O6+6O2+6H2O

(Carbon dioxide+water+light energy→glucose+oxygen+water)

The first stage of photosynthesis is a light-dependent reaction that requires solar energy that is converted to chemical energy. Chlorophyll absorbs light and drives a transfer of electrons and hydrogen from water to an acceptor called NADP⁺ (nicotinamide adenine dinucleotide phosphate), which stores the energized electrons for a short period of time. During this process water is split and oxygen gas is given off. The process of producing ATP from sunlight is called photophosphorylation. There are two forms of photophosphorylation: noncyclic photophosphorylation (Figure 3.37, A) and cyclic photophosphorylation (Figure 3.37, B).

Noncyclic photophosphorylation, the predominant route, includes two sets of pigments called photosystem I (PSI) and photosystem II (PSII). These pigments are sensitive to or are excited by slightly different wavelengths of light. Wavelengths of about 700 nm excite the chlorophyll in PSI (P700) whereas the chlorophyll of PSII (P680) is excited by wavelengths under 680 nm. The stages of noncyclic photophosphorylation are as follows:

Cyclic photophosphorylation occurs when the photo-excited electrons utilize photosystem I as an alternative path. The electrons cycle back from Fd to the cytochrome complex and then to the P700 chlorophyll. This cyclic system does generate ATP but not NADPH and no oxygen is released.

The second stage of photosynthesis, the light-independent reactions or dark reactions, takes place in the stroma within the chloroplast. The enzyme RuBisCO (ribulose-1,5-biphosphate carboxylase/oxygenase) captures CO₂ from the air and releases three-carbon sugars in a complex process called the Calvin-Benson cycle. The Calvin-Benson cycle is similar to the Krebs cycle because the starting material regenerates after molecules enter and leave the cycle. Carbon enters the cycle in the form of CO₂ and leaves in the form of sugar. The energy source for the cycle is ATP, and NADPH is the reducing power for adding high-energy electrons to make three-carbon sugars (glyceraldehyde 3-phosphate) that later combine to form glucose. The Calvin-Benson cycle is organized into three phases: carbon fixation, reduction, and regeneration of the CO₂ receptor (Figure 3.38).

Transcription

Prokaryotic transcription occurs in the cytoplasm and eukaryotic transcription takes place in the nucleus. The description or central dogma of the flow of information from genetic material was first introduced by Francis Crick in 1958 (Figure 3.39). It states that DNA transfers information to RNA and RNA then controls protein synthesis. Or, DNA makes RNA and RNA makes protein. DNA also controls its own replication (see DNA Replication, later in this chapter). The structures of DNA and RNA are discussed in Chapter 2.

The initiation of transcription is controlled by the enzyme RNA polymerase, which recognizes the beginning of a gene so that it can start mRNA synthesis at a particular DNA sequence that appears at the beginning of genes. This sequence is called a promoter. The promoter is a unidirectional sequence on one strand of the DNA and tells the RNA polymerase where to start and in which direction to continue synthesis. RNA polymerase stretches open the double helix at that point and then begins the synthesis of mRNA. This synthesis of mRNA follows the principle of complementary base pairing (see Chapter 2). Termination of transcription occurs when the polymerase recognizes a DNA sequence known as a terminator sequence. In prokaryotic cells ribosomes can begin protein synthesis with the mRNA immediately, whereas in eukaryotic cells the mRNA must leave the nucleus before it combines with the ribosomes in the cytoplasm. As stated earlier in this chapter, eukaryotic ribosomes may be free in the cytoplasm, or attached to rER.

Each mRNA molecule contains several hundred or more nucleotides complementary to the DNA template. Every three bases form a base triplet or codon and each codon is the code for a specific amino acid. DNA triplets, RNA codons, and their amino acid translation are shown in Table 3.5. However, some amino acids can be translated by different codon sequences as indicated in Table 3.6. As mRNA moves through the ribosome, the sequence of codons translates into a sequence of amino acids.

Translation

Specific enzymes and tRNA translate codons. Like other RNA molecules, tRNA is a single-stranded molecule; but it bends back in on itself to form a cloverleaf structure with an anticodon on one end (Figure 3.40). An anticodon consists of three nucleotides complementary to a specific codon on the mRNA molecule. Specific enzymes (aminoacyl-tRNA synthetase enzymes) in the cytoplasm bind specific amino acids to the ends of tRNA; and a tRNA molecule with a given anticodon can bind to a specific amino acid. Each tRNA molecule is therefore bound to one specific amino acid.

The binding of the tRNA anticodons to the codons of the mRNA, as it moves through the ribosome, forms a polypeptide chain. Translation occurs in three stages: initiation, elongation, and termination.

• Initiation: The ribosome assembles on the identified start codon (AUG—methionine) in mRNA and then each sequential base pair forms the next codon. The position of the start codon determines the open reading frame or order of codons that will be read to form a protein.

• Elongation: The first and second tRNAs bring the first and second amino acids close together. The first amino acid detaches from its tRNA and forms a peptide bond with the amino acid of the neighboring second tRNA, forming a dipeptide. When the third tRNA binds to the third codon, its amino acid binds to the second amino acid, which then detaches from its tRNA. The polypeptide chain grows as new amino acids are added to this tripeptide by the same process. This growing polypeptide chain remains attached by only one tRNA to the strand of mRNA (Figure 3.41).

• Termination: Elongation of the designated protein continues until a “stop” codon (UAA, UGA, or UAG) signals the end of the process. The building of the protein stops because there is no tRNA molecule that is complementary to the stop codon. A releasing enzyme frees the newly formed polypeptide chain from the last tRNA and the mRNA is released from the ribosome.

Binary Fission

The form of asexual reproduction by which all bacteria and most protists reproduce is binary fission. A single cell separates into two identical daughter cells, each containing an identical copy of the parental DNA. This process occurs in a stepwise fashion starting with elongation of the bacterium. Next, the bacterial chromosomal DNA, which is a single circular molecule, replicates. After this, a central transverse septum forms that divides the cell into two daughter cells (Figure 3.43). This type of reproduction normally results in two identical cells. However, bacterial DNA has a relatively high mutation rate, which is a rapid rate of genetic change that is the underlying reason for the development of antibiotic-resistant bacterial strains.

Cell Cycle and Mitosis

Eukaryotic cells undergo a cell cycle or a sequential series of events between cell divisions. The frequency of cell divisions varies between different cell types, and some cells never divide after they differentiate (i.e., nerve cells and muscle cells). The cell cycle consists of four distinct phases: the G₁ phase, S phase, G₂ phase, and M phase. The G₁ phase, S phase, and G₂ phase are collectively known as the interphase or the nondividing stage of the cell cycle (Figure 3.44). The M phase is composed of two tightly coupled processes: mitosis and cytokinesis.

• During the G₁ phase, cells carry out the metabolic activities characteristic of the tissue to which they belong. In preparation for cell division, a cell might increase the amount of cytoplasm and the number of cell organelles. Chromosomes are in their extended form, and their genes actively direct RNA synthesis. At the end of G₁, the cell commits to dividing and has reached the “point of no return.” In yeast it is called START and in multicellular eukaryotes, it is the restriction point.

• During the S phase DNA duplicates.

• During the G₂ phase the cell continues to grow and its metabolic activities prepare for mitosis. The quantity of DNA increases and the chromatin condenses to form short, thick structures that indicate the end of the phase. Now, each chromosome consists of two strands called chromatids joined together by a centromere (Figure 3.45). The two chromatids contain identical DNA base sequences because each is produced by semiconservative replication of DNA. Each chromatid becomes a separate chromosome after mitotic cell division.

• During the M phase, mitosis and cytokinesis occur. Mitosis is divided into four stages: prophase, metaphase, anaphase, and telophase (Figure 3.46). The visible characteristics of these phases are as follows:

• Prophase: The chromosomes become clearly visible by light microscopy. The centrioles migrate toward the opposite poles of the cell and each centrosome has spindle fibers extending from it. The nuclear membrane starts to disappear and the nucleolus is no longer visible.

• Metaphase: The chromosomes line up at the equator of the cell. Spindle fibers from each centriole attach to the centromeres of the chromosomes. The nuclear membrane is now absent.

• Anaphase: The centrosomes split and the sister chromatids separate as each is pulled to an opposite pole.

• Telophase: The centrosomes become longer, thinner, and less distinct. New nuclear membranes form and the nucleolus reappears. The cell membrane develops a distinct furrowing at the cell midline. Two separate nuclei are now apparent within the same cell.

• Cytokinesis: The cytoplasm divides to complete cell division.

Meiosis

Eukaryotic cells maintain a specific number of chromosomes characteristic for that species. The chromosome set exists either in a haploid state (single, unpaired) or in a diploid state (matched pair). Cells of most fungi, many algae, and some protozoans exist in the haploid state during most of their life cycle. Gametes of organisms that sexually reproduce are haploid. Cells of animals, plants, some protozoans, fungi, and algae are diploid throughout most of their life cycle. This state begins at fertilization when a female haploid gamete (egg) fuses with a male haploid gamete (sperm) to create a diploid offspring (haploid + haploid = diploid). Mitosis, however, maintains the normal chromosome number in all eukaryotic cells. Moreover, sexual reproduction in diploid organisms requires haploid chromosome numbers to produce diploid offspring. The reduction of the diploid chromosome number to a haploid state in gametes occurs during reduction division or meiosis.

In meiosis, a single duplication of chromosomes occurs and two cell divisions follow. This type of cell division is diploid → haploid in nature, and occurs only during the production of gametes, that is, sex cells. The diploid cells in the sex organs undergo two cell divisions to produce haploid sex cells. The stages of meiosis subdivide depending on whether they occur in the first or in the second meiotic cell division. These stages are prophase I, metaphase I, anaphase I, and telophase I; and prophase II, metaphase II, anaphase II, and telophase II (Figure 3.47).

It is important during meiosis that the genetic basis of the evolutionary process occurs. In other words, the significance of meiosis goes beyond the reduction of the chromosome number for sexual reproduction. First, during the lining up of the homologous pairs of chromosomes in metaphase I, each member of the pair comes from a different parent and randomly shuffles to end up in one of the daughter cells. Second, crossing-over or additional exchanges of parts of homologous chromosomes can occur in prophase I. In addition, this, together with the random lining up in metaphase I, results in genetic recombination to ensure that the gametes produced in meiosis are genetically unique. All of this provides the genetic diversity for sexually reproducing organisms that is needed to provide the characteristics that promote the survival of species over time—evolution.