Biochem for the Boards 2nd Edition

Transcription

1 Biochem for the Boards! Biochem for the Boards 2nd Edition Active Learning Workbook for the BDE 1, DDS, MA Bonus Chapter ucleotide Metabolism Socrates Publishing Co. ew York, Y Page 1

2 ucleotide Metabolism Biochem for the Boards: Bonus Chapter 1. What is a nucleotide? 2. How are nucleotides structured in chains? 3. How are purines made? 4. How are pyrimidines made? 5. How are purines recycled? 6. How are purines excreted? 1. What is a nucleotide? DA and RA are nucleic acids that are made up of chains of nucleotides. A nucleotide is a molecule that has a nitrogen base, a ribose/deoxyribose sugar, and a phosphate group. n the other hand, a nucleoside has only the nitrogenous base and the sugar and doesn t have a phosphate group. To remember which one of these make up DA and RA, think that nucleotides are TIed together to make a chain in nucleic acids. Also, recall that DA contains deoxyribose sugars in the nucleotides while RA contains ribose sugars. In the lab setting, the Feulgen reaction is used to differentiate between DA and RA because the reaction is specific for deoxyribose in DA. H H H H H Ribose H H Deoxyribose The name says it all deoxy it s ribose without one oxygen. 5 carbon H 3 carbon H H2 P Phosphate group 5 H Sugar 3 itrogenous base H2 Page 2

3 The nomenclature here can be tricky. ote below the name of the base alone versus the name of the full nucleotide it forms when it joins sugar and phosphate. ame of Base!!!! Full ucleotide ame Adenine!! Adenylic acid or Adenosine monophosphate (AMP) Guanine!! Guanylic acid or Guanosine monophosphate (GMP) Cytosine!! Cytidylic acid or Cytidine monophosphate (CMP) Uracil!!! Uridylic acid or Uridine monosphosphate (UMP) The purines are adenine and guanine and exist in both RA and DA. The pyrimidines are cytosine, thymine, and uracil. RA uses cytosine and uracil while DA uses cytosine and thymine. Don t memorize the exact structure of the bases below, but know which bases are purines and pyrimidines. Purines Pyrimidines H2 CH3 thymine adenine H2 H2 cytosine guanine Mnemonics: Pyrimidines: CUT the PY Purines: Pure As Gold uracil Page 3

4 2. How are nucleotides structured in chains? When two nucleotides are tied together to form the chain of a nucleic acid, the 5 phosphate end of one nucleotide joins with the 3 hydroxyl end of another to create a phosphodiester bond. When two separate chains come together to form DA, they connect in an antiparallel and complementary way the 3 end of the one strand meets with the 5 end of the other strand. Base sequences of a chain are usually written in the 5 to 3 direction. Phosphodiester bonds are strong and won t break by denaturation (either through ph changes or temperature changes), unlike the weaker hydrogen bonds. P P P 5 3 P type of bond P P 5 3 H type of bond otice the backbone part of the chain is an alternating phosphate group and sugar group, with the nitrogenous bases attached to the sugars. Also note that the phosphate group has a negatively charged oxygen. This negative charge makes the phosphate group hydrophilic. In the DA chain, the phosphate groups are on the outside, making the outside of the chain hydrophilic. Page 4

5 3. How are purines made? Humans mainly get our nucleotides through endogenous synthesis rather than our diet. ne way that nucleotides can be made is de novo (latin, from new ), which occurs mostly in the liver. De novo synthesis of both purines and pyrimidines requires a compound called PRPP, phosphoribosyl pyrophosphate. More on this below. For DA nucleotides, ribonucleotides are made first and are then converted to deoxyribonucleotides by the enzyme ribonucleotide reductase. An easy way to remember this is that the enzyme reduces the number of oxygens in a ribonucleotide, converting it to a deoxyribonucleotide. De ovo Purine Synthesis Remember the pentose phosphate pathway (also called the HMP shunt) from Carbohydrates: Section 3 Pyruvate Metabolism? If you haven t read it yet, this is a small but important pathway that uses an intermediate of glycolysis, glucose6p, to make ADPH and ribose5p. Ribose5P is then used to make purine bases. In summary, we can use glucose to make nucleotides by first converting it to glucose6p, and then to ribose5p through the pentose phosphate pathway. This is an important tiein so let s review it: From Diet Intermediate of Glycolysis End Product of PPP/ HMP Shunt Ribose5phosphate Phosphate group P 5 Ribose 3 H Take a moment to note that the name of the sugar is important. The name tells you immediately that the phosphate group is attached to the 5 carbon. Looking at the name of ribose5phosphate itself is an easy way to remember that the 3 end of a nucleotide is the hydroxyl end. Page 5

6 Sample Test Question: Which sugar is used to make a purine nucleotide? a) ribose1phosphate b) ribose6phosphate c) ribose5phosphate d) ribose3phosphate Hint: You should be able to rule out two of these options right away since you know that the two ends of DA are at the 5 and 3 carbons. You can also rule out option b) because ribose is a 5carbon sugar so how can the phosphate group be attached to the 6th carbon? Steps of Purine Synthesis 1. Start with R5P 2. An ATP transfers a P group, creating PRPP 3. PRPP amidotransferase transfers an amino group. 4. A few more steps occur, where THF donates a carbon and another ATP is used. This forms the intermediate IMP, which gets converted to AMP or GMP 5. The final nucleotides are formed (AMP and GMP) carbon donor Ribose 5Phosphate PRPP 5phosphoribosylamine ATP PRPP amidotransferase ATP IMP AMP GMP Important points about purine synthesis: 1. The nitrogenous base is build piece by piece on top of an existing ribose sugar 2. ATP is required 3. PRPP is an intermediate 4. THF is a carbon donor** 5. The amino acids aspartate and glutamine are involved (for AMP and GMP respectively). They donate an amino group in the last step a minor detail. **Since THF is used to make nucleotides necessary for DA synthesis, it s the target of many antimetabolite drugs, like methotrexate, used in cancer therapy. Always try to make sense out of a name so it s easier to recall which pathway the compound was associated with during your exam. PRPP is phosphoribosyl pyrophosphate. This makes sense since it comes from ribose 5phosphate with the addition of ATP, adenosine monophosphate. Even the abbreviated form has similar letters: R5P + ATP > PRPP. This will help you remember that ATP is involved too. You can also deduce that amino acids are involved based on the name 5phosphoribosylamine. Page 6

7 4. How are pyrimidines made? De ovo Pyrimidine Synthesis Recall that the term nucleotide refers to the nitrogenous basephosphatesugar unit. In the synthesis of purine nucleotides, the nitrogenous base part is build piece by piece on top of an existing ribose sugar. That s why the purine synthesis pathway starts with ribose5 phosphate. n the other hand, in pyrimidine synthesis, the nitrogenous base is made separately as a single ring and then it s attached to the ribose. The molecule that donates a ribose5p for pyrimidine synthesis is none other than PRPP. Remember, to make a deoxyribose nucleotide for DA synthesis, first a ribose nucleotide is made and then it s reduced by the enzyme,. Pyrimidine synthesis has multiple steps, so this is an overview of the most important aspects. ote that orotic acid is the acid form of orotate (the base form). You may see orotate in other resources, but they are essentially the same. carbon donor Glutamine + C2 + Aspartate H H H UMP CMP TMP ATP rotic acid donates ribose5p Important points about pyrimidine synthesis: 1. The nitrogenous base is made separately and the ribose5p is added later 2. ATP is required 3. Glutamine, Aspartate, THF and PRPP are involved (just like in purine synthesis) Review: 1. Which amino acids are involved in nucleotide synthesis? 2. Which nucleotide synthesis (purine vs pyrimidine) involves building the nitrogenous base separately and then adding a sugar? Page 7

8 5. How are purines recycled? Purines can be made de novo as shown above, but can also be recycled through salvage pathways. When nucleic acids are degraded, the purine bases can be salvaged and recycled to make new nucleotides. These salvage pathways save energy, but when there is an impairment, they can also cause serious pathology. In impairment of salvage pathways, instead of being recycled, most of the purines are shifted to excretion pathways. This is explained in more detail below. donates ribose5p 1. AMP GMP IMP 2. Adenosine Guanosine 3. Inosine Hypoxanthine 4. Guanine 1. Remember, the full nucleotide name is AMP and GMP. 2. The phosphate group and sugar group are removed, so only the nitrogenous base is left (adenosine/guanosine) 3. Adenosine deaminase or guanosine deaminase removes an ammonia group, leaving inosine and guanine. 4. These are either recycled by the enzyme HGPRT (hypoxanthineguanine phosphoribosyltransferase) or sent to excretion (see below). Where does HGPRT get the phosphoribose that it transfers? one other than PRPP! Inosine recycling has a few extra intermediates, but these are minor details. Adenosine can also be converted to AMP by another enzyme, APRT, adenine phosphoribosyl transferase. Again, PRPP is where the phosphoribose group comes from during this transfer. AMP GMP IMP Adenosine Guanosine Inosine Hypoxanthine Guanine Page 8

9 Important points about purine salvage: 1. Remember HGPRT! 2. Remember APRT The name HGPRT seems tricky, but it s easy as long as you understand instead of memorize. The G stand for guanine so you know it has to do with purines, not pyrimidines. If the enzyme is transferring a phosphoribose group, it would make sense that the enzyme is involved in nucleotide recycling because phosphate and ribose are two important groups in nucleotides. It wouldn t make sense to transfer those groups only to excrete the purine what a waste! Pathology: Leschyhan Syndrome occurs when there s a HGPRT deficiency due to an x linked recessive gene. Classic symptoms include mild mental retardation, cerebral palsy, and selfinjury. Hyperuricemia (increased levels of uric acid in the blood) also occurs since impaired purine recycling shifts purines to the excretion pathway. Pyrimidines can also recycled, using an enzyme called pyrimidine phosphoribosyltransferase. Guess where the enyzme gets the phosphoribose group from? If you didn t guess PRPP, you should do some rereading! 6. How are purines excreted? Excess purines in the diet are excreted by the kidneys. During the excretion process, purines are broken down to uric acid. Interestingly, uric acid is what makes bird droppings white! The process of purine breakdown is shown below. An important point to remember is that xanthine oxidase is the enzyme that catalyzes the final formation of uric acid. Also remember that nucleotide breakdown does T produce any ATP (whereas, ATP is produced in lipid, protein, or carbohydrate breakdown). AMP GMP inosine hypoxanthine guanine Xanthine Uric Acid enzyme Page 9

10 Use the name HGPRT to the name to remember that Hypoxanthine alone is involved in purine salvage (instead of hypoxanthine and xanthine, like is in purine excretion). H H H H Uric Acid Uric acid is a big molecule! So it s no surprise that it s not very soluble. Also, the structure looks like a purine base, so use that to remember that it s associated with purine breakdown. Pathology: Uric acid is not very soluble. In poor kidney function, uric acid isn't properly excreted and it builds up as crystals of sodium urate in the body's joints. Uric acid buildup causes the pain associated with gout. Excess uric acid can also cause kidney stones. It only takes a slightly impairment to cause a buildup. Gout is usually caused by poor kidney function, but can also be caused by impairment in purine salvage. If there are problems in the salvage pathways, more purines will be converted to uric acid for excretion. This causes a build up of uric acid in the body. I hope you enjoyed this bonus chapter of my workbook, Biochem for the Boards! Hopefully, now you see the value of using interactive exercises to help you understand instead of memorize. For the full workbook, visit Page 10