Biopolym. Cell. 2005; 21(6):485-514.
Discussions
Our shagreen leather is our problem. And we have to solve it. 6. Paying back.
1Kordium V. A.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

The problem of spatial and temporal organization of metabolic cycles in a cell is being analyzed. The unsolved questions are emphasized and the variants for their solution are suggested. The total amount of intermediate products as well as their removal from the active centers of metabolic cycle enzymes are being evaluated in view of the ideas under consideration. The removal of metabolytes is believed to be a result of the macromolecular damage. The age-related changes are explained taking into account this suggestion along with peculiarities of the mutative process.
Keywords: water in cell, metabolic cycles, chanelling, mutational process, unimportant sequences

References

[1] Kordyum VA. Our "Shagreen leather" is our problem. And we have to solve it. Biopolym Cell. 2003; 19(2):113-32.
[2] Kordyum VA. Our "Shagreen leather" is our problem. And we have to solve it. 2. The united space of organism. Biopolym Cell. 2003; 19(4):328-49.
[3] Kordyum VA. Our "Shagreen leather" is our problem. And we have to solve it. 3. A missing link. Biopolym. Cell. 2003; 19(6):473-91.
[4] Kordyum VA. Our shagreen leather is our problem, and we have to solve it. 4. «Shagreenity» that makes our skin shagreen. Biopolym Cell. 2004; 20(4):267-89.
[5] Kordyum VA. Our «Shagreen leather» is our problem. We have to solve it ourselves. 5. Forerunner. Biopolym. Cell. 2005;21(3):230-49.
[6] Metzler DE. Biochemistry. New York: Elsevier, 2001; Vol. 1. 937 p.
[7] Wiggins PM. Role of water in some biological processes. Microbiol Rev. 1990;54(4):432-49.
[8] Aliev MK, Dos Santos P, Hoerter JA, Soboll S, Tikhonov AN, Saks VA. Water content and its intracellular distribution in intact and saline perfused rat hearts revisited. Cardiovasc Res. 2002;53(1):48-58.
[9] Evdokimov IuV, Golo VL, Salianov VI, Lortkipanidze GB, Kats EI. ["Phantom" structure of solvents and packing of dual-chain nucleic acid molecules in liquid crystal dispersion particles]. Biofizika. 2000;45(6):1029-38.
[10] Luzardo MC, Amalfa F, Nu?ez AM, D?az S, Biondi De Lopez AC, Disalvo EA. Effect of trehalose and sucrose on the hydration and dipole potential of lipid bilayers. Biophys J. 2000;78(5):2452-8.
[11] Rupley JA, Careri G. Protein hydration and function. Adv Protein Chem. 1991;41:37-172.
[12] Khurgin IuI, Sherman FB, Tusukaliev U. [Isotherms of globular protein hydration under dynamic conditions]. Biokhimiia. 1977;42(3):490-8.
[13] Gurikov YuV. Current status of the water structure. Status and role of water in biological objects. M.: Nauka, 1967:5-15.
[14] Yamada T. 1H-NMR studies of the intracellular water of skeletal muscle fibers under various physiological conditions. Cell Mol Biol (Noisy-le-grand). 2001;47(5):925-33.
[15] Clegg JS. Interrelationships between water and cellular metabolism in Artemia cysts. VI. RNA and protein synthesis. J Cell Physiol. 1977;91(1):143-54.
[16] von Zglinicki T. Reliability of intracellular water and ion distributions as measured by X-ray microanalysis--a review. Scanning Microsc Suppl. 1991;5(4):S85-92.
[17] Kordyum VA. And then I sat down to write this book: It is not usual notions of human genetics. Kiev, 1993; 248 p.
[18] Metzler D. E. Biochemistry. New York: Elsevier, 2003; Vol. 2. 1973 p.
[19] Ov?di J, Saks V. On the origin of intracellular compartmentation and organized metabolic systems. Mol Cell Biochem. 2004;256-257(1-2):5-12.
[20] Negrutskii BS. The organization of protein synthesis in higher eukaryotes. Kyiv: Oberegi, 2001; 165 p.
[21] Huang X, Holden HM, Raushel FM. Channeling of substrates and intermediates in enzyme-catalyzed reactions. Annu Rev Biochem. 2001;70:149-80.
[22] Perham RN. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu Rev Biochem. 2000;69:961-1004.
[23] Tsuji SY, Wu N, Khosla C. Intermodular communication in polyketide synthases: comparing the role of protein-protein interactions to those in other multidomain proteins. Biochemistry. 2001;40(8):2317-25.
[24] Mart?n JF, Barreiro C, Gonz?lez-Lavado E, Barriuso M. Ribosomal RNA and ribosomal proteins in corynebacteria. J Biotechnol. 2003;104(1-3):41-53.
[25] Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A. Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell. 2000;102(5):615-23.
[26] M?ller WE, B?hm M, Grebenjuk VA, Skorokhod A, M?ller IM, Gamulin V. Conservation of the positions of metazoan introns from sponges to humans. Gene. 2002;295(2):299-309.
[27] Pesole G, Liuni S, Grillo G, Licciulli F, Mignone F, Gissi C, Saccone C. UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002. Nucleic Acids Res. 2002;30(1):335-40.
[28] Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF. Crystal structure of the ribosome at 5.5 A resolution. Science. 2001;292(5518):883-96.
[29] Valentin-Hansen P, Eriksen M, Udesen C. The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol. 2004;51(6):1525-33.
[30] Le SY, Zhang K, Maizel JV Jr. RNA molecules with structure dependent functions are uniquely folded. Nucleic Acids Res. 2002;30(16):3574-82.
[31] Black DL. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem. 2003;72:291-336.
[32] Scocca JR, Charron M, Shaper NL, Shaper JH. Determination of the half-life of the murine beta4-galactosyltransferase-1 mRNA in somatic cells using the tetracycline-controlled transcriptional regulation system. Biochimie. 2003;85(3-4):403-7.
[33] Erdmann VA, Szymanski M, Hochberg A, Groot N, Barciszewski J. Non-coding, mRNA-like RNAs database Y2K. Nucleic Acids Res. 2000;28(1):197-200.
[34] Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res. 2003;31(1):439-41.
[35] Vanyushin BF, Berdyshev GD. Molecular genetic mechanisms of aging. M.: Meditsina, 1977; 296 p
[36] Rudolph KL, Chang S, Lee HW, Blasco M, Gottlieb GJ, Greider C, DePinho RA. Longevity, stress response, and cancer in aging telomerase-deficient mice. Cell. 1999;96(5):701-12.
[37] Wang J, Hannon GJ, Beach DH. Risky immortalization by telomerase. Nature. 2000;405(6788):755-6.
[38] Doll? ME, Snyder WK, Dunson DB, Vijg J. Mutational fingerprints of aging. Nucleic Acids Res. 2002;30(2):545-9.
[39] Hahn 1964, 1965 (Cyted, by Vanyushin, Berdyshev) Vanyushin BF, Berdyshev GD. Molecular genetic mechanisms of aging. M.: Meditsina, 296 p.
[40] Christiansen M, Stevnsner T, Bohr VA, Clark BF, Rattan SI. Gene-specific DNA repair of pyrimidine dimers does not decline during cellular aging in vitro. Exp Cell Res. 2000;256(1):308-14.
[41] Krashennikov VE. Biological basis. Moscov, 1924.; 83 p.
[42] Vilenchik MM. Biological basis of aging and longevity. 1987. Moscow, Znanie, 176 p.
[43] Jendryczko A, Dr?zdz M. [Basic level of DNA damage in human cells]. Przegl Lek. 1989;46(5):470-3.
[44] Roguev A, Russev G. Two-wavelength fluorescence assay for DNA repair. Anal Biochem. 2000;287(2):313-8.
[45] Brachman EE, Kmiec EB. DNA replication and transcription direct a DNA strand bias in the process of targeted gene repair in mammalian cells. J Cell Sci. 2004;117(Pt 17):3867-74.
[46] Ukekawa R, Maegawa N, Mizutani E, Fujii M, Ayusawa D. Proteasome inhibitors induce changes in chromatin structure characteristic of senescent human fibroblasts. Biosci Biotechnol Biochem. 2004;68(11):2395-7.
[47] Broda E. The Evolution of Bioenergetic Processes, Pergamon, Oxford, 1975. 220 p.
[48] Chondrogianni N, Stratford FL, Trougakos IP, Friguet B, Rivett AJ, Gonos ES. Central role of the proteasome in senescence and survival of human fibroblasts: induction of a senescence-like phenotype upon its inhibition and resistance to stress upon its activation. J Biol Chem. 2003;278(30):28026-37.
[49] Riazanov AG. [Ribosome and the secret of longevity]. Mol Biol (Mosk). 2001;35(4):727-30.
[50] Cervantes RB, Stringer JR, Shao C, Tischfield JA, Stambrook PJ. Embryonic stem cells and somatic cells differ in mutation frequency and type. Proc Natl Acad Sci U S A. 2002;99(6):3586-90.
[51] Doll? ME, Snyder WK, Gossen JA, Lohman PH, Vijg J. Distinct spectra of somatic mutations accumulated with age in mouse heart and small intestine. Proc Natl Acad Sci U S A. 2000;97(15):8403-8.