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ProteinTurnoverandAminoAcidCatabolismworksheet - Protein...

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Unformatted text preview: Protein Turnover and Amino Acid Catabolism 1) Outline the process for protein digestion starting with a protein in the lumen of the intestine and ending with amino acids in the blood. 2) What is the basic cell signal for protein degradation? What is the energetic requirement for attachment of this signal? Describe the structure of the attachment. 3) How many protein activities are required to tag a protein for degradation? Show the reactions these catalyze. (Fig 23.3) 4) What is the effect of multiple ubiquitinylation? What property is displayed in multiple ubiquitinylation steps? 5) In general, what does E3 recognize (read) to determine whether a protein should be degraded? 6) What cellular assemblage degrades proteins that are ubiquitinylated? Describe the mechanism of this process. 7) What is the first step in amino acid breakdown? What cofactors/cosubstrates are required for this activity? 8) In most vertebrates, what is the ultimate fate of the nitrogen in amino acids that undergo degradation? Which organ is responsible for this transformation? When amino are broken down in peripheral tissues, how does the nitrogen reach this organ? 9) Draw the mechanism for a pyridoxaldependent transamination. 10) Which amino acids are degraded into pyruvate? Explain the mechanistic similarities in these reactions. 11) Outline the chemical intermediates in the degradation of the following amino acids: Asn, Asp. What cofactor(s) play a role in this process? What other end product may be formed from Asp. What cycle does this come from? 12) What amino acids are degraded to yield alphaketoglutarate? 13) Outline the chemical intermediates in the conversion of histidine to glutamate. What cofactor serves as the acceptor for the amidine group of imidazole ring of histidine? What other cofactors are typical one carbon acceptors/transfer agents? 14) Outline the steps in the conversion of proline and arginine to glutamate. 15) Draw the structure of Sadenosylmethionine. How is this molecule formed? What is its biological function? 16) Methionine is degraded to a four carbon molecule outline the steps in this conversion. What other amino acid is required for this transformation? What amino acid is synthesized in this process. 17) The four carbon molecule derived from methionine is converted into a three carbon molecule. What is this molecule? What cofactors are involved in this transformation? What is the redox change (if any) associated with this reaction? 18) Outline the degradative pathway for leucine. What steps in this pathway are akin to steps involved in fatty acid oxidation or synthesis. Are they more similar to fatty acid oxidation, or synthesis? 19) Show the intermediates involved in the degradation of valine, isoleucine, and lysine. How are these reaction pathways the same and how are they different from leucine degradation? 20) Name the cofactor required for hydroxylation of phenylalanine. Draw the structures of the three commonly observed forms of this cofactor. How are they related? 21) What is the consequence of a deficiency in phenylalanine hydroxylase? 22) What are two major differences between monooxygenases and dioxygenases? 23) Why is hydroxylation of an aromatic ring a necessary precursor to its cleavage? 24) What are the two major degradation products of phenylalanine/tyrosine? 25) What are the two major degradation products of tryptophan? Use a structure of tryptophan to indicate where in metabolism intermediates the carbon atoms end up in the degradation process. ...
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