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Article Evaluation

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This is an evaluation of the article Denaturation (biochemistry).

This article is part of Wikipedia:WikiProject Molecular and Cell Biology and is currently a Start-Class article.

The article discusses the concept of denaturation in biochemistry, specifically as it applies to proteins and nucleic acids. 'Protein denaturation' and 'Nucleic acid denaturation' each have their own section, each of which is broken down into further sub-sections. There is also a section for 'Common examples' and 'Denaturants'.

The article expresses a relatively neutral point of view, as the topic isn't the subject of much controversy or opinion. Potential distractions or confusions arise from the 'Common examples' section. Here, the article presents the idea that cooking food denatures some of its proteins and then gives specific examples from eggs, milk, and ceviche. This is distracting and confusing because only protein (not nucleic acid) denaturation is discussed, and it is implied that protein denaturation is the only way food is 'cooked'. This section could be removed alternatively as it doesn't contribute much understanding to the concept of denaturation. Alternatively, more examples can be added to provide a better understand of macroscopic applications of denaturation. The talk page leans towards the latter approach.

The article mentions that proteins begin folding into their native conformation after any post-translational modifications. To the best of my knowledge, this is factually incorrect; polypeptides begin folding as soon as they begin emerging from the ribosome. In the Proteins > Background subsection, quaternary structure is not mentioned as being altered by denaturation, which is a notable omission. Other concepts could use a little more background information so that a common reader can understand why certain things are happening, as opposed to just being told that they are. Specifically, a basic thermodynamic explanation of the hydrophobic effect may be beneficial.

There are a limited number of citations in this article, especially in the Protein denaturation section. It would certainly be beneficial to find my references to back the claims in the article. To the best of my knowledge, most of the un-cited claims are factually correct, though. The talk page also mentions that there are some outdated references, specifically a paper dating back to 1968.

Adding to an Article

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Added the following onto a sentence about intrinsically unstructured proteins: 'but still functionally active and tend to fold upon binding to their biological target'.

Added two citations to Denaturation (biochemistry). One of these (2) was in regards to the sentence I added above, while the other is in regards to a previously un-cited statement.

These citations are: [1]and [2].

Possible Topics

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The article Cis-regulatory element is rated as a start-class article of high importance to WikiProject Genetics. The article currently only contains a brief overview of cis-regulatory elements, one descriptive example (promoters), and the evolutionary role of them. Cis-regulatory elements are crucial to the regulation of gene expression, and there a wide variety of them that can act in many different ways. To improve this article I would describe more common cis-regulatory elements and unify them together by connecting back to the idea of regulation of gene expression. I would also dig deeper into their evolutionary role, as well as their mechanisms of action, without getting overly technical.

The article RNA extraction is a stub-class article that falls within the scope of WikiProject Molecular and Cell Biology. RNA extraction is an important technique in many molecular biology workflows. The article currently only names (but doesn't describe) common methods, and has a brief section about potential contamination. To improve this article I would expand upon the theory and methods of RNA extraction, as well as talk about downstream uses and proper handling of extracted RNA.

The article on Adenosine monophosphate is currently a start-class article that is of interest to both WikiProject Genetics and WikiProject Cell and Molecular Biology. AMP is an important regulatory nucleotide and plays a role in a wide variety of biochemical pathways. The article currently only describes its production, degradation, and cyclization. To improve this article I would discuss the metabolism of AMP, as well as its many important regulatory roles and its relation to ATP and ADP. I would also look into the evolutionary role of it.

Looks great. Keep it up! AdamCF87 (talk) 15:33, 17 October 2017 (UTC)

Nucleoside triphosphate (Article Draft)

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A nucleoside triphosphate is a molecule containing a nitrogenous base bound to a 5-carbon sugar (either ribose or deoxyribose), with three phosphate groups bound to the sugar.[1] They are the building blocks of both DNA and RNA, which are chains of nucleotides made through the processes of DNA replication and transcription.[2] Nucleoside triphosphates also serve as a source of energy for cellular reactions[3] and are involved in signalling pathways.[4]

Nucleoside triphosphates cannot be absorbed well, so they are typically synthesized within the cell.[5] Synthesis pathways differ depending on the specific nucleoside triphosphate being made, but given the many important roles of nucleoside triphosphates, synthesis is tightly regulated in all cases.[6]

Nucleoside analogues may also be used to treat viral infections.[7] For example, azidothymidine (AZT) is a nucleoside analogue used to prevent and treat HIV/AIDS.[8]

Naming

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The term nucleoside refers to a nitrogenous base linked to a 5-carbon sugar (either ribose or deoxyribose).[1] Nucleotides are nucleosides covalently linked to one or more phosphate groups.[9] To provide information about the number of phosphates, nucleotides may instead be referred to as nucleoside (mono, di, or tri) phosphates.[10] Thus, nucleoside triphosphates are a type of nucleotide.[10]

Nucleotides are commonly abbreviated with 3 letters. The first letter indicates the identity of the nitrogenous base (e.g. A for adenine, G for gaunine), the second letter indicates the number of phosphates (mono, di, tri) and the third letter is P, standing for phosphate.[11] Nucleoside triphosphates that contain ribose as the sugar are conventionally abbreviated as NTPs, while nucleoside triphosphates containing deoxyribose as the sugar are abbreviated as dNTPs. For example, dATP stands for deoxyribose adenosine triphosphate. NTPs are the building blocks of RNA, and dNTPs are the building blocks of DNA.[12]

The carbons of the sugar in a nucleoside triphosphate are numbered around the carbon ring starting from the original carbonyl of the sugar. Conventionally, the carbon numbers in a sugar are followed by the prime symbol (‘) to distinguish them from the carbons of the nitrogenous base. The nitrogenous base is linked to the 1’ carbon through a glycosidic bond, and the phosphate groups are covalently linked to the 5’ carbon.[13] The first phosphate group linked to the sugar is termed the α-phosphate, the second is the β-phosphate, and the third is the γ-phosphate.[14]

Schematic showing the structure of nucleoside triphosphates. Nucleosides consist of a 5-carbon sugar (pentose) connected to a nitrogenous base through a 1' glycosidic bond. Nucleotides are nucleosides with a variable number of phosphate groups connected to the 5' carbon. Nucleoside triphosphates are a specific type of nucleotide. This figure also shows the five common nitrogenous bases found in DNA and RNA on the right.

DNA and RNA synthesis

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In nucleic acid synthesis, the 3’ OH of a growing chain of nucleotides attacks the α-phosphate on the next NTP to be incorporated (blue), resulting in a phosphodiester linkage and the release of pyrophosphate (PPi). This figure shows DNA synthesis, but RNA synthesis occurs through the same mechanism.

The cellular processes of DNA replication and transcription involve DNA and RNA synthesis, respectively. DNA synthesis uses dNTPs as substrates, while RNA synthesis uses NTPs as substrates.[2] It should be noted that NTPs cannot be converted directly to dNTPs. DNA contains four different nitrogenous bases: adenine, guanine, cytosine and thymine. RNA also contains adenine, guanine, and cytosine, but replaces thymine with uracil.[15] Thus, DNA synthesis requires dATP, dGTP, dCTP, and dTTP as substrates, while RNA synthesis requires ATP, GTP, CTP, and UTP.

Nucleic acid synthesis is catalyzed by either DNA polymerase or RNA polymerase for DNA and RNA synthesis respectively.[16] These enzymes covalently link the free -OH group on the 3’ carbon of a growing chain of nucleotides to the α-phosphate on the 5’ carbon of the next NTP, releasing the β- and γ-phosphate groups as pyrophosphate (PPi).[17] This results in a phosphodiester linkage between the two (d)NTPs. The release of PPi provides the energy necessary for the reaction to occur.[17] It is important to note that nucleic acid synthesis occurs exclusively in the 5’ to 3’ direction.

Nucleoside triphosphate metabolism

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Given their importance in the cell, the synthesis and degradation of nucleoside triphosphates is under tight control.[6] This section focuses on nucleoside triphosphate metabolism in humans, but the process is fairly conserved among species.[18] Nucleoside triphosphates cannot be absorbed well, so all nucleoside triphosphates are typically made de novo.[19] The synthesis of ATP and GTP (purines) differs from the synthesis of CTP, TTP, and UTP (pyrimidines). Both purine and pyrimidine synthesis use phosphoribosyl pyrophosphate (PRPP) as a starting molecule.[20]

The conversion of NTPs to dNTPs can only be done in the diphosphate form. Typically a NTP has one phosphate removed to become a NDP, then is converted to a dNDP by an enzyme called ribonucleotide reductase, then a phosphate is added back to give a dNTP.[21]

Purine synthesis

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A nitrogenous base called hypoxanthine is assembled directly onto PRPP.[22] This results in a nucleotide called inosine monophosphate (IMP). IMP is then converted to either a precursor to AMP or GMP. Once AMP or GMP are formed, they can be phosphorylated by ATP to their diphosphate and triphosphate forms.[23]

Purine synthesis is regulated by the allosteric inhibition of IMP formation by the adenine or guanine nucleotides.[24] AMP and GMP also competitively inhibit the formation of their precursors from IMP.[25]

Pyrimidine synthesis

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A nitrogenous base called orotate is synthesized independently of PRPP.[25] After orotate is made it is covalently attached to PRPP. This results in a nucleotide called orotate monophosphate (OMP).[26] OMP is converted to UMP, which can then be phosphorylated by ATP to UDP and UTP. UTP can then be converted to CTP by a deamination reaction.[27] TTP is not a substrate for nucleic acid synthesis, so it is not synthesized in the cell. Instead, dTTP is made indirectly from either dUDP or dCDP after conversion to their deoxyribose forms.[20]

Pyrimidine synthesis is regulated by the allosteric inhibition of orotate synthesis by UDP and UTP. PRPP and ATP are also allosteric activators of orotate synthesis.[28]

Ribonucleotide reductase

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Ribonucleotide reductase (RNR) is the enzyme responsible for converting NTPs to dNTPs. Given that dNTPs are used in DNA replication, the activity of RNR is tightly regulated.[6] It is important to note that RNR can only process NDPs, so NTPs are first dephosphorylated to NDPs before conversion to dNDPs.[29] dNDPs are then typically re-phosphorylated. RNR has 2 subunits and 3 sites: the catalytic site, activity (A) site, and specificity (S) site.[30] The catalytic site is where the NDP to dNDP reaction takes place, the activity site determines whether or not the enzyme is active, and the specificity site determines which reaction takes place in the catalytic site.

The activity site can bind either ATP or dATP.[31] When bound to ATP, RNR is active. When ATP or dATP is bound to the S site, RNR will catalyze synthesis of dCDP and dUDP from CDP and UDP. dCDP and dUDP can go on to indirectly make dTTP. dTTP bound to the S site will catalyze synthesis of dGDP from GDP, and binding of dGDP to the S site will promote synthesis of dADP from ADP.[32] dADP is then phosphorylated to give dATP, which can bind to the A site and turn RNR off.[31]

Other cellular roles

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ATP as a source of cellular energy

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The energy released during hydrolysis of adenosine tripshophate (ATP), shown here, is frequently coupled with energetically unfavourable cellular reactions.

ATP is the primary energy currency of the cell[33]. Despite being synthesized through the metabolic pathway described above, it is primarily synthesized during both cellular respiration[34] and photosynthesis[35] by ATP synthase. ATP synthase couples the synthesis of ATP from ADP and phosphate with an electrochemical gradient generated by the pumping of protons through either the inner mitochondrial membrane (cellular respiration) or the thylakoid membrane (photosynthesis).[36] This electrochemical gradient is necessary because the formation of ATP is energetically unfavourable.

The hydrolysis of ATP to ADP and Pi proceeds as follows:[37]

This reaction is energetically favourable and releases 30.5 kJ/mol of energy[38]. In the cell, this reaction is often coupled with unfavourable reactions to provide the energy for them to proceed[39]. GTP is occasionally used for energy-coupling in a similar manner.[40]

Binding of a ligand to a G protein-coupled receptor allows GTP to bind the G protein. This causes the alpha subunit to leave and act as a downstream effector.

GTP signal transduction

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GTP is essential for signal transduction, especially with G proteins. G proteins are coupled with a cell membrane bound receptor.[41] This whole complex is called a G protein-coupled receptor. G proteins can bind either GDP or GTP. When bound to GDP, G proteins are inactive. When a ligand binds a G protein-coupled receptor, an allosteric change in the G protein is triggered, causing GDP to leave and be replaced by GTP.[42] GTP activates the alpha subunit of the G protein, causing it to dissociate from the G protein and act as a downstream effector.[42]

Nucleoside Analogues

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Nucleoside analogues can be used to treat viral infections.[43] Nucleoside analogues are nucleosides that are structurally similar (analogous) to the nucleosides used in DNA and RNA synthesis.[44] Once these nucleoside analogues enter a cell, they can become phosphorylated by a viral enzyme. The resulting nucleotides are similar enough to the nucleotides used in DNA or RNA synthesis to be incorporated into growing DNA or RNA strands, but they do not have an available 3’ OH group to attack the next nucleotide, causing chain termination.[45] This can be exploited for therapeutic uses in viral infections because viral DNA polymerase recognizes certain nucleotide analogues more readily than eukaryotic DNA polymerase.[43] For example, azidothymidine is used in the treatment of HIV/AIDS.[8] Some less selective nucleoside analogues can be used as chemotherapy agents to treat cancer,[46] such as cytosine arabinose (ara-C) in the treatment of certain forms of leukemia.[47]

Resistance to nucleoside analogues is common, and is frequently due to a mutation in the enzyme that phosphorylates the nucleoside after entry into the cell.[47] This is common in nucleoside analogues used to treat HIV/AIDS.[48]

See also

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References

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  1. ^ a b "Nucleotides and Bases - Genetics Generation". Genetics Generation. Retrieved 2017-11-11.
  2. ^ a b Chargaff, Erwin (2012-12-02). The Nucleic Acids. Elsevier. ISBN 9780323144773.
  3. ^ "Overview of ATP Hydrolysis". Khan Academy. Retrieved 2017-11-11.
  4. ^ "GPCR". Scitable. Retrieved 2017-11-11.
  5. ^ "Eating DNA: Dietary Nucleotides in Nutrition". The call of the Honeyguide. 2014-04-09. Retrieved 2017-11-11.
  6. ^ a b c Wyngaarden, James B. (1976-01-01). "Regulation of purine biosynthesis and turnover". Advances in Enzyme Regulation. 14 (Supplement C): 25–42. doi:10.1016/0065-2571(76)90006-6. PMID 184697.
  7. ^ Galmarini, C M; Mackey, J R; Dumontet, C (2001-05-24). "Nucleoside analogues: mechanisms of drug resistance and reversal strategies". Leukemia. 15 (6): 875–890. doi:10.1038/sj.leu.2402114. ISSN 1476-5551. PMID 11417472. S2CID 760764.
  8. ^ a b "Zidovudine Monograph for Professionals - Drugs.com". Drugs.com. Retrieved 2017-11-30.
  9. ^ Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James (2000). "Structure of Nucleic Acids". {{cite journal}}: Cite journal requires |journal= (help)
  10. ^ a b Secrist, J. A. (May 2001). "Nucleoside and nucleotide nomenclature". Current Protocols in Nucleic Acid Chemistry. Appendix 1: Appendix 1D. doi:10.1002/0471142700.nca01ds00. hdl:2027.42/143595. ISSN 1934-9289. PMID 18428808. S2CID 205152902.
  11. ^ "Nomenclature of Nucleosides". www.biochem.uthscsa.edu. Retrieved 2017-11-11.
  12. ^ "From DNA to RNA to protein, how does it work?". Science Explained. Retrieved 2017-11-11.
  13. ^ http://www.biosyn.com/. "Numbering convention for nucleotides". www.biosyn.com. Retrieved 2017-11-11. {{cite web}}: External link in |last= (help)
  14. ^ "SparkNotes: DNA Replication and Repair: The Chemistry of the Addition of Substrates of DNA Replication". www.sparknotes.com. Retrieved 2017-11-11.
  15. ^ "Do You Know the Differences Between DNA and RNA?". ThoughtCo. Retrieved 2017-11-11.
  16. ^ "Difference Between DNA Polymerase and RNA Polymerase". www.differencebetween.com. Retrieved 2017-11-11.
  17. ^ a b Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James (2000). "Nucleic Acid Synthesis". {{cite journal}}: Cite journal requires |journal= (help)
  18. ^ Samant, Shalaka; Lee, Hyunwoo; Ghassemi, Mahmood; Chen, Juan; Cook, James L.; Mankin, Alexander S.; Neyfakh, Alexander A. (2008-02-15). "Nucleotide Biosynthesis Is Critical for Growth of Bacteria in Human Blood". PLOS Pathogens. 4 (2): e37. doi:10.1371/journal.ppat.0040037. ISSN 1553-7374. PMC 2242838. PMID 18282099.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  19. ^ Berg, Jeremy M.; Tymoczko, John L.; Stryer, Lubert (2002). "Nucleotide Biosynthesis". {{cite journal}}: Cite journal requires |journal= (help)
  20. ^ a b "Nucleotide Metabolism: Nucleic Acid Synthesis". themedicalbiochemistrypage.org. Retrieved 2017-11-15.
  21. ^ Stubbe, JoAnne (April 1990). "Ribonucleotide Reductases: Amazing and Confusing" (PDF). The Journal of Biological Chemistry. 265 (10): 5329–5332. doi:10.1016/S0021-9258(19)39357-3. PMID 2180924.
  22. ^ Berg, Jeremy M.; Tymoczko, John L.; Stryer, Lubert (2002). "Purine Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways". {{cite journal}}: Cite journal requires |journal= (help)
  23. ^ "Purine Synthesis : Synthesis of Purine RiboNucleotides". BiochemDen.com. 2016-03-16. Retrieved 2017-11-15.
  24. ^ Berg, Jeremy M.; Tymoczko, John L.; Stryer, Lubert (2002). "Key Steps in Nucleotide Biosynthesis Are Regulated by Feedback Inhibition". {{cite journal}}: Cite journal requires |journal= (help)
  25. ^ a b NIERLICH, DONALD P.; MAGASANIK, BORIS (January 1965). "Regulation of Purine Ribonucleotide Synthesis by End Product Inhibition". The Journal of Biological Chemistry. 240: 358–365. doi:10.1016/S0021-9258(18)97657-X.
  26. ^ Moffatt, Barbara A.; Ashihara, Hiroshi (2002-04-04). "Purine and Pyrimidine Nucleotide Synthesis and Metabolism". The Arabidopsis Book / American Society of Plant Biologists. 1: e0018. doi:10.1199/tab.0018. ISSN 1543-8120. PMC 3243375. PMID 22303196.
  27. ^ "Pyrimidine Metabolism". www.cliffsnotes.com. Retrieved 2017-11-15.
  28. ^ Lane, Andrew N.; Fan, Teresa W.-M. (2015-02-27). "Regulation of mammalian nucleotide metabolism and biosynthesis". Nucleic Acids Research. 43 (4): 2466–2485. doi:10.1093/nar/gkv047. ISSN 0305-1048. PMC 4344498. PMID 25628363.
  29. ^ Kolberg, Matthias; Strand, Kari R.; Graff, Pål; Andersson, K. Kristoffer (2004-06-01). "Structure, function, and mechanism of ribonucleotide reductases". Biochimica et Biophysica Acta. 1699 (1–2): 1–34. doi:10.1016/j.bbapap.2004.02.007. ISSN 0006-3002. PMID 15158709.
  30. ^ Kolberg, Matthias; Strand, Kari R; Graff, Pål; Kristoffer Andersson, K (2004-06-01). "Structure, function, and mechanism of ribonucleotide reductases". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1699 (1): 1–34. doi:10.1016/j.bbapap.2004.02.007. PMID 15158709.
  31. ^ a b Ahmad, Faiz; Dealwis, Chris G. (2013). "The Structural Basis for the Allosteric Regulation of Ribonucleotide Reductase". Progress in Molecular Biology and Translational Science. 117: 389–410. doi:10.1016/B978-0-12-386931-9.00014-3. ISBN 9780123869319. ISSN 1877-1173. PMC 4059395. PMID 23663976.
  32. ^ Fairman, James Wesley; Wijerathna, Sanath Ranjan; Ahmad, Md Faiz; Xu, Hai; Nakano, Ryo; Jha, Shalini; Prendergast, Jay; Welin, R Martin; Flodin, Susanne (2011-02-20). "Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization". Nature Structural & Molecular Biology. 18 (3): 316–322. doi:10.1038/nsmb.2007. ISSN 1545-9985. PMC 3101628. PMID 21336276.
  33. ^ "ATP | Learn Science at Scitable". www.nature.com. Retrieved 2017-11-12.
  34. ^ "Mitochondria, Cell Energy, ATP Synthase". www.nature.com. Retrieved 2017-11-12.
  35. ^ "ATP Synthesis". Plants in Action. Retrieved 2017-11-12.
  36. ^ Jonckheere, An I.; Smeitink, Jan A. M.; Rodenburg, Richard J. T. (2012). "Mitochondrial ATP synthase: architecture, function and pathology". Journal of Inherited Metabolic Disease. 35 (2): 211–225. doi:10.1007/s10545-011-9382-9. ISSN 0141-8955. PMC 3278611. PMID 21874297.
  37. ^ Dittrich, Markus; Hayashi, Shigehiko; Schulten, Klaus (2003). "On the Mechanism of ATP Hydrolysis in F1-ATPase". Biophysical Journal. 85 (4): 2253–2266. doi:10.1016/S0006-3495(03)74650-5. ISSN 0006-3495. PMC 1303451. PMID 14507690.
  38. ^ "Overview of ATP Hydrolysis". Khan Academy. Retrieved 2017-11-12.
  39. ^ "ATP: Adenosine Triphosphate | Boundless Biology". courses.lumenlearning.com. Retrieved 2017-11-12.
  40. ^ Carvalho, Alexandra T. P.; Szeler, Klaudia; Vavitsas, Konstantinos; Åqvist, Johan; Kamerlin, Shina C. L. (2015-09-15). "Modeling the mechanisms of biological GTP hydrolysis". Archives of Biochemistry and Biophysics. Special issue in computational modeling on biological systems. 582 (Supplement C): 80–90. doi:10.1016/j.abb.2015.02.027. PMID 25731854.
  41. ^ "GPCR". www.nature.com. Retrieved 2017-11-12.
  42. ^ a b "G protein-coupled receptor (GPCR) | biochemistry". Encyclopedia Britannica. Retrieved 2017-11-12.
  43. ^ a b "Nucleoside Analogues". Molecules. Retrieved 2017-11-13.
  44. ^ Jordheim, Lars Petter; Durantel, David; Zoulim, Fabien; Dumontet, Charles (2013-05-31). "Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases". Nature Reviews Drug Discovery. 12 (6): 447–464. doi:10.1038/nrd4010. ISSN 1474-1784. PMID 23722347. S2CID 39842610.
  45. ^ Ewald, B.; Sampath, D.; Plunkett, W. (2008-10-27). "Nucleoside analogs: molecular mechanisms signaling cell death". Oncogene. 27 (50): 6522–6537. doi:10.1038/onc.2008.316. ISSN 1476-5594. PMID 18955977. S2CID 23817516.
  46. ^ Galmarini, Carlos M.; Mackey, John R.; Dumontet, Charles (July 2002). "Nucleoside analogues and nucleobases in cancer treatment". The Lancet. Oncology. 3 (7): 415–424. doi:10.1016/s1470-2045(02)00788-x. ISSN 1470-2045. PMID 12142171.
  47. ^ a b Galmarini, C M; Mackey, J R; Dumontet, C (2001-05-24). "Nucleoside analogues: mechanisms of drug resistance and reversal strategies". Leukemia. 15 (6): 875–890. doi:10.1038/sj.leu.2402114. ISSN 1476-5551. PMID 11417472. S2CID 760764.
  48. ^ Menéndez-Arias, Luis (June 2008). "Mechanisms of resistance to nucleoside analogue inhibitors of HIV-1 reverse transcriptase". Virus Research. 134 (1–2): 124–146. doi:10.1016/j.virusres.2007.12.015. ISSN 0168-1702. PMID 18272247.
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