Understanding Metabolism: An Essential Guide to Chemical Processes in Living Organisms

1. Fig. 5-1 Metabolism is the sum of all chemical processes carried out by living organisms. Anabolism = reactions that require energy to synthesize complex molecules from simpler ones. Needed for growth, reproduction and repair. Catabolism = reactions that release energy by breaking complex molecules into simpler ones that can be then reused as building blocks. Needed for energy for its life processes including movement, transport, and synthesis of complex molecules (anabolism).

2. Fig. 5-1 table All catabolic reactions involve electron transfer, capturing energy in high-energy bonds in ATP. Electron transfer is related to oxidation and reduction (redox reactions). Oxidation is the loss of electrons, gain of oxygen, loss of hydrogen, and it is exothermic, exergonic (it gives off heat energy). Reduction is the loss of oxygen, gain the electrons, gain of energy (stores energy) and is endothermic, endergonic (requires energy). When one substance gains electrons (is reduced), another must lose electrons (is oxidized). Think gain electrons = gains negative = reduction. Gaining electrons can mean gaining hydrogen or losing oxygen. 2H2 + O2 2 H2O Hydrogen is the reducing agent (electron donor) and Oxygen is the oxidizing agent. Hydrogen is oxidized.

3. Fig. 5-2 Microorganisms are very versatile in the ways in which they obtain energy. Microorganisms are categorized by the ways in which obtain energy and obtain carbon. Obtain Carbon Obtain energy Chemoheterotrophs include all infectious microorganisms. They use glycolysis, fermentaition, and aerobic respiration to obtain energy.

4. Fig. 5-3 Glycolysis and fermentation do not require oxygen (anaerobic). Aerobic respiration does require oxygen as a final electron acceptor and captures large amounts of energy from a glucose molecule as ATP as compared to glycolysis and fermentation. Photosynthetic microorganisms and plants use light energy and hydrogen from water to reduce carbon dioxide to organic substances like glucose.

5. All chemical processes in living organisms including photosynthesis, glycolysis, fermentation, and aerobic respiration, consist of a series of chemical reactions in which the product of one reaction serves as the substrate (reacting material) for the next, a metabolic pathway. Catabolic pathways capture energy and anabolic pathways make the complex molecules needed by the cell, including the enzymes needed for the metabolic pathways. Energy captured in catabolic reactions as ATP is used in anabolic pathways. Do checklist page 111.

6. Fig. 5-4 Enzymes act as catalysts – substances that remain unchanged while they speed up reactions 1000s to 1,000,000s of times. Even “spontaneous” or exothermic reaction require activation energy – the energy to get things going. Enzymes lower the activation energy required. Enzymes also allow cells to control when and how much of any particular molecule is made or broken down.

7. Fig. 5-5 Enzymes also provide a surface on which reactions can take place. The enzyme positions the reactants in such a way to enable them to react easily. Enzymes are very specific due to the shape and the electrical charges in the active site. Each enzyme binds only one substrate. Endoenzymes are intracellular and exoenzymes, made inside the cell, work outside of the cell. Random movement of molecules leads the substrate to bump into the active site of the enzyme. Because it “fits”, it remains there, forming an enzyme-substrate complex. This positions the substrate to allow the chemical reaction to take place. “fits” due to shape and chemical nature (non-covalent bonds)

8. Fig. 5-6 Enzymes are usually named by adding –ase to their substrate. Example: lipases break down lipids Many enzymes consist of a protein apoenzyme that must combine with a nonprotein coenzyme (an organic molecule) and/or a cofactor (an inorganic ion). Many coenzymes are synthesized from vitamins. Coenzymes are inorganic ions – minerals.

9. Fig. 5-8 Enzymes are controlled (usually by the cell) in several ways. Competitive inhibition Non-competitive inhibition Negative (or positive) feedback In competitive inhibition a competitive inhibitor binds reversibly to the active site, blocking the ability of the substrate to bind. This inhibition depends on the concentration of the substrate and the inhibitor. Sulfa drugs are competitive inhibitors. They compete with PABA, the substrate converted to folic acid, slowing the production of folic acid.

10. Fig. 5-9 Non-competitive (allosteric) inhibition of enzymes. The inhibitor binds to the enzyme in an area other than the active site. However, the binding of the inhibitor changes the shape of the enzyme at the active site and the substrate can not bind while the inhibitor is present. Some bind reversibly, but others bind irreversibly and permanently inactivate the enzyme. The allosteric inhibitor does not compete with the normal substrate for the active site.

11. Although not non-competitive inhibitors, lead, mercury and other heavy metals can bind to other sites on enzymes and permanently change their shape. Changing a molecules shape usually interferes with its function. The enzyme is inactivated. Feedback inhibition is the most common way in which a cell controls enzymes. When a synthetic pathway has made enough of the product, the product itself will inhibit one of the 1st enzymes in the pathway – reversible non-competitive inhibition. See checklist on page 114 and How to Ruin an Enzyme

12. Fig. 5-10 Factors That Affect Enzyme Reactions Temperature pH Concentrations of substrate, product and enzyme Substrate and enzyme move around more as temp increases so they bump into each other more often Acidic or alkaline conditions also denature enzymes – used to kill microbes

13. Chemical reactions, including enzyme- catalyzed reactions are reversible given the right circumstances. A + B  AB or AB  A + B Chemical equilibrium is reached when there is no net change in the concentrations of AB, A, or B. The concentrations of the substrates and products influence the direction and the speed (rate) of the reaction. Lots of AB will “push” the reaction toward producing A and B If A and B are used up in other reactions as soon as they are made, this will keep their concentration low and “push” the reaction in the same direction – toward A + B production

14. Fig. 5-11 Anaerobic metabolism: Glycolysis and Fermentation Glycolysis: Does not require oxygen Four major events 1.Phosphorylation 2.Breaking six-carbon sugar  2 3-carbon 3.Transfer of electrons to NAD 4.Capture of energy in ATP Increased energy Incapable of leaving the cell Uses 2 ATP

15. NADH 2 ATP made 2 ATP made Glycolysis provides relatively small amount of energy (ATP & NADH). Uses 2 ATP to produce 4 ATP. Electrons are removed from NADH during fermentation, producing NAD+ which is needed to keep glycolysis going.

16. Fig. 5-12 Fermentation = metabolism of pyruvate in the absence of oxygen. Very important because NAD+ must be recycled for glycolysis. Many kinds of fermentation are performed by a great variety of microbes including pathogens. The products are used in diagnosis. Butyric-butylic fermentation occurs in Clostridium species that cause tetanus and botulism. The production of butyric acid by Clostridium perfringens causes severe the tissue damage of gangrene What happens if pyruvic acid just accumulated in the cell? What happens if there is no NAD+?

17. Fig. 5-13 Homolactic Acid fermentation occurs in some types of bacteria called lactobacilli, in streptococci, and in mammalian muscle cells. This pathway in lactobacilli is used in making some cheeses. NAD+ can now be reused in glycolysis, step 6. NADH from step 6 of glycolysis

18. Fig. 5-14 Alcoholic fermentation is common in yeasts and is used in making bread and wine. NADH from step 6 of glycolysis NAD+ can now be reused in glycolysis, step 6.

19. The ability to ferment sugars other than glucose forms the basis of other diagnostic tests. For example, the pathogenic bacterium Staphylococcus aureus ferments mannitol (a simple sugar) and produces acid, which causes phenol red in the medium to turn yellow (see Figure 5.15). The nonpathogenic bacterium Staphylococcus epidermidis fails to ferment mannitol and does not change the color of the medium.

20. Fig. 5-16 Aerobic Respiration Both anaerobes and aerobes carry out glycolysis. Anaerobes do not use oxygen, some are killed by exposure to oxygen. Aerobes do use oxygen, some must use oxygen to survive. Microbes that can use oxygen if it is available but do not need it are facultative anaerobes. Aerobes do produce some energy during glycolysis, however, aerobes use glycolysis as a prelude to aerobic respiration – a much more productive process which requires oxygen. In prokaryotes, these reactions occur in the cytoplasm, in eukaryotes, in the matris of the mitochondria

21. The Krebs Cycle (tricarboxylic acid [TCA] cycle / citric acid cycle) is a sequence of reactions in which acetyl groups (2 carbon group) are oxidized to carbon dioxide. Hydrogen atoms are also removed by NAD+ or FAD and their electrons are transferred to coenzymes in the electron transport system which pumps the protons across a membrane creating a steep gradient. Each reaction in the cycle is controlled by a specific enzyme. The reactions (metabolic pathway) forms a cycle because oxaloacetic acid, the 1st reactant, is regenerated. Three main events: 1. The oxidation of carbon to CO2 2.The transfer of electrons tocoenzymes NADH and FADH2 3. Energy is captured in GTP

22. During glycolysis H atoms are transferred to NAD or FAD. These transfer the H atoms to electron carriers embedded in the cell membrane of bacteria or in the inner membrane of the mitochondria. Eventually these electrons combine with the final electron acceptor, oxygen, to form water. Fig. 5-19 The arrangement of the various carriers in the membrane result in the protons being pushed from the bacterial cytoplasm to outside the cell. The proton gradient created in this way is used to make ATP (oxidative phosphorylation). The electrons and protons carried by each NADH result in enough energy via the proton gradient to produce 3 ATP, while each FADH2 results in only 2 ATP. The Electron Transport Chain Oxidation/reduction

23. Eukaryotic cells make ATP via aerobic respiration in the mitochondria

24. The proton gradient created by the electron transport chain “powers” ATP synthase, which makes ATP. Like a waterfall, the protons move from high concentration to low through ATP synthase.

25. All electron transport chains are not alike, they differ from organism to organism. However all have carriers which accept only hydrogen atoms and carriers that accept only electrons – resulting in the pumping of H atoms. From the metabolism of a single glucose molecule, 10 pairs of electrons are transported by NAD (2 pairs from glycolysis, 2 pairs from pyruvic acid conversion and 6 pairs from Krebs). Two pairs are transported by FAD 10 X 3=30, 2 X 2=4, total = 34 ATP, plus 2 ATP molecules from glycolysis and 2 GTP from Krebs = 38 ATPs per glucose molecule. Compare to glycolysis and fermentation alone!

26. Fig. 5-20 Chemiosmosis occurs in and around the cell membrane in bacteria and the inner membrane of mitochondria in eukaryotic cells. Electrons are transferred along the electron transport chain, protons are pumped outside the membrane, so the ions’ concentration is higher outside. This produces a force that drives the protons back into the cell or mitochondrial matrix. In addition, there is an electrochemical gradient, with outside more positively charged (more H+ ions). The protons flow through special channels in ATP synthase, energy released is used to produce ATP.

27. Fig. 5-21 Anaerobic Respiration Some bacteria use only parts of the Krebs’ Cycle and the electron transport chain. These anaerobes do not use free oxygen as their final electron acceptor. Instead they use inorganic oxygen-containing molecules. However, this produces fewer ATP molecules. Urinalysis can be done to test for removal of one oxygen atom from nitrate to form nitrite. A positive test indicates the presence of bacteria like E. coli. Checklist page 125 See table 5.2 & 5.3

28. Fig. 5-22 Catabolism of fats Beta oxidation (oxidation of the beta carbon) Fatty acids are broken apart 2 carbons at a time to acetyl-CoA.

29. Fig. 5-24

30. Fig. 5-27 Amino acids, nucleic acid bases, and ribose are made (anabolic) from intermediates in glycolysis and from the Krebs cycle (catabolic). Therefore, these pathways are actually amphibolic. All organisms share many biochemical characteristics and require the same building blocks to make proteins and nucleic acids.

31. Fig. 5-28 Many biosynthetic pathways are complex, often requiring many reactions, each with a specific enzyme requirement. Tryptophan synthesis needs at least 13 different enzymes. Absence of a single enzyme means the microbe must take up tryptophan from the environment or die. Microbes also synthesize many carbohydrates and lipids of course - petidoglycan, etc. Microorganisms also use energy for transporting substances across membranes and for their own movement.

32. Fig. 4-32 Active transport requires energy (usually ATP). Active transport uses energy to move molecules or ion against their concentration gradient. This is like moving something up a hill, it requires energy. Active transport is important for microorganisms to move nutrients that are present in low concentrations in their environment. In Gram negative bacteria porins in the outer membrane form channels for ions and small hydrophilic metabolites (facilitated diffusion). After entering the periplasmic space, a specific periplasmic protein binds to the metabolite and allows it to be moved into the cytoplasm via cell membrane proteins then act as carriers and enzymes. They are specific for a single or a few molecules or ions, and require energy to move these molecules against their concentration gradient.

33. Group translocation reactionsmove a substance from outside to inside a cell while modifying it at the same time. Ex. Glucose is phosphorylated and can not leave the cell. Phosphotransferase system (PTS) consists of sugar-specific enzyme complexes called permeases which form a transport system through the cell membrane. PTS uses energy from the high-energy phosphate molecule phosphoenolpyruvate (PEP). PEP provides energy and a phosphate group. The enzyme transfers the phosphate to a sugar and at the same time moves the sugar across the membrane.

34. Most motile bacteria move by means of flagella Flagellated bacteria move by rotating their flagella. The energy for this appears to be provided by a proton gradient much like chemiosmosis (electron transport chain). Some glide etc. Myxococcus secrete a substance called a surfactant which lowers surface tension at one end of the bacteria. The difference in surface tension front to back causes the bacterium to glide. Cell movement requires energy