Dr.Sheldon Miller should know the metabolic pathways and the compounds involved General concepts of metabolic pathways. A single cell is a conglomerate of metabolic pathways. Roles of intermediary metabolism: This concerns the breakdown and synthesis of molecules including carbohydrates, lipids, and proteins. These compounds can come from dietary intake or synthesis within cell. in intermediary metabolism, compounds are broken down and eventually you get to the citric acid cycle and ultimately to CO2 and H20. On the Synthesis side, you see that small fragments of the degradation side compounds are used on the synthesis side, to make new proteins etc. As compounds are broken down, there are oxidative steps where chemicals are broken down and energy is relased, which is saved for the cell by coupling with reaction which conserves energy in a covalent bond. In case of ATP, acid anhydride, other things go to reduced form. The ability to capture some of the energy released during degradation is essential for all animal cells. Plants can get some energy from sun, but animals MUST get it from food etc. To summarize... Roles of degradation (catabolism) provide small carbon compounds source of energy convert compounds to excretable form role of syntheses (anabolism) maintenance of cell structure - cholesterol, phospholipids essential components in other cell functions, cofactors storage form creation - eg glucose -->glycogen converting to form to be excreted - is sometimes necessary synthesize, not degrade. Overview of metabolic pathways....biochemical things and regulation of pathway - topics covered are general and not specific to any particular pathway. see "generalized metabolic pathway" diagram. what controls what pathway a substance takes? the environment of the cell, needs of the cell, etc. eg, depending on circumstances glucose may be stored or used for energy. So, substance A is introduced to the cell via diet or synthesis. One of the early steps is usually an enzyme catalyzed rxn commiting A to take this pathway. It is a main regulatory step of the pathway, and is unique to the pathway, and is IRREVERSIBLE. other steps in the pathway are usually reversible. Product of compound can go on to be used in other pathway, used as is, excreted, stored, whatever. You can have input into a pathway, from a dietary or metabolic source; or you can have one of the intermediates in a pathway be recruited for use in another pathway. Pathways are overall unidirectional, but steps are mostly reversible. Note that synthesis and degradation of a product are NOT the same pathway; there is always at least ONE irreversible step. Le Chatelier's principle: A + B <=======> C + D if the concentration of a componenet of the rxn is altered, the concentration of other components will change to compensate for this alteration. Eg, if some A is added, rxn will shift to the right. see "maintaining a unidirectional movement" page. How does a cell control a metabolic pathway in general? eg, how does it control the rate of passage of compounds through the pathway? Irreversibility of enzyme catalyzed rxn - the committed step - other sites of metabolic control Inhibition or activation of specific enzyme in pathway - feedback inhibition - direct and allosteric - protein modification (cleavage, etc.) - specific non-metabolite inhibitor Subcellular compartmentation -separation of substance into organelles or something. Can segregate and regulate pathways Hormones and other extracellular signals Genetic Control of enzyme levels over the long term, slowly. Availability of coenzymes or substrate Tissue differences: -isoenzymes -cells' responsiveness to extracellular signals, eg, hormones. Separation (partial or complete) of competing pathways (synthesis and degradation, eg, A to G and G to A) -differences at irreversible rxn steps subcellular compartmentalization - isoenzymes and responsiveness to cellular signals -use of different coenzymes one specific pathway will not utilize all of these mechanisms, just some of them. What is the stuff you need to knwo about a metabolic pathway? Well, know the intermediate transformations taking place. knwo the source of the initial substrate. know the products, and how it/they are utilized. Know points where compounds are recruited or used by other pathways. know how pathway is regulated. This is relevant to most of the clinically used labwork in veterinary medicine. GLYCOLISIS (see handout!!!!) we do need to know the structures of d-glucose and d-fructose!! but those are the only two so far that we have to memorize. Glucose is an aldehyde, fructose is a ketone. Note that d-glucose has several asymmetric carbon atoms. The one furthest from the C=O carbonyl group. ( in glucose, the fifth one down) determines if it d or l form. the difference between glucose and galactose is at the fourth carbon, where in galactose has the OH and H substituents reversed from the way they are in glucose. Mannose differs at the C2 carbon. d-ribose is an important 5 carbon sugar used in making RNA, and deoxyribose is important in making DNA. But, most sugars in solution don't exist as a chain. Glucose in solution forms a hemiacetal ring, where the OH from the last sugar attacks the C-H bond of the first carbon. You end up with either alpha d glucose or beta d glucose, depending on if the OH is above or below the plane. see "carbohydrate structures". animals use the alpha form. plants use the beta form to make cellulose, and animals do not have the enzymes to digest this. herbivores use bacteria to digest cellulose. the 5 minute glycolysis miracle it's the major glucose breakdown pathway in animals and occurs in liver, majorly, which is where we'll discuss it. It occurs in other tissues too and is mostly the same with some regulatory differences. role of glycolysis: to provide small molecules as glucose is broken down breakdown products are used for synthesis of other molecules. also to provide energy to run synthetic reactions and cellular processes. Large amounts of bond energy are released during glucose breakdown and are captured in NAD and NADH. The energy - part of it- is captured in a covalent bond of ATP or in a covalent bond of NADH. Glycolysis occurs in cytoplasm of cell. Glucose can freely go through cell membrane very rapidly. First rxn of glycolysis is carried out by an enzyme called hexokinase (SEE HANDOUT), which phosphorylates d-glucose to glucose 6-phosphate. This is a control step, an irreversible reaction, and this form of glucose can not pass through the cell membrane, so this traps it inside the cell. This step USES ATP, uses up energy. Next step is reversible, glu 6-phosphate goes to fructose 6-phosphate by phosphoglucose isomerase. The third step is the committed step. It uses another ATP, is irreversible. Converts to fructose 1,6-biphosphate, which is unique to this pathway, and this is the main point of regulation in glycolysis.