1. Microbiology- a clinical approach by Anthony Strelkauskas et al. 2010 Chapter 3: : Essentials of metabolism

2.  It is important to have a basic understanding of metabolism because it governs the survival and growth of microorganisms.  The growth of microorganisms can have a direct effect on infectious disease.  Good metabolic function makes pathogens more successful at causing disease.  Understanding microbial growth will allow finding effective ways to inhibit microbial growth. http://www.wired.com/news/images/full/5thplace_f.j pg

4.  Metabolism is: ◦ A series of chemical processes that go on in living organisms. ◦ Used to obtain energy. ◦ Linked to growth  Carbon and energy are required for growth.  The body has two processes to obtain carbon: ◦ Autotrophy : carbon from inorganic substances ◦ Heterotrophy: carbon from other organic molecules  Energy can be gained in two major ways ◦ Phototrophy : from sun light (phototroph) ◦ Chemotrophy: through chemical reactions involving the break down of organic molecules  Nearly all infectious organisms are chemoheterotrophs.

5.  Metabolism is broken down into two parts: ◦ Catabolism – molecules are broken down through metabolic processes to release the energy stored in their chemical bonds. ◦ Anabolism – metabolic processes in which the energy derived from catabolism is used to build large organic molecules from smaller ones.  Both processes involve electron transfer and oxidation and reduction reactions.

6.  An oxidation reaction is a chemical reaction in which an atom, ion or molecule loses one or more electrons.  A reduction reaction is a chemical reaction in which an atom, ion or molecule gains one or more electrons.  Oxidation and reduction reactions always occur together. ◦ The combination of an oxidation reaction and a reduction reaction are jointly referred to as redox reactions.  When a substance is oxidized, it loses electrons.  When a substance is reduced, it gains electrons Note: loss of hydrogen = oxidation; gain of hydrogen = reduction

7.  In metabolism, respiration occurs at the cellular level and is not the same as breathing (respiration at the macroscopic level).  Cellular respiration describes catabolic processes and is divided into: ◦ Aerobic respiration – metabolism that uses oxygen ◦ Anaerobic respiration– metabolism that does not use oxygen  Technically: respiration always involves an electron transport chain

8.  Metabolic reactions occur in series of chemical reactions called pathways. ◦ The following is an example of a pathway. A is the initial substrate and E is the final product of the pathway, with B, C, and D being intermediates. A B C D E  Each step in the pathway is mediated or facilitated by a specific enzyme.

9.  Enzymes are proteins that act as catalysts for metabolic reactions, making the reaction go faster.  Each enzyme is specific for a reaction.  Enzymes are found in all living organisms and most cells contain hundreds of types which are constantly being manufactured and replaced.  Enzymes work by lowering the energy of activation.

10.  Reduce activation energy for a chemical reaction  Reaction occurs faster

11.  Enzymes have specific three dimensional shapes: if the shape changes, activity is inhibited.  The shape of the molecule provides a distinctive site called the active site. It is here that: ◦ The substrate fits into the enzyme and the reaction occurs. ◦ The enzyme and substrate interact to form the enzyme-substrate complex.  The electrical charges found at the active site are also important.  Enzymes are generally highly specific. ◦ A given enzyme catalyzes only one type of reaction. ◦ Most enzymes react with only one particular substrate.

12.  Some enzymes work on more than one substrate but in these cases the enzymes always work in a particular type of reaction. ◦ Proteases: degrade proteins ◦ Lipases: cleave lipids ◦ Nucleases: cleave nucleic acids

13.  Many enzymes can catalyze a reaction only if other substances are present at the active site. ◦ These enzymes are referred to as apoenzymes.  Co-factors are helper substances that are inorganic ions such as magnesium, zinc, or manganese.  Coenzymes are helper substances that are non-protein organic molecules.  Co-factors or coenzymes bind to the active site and change the shape of the active site so the substrate now fits.  They can also be used as carrier molecules.

14.  Two coenzyme carrier molecules frequently encountered in biological reactions are: ◦ NAD + = nicotinamide adenine dinucleotide  NADH (reduced form) ◦ FAD = flavin adenine dinucleotide  FADH 2 (reduced form)  Both are vitamins  The electrons carry the energy

15.  Targeted enzyme inhibition takes place in three ways: ◦ Competitive inhibition ◦ Allosteric inhibition ◦ Feedback inhibition

16.  The inhibitor molecule is similar in structure to the substrate and competes with the substrate to bind to the active site.  When the inhibitor has bound to the active site, the substrate cannot bind.  The binding of the competitor is reversible and dependent upon the relative numbers of inhibitor molecules and substrate molecules present.

17.  This activity also involves inhibitor molecules but they do not block the active site.  Inhibitor molecules bind to a part of the enzyme away from the active site: the allosteric site.  This binding changes the shape of the active site in such a way that it can no longer fit properly with the substrate.  The binding of some allosteric inhibitors is reversible*. *Note: lead and mercury irreversibly inhibit enzymes.

18.  Feedback inhibition is used in many of the metabolic pathways found in the cell.  The final product in a pathway accumulates and begins to bind to and inactivate the enzyme that catalyzes the first reaction of the pathway.  It is reversible and, when the level of end product decreases, the inhibition stops and the pathway begins to function again.

19.  pH ◦ Influences charges in the enzyme molecule ◦ Very low or very high pH denatures the enzyme  Temperature ◦ Slight increases increase activity, decreases inhibit the activity ◦ Extreme high temperatures break hydrogen bonding and denature enzymes  Concentration of the substrate, enzyme, product

20.  Enzymes are proteins that work in metabolism by lowering the energy of activation.  These proteins have a specific three dimensional shape and complex with the substrate they act upon at a place that is called active site.  Enzymes are highly specific and in some cases require cofactors and coenzymes to function.  Enzyme function can be regulated by competitive inhibition, allosteric, or feed back inhibition.  Temperature, pH, and the concentration of substrate all affect the function of enzymes.

21. Catabolism is the process in which A. Molecules are broken down B. Molecules are transformed into more essential components C. Molecules are built up D. Energy id decreased During a reduction reaction a substance A. Gains an electron and becomes more positively charged B. Loses an electron and becomes more negatively charged C. Gains an electron and becomes more negatively charged D. Loses an electron and becomes positively charged

22.  Catabolic processes in metabolism cause the breakdown of large organic molecules into smaller ones.  These are called fueling reactions because they cause a release of energy.  There are three important pathways by which most organisms release energy from nutrient molecules: ◦ Glycolysis ◦ Krebs cycle ◦ Electron transport chain

23.  The catabolic pathway is used by most organisms.  The best example of this pathway is glucose breakdown.  The process itself is a series of chemical reactions and involves substrate phosphorylation.  The reactions occur in the cytoplasm and do not require oxygen. ◦ 1 molecule glucose + 2 ATP  2 molecules pyruvate and 4 ATP  Four ATP molecules are produced in glycolysis ◦ The first steps of the pathway consume two ATP molecules. ◦ The net gain is 2ATP molecules/ molecule glucose.  ATP is a high energy carrier ◦ ADP + P i + energy ATP

24.  Glycolysis can lead to further pathways. ◦ Krebs cycle and cellular respiration with electron transport chain(aerobic) ◦ Fermentation (anaerobic)

25.  The Krebs cycle is also known as the tricarboxylic acid (TCA) cycle or the citric acid cycle.  It is an aerobic catabolic pathway seen in aerobic cellular respiration.  Continues from glycolysis  Pyruvate is further metabolized in this process. ◦ modified with coenzyme A to produce Acetyl-CoA  Involves electron and hydrogen shuffling, release of carbon as CO2  NADH and FADH 2 are produced and sent to the electron transport chain  Through the electron transport chain ATP is generated.

26.  The electron transport chain is a sequence of molecules. ◦ In eukaryotes, they are found in the inner mitochondrial membrane. ◦ In prokaryotes, they are organized in the plasma membrane  Electrons are transferred to a final electron acceptor. ◦ In aerobic respiration, the final acceptor is oxygen. ◦ In anaerobic respiration, the final acceptor is an inorganic oxygen-containing molecule.

27. In prokaryotes the electron transport chain is located on the cell membrane. Accumulation of H + across the membrane + -

28. Note: Cytochrome oxidase C is detected in diagnostic assays for Pseudomonas aeruginosa.

29.  As electrons are transferred along the electron transport chain, protons (H + ) are pumped out of the cell (or across inner mitochondrial membrane).  This causes the proton concentration outside the cell to be higher than inside the cell, causing a concentration gradient and a charge gradient to form.  Specialized membrane proteins allow protons to re-enter the cell. ◦ Energy is released as protons re-enter the cell. ◦ This energy is used to bind phosphate to ADP, making the high- energy molecule ATP.  36 molecules of ATP/1 molecule glucose ◦ The difference in proton concentration in this process is called the proton motive force. ◦ Important for active transport and flagella movement

30.  Fermentation is the enzymatic breakdown of carbohydrates that have been produced by glycolysis.  The final electron acceptor is an organic molecule.  This process does not require oxygen and typically occurs in the absence of oxygen.  Fermentation does not increase the yield of ATP from what it is after glycolysis (2 molecules of ATP/ 1 glucose molecule).  Different microorganisms use different fermentation pathways with varying end products.

31. No gas, also used in muscle cells

33.  Anabolic reactions are classified as biosynthetic reactions because they are used to synthesize all the biological molecules needed by the cells of living organisms.  Biosynthetic reactions form the network of pathways that produce the components required by the cell for growth and survival.  These reactions are fueled by the energy stored in high-energy bonds in ATP.  Production of carbohydrates, amino acids, lipids, nucleic acids.  These pathways are inhibited by some antibiotics: sulfonamide, trimethoprim

35.  Metabolism is the chemical process that provides or stores energy for the organism.  Metabolism can be broken down into two parts: catabolism (breaking down molecules) and anabolism (building up molecules).  Oxidation and reduction reactions involve the transfer of electrons.  Nearly all chemical processes of the cell consist of a series of chemical reactions known as a pathway.

36.  Enzymes are proteins that speed up chemical reactions by lowering the energy of activation.  Enzymes work on the basis of their three- dimensional shape. They are specific and in some cases require cofactors or coenzymes to function.  Temperature, pH, and concentration of substrate all affect enzyme function.

37.  When oxygen is involved, catabolism occurs through glycolysis, the Krebs cycle, and electron transport.  Aerobic metabolism requires oxygen and yields 38 ATP molecules from the breakdown of one molecule of glucose.  Breakdown of one molecule of glucose without oxygen via fermentation (anaerobic metabolism) yields only 2 molecules of ATP.

38. During competitive inhibition of enzyme function A. The product competes with the substrate for the action site B. ATP competes with the substrate for the active site C. A molecule can compete with the substrate for the active site D. Any molecule can compete with the substrate for the active site The final electron acceptor in aerobic respiration is A. Water B. Oxygen C. Hydrogen D. Both A and B