BMB 462 Lecture 14 Outline of Last Lecture I. Review of cholesterol/lipid transport via lipoproteinsII. Overview of Amino Acid catabolismIII. Ammonia collection in hepatocytesIV. Pyridoxal PhosphateV. Introduction to the Urea CycleOutline of Current Lecture I. Continuation of the Urea CycleII. Connections between the Urea Cycle and the TCA CycleIII. Regulation of the Urea CycleIV. Metabolism of Carbon Skeletons from amino acidsV. Carbon TransfersVI. Phenylalanine DegradationVII. The Nitrogen CycleVIII. Nitrogen FixationCurrent LectureConcepts to remembers from previous courses/lectures:- Vitamin B12 functionI. Continuation of the Urea Cyclea. In the last steps of the cycle, urea is produced via 2 cleavages. The first cleavage produces fumarate and the second gives ureai. Start with argininosuccinate. Break off four Carbon atoms that originally came as aspartate; they get broken off as fumarateii. Cleavage is done by argininosuccinaseiii. fumarate goes to TCA cycleiv. Arginine - one of the 20 common Amino Acids, but humans don't use it much as a source of Carbon for protein synthesis; mostly it is just used forurea cycle. Is considered essential because you don't produce enough of itThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.b. Arginine goes to cleavage 2i. Cut off 2 nitrogen atoms, a carbon, and an oxygen for urea, the wasteii. Regenerate ornithine to act as acceptor for next round of urea cycleiii. Cleavage done by arginaseII. Connections between the Urea Cycle and the TCA Cyclea. The 2 cycles can run independently but have important relationshipsb. Oxaloacetate - made in TCA cycle; add Nitrogen to it (amino group) to get aspartatei. Aspartate is the donor of the 2nd N-group in the urea cyclec. Fumarate – generated from the arginosuccinase reaction in the urea cycle i. It is converted to malate, which is then converted back to oxaloacetate. This results in oxidation of Carbon, producing NADH, which produces 2.5 ATP equivalents (via a redox reaction), which allows us to generate ATP bythe ETC.d. Energetics - urea requires 4 ATP to make, but when you couple it with the TCA cycle, oxidation produces 2.5 ATP equivalentsIII. Regulation of the Urea Cyclea. Regulation is needed under conditions where you eat excess protein and so have excess Nitrogen, or under starvation conditions where you're breaking down muscle mass and therefor have excess Nitrogen that wayb. Allosteric control of CPSI i. Short-term control is based on conditions in the particular cell. N acetylglutamate is created particularly for regulation (it's not an intermediate in any other pathway; produced purely for regulatory purposes)ii. Made from glutamate and acetyl-CoA. (High levels of glutamate is indicative of high levels of N, since glutamate is a key N carrier)iii. Acetylglutamate synthase - triggered by arginine, makes n-acetylglutamate. This then allosterically activates carbomyl phosphate synthetase which makes carbamoyl phosphate for the urea cycle.c. Transcriptional Control of Enzymesi. This acts as longer term control - based on demand (if you eat a big meal with a lot of protein, you get more of the enzymes and the urea cycle runs better. If there's less protein, fewer enzymes are made and therefor the urea cycle doesn't run as much)IV. Metabolism of Carbon Skeletons from amino acidsa. Overviewi. General plan: remove nitrogen by transamination, convert remaining carbon skeleton into intermediate from TCA cycle so then you can oxidize the Carbons and generate Energy from it.b. Amino acids are classified by how they're broken down/oxidized and whether or not the carbons can be used to make glucose.i. Ketogenic Amino Acids1. Only used to make ketones, cannot be used to make glucose2. i.e. Lysine, Leucine 3. Breakdown the amino acids either into acetoacetyl-CoA or acetyl-CoA a. Acetoacetyl-CoA is a ketone body and acetyl-CoA can be made into oneii. For acetyl-CoA to make glucose the cell needs to take the oxaloacetate and put it through gluconeogenesis. If you take the acetyl-CoA away from TCA cycle, it could not keep running and Energy would not be produced.c. Glucogenic Amino Acidsi. i.e. alanine. Carbon is used to make glucose (the 13 amino acids that aren't ketogenic or both are glucogenic Amino Acids)ii. Puts 3 Carbons into pyruvate, which will either be used to make oxaloacetate or acetyl-CoA. One alanine can't do both so it's considered glucogenicd. Both Ketogenic and Glucogenici. Carbon from 1 amino acid is used to make both ketone bodies and glucose/a ketone body and a glucoseii. i.e. Isoleucine, tyrosine, phenalalanine, tryptophan, threonine1. When phenalalanine is broken down part of the carbons becomes fumarate and part becomes acetoacetate.e. Know Amino acid/ketone pairs, i.e. glutamate and alpha-ketoglutarateV. Carbon Transfersa. Cofactors for One-Carbon transfersi. The cell needs to rearrange Carbon skeletons to get them to be intermediates in the TCA cycle. 1. Not all molecules immediately break down into an intermediate so have to move Carbons around, add or subtract them.ii. These do 1 Carbon transfers:iii. Activated biotin adds CO2 to some substrate using ATP (CO2 is most oxidized form of carbon) iv. Tetrahydrofolate (THF) adds Carbons in intermediate oxidation states (at either N5, or N10, or both). 1. THF picks up the carbon and brings it elsewhere2. Partially reduced.v. SAM - methyl donor. Adds CH3 groups (most reduced form of Carbon)b. Methionine Synthesis and the SAM cyclei. 1. THF donates Carbons, still donates it in intermediate oxidation state.1. The one exception to that is in making SAM, when you donate carbon in the most reduced stateii. Add methyl to homocysteine to get methionine. Requires coenzyme vitamin b12iii. To move the carbon to somewhere else, the cell needs to activate to make transfer more favourable. 1. Activate using ATP; remove all 3 Phosphate groups and attach adenosine (instead of the phosphates) to the molecule to activate it.iv. Activates molecule by producing a sulfonium ion; the positive charged sulfur makes the methyl a great leaving group. 1. This makes a very high transfer potential, so it’s very easy to transfer methyl to something elsev. Next reaction: Methyl transferases: (i.e. those used in making choline) move the methyl group from SAM to the acceptor. 1. Now back to s-adenosyl homocysteine so the last step is to regenerate the
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