Biochemistry 10.1 PDF

# Catabolism ## Introduction Metabolism encompasses all chemical reactions that an organism performs to sustain its life. Metabolic processes that break molecules down are called **catabolic processes** and typically release energy, which can be used to power various cellular processes. One use of...

# Catabolism ## Introduction Metabolism encompasses all chemical reactions that an organism performs to sustain its life. Metabolic processes that break molecules down are called **catabolic processes** and typically release energy, which can be used to power various cellular processes. One use of that energy is to build other types of molecules - such processes are called **anabolic processes**. Nearly all metabolic reactions are catalyzed by enzymes and often involve the breaking down or building up of proteins, carbohydrates, nucleic acids, and lipids. Unit 4 focuses on metabolism, with a specific focus on the catabolic pathways that release energy from carbohydrates or lipids and the anabolic pathways that store energy in carbohydrates or lipids. This lesson describes the forms that the energy released through catabolism may take between its release from molecules and its later use by the cell. One such form is adenosine triphosphate (ATP), the primary chemical unit of energy storage in most cells. ## Catabolism | Energy-containing nutrients | Catabolism | Energy-depleted end products | |---|---|---| | Carbohydrates | Break down | $CO_2$, $H_2O$, $NH_3$ | | Fats | | | | Proteins | | | | ADP + P_i produced | NAD⁺ | NADH | | | NADP⁺ | NADPH | | | FAD | FADH₂ | | | | ATP produced | ## Anabolism | Cell macromolecules | Anabolism | Precursor molecules | |---|---|---| | Proteins | Build up | Amino acids | | Polysaccharides | | Sugars | | Lipids | | Fatty acids | | Nucleic acids | | Nitrogenous bases | ## A Comparison of Catabolic and Anabolic Metabolism **Figure 10.1** A comparison of catabolic and anabolic metabolism. ## ATP and Other Cellular Sources of Energy Glucose is commonly considered the preferred fuel source for cells, yet the oxidative combustion of glucose yields approximately 2,840 kJ/mol. This amount of energy is much more than can be coupled to any individual endergonic biochemical reaction. Consequently, biochemical catabolism of biomolecules does not occur as a single combustion step, but over several enzyme-catalyzed steps (i.e., a metabolic pathway). This facilitates the release of energy in smaller portions that can be stored for later use to power one reaction at a time. ## ATP as Energy Currency Storing energy in molecules of ATP is one of the most common ways of managing the massive amount of energy released by glucose oxidation and other catabolic processes. ATP is a nucleoside triphosphate that contains a chain of three phosphate groups connected by phosphoanhydride linkages. Phosphoanhydride hydrolysis has a negative ∆G, as shown in **Figure 10.2**, but this ∆G is much smaller than that of glucose combustion. This smaller amount of energy is much more appropriate for coupling to biochemical processes. ## Phosphate Groups **Figure 10.2** ATP hydrolysis releases energy that cells can use to power endergonic biochemical processes. **Figure 10.2** ATP hydrolysis releases energy that cells can use to power endergonic biochemical processes. ## Table 10.1: Energy Yield per Mole of Glucose Combustion Compared to Aerobic Respiration | Molecule | ∆G’° (kJ/mol) | ATP yield after aerobic Respiration | Total Energy (kJ) | Efficiency of energy capture | |---|---|---|---|---| | Glucose | -2,840 (combustion) | | -2,840 | | | ATP | -30.5 (hydrolysis to ADP) | 32 | -976 | 34.4% | ## The Nucleotides are Energetically Equivalent ATP is the nucleotide most often used as energy currency, but the other common ribonucleotides (i.e., GTP, CTP, UTP) are also used to power reactions. Although the nitrogenous base differs among the four nucleotides, the energy released by hydrolysis of their phosphoanhydride linkages is essentially the same. Furthermore, ATP can be used to regenerate the other nucleoside triphosphates, making the γ-phosphate hydrolysis of any nucleoside triphosphate essentially equivalent to one unit of ATP. **Figure 10.3** provides an example of this equivalence using a step of protein translation. The ribosome uses one GTP to power peptide bond formation between an aminoacyl-tRNA and a growing peptide. The γ-phosphate of GTP is hydrolyzed to produce GDP + P_i, which releases an amount of energy essentially equivalent to the energy of ATP hydrolysis. ATP can be used to regenerate GTP; therefore, the ribosome can be said to use the equivalent of one unit of ATP to power peptide bond formation. ## Figure 10.3: Hydrolysis of GTP (or any other NTP) is energetically equivalent to hydrolysis of ATP. Some biochemical reactions require more energy input than hydrolysis of the γ-phosphate can provide. Rather than bind multiple NTP molecules, enzymes can bind a single NTP molecule but hydrolyze it at the phosphoanhydride linkage between the α- and ß-phosphates instead of at the linkage between the ß- and γ-phosphates. This results in the production of an NMP (instead of an NDP) and an inorganic pyrophosphate (PP_i) (instead of a single phosphate). PP_i is then hydrolyzed to two P_i molecules in another exergonic reaction, releasing more energy. Ultimately, the hydrolysis of an NTP to NMP + PP_i costs two units (or equivalents) of ATP. This is because ATP can be used to regenerate the used NTP by adding one phosphate back at a time. **Figure 10.4** shows the net effect of this kind of hydrolysis. **Figure 10.4** Hydrolysis of NTP to NMP + PP_i is energetically equivalent to two ATP units. ## Other High-Energy Molecules Can Regenerate ATP by Substrate-Level Phosphorylation Other molecules may facilitate ATP synthesis from ADP. For example, creatine phosphate is an important molecule in skeletal muscle. Under conditions of high energy demand, its guanidinyl phosphate group can be hydrolyzed to quickly replenish ATP stores under low-oxygen conditions. Transfer of a phosphate from one molecule to ADP to form ATP is called **substrate-level phosphorylation**. Other examples of high-energy substrates include acyl phosphates, enol phosphates, and thioesters. **Table 10.2** lists several molecules that can act as high-energy substrates in biochemical pathways commonly tested on the exam. ## Table 10.2: Examples of high-energy substrates. | High-energy substrate | Hydrolysis products | Example substrate/pathway | |---|---|---| | Phosphoric acid anhydride | R-O-P-O + HO-P-O | ATP/various | | Acyl phosphate | R-C-O + HO-P-O | 1,3-bisphosphoglycerate/glycolysis | | Enol phosphate | R-C-O + HO-P-O | Phosphoenolpyruvate/glycolysis | | Guanidinyl phosphate | R-N-C-NH2 + HO-P-O | Creatine phosphate/anaerobic muscle metabolism | | Thioester | R-C-O + HS-R’ | Succinyl-CoA/citric acid cycle | ## Other Forms of Energy Currency Aside from storing energy in ATP or ATP equivalents, the potential energy of high-energy electrons can also be stored via the redox potential (E°) of cofactors such as NADH or FADH₂. For example, the high-energy electrons of NADH enter Complex I of the electron transport chain, and the oxidation of NADH to NAD⁺ provides the energy to pump protons across the mitochondrial inner membrane, as shown in **Figure 10.5**. (See Lesson 12.2 for more on the electron transport chain and proton pumping.) ## Figure 10.5: The energy of electrons transferred during redox reactions can be used to power biochemical processes. The electrochemical gradient of charged particles (i.e., ions) contributes to the membrane potential (Lesson 3.3), which is another form of potential energy that cells can use to power endergonic processes. The energy stored in the membrane potential can be used to synthesize chemical bonds. For example, the protons pumped across the membrane by the electron transport chain create an electrochemical gradient across the mitochondrial inner membrane called the proton motive force, which powers ATP synthase. Consequently, generation of ATP in this way – that is, through a proton gradient that itself comes from oxidation of redox coenzymes – is known as oxidative phosphorylation (see Chapter 12). **Figure 10.6** illustrates the use of electrochemical gradients and the membrane potential as a cellular source of energy. ## Figure 10.6: Potential energy stored in an electrochemical gradient is freed when solutes move down their gradient. This energy can be used to power biochemical processes such as ATP synthesis. ## Concept Check 10.1 Protein synthesis (i.e., translation) at the ribosome involves numerous energy-requiring processes. One round of elongation involves: - “Charging” of a tRNA with a free amino acid (coupled to ATP → AMP + PP_i) - Peptide bond condensation (coupled to GTP → GDP + P_i) - Translocation of peptidyl-tRNA from the A site to the P site (coupled to GTP → GDP + P_i) Given these steps, what is the total net cost (in units of ATP) for adding one free amino acid to a growing peptide? ## 10.1.02: Energy of ATP Hydrolysis Concept 10.1.01 explains that the phosphoanhydride linkages of NTPs, as well as some other bonds and linkages (see Table 10.2), are considered high energy. Hydrolysis of these linkages is highly exergonic (-∆G) and often highly exothermic (-∆H), meaning it produces heat. This concept discusses the chemistry of biochemically important high-energy linkages and their hydrolysis products. Importantly, hydrolysis of a biochemical bond involves more than the simple breaking of a single covalent bond. As discussed in General Chemistry Lesson 3.5, breaking bonds always requires enthalpy input (i.e., breaking bonds is endothermic [+∆H]). However, hydrolysis also involves the formation of bonds to the atoms of the water molecule, which releases energy (i.e., forming bonds is exothermic [-∆H]). For example, in ATP hydrolysis (**Figure 10.7**), a phosphoanhydride bond and an O-H bond break, but another O-H bond forms (in the released inorganic phosphate) and a P-OH bond forms on the ß-phosphate of ADP. The energy of the bonds formed outweighs that of the bonds broken, yielding an overall exothermic process (i.e., a negative ∆H) and contributing to the favorability of the reaction. **Figure 10.7** Exothermic hydrolysis of ATP. ## Other Factors That Contribute to the Free Energy Change of Hydrolysis However, not all exothermic reactions are exergonic, and not all hydrolysis reactions are as exergonic as ATP hydrolysis. Exergonic reactions are considered energy releasing because their products have less free energy than their reactants. The magnitude of this change can be influenced by two general factors: factors that contribute to the high energy of the reactants (i.e., factors that make the reactants unstable) and factors that contribute to the low energy fo the products (i.e., factors that make the products more stable). Common contributing factors include charge-charge repulsion, ionization, resonance, and tautomerization. **Charge-charge repulsion** is an important feature of nucleoside triphosphates that contributes to their high energy. Each of the phosphate groups of the nucleotide holds at least one negative charge at physiological pH. Because like charges repel each other, this close arrangement of negative charges is relatively unstable and therefore high energy. Hydrolysis of the phosphoanhydride bond between the ß- and γ-phosphate groups allows those two groups and their negative charges to separate. Consequently, hydrolysis of an NTP is an exergonic process because it partially relieves charge-charge repulsion, thereby releasing energy (**Figure 10.8**). **Figure 10.8** Hydrolysis of a phosphoanhydride bond allows nearby negative charges to separate, stabilizing the hydrolyzed products. **Ionization** of a molecule after hydrolysis is another factor that increases the energy released. For example, **Figure 10.9** shows that hydrolysis of ATP^4- yields ADP^2- and HPO₄^2- as its direct products. However, the predominant forms of ATP and ADP under physiological conditions have formal charges of -4 and -3, respectively. After ATP hydrolysis, the ß-phosphate of ADP is quickly deprotonated by water. This spontaneous deprotonation contributes to the overall negative ∆G of hydrolysis (**Figure 10.9**). **Figure 10.9** Spontaneous (i.e., -∆G) ionization at physiological pH contributes to the exergonic nature of ATP hydrolysis. **Resonance** (see Organic Chemistry Lesson 2.7) is another stabilizing factor that contributes to the negative ∆G of ATP hydrolysis. In general, the more resonance forms a molecule has, the more stable it is. Although ATP has several resonance forms before hydrolysis, additional resonance forms are possible after hydrolysis (see **Figure 10.10**). **Figure 10.10** The ß-phosphate of ADP is more resonance stabilized than the ß-phosphate of ATP. Other high energy molecules such as acyl phosphates (e.g., 1,3-bisphosphoglycerate) and thioesters (e.g., succinyl-CoA) are also stabilized by charge separation, ionization, and resonance. **Tautomerization** is another stabilizing factor that can contribute to the exergonic nature of high-energy molecule hydrolysis. Tautomerization does not play a large role in stabilizing the products of ATP hydrolysis; however, it does explain why phosphoenolpyruvate (PEP) can serve as a high-energy molecule to power a substrate-level phosphorylation reaction at the end of glycolysis (see Lesson 11.1). This is because the phosphate group of PEP traps the molecule in its enol form. However, keto tautomers are generally much more stable than enol tautomers (see Organic Chemistry Chapter 9.4). Consequently, once PEP’s phosphate group is removed, the resulting enol form of pyruvate spontaneously tautomerizes to its keto form, stabilizing it (**Figure 10.11**). ## Figure 10.11: The spontaneous tautomerization of pyruvate to its keto form contributes to the negative ∆G of phosphoenolpyruvate hydrolysis. ## 10.1.03: Coupling of ATP Hydrolysis to Other Reactions Concepts 10.1.01 and 10.1.02 discuss the energetics of ATP hydrolysis (and hydrolysis of other high-energy substrates) as being exergonic and therefore able to power endergonic processes. Importantly, an actual hydrolysis reaction (i.e., breaking bonds by addition of water) does not need to occur to allow the potential energy stored within those molecules to be utilized. However, the energy of hydrolysis is relevant to the thermodynamics of reactions that use ATP (or its equivalents), even if hydrolysis does not occur in the reaction mechanism. Concept 4.1.03 discusses that free energy G is a state function that depends only on a system’s state and not on the path taken to achieve that state. Kinases “couple” ATP hydrolysis to substrate phosphorylation, which forms a phosphorylated substrate and ADP. However, for many kinases the actual mechanism is simply the transfer of a phosphoryl group – no hydrolysis actually occurs. Nevertheless, the thermodynamic energy of phosphoryl transfer is the same as the sum of the individual energies of ATP hydrolysis and phosphosubstrate formation (**Figure 10.12**). ## Figure 10.12: Because free energy is a state function, the free energy of hydrolysis can be considered to power a reaction, even if hydrolysis does not actually occur. Some enzymes couple ATP hydrolysis to an endergonic reaction through a series of phosphate transfers either to the substrate or to the enzyme, with the phosphate group “activating” the molecule it is attached to. Temporary phosphorylation of the enzyme can trigger a conformational change that facilitates enzyme function. For example, phosphorylation of a translocase often induces a conformational change that moves ions across a membrane against their electrochemical gradient. **Figure 10.13** shows the sodium-potassium pump, a translocase that couples ATP hydrolysis to ion movement by temporarily phosphorylating the translocase. ## Figure 10.13: ATP can power reactions by temporarily phosphorylating an enzyme to trigger a conformational change. ATP hydrolysis can also be coupled to endergonic processes through conformational changes induced by protein-ligand interactions. During muscle contraction, for example, ATP is hydrolyzed and the muscle filaments slide along each other based on their binding to ATP, ADP, or P (muscle contraction is discussed in more detail in Biology Chapter 17). ATP hydrolysis can also be indirectly coupled to an endergonic process. Electrochemical gradients and membrane potentials are a source of potential energy for powering the cell and are often generated and maintained using ATP hydrolysis. Secondary active transporters, which couple the spontaneous movement of one ion down its gradient while cotransporting a second solute against its gradient, are the most common example of this (**Figure 10.14**). ## Figure 10.14: ATP can indirectly power reactions by converting its chemical energy into the potential energy of an electrochemical gradient.