Lec 7 Pathways of Bioenergetics PDF

lecture 7 ‫البكرتاي الطبية‬ ‫ حسن محمد انيف‬.‫د‬.‫أ‬ Pathways of Bioenergetics One of the scientific community’s greatest achievements was deciphering the biochemical pathways of cells. Initial work with bacteria and yeas...

lecture 7 ‫البكرتاي الطبية‬ ‫ حسن محمد انيف‬.‫د‬.‫أ‬ Pathways of Bioenergetics One of the scientific community’s greatest achievements was deciphering the biochemical pathways of cells. Initial work with bacteria and yeasts, followed by studies with animal and plant cells, clearly demonstrated metabolic similarities and strongly supported the concept of the universality of metabolism. The study of the production and use of energy by cells is called bioenergetics, including catabolic routes that degrade nutrients and anabolic routes that are involved in cell synthesis. Acquisition of Nutrients Bacteria use various strategies for obtaining essential nutrients from the external environment and transporting these substances into the cell’s interior. For nutrients to be internalized, they must cross the bacterial cell wall and membrane. These complex structures help protect the cell from environmental insults, maintain intracellular equilibrium, and transport substances into and out of the cell. Although some key nutrients (e.g., water, oxygen, and carbon dioxide) enter the cell by simple diffusion across the cell membrane, the uptake of other substances is controlled by membrane selective permeability; still other substances use specific transport mechanisms. Active transport is among the most common methods used for the uptake of nutrients such as certain sugars, most amino acids, organic acids, and many inorganic ions. The mechanism, driven by an energy-dependent pump, involves carrier molecules embedded in the membrane portion of the cell structure. These carriers combine with the nutrients, transport them across the membrane, and release them inside the cell. Group translocation is another transport mechanism that requires energy but differs from active transport in that the nutrients being transported undergoes chemical modification. Many sugars, purines, pyrimidines, and fatty acids are transported by this mechanism. 1 lecture 7 ‫البكرتاي الطبية‬ ‫ حسن محمد انيف‬.‫د‬.‫أ‬ Production of Precursor Metabolites Once inside the cell, many nutrients serve as the raw materials from which precursor metabolites for subsequent biosynthetic processes are produced. These metabolites, listed in the Figure below, are produced through two central pathways: the Embden-Meyerhof-Parnas (EMP) pathway (glycolysis) and the tricarboxylic acid (TCA) cycle. 2 lecture 7 ‫البكرتاي الطبية‬ ‫ حسن محمد انيف‬.‫د‬.‫أ‬ The two major pathways and their relationship to one another are shown in this Figure, also the figure not shown are the alternative pathways (e.g., the Entner- Doudoroff and the pentose phosphate pathway) that play key roles in redirecting and replenishing the precursors as they are used in subsequent processes. The Entner-Doudoroff pathway catalyzes the degradation of gluconate and glucose. The gluconate is phosphorylated, dehydrated, and converted into pyruvate and glyceraldehyde, leading to ethanol production. Alternatively, the pentose phosphate pathway uses glucose to produce reduced nicotinamide adenine dinucleotide phosphate (NADPH), pentoses, and tetroses for biosynthetic reactions such as nucleoside and amino acid synthesis. The production efficiency of a bacterial cell resulting from these precursor- producing pathways can vary substantially, depending on the growth conditions and availability of nutrients. This is an important consideration, because the accurate identification of medically important bacteria often depends heavily on methods that measure the presence of products and byproducts of these metabolic pathways. 3 lecture 7 ‫البكرتاي الطبية‬ ‫ حسن محمد انيف‬.‫د‬.‫أ‬ Energy Production The third type of fueling pathway is one that produces the energy required for nearly all cellular processes, including nutrient uptake and precursor production. Energy production is accomplished by the breakdown of chemical substrates (i.e., chemical energy) through the degradative process of catabolism coupled with oxidation-reduction reactions. In this process, the energy source molecule (i.e., substrate) is oxidized as it donates electrons to an electronacceptor molecule, which is then reduced. The transfer of electrons is mediated through carrier molecules, such as nicotinamide-adenine- dinucleotide (NAD_) and nicotinamide- adenine-dinucleotide-phosphate (NADP_). The energy released by the oxidation-reduction reaction is transferred to phosphate-containing compounds, where highenergy phosphate bonds are formed. ATP is the most common of such molecules. The energy contained in this compound is eventually released by the hydrolysis of ATP under controlled conditions. The release of this chemical energy, coupled with enzymatic activities, specifically catalyzes each biochemical reaction in the cell and drives cellular reactions. The two general mechanisms for ATP production in bacterial cells are substrate- level phosphorylation and electron transport, also referred to as oxidative phosphorylation. In substrate-level phosphorylation, high-energy phosphate bonds produced by the central pathways are donated to adenosine diphosphate (ADP) to form ATP directly from the substrate as opposed to generation via the electron transport chain. In addition, pyruvate, a primary intermediate in the central pathways, serves as the initial substrate for several other pathways to generate ATP by substrate- level phosphorylation. These other pathways constitute fermentative metabolism, which does not require oxygen and produces various end products, including alcohols, acids, carbon dioxide, and hydrogen. 4 lecture 7 ‫البكرتاي الطبية‬ ‫ حسن محمد انيف‬.‫د‬.‫أ‬ The specific fermentative pathways and the end products produced vary with different bacterial species. Detection of these products is an important basis for laboratory identification of bacteria. Oxidative Phosphorylation Oxidative phosphorylation involves an electron transport system that conducts a series of electron transfers from reduced carrier molecules such as NADH2, NADPH2 and FADH2 (flavin adenine dinucleotide), produced in the central pathways (as shown in the Figure below), to a terminal electron acceptor. 5 ‫‪lecture 7‬‬ ‫البكرتاي الطبية‬ ‫أ‪.‬د‪.‬حسن محمد انيف‬ ‫‪6‬‬ lecture 7 ‫البكرتاي الطبية‬ ‫ حسن محمد انيف‬.‫د‬.‫أ‬ There are several important facets of aerobic respiration: 1. The total yield of ATP is 40: 4 from glycolysis, 2 from the TCA cycle, and 34 from electron transport. However, since 2 ATPs were expended in early glycolysis, this leaves a maximum of 38 ATPs. 2. Six carbon dioxide molecules are generated during the TCA cycle. 3. Six oxygen molecules are consumed during electron transport. 4. Six water molecules are produced in electron transport and 2 in glycolysis,but because 2 are used in the TCA cycle, this leaves a net number of 6. 7 lecture 7 ‫البكرتاي الطبية‬ ‫ حسن محمد انيف‬.‫د‬.‫أ‬ The energy produced by the series of oxidation-reduction reactions is used to generate ATP from ADP. When oxidative phosphorylation uses oxygen as the terminal electron acceptor, the process is known as aerobic respiration. Anaerobic respiration refers to processes that use final electron acceptors other than oxygen. A knowledge of which mechanisms bacteria use to generate ATP is important for designing laboratory protocols for cultivating and identifying these organisms. For example, 1- some bacteria depend solely on aerobic respiration and are unable to grow in the absence of oxygen (strictly aerobic bacteria). 2- Others can use either aerobic respiration or fermentation, depending on the availability of oxygen (facultative anaerobic bacteria). 3- For still others, oxygen is absolutely toxic (strictly anaerobic bacteria). Biosynthesis The fueling reactions essentially bring together all the raw materials needed to initiate and maintain all other cellular processes. The production of precursors and energy is accomplished through catabolic processes and the degradation of substrate molecules. The three remaining pathways for biosynthesis, polymerization, and assembly depend on anabolic metabolism. In anabolic metabolism, precursor compounds are joined for the creation of larger molecules (polymers) required for assembly of cellular structures (Figure 2-11). Biosynthetic processes use the precursor products in dozens of pathways to produce a variety of building blocks, such as amino acids, fatty acids, sugars, and nucleotides (Figure 2-11). Many of these pathways are highly complex and interdependent, whereas other pathways are completely independent. In many cases, the enzymes that drive the individual pathways are encoded on a single mRNA molecule that has been transcribed from contiguous genes in the bacterial chromosome 8 lecture 7 ‫البكرتاي الطبية‬ ‫ حسن محمد انيف‬.‫د‬.‫أ‬ As previously mentioned, bacterial genera and species vary extensively in their biosynthetic capabilities. Knowledge of these variations is necessary to use optimal conditions for growing organisms under laboratory conditions. For example, some organisms may not be capable of synthesizing an essential amino acid necessary as a building block for proteins. Without the ability to synthesize the amino acid, the bacterium must obtain the building block from the environment. Thus if the organism is cultivated in the microbiology laboratory, the amino acid must be provided in the culture medium. Polymerization and Assembly Various anabolic reactions assemble (polymerize) the building blocks into macromolecules, including lipids, lipopolysaccharides, polysaccharides, proteins, and nucleic acids. This synthesis of macromolecules is driven by energy and enzymatic activity in the cell. Similarly, energy and enzymatic activities also drive the assembly of various macromolecules into the component structures of the bacterial cell. Cellular structures are the product of all the genetic and metabolic processes discussed. 9